@article {pmid30445510, year = {2018}, author = {Shekhar Saxena, A and Salomon, MP and Matsuba, C and Yeh, SD and Baer, CF}, title = {Evolution of the mutational process under relaxed selection in Caenorhabditis elegans.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msy213}, pmid = {30445510}, issn = {1537-1719}, abstract = {The mutational process varies at many levels, from within genomes to among taxa. Many mechanisms have been linked to variation in mutation, but understanding of the evolution of the mutational process is rudimentary. Physiological condition is often implicated as a source of variation in microbial mutation rate and may contribute to mutation rate variation in multicellular organisms.Deleterious mutations are a ubiquitous source of variation in condition. We test the hypothesis that the mutational process depends on the underlying mutation load in two groups of Caenorhabditis elegans mutation accumulation (MA) lines that differ in their starting mutation loads. "First-Order MA" (O1MA) lines maintained under minimal selection for ∼250 generations were divided into high-fitness and low-fitness groups and sets of "second-order MA" (O2MA) lines derived from each O1MA line were maintained for ∼150 additional generations. Genomes of 48 O2MA lines and their progenitors were sequenced. There is significant variation among O2MA lines in base-substitution rate (µbs), but no effect of initial fitness; the indel rate is greater in high-fitness O2MA lines. Overall, µbs is positively correlated with recombination and proximity to short tandem repeats and negatively correlated with 10 bp and 1 Kb GC content. However, probability of mutation is sufficiently predicted by the three-nucleotide motif alone. ∼90% of the variance in standing nucleotide variation is explained by mutability. Total mutation rate increased in the O2MA lines, as predicted by the "drift barrier" model of mutation rate evolution. These data, combined with experimental estimates of fitness, suggest that epistasis is synergistic.}, }
@article {pmid30444659, year = {2018}, author = {Rebolleda-Gómez, M and Travisano, M}, title = {The Cost of Being Big: Local Competition, Importance of Dispersal, and Experimental Evolution of Reversal to Unicellularity.}, journal = {The American naturalist}, volume = {192}, number = {6}, pages = {731-744}, doi = {10.1086/700095}, pmid = {30444659}, issn = {1537-5323}, abstract = {Multicellularity provides multiple benefits. Nonetheless, unicellularity is ubiquitous, and there have been multiple cases of evolutionary reversal to a unicellular organization. In this article, we explore some of the costs of multicellularity as well as the possibility and dynamics of evolutionary reversals to unicellularity. We hypothesize that recently evolved multicellular organisms would face a high cost of increased competition for local resources in spatially structured environments because of larger size and increased cell densities. To test this hypothesis we conducted competition assays, computer simulations, and selection experiments using isolates of Saccharomyces cerevisiae that recently evolved multicellularity. In well-mixed environments, multicellular isolates had lower growth rates relative to their unicellular ancestor because of limitations of space and resource acquisition. In structured environments with localized resources, cells in both multicellular and unicellular isolates grew at a similar rate. Despite similar growth, higher local density of cells in multicellular groups led to increased competition and higher fitness costs in spatially structured environments. In structured environments all of the multicellular isolates rapidly evolved a predominantly unicellular life cycle, while in well-mixed environments reversal was more gradual. Taken together, these results suggest that a lack of dispersal, leading to higher local competition, might have been one of the main constraints in the evolution of early multicellular forms.}, }
@article {pmid30429351, year = {2018}, author = {Ayoubian, H and Ludwig, N and Fehlmann, T and Menegatti, J and Gröger, L and Anastasiadou, E and Trivedi, P and Keller, A and Meese, E and Grässer, FA}, title = {Infection of cell lines derived from diffuse large B-cell lymphoma (DLBCL) with the Epstein-Barr virus (EBV) alters the miRNA loading of the Ago2-complex.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JVI.01297-18}, pmid = {30429351}, issn = {1098-5514}, abstract = {Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoid tumor which is occasionally Epstein-Barr virus (EBV)-positive and is further subtyped as activated B-cell (ABC) and germinal center B-cell (GCB) DLBCL, which has implications for prognosis and treatment.We performed Ago2-RNA immunoprecipitation followed by high throughput RNA sequencing (Ago2-RIP-Seq) to capture functionally active miRNAs in EBV-negative ABC-DLBCL and GC-DLBCL cell lines and their EBV-infected counterparts. In parallel, total miRNomes of these cells were sequenced to capture the cellular miRNA profile for comparison with the functionally active profile. Selected miRNAs with differential abundance were validated using RT-qPCR and Northern Blot. We found 6 miRNAs with differential abundance (2 upregulated and 4 downregulated miRNAs) between EBV-neg. and pos. ABC-DLBCL, and 12 miRNAs with differential abundance (3 upregulated and 9 downregulated miRNAs) between EBV-neg and -pos GC-DLBCL. Eight and twelve miRNAs were confirmed using RT-qPCR in ABC-DLBCL and GC-DLBCL, respectively. Selected miRNs were analyzed in additional type I/II vs. type III EBV latency DLBCL cell lines. Furthermore, up regulation of miR-221-3p and down regulation of let-7c-5p in ABC-DLBCL and up regulation of miR-363-3p and down regulation of 423-5p in GC-DLBCL was verified using RIP-Northern blot.Our comprehensive sequence analysis of the DLBCL miRNomes identified sets of deregulated miRNAs in the Ago2-RIP-seq. Our Ago2-IP-seq miRNomes profile could be considered as an important data set for detection of deregulated functionally active miRNAs in DLBCL and could possibly lead to identification of miRNAs as biomarkers for classification of DLBCL or even as targets for personalized targeted treatment.Importance: Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive tumor of lymphoid origin which is occasionally Epstein-Barr virus (EBV)-positive. MicroRNAs are found in most multicellular organisms and even in viruses such as EBV. They regulate the synthesis of proteins by binding to their cognate messenger RNA (mRNA). MicroRNAs are tethered to their target mRNAs by "Argonaute" proteins. Here we compared the overall content of by differential loading of the Ago2-complex in comparison to the overall content of miRNAs in two DLBCL cell lines and their EBV-converted counterparts. In all cell lines, the Ago2-load was different from the overall expression of miRNAs. In addition, the loading of the Ago2-complex was changed upon infection with EBV. This indicates that the virus changes not only the overall content of miRNAs but also influences the expression of proteins by affecting the Ago-complexes.}, }
@article {pmid29475741, year = {2018}, author = {Thomas, F and Kareva, I and Raven, N and Hamede, R and Pujol, P and Roche, B and Ujvari, B}, title = {Evolved Dependence in Response to Cancer.}, journal = {Trends in ecology & evolution}, volume = {33}, number = {4}, pages = {269-276}, doi = {10.1016/j.tree.2018.01.012}, pmid = {29475741}, issn = {1872-8383}, mesh = {*Biological Evolution ; Eukaryota/*genetics ; Evolution, Molecular ; Neoplasms/*genetics/prevention & control/therapy ; *Selection, Genetic ; }, abstract = {Evolved dependence is a process through which one species becomes 'dependent' on another following a long evolutionary history of interaction. This happens when adaptations selected in the first species for interacting lead to fitness costs when the second species is not encountered. Evolved dependence is frequent in host-parasite interactions, where hosts may achieve a higher fitness in the presence of the parasite than in its absence. Since oncogenic manifestations are (i) ubiquitous across multicellular life, (ii) involved in parasitic-like interactions with their hosts, and (iii) have effectively driven the selection of numerous adaptations, it is possible that multicellular organisms display evolved dependence in response to oncogenic processes. We provide a comprehensive overview of the topic, including the implications for cancer prevention and treatment.}, }
@article {pmid30427935, year = {2018}, author = {Schneider, P and Greischar, MA and Birget, PLG and Repton, C and Mideo, N and Reece, SE}, title = {Adaptive plasticity in the gametocyte conversion rate of malaria parasites.}, journal = {PLoS pathogens}, volume = {14}, number = {11}, pages = {e1007371}, doi = {10.1371/journal.ppat.1007371}, pmid = {30427935}, issn = {1553-7374}, abstract = {Sexually reproducing parasites, such as malaria parasites, experience a trade-off between the allocation of resources to asexual replication and the production of sexual forms. Allocation by malaria parasites to sexual forms (the conversion rate) is variable but the evolutionary drivers of this plasticity are poorly understood. We use evolutionary theory for life histories to combine a mathematical model and experiments to reveal that parasites adjust conversion rate according to the dynamics of asexual densities in the blood of the host. Our model predicts the direction of change in conversion rates that returns the greatest fitness after perturbation of asexual densities by different doses of antimalarial drugs. The loss of a high proportion of asexuals is predicted to elicit increased conversion (terminal investment), while smaller losses are managed by reducing conversion (reproductive restraint) to facilitate within-host survival and future transmission. This non-linear pattern of allocation is consistent with adaptive reproductive strategies observed in multicellular organisms. We then empirically estimate conversion rates of the rodent malaria parasite Plasmodium chabaudi in response to the killing of asexual stages by different doses of antimalarial drugs and forecast the short-term fitness consequences of these responses. Our data reveal the predicted non-linear pattern, and this is further supported by analyses of previous experiments that perturb asexual stage densities using drugs or within-host competition, across multiple parasite genotypes. Whilst conversion rates, across all datasets, are most strongly influenced by changes in asexual density, parasites also modulate conversion according to the availability of red blood cell resources. In summary, increasing conversion maximises short-term transmission and reducing conversion facilitates in-host survival and thus, future transmission. Understanding patterns of parasite allocation to reproduction matters because within-host replication is responsible for disease symptoms and between-host transmission determines disease spread.}, }
@article {pmid28485371, year = {2017}, author = {Milholland, B and Dong, X and Zhang, L and Hao, X and Suh, Y and Vijg, J}, title = {Differences between germline and somatic mutation rates in humans and mice.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15183}, doi = {10.1038/ncomms15183}, pmid = {28485371}, issn = {2041-1723}, support = {P01 AG017242/AG/NIA NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Child ; Genome ; Germ-Line Mutation/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mice, Inbred C57BL ; *Mutation Rate ; }, abstract = {The germline mutation rate has been extensively studied and has been found to vary greatly between species, but much less is known about the somatic mutation rate in multicellular organisms, which remains very difficult to determine. Here, we present data on somatic mutation rates in mice and humans, obtained by sequencing single cells and clones derived from primary fibroblasts, which allows us to make the first direct comparison with germline mutation rates in these two species. The results indicate that the somatic mutation rate is almost two orders of magnitude higher than the germline mutation rate and that both mutation rates are significantly higher in mice than in humans. Our findings demonstrate both the privileged status of germline genome integrity and species-specific differences in genome maintenance.}, }
@article {pmid30423096, year = {2018}, author = {García-Jiménez, B and García, JL and Nogales, J}, title = {FLYCOP: metabolic modeling-based analysis and engineering microbial communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {17}, pages = {i954-i963}, doi = {10.1093/bioinformatics/bty561}, pmid = {30423096}, issn = {1367-4811}, abstract = {Motivation: Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential to replace engineered single strains in biotechnology applications, in pharmaceutical, chemical and living architecture sectors. In contrast to single strain engineering, the effective and high-throughput analysis and engineering of microbial consortia face the lack of knowledge, tools and well-defined workflows. This manuscript contributes to fill this important gap with a framework, called FLYCOP (FLexible sYnthetic Consortium OPtimization), which contributes to microbial consortia modeling and engineering, while improving the knowledge about how these communities work. FLYCOP selects the best consortium configuration to optimize a given goal, among multiple and diverse configurations, in a flexible way, taking temporal changes in metabolite concentrations into account.<br><br>Results: In contrast to previous systems optimizing microbial consortia, FLYCOP has novel characteristics to face up to new problems, to represent additional features and to analyze events influencing the consortia behavior. In this manuscript, FLYCOP optimizes a Synechococcus elongatus-Pseudomonas putida consortium to produce the maximum amount of bio-plastic (PHA, polyhydroxyalkanoate), and highlights the influence of metabolites exchange dynamics in a four auxotrophic Escherichia coli consortium with parallel growth. FLYCOP can also provide an explanation about biological evolution driving evolutionary engineering endeavors by describing why and how heterogeneous populations emerge from monoclonal ones.<br><br>Code reproducing the study cases described in this manuscript are available on-line: https://github.com/beatrizgj/FLYCOP.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30410727, year = {2018}, author = {Morris, JJ}, title = {What is the hologenome concept of evolution?.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {}, doi = {10.12688/f1000research.14385.1}, pmid = {30410727}, issn = {2046-1402}, abstract = {All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host-microbiome ecosystem as a &quot;holobiont&quot;. Because natural selection acts on an organism's realized phenotype, and the phenotype of a holobiont is the result of the integrated activities of both the host and all of its microbiome inhabitants, it is reasonable to think that evolution can act at the level of the holobiont and cause changes in the &quot;hologenome&quot;, or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.}, }
@article {pmid30410109, year = {2018}, author = {Pönisch, W and Eckenrode, KB and Alzurqa, K and Nasrollahi, H and Weber, C and Zaburdaev, V and Biais, N}, title = {Pili mediated intercellular forces shape heterogeneous bacterial microcolonies prior to multicellular differentiation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {16567}, doi = {10.1038/s41598-018-34754-4}, pmid = {30410109}, issn = {2045-2322}, abstract = {Microcolonies are aggregates of a few dozen to a few thousand cells exhibited by many bacteria. The formation of microcolonies is a crucial step towards the formation of more mature bacterial communities known as biofilms, but also marks a significant change in bacterial physiology. Within a microcolony, bacteria forgo a single cell lifestyle for a communal lifestyle hallmarked by high cell density and physical interactions between cells potentially altering their behaviour. It is thus crucial to understand how initially identical single cells start to behave differently while assembling in these tight communities. Here we show that cells in the microcolonies formed by the human pathogen Neisseria gonorrhoeae (Ng) present differential motility behaviors within an hour upon colony formation. Observation of merging microcolonies and tracking of single cells within microcolonies reveal a heterogeneous motility behavior: cells close to the surface of the microcolony exhibit a much higher motility compared to cells towards the center. Numerical simulations of a biophysical model for the microcolonies at the single cell level suggest that the emergence of differential behavior within a multicellular microcolony of otherwise identical cells is of mechanical origin. It could suggest a route toward further bacterial differentiation and ultimately mature biofilms.}, }
@article {pmid30404915, year = {2018}, author = {Gao, A and Shrinivas, K and Lepeudry, P and Suzuki, HI and Sharp, PA and Chakraborty, AK}, title = {Evolution of weak cooperative interactions for biological specificity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1815912115}, pmid = {30404915}, issn = {1091-6490}, abstract = {A hallmark of biological systems is that particular functions and outcomes are realized in specific contexts, such as when particular signals are received. One mechanism for mediating specificity is described by Fisher's &quot;lock and key&quot; metaphor, exemplified by enzymes that bind selectively to a particular substrate via specific finely tuned interactions. Another mechanism, more prevalent in multicellular organisms, relies on multivalent weak cooperative interactions. Its importance has recently been illustrated by the recognition that liquid-liquid phase transitions underlie the formation of membraneless condensates that perform specific cellular functions. Based on computer simulations of an evolutionary model, we report that the latter mechanism likely became evolutionarily prominent when a large number of tasks had to be performed specifically for organisms to function properly. We find that the emergence of weak cooperative interactions for mediating specificity results in organisms that can evolve to accomplish new tasks with fewer, and likely less lethal, mutations. We argue that this makes the system more capable of undergoing evolutionary changes robustly, and thus this mechanism has been repeatedly positively selected in increasingly complex organisms. Specificity mediated by weak cooperative interactions results in some useful cross-reactivity for related tasks, but at the same time increases susceptibility to misregulation that might lead to pathologies.}, }
@article {pmid30404807, year = {2018}, author = {Palmer, WH and Joosten, J and Overheul, GJ and Jansen, PW and Vermeulen, M and Obbard, DJ and Van Rij, RP}, title = {Induction and suppression of NF-κB signalling by a DNA virus of Drosophila.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JVI.01443-18}, pmid = {30404807}, issn = {1098-5514}, abstract = {Interactions between the insect immune system and RNA viruses have been extensively studied in Drosophila, where RNA interference, NF-κB and JAK-STAT pathways underlie antiviral immunity. In response to RNA interference, insect viruses have convergently evolved suppressors of this pathway that act by diverse mechanisms to permit viral replication. However, interactions between the insect immune system and DNA viruses have received less attention, primarily because few Drosophila-infecting DNA virus isolates are available. Here, we use a recently-isolated DNA virus of Drosophila melanogaster, Kallithea virus (family Nudiviridae), to probe known antiviral immune responses and virus evasion tactics in the context of DNA virus infection. We find that fly mutants for RNA interference and Immune deficiency (Imd), but not Toll, pathways are more susceptible to Kallithea virus infection. We identify the Kallithea virus-encoded protein gp83 as a potent inhibitor of Toll signalling, suggesting that Toll mediates antiviral defense against Kallithea virus infection, but that it is suppressed by the virus. We find that Kallithea virus gp83 inhibits Toll signalling through the regulation of NF-κB transcription factors. Furthermore, we find that gp83 of the closely related Drosophila innubila nudivirus (DiNV) suppresses D. melanogaster Toll signalling, suggesting an evolutionary conserved function of Toll in defense against DNA viruses. Together, these results provide a broad description of known antiviral pathways in the context of DNA virus infection and identify the first Toll pathway inhibitor in a Drosophila virus, extending the known diversity of insect virus-encoded immune inhibitors.IMPORTANCE Co-evolution of multicellular organisms and their natural viruses may lead to an intricate relationship in which host survival requires effective immunity, and virus survival depends on evasion of such responses. Insect antiviral immunity, and reciprocal virus immune suppression tactics, have been well-studied in Drosophila melanogaster, primarily during RNA, but not DNA, virus infection. Therefore, we describe interactions between a recently-isolated Drosophila DNA virus (Kallithea virus - KV) and immune processes known to control RNA viruses, such as RNAi and Imd pathways. We find that KV suppresses the Toll pathway, and identify gp83 as a KV-encoded protein that underlies this suppression. This immunosuppressive ability is conserved in another nudivirus, suggesting the Toll pathway has conserved antiviral activity against DNA nudiviruses, which have evolved suppressors in response. Together, these results indicate that DNA viruses induce and suppress NF-κB responses, and advance the application of KV as a model to study insect immunity.}, }
@article {pmid30396330, year = {2018}, author = {Joo, S and Wang, MH and Lui, G and Lee, J and Barnas, A and Kim, E and Sudek, S and Worden, AZ and Lee, JH}, title = {Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida.}, journal = {BMC biology}, volume = {16}, number = {1}, pages = {136}, doi = {10.1186/s12915-018-0605-5}, pmid = {30396330}, issn = {1741-7007}, support = {Discovery Grant 418471-12//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; KCRC 2016M1A8A1925345//Ministry of Education, Science and Technology/ ; 0843119//Division of Integrative Organismal Systems/ ; 0843506//Division of Integrative Organismal Systems/ ; GBMF 3788//Gordon and Betty Moore Foundation/ ; CAREER-1453639//Directorate for Biological Sciences/ ; }, abstract = {BACKGROUND: Complex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Homeobox TFs in the TALE superclass are deeply embedded in the gene regulatory networks that orchestrate embryogenesis. Knotted-like homeobox (KNOX) TFs, homologous to animal MEIS, have been found to drive the haploid-to-diploid transition in both unicellular green algae and land plants via heterodimerization with other TALE superclass TFs, demonstrating remarkable functional conservation of a developmental TF across lineages that diverged one billion years ago. Here, we sought to delineate whether TALE-TALE heterodimerization is ancestral to eukaryotes.<br><br>RESULTS: We analyzed TALE endowment in the algal radiations of Archaeplastida, ancestral to land plants. Homeodomain phylogeny and bioinformatics analysis partitioned TALEs into two broad groups, KNOX and non-KNOX. Each group shares previously defined heterodimerization domains, plant KNOX-homology in the KNOX group and animal PBC-homology in the non-KNOX group, indicating their deep ancestry. Protein-protein interaction experiments showed that the TALEs in the two groups all participated in heterodimerization.<br><br>CONCLUSIONS: Our study indicates that the TF dyads consisting of KNOX/MEIS and PBC-containing TALEs must have evolved early in eukaryotic evolution. Based on our results, we hypothesize that in early eukaryotes, the TALE heterodimeric configuration provided transcription-on switches via dimerization-dependent subcellular localization, ensuring execution of the haploid-to-diploid transition only when the gamete fusion is correctly executed between appropriate partner gametes. The TALE switch then diversified in the several lineages that engage in a complex multicellular organization.}, }
@article {pmid30395805, year = {2018}, author = {Ten Tusscher, K}, title = {Of mice and plants; Comparative Developmental Systems Biology.}, journal = {Developmental biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ydbio.2018.10.024}, pmid = {30395805}, issn = {1095-564X}, abstract = {Multicellular animals and plants represent independent evolutionary experiments with complex multicellular bodyplans. Differences in their life history, a mobile versus sessile lifestyle, and predominant embryonic versus postembryonic development, have led to the evolution of highly different body plans. However, also many intriguing parallels exist. Extension of the vertebrate body axis and its segmentation into somites bears striking resemblance to plant root growth and the concomittant prepatterning of lateral root competent sites. Likewise, plant shoot phyllotaxis displays similarities with vertebrate limb and digit patterning. Additionally, both plants and animals use complex signalling systems combining systemic and local signals to fine tune and coordinate organ growth across their body. Identification of these striking examples of convergent evolution provides support for the existence of general design principles: the idea that for particular patterning demands, evolution is likely to arrive at highly similar developmental patterning mechanisms. Furthermore, focussing on these parallels may aid in identifying core mechanistic principles, often obscured by the highly complex nature of multiscale patterning processes.}, }
@article {pmid30389796, year = {2018}, author = {Bull, JK and Flynn, JM and Chain, FJJ and Cristescu, ME}, title = {Fitness and Genomic Consequences of Chronic Exposure to Low Levels of Copper and Nickel in Daphnia pulex Mutation Accumulation Lines.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1534/g3.118.200797}, pmid = {30389796}, issn = {2160-1836}, abstract = {In at least some unicellular organisms, mutation rates are temporarily raised upon exposure to environmental stress, potentially contributing to the evolutionary response to stress. Whether this is true for multicellular organisms, however, has received little attention. This study investigated the effects of chronic mild stress, in the form of low-level copper and nickel exposure, on mutational processes in Daphnia pulex using a combination of mutation accumulation, whole genome sequencing and life-history assays. After over 100 generations of mutation accumulation, we found no effects of metal exposure on the rates of single nucleotide mutations and of loss of heterozygosity events, the two mutation classes that occurred in sufficient numbers to allow statistical analysis. Similarly, rates of decline in fitness, as measured by intrinsic rate of population increase and of body size at first reproduction, were negligibly affected by metal exposure. We can reject the possibility that Daphnia were insufficiently stressed to invoke genetic responses as we have previously shown rates of large-scale deletions and duplications are elevated under metal exposure in this experiment. Overall, the mutation accumulation lines did not significantly depart from initial values for phenotypic traits measured, indicating the lineage used was broadly mutationally robust. Taken together, these results indicate that the mutagenic effects of chronic low-level exposure to these metals are restricted to certain mutation classes and that fitness consequences are likely minor and therefore unlikely to be relevant in determining the evolutionary responses of populations exposed to these stressors.}, }
@article {pmid30386324, year = {2018}, author = {Yap, GS and Gause, WC}, title = {Helminth Infections Induce Tissue Tolerance Mitigating Immunopathology but Enhancing Microbial Pathogen Susceptibility.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {2135}, doi = {10.3389/fimmu.2018.02135}, pmid = {30386324}, issn = {1664-3224}, abstract = {Helminths are ubiquitous and have chronically infected vertebrates throughout their evolution. As such helminths have likely exerted considerable selection pressure on our immune systems. The large size of multicellular helminths and their limited replicative capacity in the host necessarily elicits different host protective mechanisms than the immune response evoked by microbial pathogens such as bacteria, viruses and intracellular parasites. The cellular damage resulting from helminth migration through tissues is a major trigger of the type 2 and regulatory immune responses, which activates wound repair mechanisms that increases tissue tolerance to injury and resistance mechanisms that enhance resistance to further colonization with larval stages. While these wound healing and anti-inflammatory responses may be beneficial to the helminth infected host, they may also compromise the host's ability to mount protective immune responses to microbial pathogens. In this review we will first describe helminth-induced tolerance mechanisms that develop in specific organs including the lung and the intestine, and how adaptive immunity may contribute to these responses through differential activation of T cells in the secondary lymphoid organs. We will then integrate studies that have examined how the immune response is modulated in these specific tissues during coinfection of helminths with viruses, protozoa, and bacteria.}, }
@article {pmid30377252, year = {2018}, author = {Darris, C and Revert, F and Revert-Ros, F and Gozalbo-Rovira, R and Feigley, A and Fidler, A and Lopez-Pascual, E and Saus, J and Hudson, B}, title = {Unicellular ancestry and mechanisms of diversification of Goodpasture-antigen binding protein.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1074/jbc.RA118.006225}, pmid = {30377252}, issn = {1083-351X}, abstract = {The emergence of the basement membrane (BM), a specialized form of extracellular matrix, was essential in the unicellular transition to multicellularity. Yet, the mechanism is unknown. Goodpasture antigen-binding protein (GPBP), aBM protein, was uniquely poised to play diverse roles in this transition owing to its multiple isoforms (GPBP-1, -2 and -3) with varied intracellular and extracellular functions (ceramide trafficker and protein kinase). We sought to determine the evolutionary origin of GPBP isoforms. Our findings reveal the presence of GPBP in unicellular protists, with GPBP-2 as the most ancient isoform.In vertebrates GPBP-1 assumed extracellular function which is further enhanced by membrane bound GPBP-3 in mammalians, while GPBP-2 retained intracellular function. Moreover, GPBP-2 possesses a dual intracellular/extracellular functionin cnidarians, an early non-bilaterian group. We conclude that GPBP functioning both inside and outside the cell was of fundamental importance for the evolutionary transition to animal multicellularity and tissue evolution.}, }
@article {pmid29892951, year = {2018}, author = {Gao, Q and Xu, S and Zhu, X and Wang, L and Yang, Z and Zhao, X}, title = {Genome-wide identification and characterization of the RIO atypical kinase family in plants.}, journal = {Genes &amp; genomics}, volume = {40}, number = {6}, pages = {669-683}, doi = {10.1007/s13258-018-0658-4}, pmid = {29892951}, issn = {2092-9293}, support = {31601385//National Natural Science Foundation of China/International ; 2016ZX08012-002//National Science and Technology Major Project/International ; 2014AA10A601-5//National High-tech R&amp;D Program/International ; BK20160429//Natural Science Foundation of Jiangsu Province/International ; 16KJB210001//Natural Science Research Project in Universities of Jiangsu Province/International ; PPZY2015A018//Top-notch Academic Programs Project of Jiangsu Higher Education Institutions/International ; }, mesh = {Amino Acid Sequence/genetics ; Arabidopsis/genetics ; Gene Expression Regulation, Plant/genetics ; Genes, Plant/genetics ; Multigene Family ; Oryza/genetics ; Phylogeny ; Plant Proteins/genetics ; Plants/genetics ; Protein-Serine-Threonine Kinases/*genetics/metabolism ; Sequence Alignment/methods ; Transcriptome/genetics ; Viridiplantae/*genetics ; Zea mays/genetics ; }, abstract = {Members of the right open reading frame (RIO) atypical kinase family are present in all three domains of life. In eukaryotes, three subfamilies have been identified: RIO1, RIO2, and RIO3. Studies have shown that the yeast and human RIO1 and RIO2 kinases are essential for the biogenesis of small ribosomal subunits. Thus far, RIO3 has been found only in multicellular eukaryotes. In this study, we systematically identified members of the RIO gene family in 37 species representing the major evolutionary lineages in Viridiplantae. A total of 84 RIO genes were identified; among them, 41 were classified as RIO1 and 43 as RIO2. However, no RIO3 gene was found in any of the species examined. Phylogenetic trees constructed for plant RIO1 and RIO2 proteins were generally congruent with the species phylogeny. Subcellular localization analyses showed that the plant RIO proteins were localized mainly in the nucleus and/or cytoplasm. Expression profile analysis of rice, maize, and Arabidopsis RIO genes in different tissues revealed similar expression patterns between RIO1 and RIO2 genes, and their expression levels were high in certain tissues. In addition, the expressions of plant RIO genes were regulated by two drugs: mycophenolic acid and actinomycin D. Function prediction using genome-wide coexpression analysis revealed that most plant RIO genes may be involved in ribosome biogenesis. Our results will be useful for the evolutionary analysis of the ancient RIO kinase family and provide a basis for further functional characterization of RIO genes in plants.}, }
@article {pmid29850801, year = {2018}, author = {Nishiyama, E and Ohshima, K}, title = {Cross-Kingdom Commonality of a Novel Insertion Signature of RTE-Related Short Retroposons.}, journal = {Genome biology and evolution}, volume = {10}, number = {6}, pages = {1471-1483}, doi = {10.1093/gbe/evy098}, pmid = {29850801}, issn = {1759-6653}, mesh = {Animals ; DNA Transposable Elements/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Plant/genetics ; Lizards/genetics ; Long Interspersed Nucleotide Elements/genetics ; Magnoliopsida/genetics ; Mammals/genetics ; Microsatellite Repeats/genetics ; Mutagenesis, Insertional/methods ; Phylogeny ; Retroelements/*genetics ; Reverse Transcription/genetics ; Short Interspersed Nucleotide Elements/genetics ; }, abstract = {In multicellular organisms, such as vertebrates and flowering plants, horizontal transfer (HT) of genetic information is thought to be a rare event. However, recent findings unveiled unexpectedly frequent HT of RTE-clade LINEs. To elucidate the molecular footprints of the genomic integration machinery of RTE-related retroposons, the sequence patterns surrounding the insertion sites of plant Au-like SINE families were analyzed in the genomes of a wide variety of flowering plants. A novel and remarkable finding regarding target site duplications (TSDs) for SINEs was they start with thymine approximately one helical pitch (ten nucleotides) downstream of a thymine stretch. This TSD pattern was found in RTE-clade LINEs, which share the 3'-end sequence of these SINEs, in the genome of leguminous plants. These results demonstrably show that Au-like SINEs were mobilized by the enzymatic machinery of RTE-clade LINEs. Further, we discovered the same TSD pattern in animal SINEs from lizard and mammals, in which the RTE-clade LINEs sharing the 3'-end sequence with these animal SINEs showed a distinct TSD pattern. Moreover, a significant correlation was observed between the first nucleotide of TSDs and microsatellite-like sequences found at the 3'-ends of SINEs and LINEs. We propose that RTE-encoded protein could preferentially bind to a DNA region that contains a thymine stretch to cleave a phosphodiester bond downstream of the stretch. Further, determination of cleavage sites and/or efficiency of primer sites for reverse transcription may depend on microsatellite-like repeats in the RNA template. Such a unique mechanism may have enabled retroposons to successfully expand in frontier genomes after HT.}, }
@article {pmid30368592, year = {2018}, author = {Niklas, KJ and Wayne, R and Benítez, M and Newman, SA}, title = {Polarity, planes of cell division, and the evolution of plant multicellularity.}, journal = {Protoplasma}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00709-018-1325-y}, pmid = {30368592}, issn = {1615-6102}, abstract = {Organisms as diverse as bacteria, fungi, plants, and animals manifest a property called &quot;polarity.&quot; The literature shows that polarity emerges as a consequence of different mechanisms in different lineages. However, across all unicellular and multicellular organisms, polarity is evident when cells, organs, or organisms manifest one or more of the following: orientation, axiation, and asymmetry. Here, we review the relationships among these three features in the context of cell division and the evolution of multicellular polarity primarily in plants (defined here to include the algae). Data from unicellular and unbranched filamentous organisms (e.g., Chlamydomonas and Ulothrix) show that cell orientation and axiation are marked by cytoplasmic asymmetries. Branched filamentous organisms (e.g., Cladophora and moss protonema) require an orthogonal reorientation of axiation, or a localized cell asymmetry (e.g., &quot;tip&quot; growth in pollen tubes and fungal hyphae). The evolution of complex multicellular meristematic polarity required a third reorientation of axiation. These transitions show that polarity and the orientation of the future plane(s) of cell division are dyadic dynamical patterning modules that were critical for multicellular eukaryotic organisms.}, }
@article {pmid30362942, year = {2018}, author = {Castiglione, GM and Chang, BS}, title = {Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, doi = {10.7554/eLife.35957}, pmid = {30362942}, issn = {2050-084X}, support = {Discovery grant//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Trade-offs between protein stability and activity can restrict access to evolutionary trajectories, but widespread epistasis may facilitate indirect routes to adaptation. This may be enhanced by natural environmental variation, but in multicellular organisms this process is poorly understood. We investigated a paradoxical trajectory taken during the evolution of tetrapod dim-light vision, where in the rod visual pigment rhodopsin, E122 was fixed 350 million years ago, a residue associated with increased active-state (MII) stability but greatly diminished rod photosensitivity. Here, we demonstrate that high MII stability could have likely evolved without E122, but instead, selection appears to have entrenched E122 in tetrapods via epistatic interactions with nearby coevolving sites. In fishes by contrast, selection may have exploited these epistatic effects to explore alternative trajectories, but via indirect routes with low MII stability. Our results suggest that within tetrapods, E122 and high MII stability cannot be sacrificed-not even for improvements to rod photosensitivity.}, }
@article {pmid30357728, year = {2018}, author = {Fitzgerald, RS}, title = {O2/CO2: Biological Detection to Homeostatic Control.}, journal = {Advances in experimental medicine and biology}, volume = {1071}, number = {}, pages = {1-12}, doi = {10.1007/978-3-319-91137-3_1}, pmid = {30357728}, issn = {0065-2598}, abstract = {Oxygen (O2) and Carbon Dioxide (CO2) are the two gases to be detected and controlled. Of interest might be a query of the evolutionary origin of each. From the cooling of the Big Bang (~13.8 Billion Years Ago [BYA]) came a quark-gluon plasma from which protons and neutrons emerged, producing H, He, Li. As H and He collapsed into the first stars at ~13.3 BYA carbon and monatomic oxygen were generated. Some 3 billion years ago greater amounts of diatomic oxygen (O2) were provided by earth's photosynthesizing bacteria until earth's atmosphere had sufficient amounts to sustain the life processes of multicellular animals, and finally higher vertebrates. Origin of CO2 is somewhat unclear, though it probably came from the erupting early volcanoes. Photosynthesis produced sugars with O2 a waste product. Animal life took sugars and O2 needed for life. Clearly, animal detection and control of each was critical. Many chapters involving great heroes describe phases involved in detecting each, both in the CNS and in peripheral detectors. The carotid body (CB) has played a crucial role in the detection of each. What reflex responses the stimulated CB generates, and the mechanisms as to how it does so have been a fascinating story over the last 1.5 centuries, but principally over the last 50 years. Explorations to detect these gases have proceeded from the organismal/system/ organ levels down to the sub-cell and genetic levels.}, }
@article {pmid30348074, year = {2018}, author = {Kin, K and Forbes, G and Cassidy, A and Schaap, P}, title = {Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {764}, doi = {10.1186/s12864-018-5146-3}, pmid = {30348074}, issn = {1471-2164}, support = {742288//H2020 European Research Council/ ; ALTF 295-2015//European Molecular Biology Organization/ ; H28-1002//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: A major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types. During Dictyostelid evolution novel specialization occurred within taxon group 4. We here aim to retrace the nature and ancestry of the novel &quot;cup&quot; cells by comparing their transcriptome to that of other cell types.<br><br>RESULTS: RNA-Seq was performed on purified mature spore, stalk and cup cells and on vegetative amoebas. Clustering and phylogenetic analyses showed that cup cells were most similar to stalk cells, suggesting that they share a common ancestor. The affinity between cup and stalk cells was also evident from promoter-reporter studies of newly identified cell-type genes, which revealed late expression in cups of many stalk genes. However, GO enrichment analysis reveal the unexpected prominence of GTPase mediated signalling in cup cells, in contrast to enrichment of autophagy and cell wall synthesis related transcripts in stalk cells. Combining the cell type RNA-Seq data with developmental expression profiles revealed complex expression dynamics in each cell type as well as genes exclusively expressed during terminal differentiation. Most notable were nine related hssA-like genes that were highly and exclusively expressed in cup cells.<br><br>CONCLUSIONS: This study reveals the unique transcriptomes of the mature cup, stalk and spore cells of D. discoideum and provides insight into the ancestry of cup cells and roles in signalling that were not previously realized. The data presented in this study will serve as an important resource for future studies into the regulation and evolution of cell type specialization.}, }
@article {pmid30336184, year = {2018}, author = {Miller, WB and Torday, JS and Baluška, F}, title = {Biological Evolution as Defense of 'Self'.}, journal = {Progress in biophysics and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pbiomolbio.2018.10.002}, pmid = {30336184}, issn = {1873-1732}, abstract = {Although the origin of self-referential consciousness is unknown, it can be argued that the instantiation of self-reference was the commencement the living state as phenomenal experientiality. As self-referential cognition is demonstrated by all living organisms, life can be equated with the sustenance of cellular homeostasis in the continuous defense of 'self'. It is proposed that the epicenter of 'self' is perpetually embodied within the basic cellular form in which it was instantiated. Cognition-Based Evolution argues that all of biological and evolutionary development represents the perpetual autopoietic defense of self-referential basal cellular states of homeostatic preference. The means by which these states are attained and maintained is through self-referential measurement of information and its communication. The multicellular forms, either as biofilms or holobionts, represent the cellular attempt to achieve maximum states of informational distinction and energy efficiency through individual and collective means. In this frame, consciousness, self-consciousness and intelligence can be identified as forms of collective cellular phenotype directed towards the defense of fundamental cellular self-reference.}, }
@article {pmid30325443, year = {2018}, author = {Skaldin, M and Tuittila, M and Zavialov, AV and Zavialov, AV}, title = {Secreted bacterial adenosine deaminase is an evolutionary precursor of adenosine deaminase growth factor.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msy193}, pmid = {30325443}, issn = {1537-1719}, abstract = {Adenosine deaminases (ADAs) play a pivotal role in regulating the level of adenosine, an important signaling molecule that controls a variety of cellular responses. Two distinct ADAs, ADA1 and adenosine deaminase growth factor (ADGF aka ADA2), are known. Cytoplasmic ADA1 plays a key role in purine metabolism and is widely distributed from prokaryotes to mammals. On the other hand, secreted ADGF/ADA2 is a cell-signaling protein that was thought to be present only in multicellular organisms. Here, we discovered a bacterial homologue of ADGF/ADA2. Bacterial and eukaryotic ADGF/ADA2 possess the dimerization and PRB domains characteristic for the family, have nearly identical catalytic sites, and show similar catalytic characteristics. Most surprisingly, the bacterial enzyme has a signal sequence similar to that of eukaryotic ADGF/ADA2 and is specifically secreted into the extracellular space, where it may potentially control the level of extracellular adenosine. This finding provides the first example of evolution of an extracellular eukaryotic signaling protein from a secreted bacterial analogue with identical activity and suggests a potential role of ADGF/ADA2 in bacterial communication.}, }
@article {pmid30318349, year = {2018}, author = {Bråte, J and Neumann, RS and Fromm, B and Haraldsen, AAB and Tarver, JE and Suga, H and Donoghue, PCJ and Peterson, KJ and Ruiz-Trillo, I and Grini, PE and Shalchian-Tabrizi, K}, title = {Unicellular Origin of the Animal MicroRNA Machinery.}, journal = {Current biology : CB}, volume = {28}, number = {20}, pages = {3288-3295.e5}, doi = {10.1016/j.cub.2018.08.018}, pmid = {30318349}, issn = {1879-0445}, abstract = {The emergence of multicellular animals was associated with an increase in phenotypic complexity and with the acquisition of spatial cell differentiation and embryonic development. Paradoxically, this phenotypic transition was not paralleled by major changes in the underlying developmental toolkit and regulatory networks. In fact, most of these systems are ancient, established already in the unicellular ancestors of animals [1-5]. In contrast, the Microprocessor protein machinery, which is essential for microRNA (miRNA) biogenesis in animals, as well as the miRNA genes themselves produced by this Microprocessor, have not been identified outside of the animal kingdom [6]. Hence, the Microprocessor, with the key proteins Pasha and Drosha, is regarded as an animal innovation [7-9]. Here, we challenge this evolutionary scenario by investigating unicellular sister lineages of animals through genomic and transcriptomic analyses. We identify in Ichthyosporea both Drosha and Pasha (DGCR8 in vertebrates), indicating that the Microprocessor complex evolved long before the last common ancestor of animals, consistent with a pre-metazoan origin of most of the animal developmental gene elements. Through small RNA sequencing, we also discovered expressed bona fide miRNA genes in several species of the ichthyosporeans harboring the Microprocessor. A deep, pre-metazoan origin of the Microprocessor and miRNAs comply with a view that the origin of multicellular animals was not directly linked to the innovation of these key regulatory components.}, }
@article {pmid30309963, year = {2018}, author = {Armon, S and Bull, MS and Aranda-Diaz, A and Prakash, M}, title = {Ultrafast epithelial contractions provide insights into contraction speed limits and tissue integrity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1802934115}, pmid = {30309963}, issn = {1091-6490}, abstract = {By definition of multicellularity, all animals need to keep their cells attached and intact, despite internal and external forces. Cohesion between epithelial cells provides this key feature. To better understand fundamental limits of this cohesion, we study the epithelium mechanics of an ultrathin (∼25 μm) primitive marine animal Trichoplax adhaerens, composed essentially of two flat epithelial layers. With no known extracellular matrix and no nerves or muscles, T. adhaerens has been claimed to be the &quot;simplest known living animal,&quot; yet is still capable of coordinated locomotion and behavior. Here we report the discovery of the fastest epithelial cellular contractions known in any metazoan, to be found in T. adhaerens dorsal epithelium (50% shrinkage of apical cell area within one second, at least an order of magnitude faster than other known examples). Live imaging reveals emergent contractile patterns that are mostly sporadic single-cell events, but also include propagating contraction waves across the tissue. We show that cell contraction speed can be explained by current models of nonmuscle actin-myosin bundles without load, while the tissue architecture and unique mechanical properties are softening the tissue, minimizing the load on a contracting cell. We propose a hypothesis, in which the physiological role of the contraction dynamics is to resist external stresses while avoiding tissue rupture (&quot;active cohesion&quot;), a concept that can be further applied to engineering of active materials.}, }
@article {pmid30295813, year = {2018}, author = {Sperling, EA and Stockey, RG}, title = {The Temporal and Environmental Context of Early Animal Evolution: Considering All the Ingredients of an &quot;Explosion&quot;.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {605-622}, doi = {10.1093/icb/icy088}, pmid = {30295813}, issn = {1557-7023}, abstract = {Animals originated and evolved during a unique time in Earth history-the Neoproterozoic Era. This paper aims to discuss (1) when landmark events in early animal evolution occurred, and (2) the environmental context of these evolutionary milestones, and how such factors may have affected ecosystems and body plans. With respect to timing, molecular clock studies-utilizing a diversity of methodologies-agree that animal multicellularity had arisen by ∼800 million years ago (Ma) (Tonian period), the bilaterian body plan by ∼650 Ma (Cryogenian), and divergences between sister phyla occurred ∼560-540 Ma (late Ediacaran). Most purported Tonian and Cryogenian animal body fossils are unlikely to be correctly identified, but independent support for the presence of pre-Ediacaran animals is recorded by organic geochemical biomarkers produced by demosponges. This view of animal origins contrasts with data from the fossil record, and the taphonomic question of why animals were not preserved (if present) remains unresolved. Neoproterozoic environments demanding small, thin, body plans, and lower abundance/rarity in populations may have played a role. Considering environmental conditions, geochemical data suggest that animals evolved in a relatively low-oxygen ocean. Here, we present new analyses of sedimentary total organic carbon contents in shales suggesting that the Neoproterozoic ocean may also have had lower primary productivity-or at least lower quantities of organic carbon reaching the seafloor-compared with the Phanerozoic. Indeed, recent modeling efforts suggest that low primary productivity is an expected corollary of a low-O2 world. Combined with an inability to inhabit productive regions in a low-O2 ocean, earliest animal communities would likely have been more food limited than generally appreciated, impacting both ecosystem structure and organismal behavior. In light of this, we propose the &quot;fire triangle&quot; metaphor for environmental influences on early animal evolution. Moving toward consideration of all environmental aspects of the Cambrian radiation (fuel, heat, and oxidant) will ultimately lead to a more holistic view of the event.}, }
@article {pmid30288746, year = {2018}, author = {Stiller, JW and Yang, C and Collén, J and Kowalczyk, N and Thompson, BE}, title = {Evolution and expression of core SWI/SNF genes in red algae.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.12795}, pmid = {30288746}, issn = {1529-8817}, support = {0741907//NSF Research Collaboration Network/ ; DE-AC02-05CH11231//U.S. Department of Energy Joint Genome Institute/ ; }, abstract = {Red algae are the oldest identifiable multicellular eukaryotes, with a fossil record dating back more than a billion years. During that time two major rhodophyte lineages, bangiophytes and florideophytes, have evolved varied levels of morphological complexity. These two groups are distinguished, in part, by different patterns of multicellular development, with florideophytes exhibiting a far greater diversity of morphologies. Interestingly, during their long evolutionary history, there is no record of a rhodophyte achieving the kinds of cellular and tissue-specific differentiation present in other multicellular algal lineages. To date, the genetic underpinnings of unique aspects of red algal development are largely unexplored; however, they must reflect the complements and patterns of expression of key regulatory genes. Here we report comparative evolutionary and gene expression analyses of core subunits of the SWI/SNF chromatin-remodeling complex, which is implicated in cell differentiation and developmental regulation in more well studied multicellular groups. Our results suggest that a single, canonical SWI/SNF complex was present in the rhodophyte ancestor, with gene duplications and evolutionary diversification of SWI/SNF subunits accompanying the evolution of multicellularity in the common ancestor of bangiophytes and florideophytes. Differences in how SWI/SNF chromatin remodeling evolved subsequently, in particular gene losses and more rapid divergence of SWI3 and SNF5 in bangiophytes, could help to explain why they exhibit a more limited range of morphological complexity than their florideophyte cousins.}, }
@article {pmid30283698, year = {2018}, author = {Godwin, JL and Spurgin, LG and Michalczyk, Ł and Martin, OY and Lumley, AJ and Chapman, T and Gage, MJG}, title = {Lineages evolved under stronger sexual selection show superior ability to invade conspecific competitor populations.}, journal = {Evolution letters}, volume = {2}, number = {5}, pages = {511-523}, doi = {10.1002/evl3.80}, pmid = {30283698}, issn = {2056-3744}, abstract = {Despite limitations on offspring production, almost all multicellular species use sex to reproduce. Sex gives rise to sexual selection, a widespread force operating through competition and choice within reproduction, however, it remains unclear whether sexual selection is beneficial for total lineage fitness, or if it acts as a constraint. Sexual selection could be a positive force because of selection on improved individual condition and purging of mutation load, summing into lineages with superior fitness. On the other hand, sexual selection could negate potential net fitness through the actions of sexual conflict, or because of tensions between investment in sexually selected and naturally selected traits. Here, we explore these ideas using a multigenerational invasion challenge to measure consequences of sexual selection for the overall net fitness of a lineage. After applying experimental evolution under strong versus weak regimes of sexual selection for 77 generations with the flour beetle Tribolium castaneum, we measured the overall ability of introductions from either regime to invade into conspecific competitor populations across eight generations. Results showed that populations from stronger sexual selection backgrounds had superior net fitness, invading more rapidly and completely than counterparts from weak sexual selection backgrounds. Despite comprising only 10% of each population at the start of the invasion experiment, colonizations from strong sexual selection histories eventually achieved near-total introgression, almost completely eliminating the original competitor genotype. Population genetic simulations using the design and parameters of our experiment indicate that this invasion superiority could be explained if strong sexual selection had improved both juvenile and adult fitness, in both sexes. Using a combination of empirical and modeling approaches, our findings therefore reveal positive and wide-reaching impacts of sexual selection for net population fitness when facing the broad challenge of invading competitor populations across multiple generations.}, }
@article {pmid30281390, year = {2018}, author = {Booth, DS and Szmidt-Middleton, H and King, N}, title = {Choanoflagellate transfection illuminates their cell biology and the ancestry of animal septins.}, journal = {Molecular biology of the cell}, volume = {}, number = {}, pages = {mbcE18080514}, doi = {10.1091/mbc.E18-08-0514}, pmid = {30281390}, issn = {1939-4586}, abstract = {As the closest living relatives of animals, choanoflagellates offer unique insights into animal origins and core mechanisms underlying animal cell biology. However, unlike traditional model organisms, such as yeast, flies and worms, choanoflagellates have been refractory to DNA delivery methods for expressing foreign genes. Here we report the establishment of a robust method for expressing transgenes in the choanoflagellate Salpingoeca rosetta, overcoming barriers that have previously hampered DNA delivery and expression. To demonstrate how this method accelerates the study of S. rosetta cell biology, we engineered a panel of fluorescent protein markers that illuminate key features of choanoflagellate cells. We then investigated the localization of choanoflagellate septins, a family of GTP-binding cytoskeletal proteins that are hypothesized to regulate multicellular rosette development in S. rosetta. Fluorescently tagged septins localized to the basal pole of S. rosetta single cells and rosettes in a pattern resembling septin localization in animal epithelia. The establishment of transfection in S. rosetta and its application to the study of septins represent critical advances in the growth of S. rosetta as an experimental model for investigating choanoflagellate cell biology, core mechanisms underlying animal cell biology, and the origin of animals.}, }
@article {pmid30280251, year = {2018}, author = {Zhou, W and Gao, B and Zhu, S}, title = {Did cis- and trans-defensins derive from a common ancestor?.}, journal = {Immunogenetics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00251-018-1086-y}, pmid = {30280251}, issn = {1432-1211}, support = {31570773//National Natural Science Foundation of China/ ; 31870766//National Natural Science Foundation of China/ ; }, abstract = {Defensins are small, cysteine-rich, cationic antimicrobial peptides, serving as effectors of the innate immune system and modulators of the adaptive immune system. They extensively exist in multicellular organisms and are divided into cis and trans according to their disulfide bridge connectivity patterns. It has been proposed that these two types of defensins convergently originated from different ancestors. Here, we report the discovery of a structural signature involved in the formation of the cysteine-stabilized α-helix/β-sheet (CSαβ) fold of the cis-defensins in some trans-β-defensins, with only one amino acid indel (CXC vs. CC. C, cysteine; X, any amino acid). The indel of the X residue in the structural signature provides a possible explanation as to why cis- and trans-defensins possess different folds and connectivity patterns of disulfide bridges formed in evolution. Although our attempt to convert the structure type of a present-day trans-defensin with the X residue deleted was unsuccessful due to the low solubility of the synthetic peptide, a combination of data from structural signature, function, and phylogenetic distribution suggests that these defensins may have descended from a common ancestor. In this evolutionary scenario, we propose that a progenitor cis-scaffold might gradually evolve into a trans-defensin after deleting the X residue in specific lineages. This proposal adds a new dimension to more deeply studying the evolutionary relationship of defensins with different folds and of other distantly related proteins.}, }
@article {pmid30271390, year = {2018}, author = {Teng, Z and Zhang, Y and Zhang, W and Pan, H and Xu, J and Huang, H and Xiao, T and Wu, LF}, title = {Diversity and Characterization of Multicellular Magnetotactic Prokaryotes From Coral Reef Habitats of the Paracel Islands, South China Sea.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2135}, doi = {10.3389/fmicb.2018.02135}, pmid = {30271390}, issn = {1664-302X}, abstract = {While multicellular magnetotactic prokaryotes (MMPs) are ubiquitous in marine environments, the diversity of MMPs in sediments of coral reef ecosystems has rarely been reported. In this study, we made an investigation on the diversity and characteristics of MMPs in sediments at 11 stations in coral reef habitats of the Paracel Islands. The results showed that MMPs were present at nine stations, with spherical mulberry-like MMPs (s-MMPs) found at all stations and ellipsoidal pineapple-like MMPs (e-MMPs) found at seven stations. The maximum abundance of MMPs was 6 ind./cm3. Phylogenetic analysis revealed the presence of one e-MMP species and five s-MMP species including two species of a new genus. The results indicate that coral reef habitats of the Paracel Islands have a high diversity of MMPs that bio-mineralize multiple intracellular chains of iron crystals and play important role in iron cycling in such oligotrophic environment. These observations provide new perspective of the diversity of MMPs in general and expand knowledge of the occurrence of MMPs in coral reef habitats.}, }
@article {pmid30270425, year = {2018}, author = {Joshi, J and Guttal, V}, title = {Demographic noise and cost of greenbeard can facilitate greenbeard cooperation.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1111/evo.13615}, pmid = {30270425}, issn = {1558-5646}, support = {DBT-IISc partnership program//Department of Biotechnology , Ministry of Science and Technology/ ; DST-FIST//Department of Science and Technology, Ministry of Science and Technology/ ; Mathematical Biology Phase II (SR/S4/MS:799/12)//Department of Science and Technology, Ministry of Science and Technology/ ; ICTS/Prog-PGE2018/03//International Centre for Theoretical Sciences/ ; }, abstract = {Cooperation among organisms, where cooperators suffer a personal cost to benefit others, is ubiquitous in nature. Greenbeard is a key mechanism for the evolution of cooperation, where a single gene or a set of linked genes codes for both cooperation and a phenotypic tag (metaphorically called &quot;green beard&quot;). Greenbeard cooperation is typically thought to decline over time since defectors can also evolve the tag. However, models of tag-based cooperation typically ignore two key realistic features: populations are finite, and that phenotypic tags can be costly. We develop an analytical model for coevolutionary dynamics of two evolvable traits in finite populations with mutations: costly cooperation and a costly tag. We show that an interplay of demographic noise and cost of the tag can induce coevolutionary cycling, where the evolving population does not reach a steady state but spontaneously switches between cooperative tag-carrying and noncooperative tagless states. Such dynamics allows the tag to repeatedly reappear even after it is invaded by defectors. Thus, we highlight the surprising possibility that the cost of the tag, together with demographic noise, can facilitate the evolution of greenbeard cooperation. We discuss implications of these findings in the context of the evolution of quorum sensing and multicellularity.}, }
@article {pmid30254228, year = {2018}, author = {Chen, X and Köllner, TG and Shaulsky, G and Jia, Q and Dickschat, JS and Gershenzon, J and Chen, F}, title = {Diversity and Functional Evolution of Terpene Synthases in Dictyostelid Social Amoebae.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14361}, doi = {10.1038/s41598-018-32639-0}, pmid = {30254228}, issn = {2045-2322}, abstract = {Dictyostelids, or social amoebae, have a unique life style in forming multicellular fruiting bodies from unicellular amoeboids upon starvation. Recently, dictyostelids were found to contain terpene synthase (TPS) genes, a gene type of secondary metabolism previously known to occur only in plants, fungi and bacteria. Here we report an evolutionary functional study of dictyostelid TPS genes. The number of TPS genes in six species of dictyostelids examined ranges from 1 to 19; and the model species Dictyostelium purpureum contains 12 genes. Using in vitro enzyme assays, the 12 TPS genes from D. purpureum were shown to encode functional enzymes with distinct product profiles. The expression of the 12 TPS genes in D. purpureum is developmentally regulated. During multicellular development, D. purpureum releases a mixture of volatile terpenes dominated by sesquiterpenes that are the in vitro products of a subset of the 12 TPS genes. The quality and quantity of the terpenes released from D. purpureum, however, bear little resemblance to those of D. discoideum, a closely related dictyostelid. Despite these variations, the conserved clade of dictyostelid TPSs, which have an evolutionary distance of more than 600 million years, has the same biochemical function, catalyzing the formation of a sesquiterpene protoillud-7-ene. Taken together, our results indicate that the dynamic evolution of dictyostelid TPS genes includes both purifying selection of an orthologous group and species-specific expansion with functional divergence. Consequently, the terpenes produced by these TPSs most likely have conserved as well as species-adaptive biological functions as chemical languages in dictyostelids.}, }
@article {pmid30231028, year = {2018}, author = {Lau, AYT and Cheng, X and Cheng, CK and Nong, W and Cheung, MK and Chan, RH and Hui, JHL and Kwan, HS}, title = {Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0198234}, doi = {10.1371/journal.pone.0198234}, pmid = {30231028}, issn = {1932-6203}, abstract = {Coprinopsis cinerea is a model mushroom particularly suited for the study of fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) have been extensively studied in animals and plants for their essential roles in post-transcriptional regulation of gene expression, miRNAs in fungi are less well characterized and their potential roles in controlling mushroom development remain unknown. To identify miRNA-like RNAs (milRNAs) in C. cinerea and explore their expression patterns during the early developmental transition of mushroom development, small RNA libraries of vegetative mycelium and primordium were generated and putative milRNA candidates were identified following the standards of miRNA prediction in animals and plants. Two out of 22 novel predicted milRNAs, cci-milR-12c and cci-milR-13e-5p, were validated by northern blot and stem-loop reverse transcription real-time PCR. Cci-milR-12c was differentially expressed whereas the expression levels of cci-milR-13e-5p were similar in the two developmental stages. Target prediction of the validated milRNAs resulted in genes associated with fruiting body development, including pheromone, hydrophobin, cytochrome P450, and protein kinase. Essential genes for miRNA biogenesis, including three coding for Dicer-like (DCL), one for Argonaute (AGO), one for AGO-like and one for quelling deficient-2 (QDE-2) proteins, were also identified in the C. cinerea genome. Phylogenetic analysis showed that the DCL and AGO proteins of C. cinerea were more closely related to those in other basidiomycetes and ascomycetes than to those in animals and plants. Taken together, our findings provided the first evidence for milRNAs in the model mushroom and their potential roles in regulating fruiting body development. New information on the evolutionary relationship of milRNA biogenesis proteins across kingdoms has also provided new insights for guiding further functional and evolutionary studies of miRNAs.}, }
@article {pmid30225080, year = {2018}, author = {Herron, MD and Ratcliff, WC and Boswell, J and Rosenzweig, F}, title = {Genetics of a de novo origin of undifferentiated multicellularity.}, journal = {Royal Society open science}, volume = {5}, number = {8}, pages = {180912}, doi = {10.1098/rsos.180912}, pmid = {30225080}, issn = {2054-5703}, abstract = {The evolution of multicellularity was a major transition in evolution and set the stage for unprecedented increases in complexity, especially in land plants and animals. Here, we explore the genetics underlying a de novo origin of multicellularity in a microbial evolution experiment carried out on the green alga Chlamydomonas reinhardtii. We show that large-scale changes in gene expression underlie the transition to a multicellular life cycle. Among these, changes to genes involved in cell cycle and reproductive processes were overrepresented, as were changes to C. reinhardtii-specific and volvocine-specific genes. These results suggest that the genetic basis for the experimental evolution of multicellularity in C. reinhardtii has both lineage-specific and shared features, and that the shared features have more in common with C. reinhardtii's relatives among the volvocine algae than with other multicellular green algae or land plants.}, }
@article {pmid30220504, year = {2018}, author = {De Clerck, O and Kao, SM and Bogaert, KA and Blomme, J and Foflonker, F and Kwantes, M and Vancaester, E and Vanderstraeten, L and Aydogdu, E and Boesger, J and Califano, G and Charrier, B and Clewes, R and Del Cortona, A and D'Hondt, S and Fernandez-Pozo, N and Gachon, CM and Hanikenne, M and Lattermann, L and Leliaert, F and Liu, X and Maggs, CA and Popper, ZA and Raven, JA and Van Bel, M and Wilhelmsson, PKI and Bhattacharya, D and Coates, JC and Rensing, SA and Van Der Straeten, D and Vardi, A and Sterck, L and Vandepoele, K and Van de Peer, Y and Wichard, T and Bothwell, JH}, title = {Insights into the Evolution of Multicellularity from the Sea Lettuce Genome.}, journal = {Current biology : CB}, volume = {28}, number = {18}, pages = {2921-2933.e5}, doi = {10.1016/j.cub.2018.08.015}, pmid = {30220504}, issn = {1879-0445}, abstract = {We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance &quot;green tides.&quot; Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage.}, }
@article {pmid30218496, year = {2018}, author = {Kulkarni, P and Uversky, VN}, title = {Intrinsically Disordered Proteins: The Dark Horse of the Dark Proteome.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e1800061}, doi = {10.1002/pmic.201800061}, pmid = {30218496}, issn = {1615-9861}, abstract = {A good portion of the 'protein universe' embodies the 'dark proteome'. The latter comprises proteins not amenable to experimental structure determination by existing means and inaccessible to homology modeling. Hence, the dark proteome has remained largely unappreciated. Intrinsically disordered proteins (IDPs) that lack rigid 3D structure are a major component of this dark proteome across all three kingdoms of life. Despite lack of structure, IDPs play critical roles in numerous important biological processes. Furthermore, IDPs serve as crucial constituents of proteinaceous membrane-less organelles (PMLOs), where they often serve as drivers and controllers of biological liquid-liquid phase transitions responsible for the PMLO biogenesis. In this perspective, the role of IDPs is discussed in i) the origin of prebiotic life and the evolution of the first independent primordial living unit akin to Tibor Gánti's chemoton, which preceded the Last Universal Common Ancestor (LUCA), ii) role in multicellularity and hence, in major evolutionary transitions, and iii), their role in phenotypic switching, and the emergence of new traits and adaptive opportunities via non-genetic, protein-based mechanisms. The emerging picture suggests that despite being major constituents of the dark matter, IDPs may be the dark horse in the protein universe.}, }
@article {pmid30214674, year = {2018}, author = {Baluška, F and Miller, WB}, title = {Senomic view of the cell: Senome versus Genome.}, journal = {Communicative &amp; integrative biology}, volume = {11}, number = {3}, pages = {1-9}, doi = {10.1080/19420889.2018.1489184}, pmid = {30214674}, issn = {1942-0889}, abstract = {In the legacy of Thomas Henry Huxley, and his 'epigenetic' philosophy of biology, cells are proposed to represent a trinity of three memory-storing media: Senome, Epigenome, and Genome that together comprise a cell-wide informational architecture. Our current preferential focus on the Genome needs to be complemented by a similar focus on the Epigenome and a here proposed Senome, representing the sum of all the sensory experiences of the cognitive cell and its sensing apparatus. Only then will biology be in a position to embrace the whole complexity of the eukaryotic cell, understanding its true nature which allows the communicative assembly of cells in the form of sentient multicellular organisms.}, }
@article {pmid30212236, year = {2018}, author = {Zhang, L and Vijg, J}, title = {Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging.}, journal = {Annual review of genetics}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-genet-120417-031501}, pmid = {30212236}, issn = {1545-2948}, abstract = {DNA mutations as a consequence of errors during DNA damage repair, replication, or mitosis are the substrate for evolution. In multicellular organisms, mutations can occur in the germline and also in somatic tissues, where they are associated with cancer and other chronic diseases and possibly with aging. Recent advances in high-throughput sequencing have made it relatively easy to study germline de novo mutations, but in somatic cells, the vast majority of mutations are low-abundant and can be detected only in clonal lineages, such as tumors, or single cells. Here we review recent results on somatic mutations in normal human and animal tissues with a focus on their possible functional consequences. Expected final online publication date for the Annual Review of Genetics Volume 52 is November 23, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid30177944, year = {2018}, author = {Yruela, I and Contreras-Moreira, B and Dunker, AK and Niklas, KJ}, title = {Evolution of Protein Ductility in Duplicated Genes of Plants.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1216}, doi = {10.3389/fpls.2018.01216}, pmid = {30177944}, issn = {1664-462X}, abstract = {Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of diverse phylogenetic lineages have revealed: (1) that protein ductility increases in concert with organismic complexity, and (2) that distributions of IDPs and IDRs along the chromosomes of plant species are non-random and correlate with variations in the rates of the genetic recombination and chromosomal rearrangement. Here, we show that approximately 50% of aligned residues in paralogs across a spectrum of algae, bryophytes, monocots, and eudicots are IDRs and that a high proportion (ca. 60%) are in disordered segments greater than 30 residues. When three types of IDRs are distinguished (i.e., identical, similar and variable IDRs) we find that species with large numbers of chromosome and endoduplicated genes exhibit paralogous sequences with a higher frequency of identical IDRs, whereas species with small chromosomes numbers exhibit paralogous sequences with a higher frequency of similar and variable IDRs. These results are interpreted to indicate that genome duplication events influence the distribution of IDRs along protein sequences and likely favor the presence of identical IDRs (compared to similar IDRs or variable IDRs). We discuss the evolutionary implications of gene duplication events in the context of ductile/disordered residues and segments, their conservation, and their effects on functionality.}, }
@article {pmid30172691, year = {2018}, author = {Olejarz, J and Kaveh, K and Veller, C and Nowak, MA}, title = {Selection for synchronized cell division in simple multicellular organisms.}, journal = {Journal of theoretical biology}, volume = {457}, number = {}, pages = {170-179}, doi = {10.1016/j.jtbi.2018.08.038}, pmid = {30172691}, issn = {1095-8541}, abstract = {The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular organism requires multiple rounds of cell division, a natural question is whether these cell divisions should be synchronous or not. We study a population model in which there compete simple multicellular organisms that grow by either synchronous or asynchronous cell divisions. We demonstrate that natural selection can act differently on synchronous and asynchronous cell division, and we offer intuition for why these phenotypes are generally not neutral variants of each other.}, }
@article {pmid30171399, year = {2018}, author = {Liu, Y and Liu, D and Khan, AR and Liu, B and Wu, M and Huang, L and Wu, J and Song, G and Ni, H and Ying, H and Yu, H and Gan, Y}, title = {NbGIS regulates glandular trichome initiation through GA signaling in tobacco.}, journal = {Plant molecular biology}, volume = {98}, number = {1-2}, pages = {153-167}, doi = {10.1007/s11103-018-0772-3}, pmid = {30171399}, issn = {1573-5028}, support = {31570183; 31529001; 31661143004//National Natural Science Foundation of China/ ; LZ15C020001//Zhejiang Provincial Natural Science Foundation of China/ ; 2015CB150200//Major State Basic Research Development Program/ ; 2016YFD0100701//the National Key R &amp; D Program of China/ ; }, mesh = {Amino Acid Sequence ; Biosynthetic Pathways/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Gibberellins/biosynthesis/*metabolism ; Phenotype ; Phylogeny ; Plant Development/genetics ; Plant Proteins/chemistry/*metabolism ; Plant Shoots/physiology ; Plants, Genetically Modified ; *Signal Transduction ; Tobacco/genetics/growth &amp; development/*metabolism ; Trichomes/*growth &amp; development/*metabolism/ultrastructure ; }, abstract = {KEY MESSAGE: A novel gene NbGIS positively regulates glandular trichome initiation through GA Signaling in tobacco. NbMYB123-like regulates glandular trichome initiation by acting downstream of NbGIS in tobacco. Glandular trichome is a specialized multicellular structure which has capability to synthesize and secrete secondary metabolites and protects plants from biotic and abiotic stresses. Our previous results revealed that a C2H2 zinc-finger transcription factor GIS and its sub-family genes act upstream of GL3/EGL3-GL1-TTG1 transcriptional activator complex to regulate trichome initiation in Arabidopsis. In this present study, we found that NbGIS could positively regulate glandular trichome development in Nicotiana benthamiana (tobacco). Our result demonstrated that 35S:NbGIS lines exhibited much higher densities of trichome on leaves, main stems, lateral branches and sepals than WT plants, while NbGIS:RNAi lines had the opposite phenotypes. Furthermore, our results also showed that NbGIS was required in response to GA signal to control glandular trichome initiation in Nicotiana benthamiana. In addition, our results also showed that NbGIS significantly influenced GA accumulation and expressions of marker genes of the GA biosynthesis, might result in the changes of growth and maturation in tobacco. Lastly, our results also showed that NbMYB123-like regulated glandular trichome initiation in tobacco by acting downstream of NbGIS. These findings provide new insights to discover the molecular mechanism by which C2H2 transcriptional factors regulates glandular trichome initiation through GA signaling pathway in tobacco.}, }
@article {pmid30170750, year = {2018}, author = {Atkinson, SD and Bartholomew, JL and Lotan, T}, title = {Myxozoans: Ancient metazoan parasites find a home in phylum Cnidaria.}, journal = {Zoology (Jena, Germany)}, volume = {129}, number = {}, pages = {66-68}, doi = {10.1016/j.zool.2018.06.005}, pmid = {30170750}, issn = {1873-2720}, mesh = {Animals ; Biological Evolution ; Cnidaria/*parasitology ; Host-Parasite Interactions ; Myxozoa/genetics/*physiology ; Parasites ; }, abstract = {Myxozoans are endoparasites with complex life cycles that alternate between invertebrate and vertebrate hosts. Though considered protozoans for over 150 years, they are now recognized as metazoans, given their multicellularity and ultrastructural features. In recognition of synapomorphies and cnidarian-specific genes, myxozoans were placed recently within the phylum Cnidaria. Although they have lost genetic and structural complexity on the path to parasitism, myxozoans have retained characteristic cnidarian cnidocysts, but use them for initiating host infection. Myxozoans represent at least 20% of phylum Cnidaria, but as a result of rapid evolution, extensive diversification and host specialization, they are probably at least as diverse as their free-living relatives. The ability of myxozoans to infect freshwater, marine and terrestrial hosts implies that Cnidaria are no longer constrained to the aquatic environment.}, }
@article {pmid30159848, year = {2018}, author = {Chi, C and Wang, L and Lan, W and Zhao, L and Su, Y}, title = {PpV, acting via the JNK pathway, represses apoptosis during normal development of Drosophila wing.}, journal = {Apoptosis : an international journal on programmed cell death}, volume = {23}, number = {9-10}, pages = {554-562}, doi = {10.1007/s10495-018-1479-2}, pmid = {30159848}, issn = {1573-675X}, support = {201612010//Fundamental Research Funds for the Central Universities/ ; 201762003//Fundamental Research Funds for the Central Universities/ ; 201562029//Fundamental Research Funds for the Central Universities/ ; 31701274//National Natural Science Foundation of China/ ; 2017M612349//China Postdoctoral Science Foundation/ ; }, abstract = {Apoptosis is one of the main fundamental biological processes required for development of multicellular organisms. Inappropriate regulation of apoptosis can lead to severe developmental abnormalities and diseases. Therefore, the control of apoptosis, not only for its activation but also for its inhibition, is critically important during development. In contrast to the extensive studies of apoptosis induction, its inhibitory mechanisms that are even more vital in certain populations of cells actually are very far from being well understood. Here we report an inhibitory role of protein phosphatase V (PpV), a serine/threonine protein phosphatase, in controlling the apoptosis during Drosophila wing development. We observed that inhibition of ppv by RNAi in wing imaginal discs induced ectopic cell death and caspase activation, thus, resulted in a defective adult wing. Moreover, knocking-down ppv triggered the activation of c-Jun N-terminal kinase (JNK) signal, an evolutionarily conserved intracellular signaling that has been implicated to modulate the apoptotic machinery in many biological and experimental systems. Disrupting the JNK signal transduction was adequate to suppress the ppv effects for wing development. Together, we provided the evidence to demonstrate that ppv is required for normal wing development in maintaining the silence of apoptotic signal possibly through JNK pathway.}, }
@article {pmid30149856, year = {2018}, author = {Strauss, J and Wilkinson, C and Vidilaseris, K and Harborne, SPD and Goldman, A}, title = {A Simple Strategy to Determine the Dependence of Membrane-Bound Pyrophosphatases on K+ as a Cofactor.}, journal = {Methods in enzymology}, volume = {607}, number = {}, pages = {131-156}, doi = {10.1016/bs.mie.2018.04.018}, pmid = {30149856}, issn = {1557-7988}, abstract = {Membrane-bound pyrophosphatases (mPPases) couple pyrophosphate hydrolysis to H+ and/or Na+ pumping across membranes and are found in all domains of life except for multicellular animals including humans. They are important for development and stress resistance in plants. Furthermore, mPPases play a role in virulence of human pathogens that cause severe diseases such as malaria and African sleeping sickness. Sequence analysis, functional studies, and recently solved crystal structures have contributed to the understanding of the mPPase catalytic cycle. However, several key mechanistic features remain unknown. During evolution, several subgroups of mPPases differing in their pumping specificity and cofactor dependency arose. mPPases are classified into one of five subgroups, usually by sequence analysis. However, classification based solely on sequence has been inaccurate in several instances due to our limited understanding of the molecular mechanism of mPPases. Thus, pumping specificity and cofactor dependency of mPPases require experimental confirmation. Here, we describe a simple method for the determination of K+ dependency in mPPases using a hydrolytic activity assay. By coupling these dependency studies with site-directed mutagenesis, we have begun to build a better understanding of the molecular mechanisms of mPPases. We optimized the assay for thermostable mPPases that are commonly used as model systems in our lab, but the method is equally applicable to mesophilic mPPases with minor modifications.}, }
@article {pmid30134151, year = {2018}, author = {Stone, R and Portegys, T and Mikhailovsky, G and Alicea, B}, title = {Origins of the Embryo: Self-organization through cybernetic regulation.}, journal = {Bio Systems}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biosystems.2018.08.005}, pmid = {30134151}, issn = {1872-8324}, abstract = {The construction of an embryo from a single cell precursor is a highly complex process. Evolutionary emergence of the first embryos is even more complex, and involves both a transition to multicellularity along with the establishment of developmental mechanisms. We propose that embryogenesis relies on a community of cells conforming to a regulatory model of emergent multicellularity. This model draws together multiple threads in the scientific literature, from complexity theory to cybernetics, and from thermodynamic entropy to artificial life. All of these strands come together to inform a model of goal-oriented regulation for emergent structures in early life. This is an important step in the evolution of early life, as well as the emergence of complex life in the earliest habitats. Our model, called the cybernetic embryo, allows for a systems-level view of the embryogenetic process.}, }
@article {pmid30125231, year = {2018}, author = {Hanschen, ER and Herron, MD and Wiens, JJ and Nozaki, H and Michod, RE}, title = {Multicellularity Drives the Evolution of Sexual Traits.}, journal = {The American naturalist}, volume = {192}, number = {3}, pages = {E93-E105}, doi = {10.1086/698301}, pmid = {30125231}, issn = {1537-5323}, abstract = {From the male peacock's tail plumage to the floral displays of flowering plants, traits related to sexual reproduction are often complex and exaggerated. Why has sexual reproduction become so complicated? Why have such exaggerated sexual traits evolved? Early work posited a connection between multicellularity and sexual traits such as anisogamy (i.e., the evolution of small sperm and large eggs). Anisogamy then drives the evolution of other forms of sexual dimorphism. Yet the relationship between multicellularity and the evolution of sexual traits has not been empirically tested. Given their extensive variation in both multicellular complexity and sexual systems, the volvocine green algae offer a tractable system for understanding the interrelationship of multicellular complexity and sex. Here we show that species with greater multicellular complexity have a significantly larger number of derived sexual traits, including anisogamy, internal fertilization, and secondary sexual dimorphism. Our results demonstrate that anisogamy repeatedly evolved from isogamous multicellular ancestors and that anisogamous species are larger and produce larger zygotes than isogamous species. In the volvocine algae, the evolution of multicellularity likely drives the evolution of anisogamy, and anisogamy subsequently drives secondary sexual dimorphism. Multicellularity may set the stage for the overall diversity of sexual complexity throughout the Tree of Life.}, }
@article {pmid30109121, year = {2018}, author = {Wang, X and Zhu, W and Chang, P and Wu, H and Liu, H and Chen, J}, title = {Merge and separation of NuA4 and SWR1 complexes control cell fate plasticity in Candida albicans.}, journal = {Cell discovery}, volume = {4}, number = {}, pages = {45}, doi = {10.1038/s41421-018-0043-0}, pmid = {30109121}, issn = {2056-5968}, support = {R01 AI099190/AI/NIAID NIH HHS/United States ; R01 GM117111/GM/NIGMS NIH HHS/United States ; }, abstract = {Phenotypic plasticity is common in development. Candida albicans, a polymorphic fungal pathogen of humans, possesses the unique ability to achieve rapid and reversible cell fate between unicellular form (yeast) and multicellular form (hypha) in response to environmental cues. The NuA4 histone acetyltransferase activity and Hda1 histone deacetylase activity have been reported to be required for hyphal initiation and maintenance. However, how Hda1 and NuA4 regulate hyphal elongation is not clear. NuA4 histone acetyltransferase and SWR1 chromatin remodeling complexes are conserved from yeast to human, which may have merged together to form a larger TIP60 complex since the origin of metazoan. In this study, we show a dynamic merge and separation of NuA4 and SWR1 complexes in C. albicans. NuA4 and SWR1 merge together in yeast state and separate into two distinct complexes in hyphal state. We demonstrate that acetylation of Eaf1 K173 controls the interaction between the two complexes. The YEATS domain of Yaf9 in C. albicans can recognize an acetyl-lysine of the Eaf1 and mediate the Yaf9-Eaf1 interaction. The reversible acetylation and deacetylation of Eaf1 by Esa1 and Hda1 control the merge and separation of NuA4 and SWR1, and this regulation is triggered by Brg1 recruitment of Hda1 to chromatin in response nutritional signals that sustain hyphal elongation. We have also observed an orchestrated promoter association of Esa1, Hda1, Swr1, and H2A.Z during the reversible yeast-hyphae transitions. This is the first discovery of a regulated merge of the NuA4 and SWR1 complexes that controls cell fate determination and this regulation may be conserved in polymorphic fungi.}, }
@article {pmid30103474, year = {2018}, author = {Mattick, JS}, title = {The State of Long Non-Coding RNA Biology.}, journal = {Non-coding RNA}, volume = {4}, number = {3}, pages = {}, doi = {10.3390/ncrna4030017}, pmid = {30103474}, issn = {2311-553X}, abstract = {Transcriptomic studies have demonstrated that the vast majority of the genomes of mammals and other complex organisms is expressed in highly dynamic and cell-specific patterns to produce large numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Despite well characterized examples, their scaling with developmental complexity, and many demonstrations of their association with cellular processes, development and diseases, lncRNAs are still to be widely accepted as major players in gene regulation. This may reflect an underappreciation of the extent and precision of the epigenetic control of differentiation and development, where lncRNAs appear to have a central role, likely as organizational and guide molecules: most lncRNAs are nuclear-localized and chromatin-associated, with some involved in the formation of specialized subcellular domains. I suggest that a reassessment of the conceptual framework of genetic information and gene expression in the 4-dimensional ontogeny of spatially organized multicellular organisms is required. Together with this and further studies on their biology, the key challenges now are to determine the structure⁻function relationships of lncRNAs, which may be aided by emerging evidence of their modular structure, the role of RNA editing and modification in enabling epigenetic plasticity, and the role of RNA signaling in transgenerational inheritance of experience.}, }
@article {pmid30102347, year = {2018}, author = {Gaouda, H and Hamaji, T and Yamamoto, K and Kawai-Toyooka, H and Suzuki, M and Noguchi, H and Minakuchi, Y and Toyoda, A and Fujiyama, A and Nozaki, H and Smith, DR}, title = {Exploring the Limits and Causes of Plastid Genome Expansion in Volvocine Green Algae.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2248-2254}, doi = {10.1093/gbe/evy175}, pmid = {30102347}, issn = {1759-6653}, abstract = {Plastid genomes are not normally celebrated for being large. But researchers are steadily uncovering algal lineages with big and, in rare cases, enormous plastid DNAs (ptDNAs), such as volvocine green algae. Plastome sequencing of five different volvocine species has revealed some of the largest, most repeat-dense plastomes on record, including that of Volvox carteri (∼525 kb). Volvocine algae have also been used as models for testing leading hypotheses on organelle genome evolution (e.g., the mutational hazard hypothesis), and it has been suggested that ptDNA inflation within this group might be a consequence of low mutation rates and/or the transition from a unicellular to multicellular existence. Here, we further our understanding of plastome size variation in the volvocine line by examining the ptDNA sequences of the colonial species Yamagishiella unicocca and Eudorina sp. NIES-3984 and the multicellular Volvox africanus, which are phylogenetically situated between species with known ptDNA sizes. Although V. africanus is closely related and similar in multicellular organization to V. carteri, its ptDNA was much less inflated than that of V. carteri. Synonymous- and noncoding-site nucleotide substitution rate analyses of these two Volvox ptDNAs suggest that there are drastically different plastid mutation rates operating in the coding versus intergenic regions, supporting the idea that error-prone DNA repair in repeat-rich intergenic spacers is contributing to genome expansion. Our results reinforce the idea that the volvocine line harbors extremes in plastome size but ultimately shed doubt on some of the previously proposed hypotheses for ptDNA inflation within the lineage.}, }
@article {pmid30099198, year = {2018}, author = {Lazzari, G and Nicolas, V and Matsusaki, M and Akashi, M and Couvreur, P and Mura, S}, title = {Multicellular spheroid based on a triple co-culture: A novel 3D model to mimic pancreatic tumor complexity.}, journal = {Acta biomaterialia}, volume = {78}, number = {}, pages = {296-307}, doi = {10.1016/j.actbio.2018.08.008}, pmid = {30099198}, issn = {1878-7568}, abstract = {The preclinical drug screening of pancreatic cancer treatments suffers from the absence of appropriate models capable to reproduce in vitro the heterogeneous tumor microenvironment and its stiff desmoplasia. Driven by this pressing need, we describe in this paper the conception and the characterization of a novel 3D tumor model consisting of a triple co-culture of pancreatic cancer cells (PANC-1), fibroblasts (MRC-5) and endothelial cells (HUVEC), which assembled to form a hetero-type multicellular tumor spheroid (MCTS). By histological analyses and Selective Plain Illumination Microscopy (SPIM) we have monitored the spatial distribution of each cell type and the evolution of the spheroid composition. Results revealed the presence of a core rich in fibroblasts and fibronectin in which endothelial cells were homogeneously distributed. The integration of the three cell types enabled to reproduce in vitro with fidelity the influence of the surrounding environment on the sensitivity of cancer cells to chemotherapy. To our knowledge, this is the first time that a scaffold-free pancreatic cancer spheroid model combining both tumor and multiple stromal components has been designed. It holds the possibility to become an advantageous tool for a pertinent assessment of the efficacy of various therapeutic strategies.<br><br>STATEMENT OF SIGNIFICANCE: Pancreatic tumor microenvironment is characterized by abundant fibrosis and aberrant vasculature. Aiming to reproduce in vitro these features, cancer cells have been already co-cultured with fibroblasts or endothelial cells separately but the integration of both these essential components of the pancreatic tumor microenvironment in a unique system, although urgently needed, was still missing. In this study, we successfully integrated cellular and acellular microenvironment components (i.e., fibroblasts, endothelial cells, fibronectin) in a hetero-type scaffold-free multicellular tumor spheroid. This new 3D triple co-culture model closely mimicked the resistance to treatments observed in vivo, resulting in a reduction of cancer cell sensitivity to the anticancer treatment.}, }
@article {pmid30089142, year = {2018}, author = {Tverskoi, D and Makarenkov, V and Aleskerov, F}, title = {Modeling functional specialization of a cell colony under different fecundity and viability rates and resource constraint.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0201446}, doi = {10.1371/journal.pone.0201446}, pmid = {30089142}, issn = {1932-6203}, abstract = {The emergence of functional specialization is a core problem in biology. In this work we focus on the emergence of reproductive (germ) and vegetative viability-enhancing (soma) cell functions (or germ-soma specialization). We consider a group of cells and assume that they contribute to two different evolutionary tasks, fecundity and viability. The potential of cells to contribute to fitness components is traded off. As embodied in current models, the curvature of the trade-off between fecundity and viability is concave in small-sized organisms and convex in large-sized multicellular organisms. We present a general mathematical model that explores how the division of labor in a cell colony depends on the trade-off curvatures, a resource constraint and different fecundity and viability rates. Moreover, we consider the case of different trade-off functions for different cells. We describe the set of all possible solutions of the formulated mathematical programming problem and show some interesting examples of optimal specialization strategies found for our objective fitness function. Our results suggest that the transition to specialized organisms can be achieved in several ways. The evolution of Volvocalean green algae is considered to illustrate the application of our model. The proposed model can be generalized to address a number of important biological issues, including the evolution of specialized enzymes and the emergence of complex organs.}, }
@article {pmid30086318, year = {2018}, author = {Furumizu, C and Hirakawa, Y and Bowman, JL and Sawa, S}, title = {3D Body Evolution: Adding a New Dimension to Colonize the Land.}, journal = {Current biology : CB}, volume = {28}, number = {15}, pages = {R838-R840}, doi = {10.1016/j.cub.2018.06.040}, pmid = {30086318}, issn = {1879-0445}, abstract = {Complex multicellular plant bodies evolved in both generations of land plants. A new study demonstrates that CLAVATA3-like peptides function via conserved receptors in Physcomitrella patens as key molecules for morphological innovation of 3D growth in land plants.}, }
@article {pmid30082786, year = {2018}, author = {Li, Z and Fu, X and Wang, Y and Liu, R and He, Y}, title = {Polycomb-mediated gene silencing by the BAH-EMF1 complex in plants.}, journal = {Nature genetics}, volume = {50}, number = {9}, pages = {1254-1261}, doi = {10.1038/s41588-018-0190-0}, pmid = {30082786}, issn = {1546-1718}, abstract = {Polycomb proteins implement genome-wide transcriptional repression in multicellular organisms. The evolutionarily conserved Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) that is read and effected by Polycomb repressive complex 1 (PRC1) in animals, but the interpretation of this mark remains unclear in plants. Here we report that in the eudicot Arabidopsis thaliana two homologous BAH (Bromo adjacent homology) domain-containing proteins form a plant-specific complex with EMBRYONIC FLOWER 1 (EMF1), and that the BAH-EMF1 complex (BAH-EMF1c) reads and effects the H3K27me3 mark and mediates genome-wide transcriptional repression. Furthermore, in the monocot rice a homolog of the Arabidopsis BAH-domain proteins also binds methylated H3K27 and forms a complex with the rice homolog of EMF1, suggesting that BAH-EMF1c is conserved in flowering plants. Therefore, our results show that the plant-specific BAH-EMF1c fulfills PRC1-like functions in higher plants, suggesting a convergent evolution of PRC1 activity in plants and animals.}, }
@article {pmid30078827, year = {2018}, author = {Oka, M and Yoneda, Y}, title = {Importin α: functions as a nuclear transport factor and beyond.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {94}, number = {7}, pages = {259-274}, doi = {10.2183/pjab.94.018}, pmid = {30078827}, issn = {1349-2896}, mesh = {Active Transport, Cell Nucleus ; Animals ; Cell Nucleus/*metabolism ; Humans ; Neurons/cytology/metabolism ; Nuclear Pore/metabolism ; alpha Karyopherins/*metabolism ; }, abstract = {Nucleocytoplasmic transport is an essential process in eukaryotes. The molecular mechanisms underlying nuclear transport that involve the nuclear transport receptor, small GTPase Ran, and the nuclear pore complex are highly conserved from yeast to humans. On the other hand, it has become clear that the nuclear transport system diverged during evolution to achieve various physiological functions in multicellular eukaryotes. In this review, we first summarize the molecular mechanisms of nuclear transport and how these were elucidated. Then, we focus on the diverse functions of importin α, which acts not merely an import factor but also as a multi-functional protein contributing to a variety of cellular functions in higher eukaryotes.}, }
@article {pmid30072980, year = {2018}, author = {Sharma, G and Burrows, LL and Singer, M}, title = {Diversity and Evolution of Myxobacterial Type IV Pilus Systems.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1630}, doi = {10.3389/fmicb.2018.01630}, pmid = {30072980}, issn = {1664-302X}, abstract = {Type IV pili (T4P) are surface-exposed protein fibers that play key roles in the bacterial life cycle via surface attachment/adhesion, biofilm formation, motility, and development. The order Myxococcales (myxobacteria) are members of the class Deltaproteobacteria and known for their large genome size and complex social behaviors, including gliding motility, fruiting body formation, biofilm production, and prey hunting. Myxococcus xanthus, the best-characterized member of the order, relies on the appropriate expression of 17 type IVa (T4aP) genes organized in a single cluster plus additional genes (distributed throughout the genome) for social motility and development. Here, we compared T4aP genes organization within the myxobacteria to understand their evolutionary origins and diversity. We found that T4aP genes are organized as large clusters in suborder Cystobacterineae, whereas in other two suborders Sorangiineae and Nannocystineae, these genes are dispersed throughout the genome. Based on the genomic organization, the phylogeny of conserved proteins, and synteny studies among 28 myxobacterial and 66 Proteobacterial genomes, we propose an evolutionary model for the origin of myxobacterial T4aP genes independently from other orders in class Deltaproteobacteria. Considering a major role for T4P, this study further proposes the origins and evolution of social motility in myxobacteria and provides a foundation for understanding how complex-behavioral traits, such as gliding motility, multicellular development, etc., might have evolved in this diverse group of complex organisms.}, }
@article {pmid30068565, year = {2018}, author = {Bornens, M}, title = {Cell polarity: having and making sense of direction-on the evolutionary significance of the primary cilium/centrosome organ in Metazoa.}, journal = {Open biology}, volume = {8}, number = {8}, pages = {}, doi = {10.1098/rsob.180052}, pmid = {30068565}, issn = {2046-2441}, abstract = {Cell-autonomous polarity in Metazoans is evolutionarily conserved. I assume that permanent polarity in unicellular eukaryotes is required for cell motion and sensory reception, integration of these two activities being an evolutionarily constrained function. Metazoans are unique in making cohesive multicellular organisms through complete cell divisions. They evolved a primary cilium/centrosome (PC/C) organ, ensuring similar functions to the basal body/flagellum of unicellular eukaryotes, but in different cells, or in the same cell at different moments. The possibility that this innovation contributed to the evolution of individuality, in being instrumental in the early specification of the germ line during development, is further discussed. Then, using the example of highly regenerative organisms like planarians, which have lost PC/C organ in dividing cells, I discuss the possibility that part of the remodelling necessary to reach a new higher-level unit of selection in multi-cellular organisms has been triggered by conflicts among individual cell polarities to reach an organismic polarity. Finally, I briefly consider organisms with a sensorimotor organ like the brain that requires exceedingly elongated polarized cells for its activity. I conclude that beyond critical consequences for embryo development, the conservation of cell-autonomous polarity in Metazoans had far-reaching implications for the evolution of individuality.}, }
@article {pmid30066215, year = {2018}, author = {Stencel, A and Wloch-Salamon, DM}, title = {Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12064-018-0268-3}, pmid = {30066215}, issn = {1611-7530}, support = {2018/28/T/HS1/00201//Narodowe Centrum Nauki/ ; Opus 2017/25/B/NZ8/01035//Narodowe Centrum Nauki/ ; DS/762 - K/ZDS/007338//Uniwersytet Jagielloński w Krakowie/ ; }, abstract = {Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated. In this paper, we argue, firstly, that only a very small number of symbiotic microorganisms are sufficiently integrated into multicellular organisms to act in concert with them as units of selection, thus rendering claims that holobionts are units of selection invalid. Secondly, even though holobionts are not units of selection, they can still constitute genuine units from an evolutionary perspective, provided we accept certain constraints: mainly, they should be considered units of co-operation. Thirdly, we propose a reconciliation of the role of symbiotic microorganisms with the theory of speciation through the use of a developed framework. Mainly, we will argue that, in order to understand the role of microorganisms in the speciation of multicellular organisms, it is not necessary to consider holobionts units of selection; it is sufficient to consider them units of co-operation.}, }
@article {pmid30065707, year = {2018}, author = {Chen, H and Zhang, SD and Chen, L and Cai, Y and Zhang, WJ and Song, T and Wu, LF}, title = {Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1569}, doi = {10.3389/fmicb.2018.01569}, pmid = {30065707}, issn = {1664-302X}, abstract = {Magnetotactic bacteria (MTB) are a diverse group of microorganisms capable of using geomagnetic fields for navigation. This magnetotactic behavior can help microorganisms move toward favorable habitats for optimal growth and reproduction. A comprehensive understanding of the magnetotactic mechanism at molecular levels requires highly efficient genomic editing tools, which remain underdeveloped in MTB. Here, we adapted an engineered CRISPR-Cas9 system for efficient inactivation of genes in a widely used MTB model strain, Magnetospirillum magneticum AMB-1. By combining a nuclease-deficient Cas9 (dCas9) and single-guide RNA (sgRNA), a CRISPR interference system was successfully developed to repress amb0994 expression. Furthermore, we constructed an in-frame deletion mutant of amb0994 by developing a CRISPR-Cas9 system. This mutant produces normal magnetosomes; however, its response to abrupt magnetic field reversals is faster than wild-type strain. This behavioral difference is probably a consequence of altered flagella function, as suggested with our dynamics simulation study by modeling M. magneticum AMB-1 cell as an ellipsoid. These data indicate that, Amb0994 is involved in the cellular response to magnetic torque changes via controlling flagella. In summary, this study, besides contributing to a better understanding of magnetotaxis mechanism, demonstrated the CRISPR-(d)Cas9 system as a useful genetic tool for efficient genome editing in MTB.}, }
@article {pmid30061903, year = {2018}, author = {Benítez, M and Hernández-Hernández, V and Newman, SA and Niklas, KJ}, title = {Dynamical Patterning Modules, Biogeneric Materials, and the Evolution of Multicellular Plants.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {871}, doi = {10.3389/fpls.2018.00871}, pmid = {30061903}, issn = {1664-462X}, abstract = {Comparative analyses of developmental processes across a broad spectrum of organisms are required to fully understand the mechanisms responsible for the major evolutionary transitions among eukaryotic photosynthetic lineages (defined here as the polyphyletic algae and the monophyletic land plants). The concepts of dynamical patterning modules (DPMs) and biogeneric materials provide a framework for studying developmental processes in the context of such comparative analyses. In the context of multicellularity, DPMs are defined as sets of conserved gene products and molecular networks, in conjunction with the physical morphogenetic and patterning processes they mobilize. A biogeneric material is defined as mesoscale matter with predictable morphogenetic capabilities that arise from complex cellular conglomerates. Using these concepts, we outline some of the main events and transitions in plant evolution, and describe the DPMs and biogeneric properties associated with and responsible for these transitions. We identify four primary DPMs that played critical roles in the evolution of multicellularity (i.e., the DPMs responsible for cell-to-cell adhesion, identifying the future cell wall, cell differentiation, and cell polarity). Three important conclusions emerge from a broad phyletic comparison: (1) DPMs have been achieved in different ways, even within the same clade (e.g., phycoplastic cell division in the Chlorophyta and phragmoplastic cell division in the Streptophyta), (2) DPMs had their origins in the co-option of molecular species present in the unicellular ancestors of multicellular plants, and (3) symplastic transport mediated by intercellular connections, particularly plasmodesmata, was critical for the evolution of complex multicellularity in plants.}, }
@article {pmid30061561, year = {2018}, author = {Stewart, AD and Rice, WR}, title = {Arrest of sex-specific adaptation during the evolution of sexual dimorphism in Drosophila.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {9}, pages = {1507-1513}, doi = {10.1038/s41559-018-0613-4}, pmid = {30061561}, issn = {2397-334X}, abstract = {Sexually antagonistic selection arises when a trait expressed in both sexes (a shared trait) is selected towards different, sex-specific optima. Sex-discordant selection causes different alleles to be favoured in each sex (intralocus sexual conflict). A key parameter responsible for generating this conflict is the intersexual genetic correlation (rMF), which determines the degree to which heritable genetic variation for the shared trait produces a similar phenotype in both sexes. A strong, positive rMF interferes with adaptation when there is sex-discordant selection. In principle, the rMF can evolve in response to sex-discordant selection: the faster it declines, the faster the resolution of intralocus sexual conflict. Here, we use Drosophila melanogaster to quantify the time scale over which a strong, positive rMF impedes a response to sex-discordant selection for a canonical quantitative trait (body size) with an exceptionally long (250 generations) selection experiment for a complex multicellular organism. We found that, compared with rapid and substantial evolution under sex-concordant selection, a high rMF arrested sex-specific adaptation for 100 generations in females and a minimum of 250 generations in males. Our study demonstrates that a high rMF can lead to a protracted period of adaptive stalemate during the evolution of sexual dimorphism.}, }
@article {pmid30059538, year = {2018}, author = {Waldron, FM and Stone, GN and Obbard, DJ}, title = {Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes.}, journal = {PLoS genetics}, volume = {14}, number = {7}, pages = {e1007533}, doi = {10.1371/journal.pgen.1007533}, pmid = {30059538}, issn = {1553-7404}, abstract = {RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga-which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.}, }
@article {pmid30028958, year = {2018}, author = {Campbell, FC and Loughrey, MB and McClements, J and Deevi, RK and Javadi, A and Rainey, L}, title = {Mechanistic Insights into Colorectal Cancer Phenomics from Fundamental and Organotypic Model Studies.}, journal = {The American journal of pathology}, volume = {188}, number = {9}, pages = {1936-1948}, doi = {10.1016/j.ajpath.2018.05.021}, pmid = {30028958}, issn = {1525-2191}, abstract = {Colorectal cancer (CRC) diagnosis and prognostic stratification are based on histopathologic assessment of cell or nuclear pleomorphism, aberrant mitotic figures, altered glandular architecture, and other phenomic abnormalities. This complexity is driven by oncogenic perturbation of tightly coordinated spatiotemporal signaling to disrupt multiple scales of tissue organization. This review clarifies molecular and cellular mechanisms underlying common CRC histologic features and helps understand how the CRC genome controls core aspects of tumor aggressiveness. It further explores a spatiotemporal framework for CRC phenomics based on regulation of living cells in fundamental and organotypic model systems. The review also discusses tissue homeostasis, considers distinct classes of oncogenic perturbations, and evolution of cellular or multicellular cancer phenotypes. It further explores the molecular controls of cribriform, micropapillary, and high-grade CRC morphology in organotypic culture models and assesses relevant translational studies. In addition, the review delves into complexities of morphologic plasticity whereby a single molecular signature generates heterogeneous cancer phenotypes, and, conversely, morphologically homogeneous tumors show substantive molecular diversity. Principles outlined may aid mechanistic interpretation of omics data in a setting of cancer pathology, provide insight into CRC consensus molecular subtypes, and better define principles for CRC prognostic stratification.}, }
@article {pmid29992410, year = {2018}, author = {Leong, SP and Aktipis, A and Maley, C}, title = {Cancer initiation and progression within the cancer microenvironment.}, journal = {Clinical &amp; experimental metastasis}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10585-018-9921-y}, pmid = {29992410}, issn = {1573-7276}, abstract = {Within the cancer microenvironment, the growth and proliferation of cancer cells in the primary site as well as in the metastatic site represent a global biological phenomenon. To understand the growth, proliferation and progression of cancer either by local expansion and/or metastasis, it is important to understand the cancer microenvironment and host response to cancer growth. Melanoma is an excellent model to study the interaction of cancer initiation and growth in relationship to its microenvironment. Social evolution with cooperative cellular groups within an organism is what gives rise to multicellularity in the first place. Cancer cells evolve to exploit their cellular environment. The foundations of multicellular cooperation break down in cancer because those cells that misbehave have an evolutionary advantage over their normally behaving neighbors. It is important to classify evolutionary and ecological aspects of cancer growth, thus, data for cancer growth and outcomes need to be collected to define these parameters so that accurate predictions of how cancer cells may proliferate and metastasize can be developed.}, }
@article {pmid29966484, year = {2018}, author = {Liao, Z and Kjellin, J and Hoeppner, MP and Grabherr, M and Söderbom, F}, title = {Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.}, journal = {RNA biology}, volume = {15}, number = {7}, pages = {937-954}, doi = {10.1080/15476286.2018.1481697}, pmid = {29966484}, issn = {1555-8584}, abstract = {Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3'-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.}, }
@article {pmid29961831, year = {2018}, author = {Zhao, J and Yuan, S and Gao, B and Zhu, S}, title = {Molecular diversity of fungal inhibitor cystine knot peptides evolved by domain repeat and fusion.}, journal = {FEMS microbiology letters}, volume = {365}, number = {15}, pages = {}, doi = {10.1093/femsle/fny158}, pmid = {29961831}, issn = {1574-6968}, abstract = {Peptides with the inhibitor cystine knot (ICK) motif are extensively present in animals and plants where they exert a diversity of biological functions. However, few studies have been undertaken on this class of peptides in fungi. In this work, we identify a total of 386 fungal ICK peptides and proteins containing this motif by computational data mining of fungal genome databases, which exhibit 14 different exon-intron structures. According to their domain architectures, these proteins are classified into three distinct structural types, including single domains, tandem repeat domains and fusion domains, in which six families belonging to single or tandem repeat domains show remarkable sequence similarity to those from animals and plants, suggesting their orthologous relationship. Extremely high molecular diversity in fungal ICKs might be attributable to different genetic mechanisms, such as gene/domain duplication and fusion. This work not only enlarges the number of ICK peptides in multicellular organisms, but also uncovers their complex evolutionary history in a specific lineage.}, }
@article {pmid29954963, year = {2018}, author = {Pennisi, E}, title = {Is cancer a breakdown of multicellularity?.}, journal = {Science (New York, N.Y.)}, volume = {360}, number = {6396}, pages = {1391}, doi = {10.1126/science.360.6396.1391}, pmid = {29954963}, issn = {1095-9203}, mesh = {*Biological Evolution ; Carcinogenesis/genetics/*pathology ; Gene Regulatory Networks ; Humans ; Neoplasms/genetics/*pathology ; }, }
@article {pmid29942020, year = {2018}, author = {Sebé-Pedrós, A and Chomsky, E and Pang, K and Lara-Astiaso, D and Gaiti, F and Mukamel, Z and Amit, I and Hejnol, A and Degnan, BM and Tanay, A}, title = {Early metazoan cell type diversity and the evolution of multicellular gene regulation.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {7}, pages = {1176-1188}, doi = {10.1038/s41559-018-0575-6}, pmid = {29942020}, issn = {2397-334X}, abstract = {A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement cell-type-specific functions. However, the evolution of metazoan cell types and their underlying gene regulatory programmes remains largely uncharacterized. Here, we use whole-organism single-cell RNA sequencing to map cell-type-specific transcription in Porifera (sponges), Ctenophora (comb jellies) and Placozoa species. We describe the repertoires of cell types in these non-bilaterian animals, uncovering diverse instances of previously unknown molecular signatures, such as multiple types of peptidergic cells in Placozoa. Analysis of the regulatory programmes of these cell types reveals variable levels of complexity. In placozoans and poriferans, sequence motifs in the promoters are predictive of cell-type-specific programmes. By contrast, the generation of a higher diversity of cell types in ctenophores is associated with lower specificity of promoter sequences and the existence of distal regulatory elements. Our findings demonstrate that metazoan cell types can be defined by networks of transcription factors and proximal promoters, and indicate that further genome regulatory complexity may be required for more diverse cell type repertoires.}, }
@article {pmid29939836, year = {2018}, author = {Pashov, A and Hernandez Puente, CV and Ibrahim, SM and Monzavi-Karbassi, B and Makhoul, I and Kieber-Emmons, T}, title = {Thinking Cancer.}, journal = {Monoclonal antibodies in immunodiagnosis and immunotherapy}, volume = {37}, number = {3}, pages = {117-125}, doi = {10.1089/mab.2018.0014}, pmid = {29939836}, issn = {2167-9436}, mesh = {Animals ; Anthroposophy ; Autoantibodies/biosynthesis/genetics ; B7-H1 Antigen/*genetics/immunology ; Cell Transformation, Neoplastic/*genetics/immunology/pathology ; *Epigenesis, Genetic ; *Gene Expression Regulation, Neoplastic ; Gene-Environment Interaction ; Homeostasis/genetics/immunology ; Humans ; Immunity, Innate ; Interferon-gamma/genetics/immunology ; Mutation ; Neoplasm Proteins/*genetics/immunology ; Neoplasms/*genetics/immunology/pathology ; }, abstract = {Evolutionary theories are necessarily invoked for understanding cancer development at the level of species, at the level of cells and tissues, and for developing effective therapies. It is crucial to view cancer in a Darwinian light, where the differential survival of individual cells is based on heritable variations. In the process of this somatic evolution, multicellularity controls are overridden by cancer cells, which become increasingly autonomous. Ecological epigenetics also helps understand how rogue cells that have basically the same DNA as their normal cell counterpart overcome the tissue homeostasis. As we struggle to wrap our minds around the complexity of these phenomena, we apply often times anthropomorphic terms, such as subversion, hijacking, or hacking, to describe especially the most complex among them-the interaction of tumors with the immune system. In this commentary we highlight examples of the anthropomorphic thinking of cancer and try to put into context the relative meaning of terms and the mechanisms that are oftentimes invoked to justify those terms.}, }
@article {pmid29938763, year = {2018}, author = {Funayama, N}, title = {The cellular and molecular bases of the sponge stem cell systems underlying reproduction, homeostasis and regeneration.}, journal = {The International journal of developmental biology}, volume = {62}, number = {6-7-8}, pages = {513-525}, doi = {10.1387/ijdb.180016nf}, pmid = {29938763}, issn = {1696-3547}, abstract = {The evolution of multicellular organisms is generally thought (and seems likely) to have been accompanied by the evolution of a stem cell system. Sponges, some of the early-evolved metazoans, have totipotent/pluripotent stem cells. Thus, uncovering the cellular and molecular bases of the sponge stem cells will not only be crucial for understanding the ancestral gene repertoire of animal stem cells, but will also give us clues to understanding the evolution of molecular mechanisms for maintaining multipotency (pluripotency) and differentiation ability during animal evolution. Sponges (Porifera) are a large phylum that includes an enormous number of species, whose cellular compositions and life cycles show striking variations. In the last decade, methodologies for molecular studies and sequencing resources have dramatically advanced and made it possible to clearly define stem cells in sponges in cellular and molecular terms. In this review, together with recent studies of sponges in various classes, the following issues will be discussed: i) recent findings that revealed that the previously proposed model that &quot;archeocytes and choanocytes are the two types of stem cells&quot; originally based on work in demosponges can be applied as a unified view of the stem cell system in sponges that have various cellular organizations, ii) the fact that sponge cells are more plastic than previously thought, as shown by recent studies of sponge regeneration both from dissociated cells and upon injury, and iii) the importance of transdifferentiation in sponge stem cell systems and regeneration.}, }
@article {pmid29930939, year = {2018}, author = {Fiore, APZP and Ribeiro, PF and Bruni-Cardoso, A}, title = {Sleeping Beauty and the Microenvironment Enchantment: Microenvironmental Regulation of the Proliferation-Quiescence Decision in Normal Tissues and in Cancer Development.}, journal = {Frontiers in cell and developmental biology}, volume = {6}, number = {}, pages = {59}, doi = {10.3389/fcell.2018.00059}, pmid = {29930939}, issn = {2296-634X}, abstract = {Cells from prokaryota to the more complex metazoans cease proliferating at some point in their lives and enter a reversible, proliferative-dormant state termed quiescence. The appearance of quiescence in the course of evolution was essential to the acquisition of multicellular specialization and compartmentalization and is also a central aspect of tissue function and homeostasis. But what makes a cell cease proliferating even in the presence of nutrients, growth factors, and mitogens? And what makes some cells &quot;wake up&quot; when they should not, as is the case in cancer? Here, we summarize and discuss evidence showing how microenvironmental cues such as those originating from metabolism, extracellular matrix (ECM) composition and arrangement, neighboring cells and tissue architecture control the cellular proliferation-quiescence decision, and how this complex regulation is corrupted in cancer.}, }
@article {pmid29914363, year = {2018}, author = {Dunning Hotopp, JC}, title = {Grafting or pruning in the animal tree: lateral gene transfer and gene loss?.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {470}, doi = {10.1186/s12864-018-4832-5}, pmid = {29914363}, issn = {1471-2164}, support = {R01 CA206188/CA/NCI NIH HHS/United States ; ABI-1457957//National Science Foundation/ ; 1-R01-CA206188//National Cancer Institute/ ; }, abstract = {BACKGROUND: Lateral gene transfer (LGT), also known as horizontal gene transfer, into multicellular eukaryotes with differentiated tissues, particularly gonads, continues to be met with skepticism by many prominent evolutionary and genomic biologists. A detailed examination of 26 animal genomes identified putative LGTs in invertebrate and vertebrate genomes, concluding that there are fewer predicted LGTs in vertebrates/chordates than invertebrates, but there is still evidence of LGT into chordates, including humans. More recently, a reanalysis of a subset of these putative LGTs into vertebrates concluded that there is not horizontal gene transfer in the human genome. One of the genes in dispute is an N-acyl-aromatic-L-amino acid amidohydrolase (ENSG00000132744), which encodes ACY3. This gene was initially identified as a putative bacteria-chordate LGT but was later debunked as it has a significant BLAST match to a more recently deposited genome of Saccoglossus kowalevskii, a flatworm, Metazoan, and hemichordate.<br><br>RESULTS: Using BLAST searches, HMM searches, and phylogenetics to assess the evidence for LGT, gene loss, and rate variation in ACY3/ASPA homologues, the most parsimonious explanation for the distribution of ACY3/ASPA genes in eukaryotes involves both gene loss and bacteria-animal LGT, albeit LGT that occurred hundreds of millions of years ago prior to the divergence of gnathostomes.<br><br>CONCLUSIONS: ACY3/ASPA is most likely a bacteria-animal LGT. LGTs at these time scales in the ancestors of humans are not unexpected given the many known, well-characterized, and adaptive LGTs from bacteria to insects and nematodes.}, }
@article {pmid29906914, year = {2018}, author = {Kang, C and Aguilar, B and Shmulevich, I}, title = {Emergence of diversity in homogeneous coupled Boolean networks.}, journal = {Physical review. E}, volume = {97}, number = {5-1}, pages = {052415}, doi = {10.1103/PhysRevE.97.052415}, pmid = {29906914}, issn = {2470-0053}, mesh = {Evolution, Molecular ; *Gene Regulatory Networks ; *Models, Genetic ; }, abstract = {The origin of multicellularity in metazoa is one of the fundamental questions of evolutionary biology. We have modeled the generic behaviors of gene regulatory networks in isogenic cells as stochastic nonlinear dynamical systems-coupled Boolean networks with perturbation. Model simulations under a variety of dynamical regimes suggest that the central characteristic of multicellularity, permanent spatial differentiation (diversification), indeed can arise. Additionally, we observe that diversification is more likely to occur near the critical regime of Lyapunov stability.}, }
@article {pmid29906891, year = {2018}, author = {Jacobeen, S and Graba, EC and Brandys, CG and Day, TC and Ratcliff, WC and Yunker, PJ}, title = {Geometry, packing, and evolutionary paths to increased multicellular size.}, journal = {Physical review. E}, volume = {97}, number = {5-1}, pages = {050401}, doi = {10.1103/PhysRevE.97.050401}, pmid = {29906891}, issn = {2470-0053}, abstract = {The evolutionary transition to multicellularity transformed life on earth, heralding the evolution of large, complex organisms. Recent experiments demonstrated that laboratory-evolved multicellular &quot;snowflake yeast&quot; readily overcome the physical barriers that limit cluster size by modifying cellular geometry [Jacobeen et al., Nat. Phys. 14, 286 (2018)10.1038/s41567-017-0002-y]. However, it is unclear why this route to large size is observed, rather than an evolved increase in intercellular bond strength. Here, we use a geometric model of the snowflake yeast growth form to examine the geometric efficiency of increasing size by modifying geometry and bond strength. We find that changing geometry is a far more efficient route to large size than evolving increased intercellular adhesion. In fact, increasing cellular aspect ratio is on average ∼13 times more effective than increasing bond strength at increasing the number of cells in a cluster. Modifying other geometric parameters, such as the geometric arrangement of mother and daughter cells, also had larger effects on cluster size than increasing bond strength. Simulations reveal that as cells reproduce, internal stress in the cluster increases rapidly; thus, increasing bond strength provides diminishing returns in cluster size. Conversely, as cells become more elongated, cellular packing density within the cluster decreases, which substantially decreases the rate of internal stress accumulation. This suggests that geometrically imposed physical constraints may have been a key early selective force guiding the emergence of multicellular complexity.}, }
@article {pmid29891718, year = {2018}, author = {Smith, CCR and Tittes, S and Mendieta, JP and Collier-Zans, E and Rowe, HC and Rieseberg, LH and Kane, NC}, title = {Genetics of alternative splicing evolution during sunflower domestication.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {26}, pages = {6768-6773}, doi = {10.1073/pnas.1803361115}, pmid = {29891718}, issn = {1091-6490}, mesh = {*Alternative Splicing ; Domestication ; *Evolution, Molecular ; Helianthus/*genetics ; Plant Breeding ; Plant Proteins/genetics/metabolism ; Protein Isoforms/genetics/metabolism ; Quantitative Trait Loci ; RNA, Plant/*genetics ; Spliceosomes ; Transcriptome ; }, abstract = {Alternative splicing enables organisms to produce the diversity of proteins necessary for multicellular life by using relatively few protein-coding genes. Although differences in splicing have been identified among divergent taxa, the shorter-term evolution of splicing is understudied. The origins of novel splice forms, and the contributions of alternative splicing to major evolutionary transitions, are largely unknown. This study used transcriptomes of wild and domesticated sunflowers to examine splice differentiation and regulation during domestication. We identified substantial splicing divergence between wild and domesticated sunflowers, mainly in the form of intron retention. Transcripts with divergent splicing were enriched for seed-development functions, suggesting that artificial selection impacted splicing patterns. Mapping of quantitative trait loci (QTLs) associated with 144 differential splicing cases revealed primarily trans-acting variation affecting splicing patterns. A large proportion of identified QTLs contain known spliceosome proteins and are associated with splicing variation in multiple genes. Examining a broader set of wild and domesticated sunflower genotypes revealed that most differential splicing patterns in domesticated sunflowers likely arose from standing variation in wild Helianthus annuus and gained frequency during the domestication process. However, several domesticate-associated splicing patterns appear to be introgressed from other Helianthus species. These results suggest that sunflower domestication involved selection on pleiotropic regulatory alleles. More generally, our findings indicate that substantial differences in isoform abundances arose rapidly during a recent evolutionary transition and appear to contribute to adaptation and population divergence.}, }
@article {pmid29889237, year = {2018}, author = {Leys, SP and Kahn, AS}, title = {Oxygen and the Energetic Requirements of the First Multicellular Animals.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {666-676}, doi = {10.1093/icb/icy051}, pmid = {29889237}, issn = {1557-7023}, abstract = {The appearance of multicellular animals during the Neoproterozoic Era is thought to have coincided with oxygenation of the oceans; however, we know little about the physiological needs of early animals or about the environment they lived in. Approaches using biomarkers, fossils, and phylogenomics have provided some hints of the types of animals that may have been present during the Neoproterozoic, but extant animals are our best modern links to the theoretical ancestors of animals. Neoproterozoic oceans were low energy habitats, with low oxygen concentrations and sparse food availability for the first animals. We examined tolerance of extant ctenophores and sponges-as representatives of extant lineages of the earliest known metazoan groups-to feeding and oxygen use. A review of respiration rates in species across several phyla suggests that suspension feeders in general have a wide range of metabolic rates, but sponges have some of the highest of invertebrates and ctenophores some of the lowest. Our own studies on the metabolism of two groups of deep water sponges show that sponges have different approaches to deal with the cost of filtration and low food availability. We also confirmed that deep water sponges tolerate periods of hypoxia, but at the cost of filtration, indicating that normal feeding is energetically expensive. Predictions of oxygen levels in the Neoproterozoic suggest the last common ancestor of multicellular animals was unlikely to have filtered like modern sponges. Getting enough food at low oxygen would have been a more important driver of the evolution of early body plans.}, }
@article {pmid29880641, year = {2018}, author = {Miller, PW and Pokutta, S and Mitchell, JM and Chodaparambil, JV and Clarke, DN and Nelson, WJ and Weis, WI and Nichols, SA}, title = {Analysis of a vinculin homolog in a sponge (phylum Porifera) reveals that vertebrate-like cell adhesions emerged early in animal evolution.}, journal = {The Journal of biological chemistry}, volume = {293}, number = {30}, pages = {11674-11686}, doi = {10.1074/jbc.RA117.001325}, pmid = {29880641}, issn = {1083-351X}, support = {P41 GM103393/GM/NIGMS NIH HHS/United States ; R01 GM114462/GM/NIGMS NIH HHS/United States ; R35 GM118064/GM/NIGMS NIH HHS/United States ; }, abstract = {The evolution of cell-adhesion mechanisms in animals facilitated the assembly of organized multicellular tissues. Studies in traditional animal models have revealed two predominant adhesion structures, the adherens junction (AJ) and focal adhesions (FAs), which are involved in the attachment of neighboring cells to each other and to the secreted extracellular matrix (ECM), respectively. The AJ (containing cadherins and catenins) and FAs (comprising integrins, talin, and paxillin) differ in protein composition, but both junctions contain the actin-binding protein vinculin. The near ubiquity of these structures in animals suggests that AJ and FAs evolved early, possibly coincident with multicellularity. However, a challenge to this perspective is that previous studies of sponges-a divergent animal lineage-indicate that their tissues are organized primarily by an alternative, sponge-specific cell-adhesion mechanism called &quot;aggregation factor.&quot; In this study, we examined the structure, biochemical properties, and tissue localization of a vinculin ortholog in the sponge Oscarella pearsei (Op). Our results indicate that Op vinculin localizes to both cell-cell and cell-ECM contacts and has biochemical and structural properties similar to those of vertebrate vinculin. We propose that Op vinculin played a role in cell adhesion and tissue organization in the last common ancestor of sponges and other animals. These findings provide compelling evidence that sponge tissues are indeed organized like epithelia in other animals and support the notion that AJ- and FA-like structures extend to the earliest periods of animal evolution.}, }
@article {pmid29875290, year = {2018}, author = {Ye, AY and Dou, Y and Yang, X and Wang, S and Huang, AY and Wei, L}, title = {A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations.}, journal = {Genome research}, volume = {28}, number = {7}, pages = {943-951}, doi = {10.1101/gr.230003.117}, pmid = {29875290}, issn = {1549-5469}, mesh = {Alleles ; Child ; Female ; Genome, Human/genetics ; Humans ; Male ; Mosaicism ; Mutation/*genetics ; Mutation Rate ; Pedigree ; Polymorphism, Single Nucleotide/*genetics ; }, abstract = {The allele fraction (AF) distribution, occurrence rate, and evolutionary contribution of postzygotic single-nucleotide mosaicisms (pSNMs) remain largely unknown. In this study, we developed a mathematical model to describe the accumulation and AF drift of pSNMs during the development of multicellular organisms. By applying the model, we quantitatively analyzed two large-scale data sets of pSNMs identified from human genomes. We found that the postzygotic mutation rate per cell division during early embryogenesis, especially during the first cell division, was higher than the average mutation rate in either male or female gametes. We estimated that the stochastic cell death rate per cell cleavage during human embryogenesis was ∼5%, and parental pSNMs occurring during the first three cell divisions contributed to ∼10% of the de novo mutations observed in children. We further demonstrated that the genomic profiles of pSNMs could be used to measure the divergence distance between tissues. Our results highlight the importance of pSNMs in estimating recurrence risk and clarified the quantitative relationship between postzygotic and de novo mutations.}, }
@article {pmid29866913, year = {2018}, author = {Grüter, C and Jongepier, E and Foitzik, S}, title = {Insect societies fight back: the evolution of defensive traits against social parasites.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {373}, number = {1751}, pages = {}, doi = {10.1098/rstb.2017.0200}, pmid = {29866913}, issn = {1471-2970}, abstract = {Insect societies face many social parasites that exploit their altruistic behaviours or their resources. Due to the fitness costs these social parasites incur, hosts have evolved various behavioural, chemical, architectural and morphological defence traits. Similar to bacteria infecting multicellular hosts, social parasites have to successfully go through several steps to exploit their hosts. Here, we review how social insects try to interrupt this sequence of events. They can avoid parasite contact by choosing to nest in parasite-free locales or evade attacks by adapting their colony structure. Once social parasites attack, hosts attempt to detect them, which can be facilitated by adjustments in colony odour. If social parasites enter the nest, hosts can either aggressively defend their colony or take their young and flee. Nest structures are often shaped to prevent social parasite invasion or to safeguard host resources. Finally, if social parasites successfully establish themselves in host nests, hosts can rebel by killing the parasite brood or by reproducing in the parasites' presence. Hosts of social parasites can therefore develop multiple traits, leading to the evolution of complex defence portfolios of co-dependent traits. Social parasites can respond to these multi-level defences with counter-adaptations, potentially leading to geographical mosaics of coevolution.This article is part of the Theo Murphy meeting issue 'Evolution of pathogen and parasite avoidance behaviours'.}, }
@article {pmid29860723, year = {2018}, author = {Mustafin, RN and Khusnutdinova, EK}, title = {[Epigenetic hypothesis of the role of peptides in aging.].}, journal = {Advances in gerontology = Uspekhi gerontologii}, volume = {31}, number = {1}, pages = {10-20}, pmid = {29860723}, issn = {1561-9125}, abstract = {In regulation of gene expression in the ontogenesis of multicellular eukaryotes, in addition to transcription factors, an important role is played by epigenetic factors that control the release of genetic information in each cell division. Many binding sites for the transcription factors were derived from transposons sequences. Mobile elements are also important sources of non-coding RNA. Due to this, transposons have an indirect effect on gene expression and genome methylation. In evolution, transposons serve as important sources for the origin of new protein and proteins domains. A number of studies have identified that long non-coding RNAs and microRNAs can be translated into functional peptides. At the same time, transposons remain active in the hypothalamus of adult humans, which is consistent with the transcription of non-coding RNAs in these structures, which may be key in aging.}, }
@article {pmid29856957, year = {2018}, author = {Sebé-Pedrós, A and Saudemont, B and Chomsky, E and Plessier, F and Mailhé, MP and Renno, J and Loe-Mie, Y and Lifshitz, A and Mukamel, Z and Schmutz, S and Novault, S and Steinmetz, PRH and Spitz, F and Tanay, A and Marlow, H}, title = {Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq.}, journal = {Cell}, volume = {173}, number = {6}, pages = {1520-1534.e20}, doi = {10.1016/j.cell.2018.05.019}, pmid = {29856957}, issn = {1097-4172}, abstract = {The emergence and diversification of cell types is a leading factor in animal evolution. So far, systematic characterization of the gene regulatory programs associated with cell type specificity was limited to few cell types and few species. Here, we perform whole-organism single-cell transcriptomics to map adult and larval cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal with complex tissue-level body-plan organization. We uncover eight broad cell classes in Nematostella, including neurons, cnidocytes, and digestive cells. Each class comprises different subtypes defined by the expression of multiple specific markers. In particular, we characterize a surprisingly diverse repertoire of neurons, which comparative analysis suggests are the result of lineage-specific diversification. By integrating transcription factor expression, chromatin profiling, and sequence motif analysis, we identify the regulatory codes that underlie Nematostella cell-specific expression. Our study reveals cnidarian cell type complexity and provides insights into the evolution of animal cell-specific genomic regulation.}, }
@article {pmid29853554, year = {2018}, author = {Toda, S and Blauch, LR and Tang, SKY and Morsut, L and Lim, WA}, title = {Programming self-organizing multicellular structures with synthetic cell-cell signaling.}, journal = {Science (New York, N.Y.)}, volume = {361}, number = {6398}, pages = {156-162}, doi = {10.1126/science.aat0271}, pmid = {29853554}, issn = {1095-9203}, support = {K99 EB021030/EB/NIBIB NIH HHS/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; T32 GM008412/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Artificial Cells ; Cell Adhesion ; *Cell Communication ; Cell Engineering/*methods ; *Cells ; *Morphogenesis ; Signal Transduction ; Spheroids, Cellular/cytology/physiology ; }, abstract = {A common theme in the self-organization of multicellular tissues is the use of cell-cell signaling networks to induce morphological changes. We used the modular synNotch juxtacrine signaling platform to engineer artificial genetic programs in which specific cell-cell contacts induced changes in cadherin cell adhesion. Despite their simplicity, these minimal intercellular programs were sufficient to yield assemblies with hallmarks of natural developmental systems: robust self-organization into multidomain structures, well-choreographed sequential assembly, cell type divergence, symmetry breaking, and the capacity for regeneration upon injury. The ability of these networks to drive complex structure formation illustrates the power of interlinking cell signaling with cell sorting: Signal-induced spatial reorganization alters the local signals received by each cell, resulting in iterative cycles of cell fate branching. These results provide insights into the evolution of multicellularity and demonstrate the potential to engineer customized self-organizing tissues or materials.}, }
@article {pmid29851258, year = {2018}, author = {Schaefke, B and Sun, W and Li, YS and Fang, L and Chen, W}, title = {The evolution of posttranscriptional regulation.}, journal = {Wiley interdisciplinary reviews. RNA}, volume = {}, number = {}, pages = {e1485}, doi = {10.1002/wrna.1485}, pmid = {29851258}, issn = {1757-7012}, abstract = {&quot;DNA makes RNA makes protein.&quot; After transcription, mRNAs undergo a series of intertwining processes to be finally translated into functional proteins. The &quot;posttranscriptional&quot; regulation (PTR) provides cells an extended option to fine-tune their proteomes. To meet the demands of complex organism development and the appropriate response to environmental stimuli, every step in these processes needs to be finely regulated. Moreover, changes in these regulatory processes are important driving forces underlying the evolution of phenotypic differences across different species. The major PTR mechanisms discussed in this review include the regulation of splicing, polyadenylation, decay, and translation. For alternative splicing and polyadenylation, we mainly discuss their evolutionary dynamics and the genetic changes underlying the regulatory differences in cis-elements versus trans-factors. For mRNA decay and translation, which, together with transcription, determine the cellular RNA or protein abundance, we focus our discussion on how their divergence coordinates with transcriptional changes to shape the evolution of gene expression. Then to highlight the importance of PTR in the evolution of higher complexity, we focus on their roles in two major phenomena during eukaryotic evolution: the evolution of multicellularity and the division of labor between different cell types and tissues; and the emergence of diverse, often highly specialized individual phenotypes, especially those concerning behavior in eusocial insects. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution Translation > Translation Regulation RNA Processing > Splicing Regulation/Alternative Splicing.}, }
@article {pmid29846592, year = {2018}, author = {Paps, J}, title = {What Makes an Animal? The Molecular Quest for the Origin of the Animal Kingdom.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {654-665}, doi = {10.1093/icb/icy036}, pmid = {29846592}, issn = {1557-7023}, abstract = {What makes an animal? To find the answer we need to integrate data from disciplines such as phylogenetics, paleontology, ecology, development, anatomy, and physiology, as well as molecular biology and genomics. Knowledge of which groups branched before and after the origin of animals is essential. Recent advances in molecular phylogenetics, together with the discovery of new eukaryotic lineages, have drawn a new picture of the ancestry of animals. The nature of the early diverging animal lineages and the timing of the transition are in a state of flux. Various factors have been linked to this striking transition to multicellularity, including changes in environmental conditions and the ecological interactions between unicellular eukaryotes. The current wealth of genomic data has also shed new light on this question. The analysis of the genome of various close relatives of animals has revealed the importance that recycling of ancient genes into metazoan biological functions played into animal origins. A recent study reconstructing the genome of the last common ancestor of extant animals has unveiled an unprecedented emergence of new genes, highlighting the role of genomic novelty in the origin of metazoans.}, }
@article {pmid29844338, year = {2018}, author = {Pinhal, D and Bovolenta, LA and Moxon, S and Oliveira, AC and Nachtigall, PG and Acencio, ML and Patton, JG and Hilsdorf, AWS and Lemke, N and Martins, C}, title = {Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8248}, doi = {10.1038/s41598-018-26607-x}, pmid = {29844338}, issn = {2045-2322}, abstract = {MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs.}, }
@article {pmid29807994, year = {2018}, author = {Cooper, GA and West, SA}, title = {Division of labour and the evolution of extreme specialization.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {7}, pages = {1161-1167}, doi = {10.1038/s41559-018-0564-9}, pmid = {29807994}, issn = {2397-334X}, abstract = {Division of labour is a common feature of social groups, from biofilms to complex animal societies. However, we lack a theoretical framework that can explain why division of labour has evolved on certain branches of the tree of life but not others. Here, we model the division of labour over a cooperative behaviour, considering both when it should evolve and the extent to which the different types should become specialized. We found that: (1) division of labour is usually-but not always-favoured by high efficiency benefits to specialization and low within-group conflict; and (2) natural selection favours extreme specialization, where some individuals are completely dependent on the helping behaviour of others. We make a number of predictions, several of which are supported by the existing empirical data, from microbes and animals, while others suggest novel directions for empirical work. More generally, we show how division of labour can lead to mutual dependence between different individuals and hence drive major evolutionary transitions, such as those to multicellularity and eusociality.}, }
@article {pmid29802408, year = {2018}, author = {Reeves, MQ and Kandyba, E and Harris, S and Del Rosario, R and Balmain, A}, title = {Multicolour lineage tracing reveals clonal dynamics of squamous carcinoma evolution from initiation to metastasis.}, journal = {Nature cell biology}, volume = {20}, number = {6}, pages = {699-709}, doi = {10.1038/s41556-018-0109-0}, pmid = {29802408}, issn = {1476-4679}, abstract = {Tumour cells are subjected to evolutionary selection pressures during progression from initiation to metastasis. We analysed the clonal evolution of squamous skin carcinomas induced by DMBA/TPA treatment using the K5CreER-Confetti mouse and stage-specific lineage tracing. We show that benign tumours are polyclonal, but only one population contains the Hras driver mutation. Thus, benign papillomas are monoclonal in origin but recruit neighbouring epithelial cells during growth. Papillomas that never progress to malignancy retain several distinct clones, whereas progression to carcinoma is associated with a clonal sweep. Newly generated clones within carcinomas demonstrate intratumoural invasion and clonal intermixing, often giving rise to metastases containing two or more distinct clones derived from the matched primary tumour. These data demonstrate that late-stage tumour progression and dissemination are governed by evolutionary selection pressures that operate at a multicellular level and, therefore, differ from the clonal events that drive initiation and the benign-malignant transition.}, }
@article {pmid29797026, year = {2018}, author = {Hauser, CJ and Otterbein, LE}, title = {Danger signals from mitochondrial DAMPS in trauma and post-injury sepsis.}, journal = {European journal of trauma and emergency surgery : official publication of the European Trauma Society}, volume = {44}, number = {3}, pages = {317-324}, doi = {10.1007/s00068-018-0963-2}, pmid = {29797026}, issn = {1863-9941}, support = {W81XWH-16-1-0464//U.S. Department of Defense/ ; }, mesh = {Alarmins/*immunology ; Animals ; Humans ; Immunity, Innate ; Inflammation/*immunology ; Mitochondria/*immunology ; Signal Transduction/immunology ; Wounds and Injuries/*immunology ; }, abstract = {In all multicellular organisms, immediate host responses to both sterile and infective threat are initiated by very primitive systems now grouped together under the general term 'danger responses'. Danger signals are generated when primitive 'pattern recognition receptors' (PRR) encounter activating 'alarmins'. These molecular species may be of pathogenic infective origin (pathogen-associated molecular patterns) or of sterile endogenous origin (danger-associated molecular patterns). There are many sterile and infective alarmins and there is considerable overlap in their ability to activate PRR, but in all cases the end result is inflammation. It is the overlap between sterile and infective signals acting via a relatively limited number of PRR that generally underlies the great clinical similarity we see between sterile and infective systemic inflammatory responses. Mitochondria (MT) are evolutionarily derived from bacteria, and thus they sit at the crossroads between sterile and infective danger signal pathways. Many of the molecular species in mitochondria are alarmins, and so the release of MT from injured cells results in a wide variety of inflammatory events. This paper discusses the known participation of MT in inflammation and reviews what is known about how the major.}, }
@article {pmid29789717, year = {2018}, author = {Al Habyan, S and Kalos, C and Szymborski, J and McCaffrey, L}, title = {Multicellular detachment generates metastatic spheroids during intra-abdominal dissemination in epithelial ovarian cancer.}, journal = {Oncogene}, volume = {37}, number = {37}, pages = {5127-5135}, doi = {10.1038/s41388-018-0317-x}, pmid = {29789717}, issn = {1476-5594}, abstract = {Ovarian cancer is the most lethal gynecological cancer, where survival rates have had modest improvement over the last 30 years. Metastasis of cancer cells is a major clinical problem, and patient mortality occurs when ovarian cancer cells spread beyond the confinement of ovaries. Disseminated ovarian cancer cells typically spread within the abdomen, where ascites accumulation aids in their transit. Metastatic ascites contain multicellular spheroids, which promote chemo-resistance and recurrence. However, little is known about the origin and mechanisms through which spheroids arise. Using live-imaging of 3D culture models and animal models, we report that epithelial ovarian cancer (EOC) cells, the most common type of ovarian cancer, can spontaneously detach as either single cells or clusters. We report that clusters are more resistant to anoikis and have a potent survival advantage over single cells. Using in vivo lineage tracing, we found that multicellular spheroids arise preferentially from collective detachment, rather than aggregation in the abdomen. Finally, we report that multicellular spheroids from collective detachment are capable of seeding intra-abdominal metastases that retain intra-tumoral heterogeneity from the primary tumor.}, }
@article {pmid29788279, year = {2018}, author = {Tarver, JE and Taylor, RS and Puttick, MN and Lloyd, GT and Pett, W and Fromm, B and Schirrmeister, BE and Pisani, D and Peterson, KJ and Donoghue, PCJ}, title = {Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss.}, journal = {Genome biology and evolution}, volume = {10}, number = {6}, pages = {1457-1470}, doi = {10.1093/gbe/evy096}, pmid = {29788279}, issn = {1759-6653}, abstract = {microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.}, }
@article {pmid29775683, year = {2018}, author = {Dechristé, G and Fehrenbach, J and Griseti, E and Lobjois, V and Poignard, C}, title = {Viscoelastic modeling of the fusion of multicellular tumor spheroids in growth phase.}, journal = {Journal of theoretical biology}, volume = {454}, number = {}, pages = {102-109}, doi = {10.1016/j.jtbi.2018.05.005}, pmid = {29775683}, issn = {1095-8541}, abstract = {BACKGROUND: Since several decades, the experiments have highlighted the analogy of fusing cell aggregates with liquid droplets. The physical macroscopic models have been derived under incompressible assumptions. The aim of this paper is to provide a 3D model of growing spheroids, which is more relevant regarding embryo cell aggregates or tumor cell spheroids.<br><br>METHODS: We extend the past approach to a compressible 3D framework in order to account for the tumor spheroid growth. We exhibit the crucial importance of the effective surface tension, and of the inner pressure of the spheroid to describe precisely the fusion. The experimental data were obtained on spheroids of colon carcinoma human cells (HCT116 cell line). After 3 or 6 days of culture, two identical spheroids were transferred in one well and their fusion was monitored by live videomicroscopy acquisition each 2 h during 72 h. From these images the neck radius and the diameter of the assembly of the fusing spheroids are extracted.<br><br>RESULTS: The numerical model is fitted with the experiments. It is worth noting that the time evolution of both neck radius and spheroid diameter are quantitatively obtained. The interesting feature lies in the fact that such measurements characterise the macroscopic rheological properties of the tumor spheroids.<br><br>CONCLUSIONS: The experimental determination of the kinetics of neck radius and overall diameter during spheroids fusion characterises the rheological properties of the spheroids. The consistency of the model is shown by fitting the model with two different experiments, enhancing the importance of both surface tension and cell proliferation.<br><br>GENERAL SIGNIFICANCE: The paper sheds new light on the macroscopic rheological properties of tumor spheroids. It emphasizes the role of the surface tension and the inner pressure in the fusion of growing spheroid. Under geometrical assumptions, the model reduces to a 2-parameter differential equation fit with experimental measurements. The 3-D partial differential system makes it possible to study the fusion of spheroids in non-symmetrical or more general frameworks.}, }
@article {pmid29760902, year = {2018}, author = {Quintero-Galvis, JF and Paleo-López, R and Solano-Iguaran, JJ and Poupin, MJ and Ledger, T and Gaitan-Espitia, JD and Antoł, A and Travisano, M and Nespolo, RF}, title = {Exploring the evolution of multicellularity in Saccharomyces cerevisiae under bacteria environment: An experimental phylogenetics approach.}, journal = {Ecology and evolution}, volume = {8}, number = {9}, pages = {4619-4630}, doi = {10.1002/ece3.3979}, pmid = {29760902}, issn = {2045-7758}, abstract = {There have been over 25 independent unicellular to multicellular evolutionary transitions, which have been transformational in the complexity of life. All of these transitions likely occurred in communities numerically dominated by unicellular organisms, mostly bacteria. Hence, it is reasonable to expect that bacteria were involved in generating the ecological conditions that promoted the stability and proliferation of the first multicellular forms as protective units. In this study, we addressed this problem by analyzing the occurrence of multicellularity in an experimental phylogeny of yeasts (Sacharomyces cerevisiae) a model organism that is unicellular but can generate multicellular clusters under some conditions. We exposed a single ancestral population to periodic divergences, coevolving with a cocktail of environmental bacteria that were inoculated to the environment of the ancestor, and compared to a control (no bacteria). We quantified culturable microorganisms to the level of genera, finding up to 20 taxa (all bacteria) that competed with the yeasts during diversification. After 600 generations of coevolution, the yeasts produced two types of multicellular clusters: clonal and aggregative. Whereas clonal clusters were present in both treatments, aggregative clusters were only present under the bacteria treatment and showed significant phylogenetic signal. However, clonal clusters showed different properties if bacteria were present as follows: They were more abundant and significantly smaller than in the control. These results indicate that bacteria are important modulators of the occurrence of multicellularity, providing support to the idea that they generated the ecological conditions-promoting multicellularity.}, }
@article {pmid29755113, year = {2018}, author = {Jézéquel, P and Campone, M}, title = {Comment on &quot;How the evolution of multicellularity set the stage for cancer&quot;.}, journal = {British journal of cancer}, volume = {119}, number = {1}, pages = {133-134}, doi = {10.1038/s41416-018-0091-0}, pmid = {29755113}, issn = {1532-1827}, }
@article {pmid29752387, year = {2018}, author = {Parra-Acero, H and Ros-Rocher, N and Perez-Posada, A and Kożyczkowska, A and Sánchez-Pons, N and Nakata, A and Suga, H and Najle, SR and Ruiz-Trillo, I}, title = {Transfection of Capsaspora owczarzaki, a close unicellular relative of animals.}, journal = {Development (Cambridge, England)}, volume = {145}, number = {10}, pages = {}, doi = {10.1242/dev.162107}, pmid = {29752387}, issn = {1477-9129}, mesh = {Animals ; Biological Evolution ; DNA/*genetics ; Evolution, Molecular ; Gene Expression Regulation/genetics ; Genome, Protozoan/*genetics ; Mesomycetozoea/*genetics ; Plasmids/*genetics ; Transfection/*methods ; }, abstract = {How animals emerged from their unicellular ancestor remains a major evolutionary question. New genome data from the closest unicellular relatives of animals have provided important insights into the evolution of animal multicellularity. We know that the unicellular ancestor of animals had an unexpectedly complex genetic repertoire, including many genes that are key to animal development and multicellularity. Thus, assessing the function of these genes among unicellular relatives of animals is key to understanding how they were co-opted at the onset of the Metazoa. However, such analyses have been hampered by the lack of genetic tools. Progress has been made in choanoflagellates and teretosporeans, two of the three lineages closely related to animals, whereas no tools are yet available for functional analysis in the third lineage: the filastereans. Importantly, filastereans have a striking repertoire of genes involved in transcriptional regulation and other developmental processes. Here, we describe a reliable transfection method for the filasterean Capsaspora owczarzaki We also provide a set of constructs for visualising subcellular structures in live cells. These tools convert Capsaspora into a unique experimentally tractable organism to use to investigate the origin and evolution of animal multicellularity.}, }
@article {pmid29738987, year = {2018}, author = {Tasic, B}, title = {Single cell transcriptomics in neuroscience: cell classification and beyond.}, journal = {Current opinion in neurobiology}, volume = {50}, number = {}, pages = {242-249}, doi = {10.1016/j.conb.2018.04.021}, pmid = {29738987}, issn = {1873-6882}, abstract = {Biology has been facing a daunting problem since the cell was understood to be the building block of metazoans: how do we study multicellular systems, when a universal approach to characterize their building blocks and classify them does not exist? Metazoan diversity has not helped: there are many model and non-model organisms, developmental and adult stages, healthy and diseased states. Here, I review the application of single cell transcriptomics to cell classification in neuroscience and its corollaries: the differentially expressed genes discovered in this process are a treasure trove for understanding cell type function and enabling specific access to those types. The advancements and widespread adoption of single-cell transcriptomics are bound to transform our understanding of neural system development, function, pathology and evolution.}, }
@article {pmid29735660, year = {2018}, author = {Elsner, D and Meusemann, K and Korb, J}, title = {Longevity and transposon defense, the case of termite reproductives.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {21}, pages = {5504-5509}, doi = {10.1073/pnas.1804046115}, pmid = {29735660}, issn = {1091-6490}, mesh = {Animals ; *DNA Transposable Elements ; *Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Isoptera/*genetics ; *Longevity ; RNA, Small Interfering/*genetics ; *Reproduction ; }, abstract = {Social insects are promising new models in aging research. Within single colonies, longevity differences of several magnitudes exist that can be found elsewhere only between different species. Reproducing queens (and, in termites, also kings) can live for several decades, whereas sterile workers often have a lifespan of a few weeks only. We studied aging in the wild in a highly social insect, the termite Macrotermes bellicosus, which has one of the most pronounced longevity differences between reproductives and workers. We show that gene-expression patterns differed little between young and old reproductives, implying negligible aging. By contrast, old major workers had many genes up-regulated that are related to transposable elements (TEs), which can cause aging. Strikingly, genes from the PIWI-interacting RNA (piRNA) pathway, which are generally known to silence TEs in the germline of multicellular animals, were down-regulated only in old major workers but not in reproductives. Continued up-regulation of the piRNA defense commonly found in the germline of animals can explain the long life of termite reproductives, implying somatic cooption of germline defense during social evolution. This presents a striking germline/soma analogy as envisioned by the superorganism concept: the reproductives and workers of a colony reflect the germline and soma of multicellular animals, respectively. Our results provide support for the disposable soma theory of aging.}, }
@article {pmid29731304, year = {2018}, author = {Maclean, AE and Hertle, AP and Ligas, J and Bock, R and Balk, J and Meyer, EH}, title = {Absence of Complex I Is Associated with Diminished Respiratory Chain Function in European Mistletoe.}, journal = {Current biology : CB}, volume = {28}, number = {10}, pages = {1614-1619.e3}, doi = {10.1016/j.cub.2018.03.036}, pmid = {29731304}, issn = {1879-0445}, abstract = {Parasitism is a life history strategy found across all domains of life whereby nutrition is obtained from a host. It is often associated with reductive evolution of the genome, including loss of genes from the organellar genomes [1, 2]. In some unicellular parasites, the mitochondrial genome (mitogenome) has been lost entirely, with far-reaching consequences for the physiology of the organism [3, 4]. Recently, mitogenome sequences of several species of the hemiparasitic plant mistletoe (Viscum sp.) have been reported [5, 6], revealing a striking loss of genes not seen in any other multicellular eukaryotes. In particular, the nad genes encoding subunits of respiratory complex I are all absent and other protein-coding genes are also lost or highly diverged in sequence, raising the question what remains of the respiratory complexes and mitochondrial functions. Here we show that oxidative phosphorylation (OXPHOS) in European mistletoe, Viscum album, is highly diminished. Complex I activity and protein subunits of complex I could not be detected. The levels of complex IV and ATP synthase were at least 5-fold lower than in the non-parasitic model plant Arabidopsis thaliana, whereas alternative dehydrogenases and oxidases were higher in abundance. Carbon flux analysis indicates that cytosolic reactions including glycolysis are greater contributors to ATP synthesis than the mitochondrial tricarboxylic acid (TCA) cycle. Our results describe the extreme adjustments in mitochondrial functions of the first reported multicellular eukaryote without complex I.}, }
@article {pmid29730580, year = {2018}, author = {Vijay, K}, title = {Toll-like receptors in immunity and inflammatory diseases: Past, present, and future.}, journal = {International immunopharmacology}, volume = {59}, number = {}, pages = {391-412}, doi = {10.1016/j.intimp.2018.03.002}, pmid = {29730580}, issn = {1878-1705}, mesh = {Animals ; Genetic Predisposition to Disease ; Humans ; *Immunity, Innate ; Infection/genetics/immunology ; Inflammation/genetics/*immunology ; Polymorphism, Genetic ; Toll-Like Receptors/genetics/*immunology ; }, abstract = {The immune system is a very diverse system of the host that evolved during evolution to cope with various pathogens present in the vicinity of environmental surroundings inhabited by multicellular organisms ranging from achordates to chordates (including humans). For example, cells of immune system express various pattern recognition receptors (PRRs) that detect danger via recognizing specific pathogen-associated molecular patterns (PAMPs) and mount a specific immune response. Toll-like receptors (TLRs) are one of these PRRs expressed by various immune cells. However, they were first discovered in the Drosophila melanogaster (common fruit fly) as genes/proteins important in embryonic development and dorso-ventral body patterning/polarity. Till date, 13 different types of TLRs (TLR1-TLR13) have been discovered and described in mammals since the first discovery of TLR4 in humans in late 1997. This discovery of TLR4 in humans revolutionized the field of innate immunity and thus the immunology and host-pathogen interaction. Since then TLRs are found to be expressed on various immune cells and have been targeted for therapeutic drug development for various infectious and inflammatory diseases including cancer. Even, Single nucleotide polymorphisms (SNPs) among various TLR genes have been identified among the different human population and their association with susceptibility/resistance to certain infections and other inflammatory diseases. Thus, in the present review the current and future importance of TLRs in immunity, their pattern of expression among various immune cells along with TLR based therapeutic approach is reviewed.}, }
@article {pmid29718307, year = {2018}, author = {Tarhan, LG and Droser, ML and Cole, DB and Gehling, JG}, title = {Ecological Expansion and Extinction in the Late Ediacaran: Weighing the Evidence for Environmental and Biotic Drivers.}, journal = {Integrative and comparative biology}, volume = {58}, number = {4}, pages = {688-702}, doi = {10.1093/icb/icy020}, pmid = {29718307}, issn = {1557-7023}, abstract = {The Ediacara Biota, Earth's earliest communities of complex, macroscopic, multicellular organisms, appeared during the late Ediacaran Period, just prior to the Cambrian Explosion. Ediacara fossil assemblages consist of exceptionally preserved soft-bodied forms of enigmatic morphology and affinity which nonetheless represent a critical stepping-stone in the evolution of complex animal ecosystems. The Ediacara Biota has historically been divided into three successive Assemblages-the Avalon, the White Sea, and the Nama. Although the oldest (Avalon) Assemblage documents the initial appearance of several groups of Ediacara taxa, the two younger (White Sea and Nama) Assemblages record a particularly striking suite of ecological innovations, including the appearance of diverse Ediacara body plans-in tandem with the rise of bilaterian animals-as well as the emergence of novel ecological strategies such as movement, sexual reproduction, biomineralization, and the development of dense, heterogeneous benthic communities. Many of these ecological innovations appear to be linked to adaptations to heterogeneous substrates and shallow and energetic marine settings. In spite of these innovations, the majority of Ediacara taxa disappear by the end of the Ediacaran, with interpretations for this disappearance historically ranging from the closing of preservational windows to environmentally or biotically mediated extinction. However, in spite of the unresolved affinity and eventual extinction of individual Ediacara taxa, these distinctive ecological strategies persist across the Ediacaran-Cambrian boundary and are characteristic of younger animal-dominated communities of the Phanerozoic. The late Ediacaran emergence of these strategies may, therefore, have facilitated subsequent radiations of the Cambrian. In this light, the Ediacaran and Cambrian Periods, although traditionally envisioned as separate worlds, are likely to have been part of an ecological and evolutionary continuum.}, }
@article {pmid29688518, year = {2018}, author = {Lee, J and Yang, EC and Graf, L and Yang, JH and Qiu, H and Zelzion, U and Chan, CX and Stephens, TG and Weber, APM and Boo, GH and Boo, SM and Kim, KM and Shin, Y and Jung, M and Lee, SJ and Yim, HS and Lee, JH and Bhattacharya, D and Yoon, HS}, title = {Analysis of the Draft Genome of the Red Seaweed Gracilariopsis chorda Provides Insights into Genome Size Evolution in Rhodophyta.}, journal = {Molecular biology and evolution}, volume = {35}, number = {8}, pages = {1869-1886}, doi = {10.1093/molbev/msy081}, pmid = {29688518}, issn = {1537-1719}, abstract = {Red algae (Rhodophyta) underwent two phases of large-scale genome reduction during their early evolution. The red seaweeds did not attain genome sizes or gene inventories typical of other multicellular eukaryotes. We generated a high-quality 92.1 Mb draft genome assembly from the red seaweed Gracilariopsis chorda, including methylation and small (s)RNA data. We analyzed these and other Archaeplastida genomes to address three questions: 1) What is the role of repeats and transposable elements (TEs) in explaining Rhodophyta genome size variation, 2) what is the history of genome duplication and gene family expansion/reduction in these taxa, and 3) is there evidence for TE suppression in red algae? We find that the number of predicted genes in red algae is relatively small (4,803-13,125 genes), particularly when compared with land plants, with no evidence of polyploidization. Genome size variation is primarily explained by TE expansion with the red seaweeds having the largest genomes. Long terminal repeat elements and DNA repeats are the major contributors to genome size growth. About 8.3% of the G. chorda genome undergoes cytosine methylation among gene bodies, promoters, and TEs, and 71.5% of TEs contain methylated-DNA with 57% of these regions associated with sRNAs. These latter results suggest a role for TE-associated sRNAs in RNA-dependent DNA methylation to facilitate silencing. We postulate that the evolution of genome size in red algae is the result of the combined action of TE spread and the concomitant emergence of its epigenetic suppression, together with other important factors such as changes in population size.}, }
@article {pmid29687636, year = {2018}, author = {Liu, J and Zhang, W and Du, H and Leng, X and Li, JH and Pan, H and Xu, J and Wu, LF and Xiao, T}, title = {Seasonal changes in the vertical distribution of two types of multicellular magnetotactic prokaryotes in the sediment of Lake Yuehu, China.}, journal = {Environmental microbiology reports}, volume = {10}, number = {4}, pages = {475-484}, doi = {10.1111/1758-2229.12652}, pmid = {29687636}, issn = {1758-2229}, abstract = {There are two genetically distinct morphological types of multicellular magnetotactic prokaryotes (MMPs) in the intertidal zone of Lake Yuehu (China): ellipsoidal MMPs (eMMPs) and spherical MMPs (sMMPs). We studied the vertical distribution of both types of MMPs in the sediment at Lake Yuehu during 1 year. Both types of MMPs were observed at sediment depths ranging from 1 to 34 cm, depending on the seasons. The eMMPs distributed at depths of 2-34 cm during spring, 1-11 cm during summer, 2-21 cm during autumn and 9-32 cm during winter. The eMMP species Candidatus Magnetananas rongchenensis, with magnetite magnetosomes, dominated at all distribution depths. These results suggested that Ca. M. rongchenensis migrated vertically during four seasons. The vertical profiles of oxidation-reduction potential (ORP) in Lake Yuehu changed seasonally, and these changes coincided with the seasonal distribution of MMPs, suggesting that the ORP affected the vertical distribution of MMPs. In addition, high concentrations of ammonium and silicate were associated with low abundances of MMPs.}, }
@article {pmid29686411, year = {2018}, author = {Marín, I}, title = {Origin and evolution of fungal HECT ubiquitin ligases.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6419}, doi = {10.1038/s41598-018-24914-x}, pmid = {29686411}, issn = {2045-2322}, abstract = {Ubiquitin ligases (E3s) are basic components of the eukaryotic ubiquitination system. In this work, the emergence and diversification of fungal HECT ubiquitin ligases is described. Phylogenetic and structural data indicate that six HECT subfamilies (RSP5, TOM1, UFD4, HUL4, HUL4A and HUL5) existed in the common ancestor of all fungi. These six subfamilies have evolved very conservatively, with only occasional losses and duplications in particular fungal lineages. However, an early, drastic reduction in the number of HECT genes occurred in microsporidians, in parallel to the reduction of their genomes. A significant correlation between the total number of genes and the number of HECT-encoding genes present in fungi has been observed. However, transitions from unicellularity to multicellularity or vice versa apparently had no effect on the evolution of this family. Likely orthologs or co-orthologs of all fungal HECT genes have been detected in animals. Four genes are deduced to be present in the common ancestor of fungi, animals and plants. Protein-protein interactions detected in both the yeast Saccharomyces cerevisiae and humans suggest that some ancient functions of HECT proteins have been conserved since the animals/fungi split.}, }
@article {pmid29686139, year = {2018}, author = {Wang, Y and Gao, Y and Li, C and Gao, H and Zhang, CC and Xu, X}, title = {Three Substrains of the Cyanobacterium Anabaena sp. Strain PCC 7120 Display Divergence in Genomic Sequences and hetC Function.}, journal = {Journal of bacteriology}, volume = {200}, number = {13}, pages = {}, doi = {10.1128/JB.00076-18}, pmid = {29686139}, issn = {1098-5530}, abstract = {Anabaena sp. strain PCC 7120 is a model strain for molecular studies of cell differentiation and patterning in heterocyst-forming cyanobacteria. Subtle differences in heterocyst development have been noticed in different laboratories working on the same organism. In this study, 360 mutations, including single nucleotide polymorphisms (SNPs), small insertion/deletions (indels; 1 to 3 bp), fragment deletions, and transpositions, were identified in the genomes of three substrains. Heterogeneous/heterozygous bases were also identified due to the polyploidy nature of the genome and the multicellular morphology but could be completely segregated when plated after filament fragmentation by sonication. hetC is a gene upregulated in developing cells during heterocyst formation in Anabaena sp. strain PCC 7120 and found in approximately half of other heterocyst-forming cyanobacteria. Inactivation of hetC in 3 substrains of Anabaena sp. PCC 7120 led to different phenotypes: the formation of heterocysts, differentiating cells that keep dividing, or the presence of both heterocysts and dividing differentiating cells. The expression of P hetZ -gfp in these hetC mutants also showed different patterns of green fluorescent protein (GFP) fluorescence. Thus, the function of hetC is influenced by the genomic background and epistasis and constitutes an example of evolution under way.IMPORTANCE Our knowledge about the molecular genetics of heterocyst formation, an important cell differentiation process for global N2 fixation, is mostly based on studies with Anabaena sp. strain PCC 7120. Here, we show that rapid microevolution is under way in this strain, leading to phenotypic variations for certain genes related to heterocyst development, such as hetC This study provides an example for ongoing microevolution, marked by multiple heterogeneous/heterozygous single nucleotide polymorphisms (SNPs), in a multicellular multicopy-genome microorganism.}, }
@article {pmid29685747, year = {2018}, author = {Miller, WB and Torday, JS}, title = {Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution.}, journal = {Progress in biophysics and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pbiomolbio.2018.04.006}, pmid = {29685747}, issn = {1873-1732}, abstract = {Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity.}, }
@article {pmid29675836, year = {2018}, author = {Nagy, LG and Kovács, GM and Krizsán, K}, title = {Complex multicellularity in fungi: evolutionary convergence, single origin, or both?.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {4}, pages = {1778-1794}, doi = {10.1111/brv.12418}, pmid = {29675836}, issn = {1469-185X}, support = {P2014/12//Hungarian Academy of Sciences/ ; ERC_HU Grant #118722//NRDI Office/ ; }, abstract = {Complex multicellularity represents the most advanced level of biological organization and it has evolved only a few times: in metazoans, green plants, brown and red algae and fungi. Compared to other lineages, the evolution of multicellularity in fungi follows different principles; both simple and complex multicellularity evolved via unique mechanisms not found in other lineages. Herein we review ecological, palaeontological, developmental and genomic aspects of complex multicellularity in fungi and discuss general principles of the evolution of complex multicellularity in light of its fungal manifestations. Fungi represent the only lineage in which complex multicellularity shows signatures of convergent evolution: it appears 8-11 times in distinct fungal lineages, which show a patchy phylogenetic distribution yet share some of the genetic mechanisms underlying complex multicellular development. To explain the patchy distribution of complex multicellularity across the fungal phylogeny we identify four key observations: the large number of apparently independent complex multicellular clades; the lack of documented phenotypic homology between these clades; the conservation of gene circuits regulating the onset of complex multicellular development; and the existence of clades in which the evolution of complex multicellularity is coupled with limited gene family diversification. We discuss how these patterns and known genetic aspects of fungal development can be reconciled with the genetic theory of convergent evolution to explain the pervasive occurrence of complex multicellularity across the fungal tree of life.}, }
@article {pmid29675831, year = {2018}, author = {Kauko, A and Lehto, K}, title = {Eukaryote specific folds: Part of the whole.}, journal = {Proteins}, volume = {86}, number = {8}, pages = {868-881}, doi = {10.1002/prot.25517}, pmid = {29675831}, issn = {1097-0134}, abstract = {The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor. Despite of this, there exists a large number of protein families and folds found only in eukaryotes. In this study, we have analyzed structural superfamilies and folds that probably appeared during eukaryogenesis. These folds typically represent relatively small binding domains of larger multidomain proteins. They are commonly involved in biological processes that are particularly complex in eukaryotes, such as signaling, trafficking/cytoskeleton, ubiquitination, transcription and RNA processing, but according to recent studies, these processes also have prokaryotic roots. Thus the folds originating from an eukaryotic stem seem to represent accessory parts that have contributed in the expansion of several prokaryotic processes to a new level of complexity. This might have taken place as a co-evolutionary process where increasing complexity and fold innovations have supported each other.}, }
@article {pmid29663630, year = {2018}, author = {Albuquerque, TAF and Drummond do Val, L and Doherty, A and de Magalhães, JP}, title = {From humans to hydra: patterns of cancer across the tree of life.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {3}, pages = {1715-1734}, doi = {10.1111/brv.12415}, pmid = {29663630}, issn = {1469-185X}, support = {//Wellcome Trust/United Kingdom ; }, abstract = {Cancer is a disease of multicellularity; it originates when cells become dysregulated due to mutations and grow out of control, invading other tissues and provoking discomfort, disability, and eventually death. Human life expectancy has greatly increased in the last two centuries, and consequently so has the incidence of cancer. However, how cancer patterns in humans compare to those of other species remains largely unknown. In this review, we search for clues about cancer and its evolutionary underpinnings across the tree of life. We discuss data from a wide range of species, drawing comparisons with humans when adequate, and interpret our findings from an evolutionary perspective. We conclude that certain cancers are uniquely common in humans, such as lung, prostate, and testicular cancer; while others are common across many species. Lymphomas appear in almost every animal analysed, including in young animals, which may be related to pathogens imposing selection on the immune system. Cancers unique to humans may be due to our modern environment or may be evolutionary accidents: random events in the evolution of our species. Finally, we find that cancer-resistant animals such as whales and mole-rats have evolved cellular mechanisms that help them avoid neoplasia, and we argue that there are multiple natural routes to cancer resistance.}, }
@article {pmid29662839, year = {2018}, author = {Dhakshinamoorthy, R and Bitzhenner, M and Cosson, P and Soldati, T and Leippe, M}, title = {The Saposin-Like Protein AplD Displays Pore-Forming Activity and Participates in Defense Against Bacterial Infection During a Multicellular Stage of Dictyostelium discoideum.}, journal = {Frontiers in cellular and infection microbiology}, volume = {8}, number = {}, pages = {73}, doi = {10.3389/fcimb.2018.00073}, pmid = {29662839}, issn = {2235-2988}, abstract = {Due to their archaic life style and microbivor behavior, amoebae may represent a source of antimicrobial peptides and proteins. The amoebic protozoon Dictyostelium discoideum has been a model organism in cell biology for decades and has recently also been used for research on host-pathogen interactions and the evolution of innate immunity. In the genome of D. discoideum, genes can be identified that potentially allow the synthesis of a variety of antimicrobial proteins. However, at the protein level only very few antimicrobial proteins have been characterized that may interact directly with bacteria and help in fighting infection of D. discoideum with potential pathogens. Here, we focus on a large group of gene products that structurally belong to the saposin-like protein (SAPLIP) family and which members we named provisionally Apls (amoebapore-like peptides) according to their similarity to a comprehensively studied antimicrobial and cytotoxic pore-forming protein of the protozoan parasite Entamoeba histolytica. We focused on AplD because it is the only Apl gene that is reported to be primarily transcribed further during the multicellular stages such as the mobile slug stage. Upon knock-out (KO) of the gene, aplD- slugs became highly vulnerable to virulent Klebsiella pneumoniae. AplD- slugs harbored bacterial clumps in their interior and were unable to slough off the pathogen in their slime sheath. Re-expression of AplD in aplD- slugs rescued the susceptibility toward K. pneumoniae. The purified recombinant protein rAplD formed pores in liposomes and was also capable of permeabilizing the membrane of live Bacillus megaterium. We propose that the multifarious Apl family of D. discoideum comprises antimicrobial effector polypeptides that are instrumental to interact with bacteria and their phospholipid membranes. The variety of its members would allow a complementary and synergistic action against a variety of microbes, which the amoeba encounters in its environment.}, }
@article {pmid29644800, year = {2018}, author = {Mincarelli, L and Lister, A and Lipscombe, J and Macaulay, IC}, title = {Defining Cell Identity with Single-Cell Omics.}, journal = {Proteomics}, volume = {18}, number = {18}, pages = {e1700312}, doi = {10.1002/pmic.201700312}, pmid = {29644800}, issn = {1615-9861}, abstract = {Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation-most notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.}, }
@article {pmid29641448, year = {2018}, author = {Zheng, S and Long, J and Liu, Z and Tao, W and Wang, D}, title = {Identification and Evolution of TGF-β Signaling Pathway Members in Twenty-Four Animal Species and Expression in Tilapia.}, journal = {International journal of molecular sciences}, volume = {19}, number = {4}, pages = {}, doi = {10.3390/ijms19041154}, pmid = {29641448}, issn = {1422-0067}, mesh = {Activin Receptors, Type I/genetics/metabolism ; Animals ; *Evolution, Molecular ; Fish Proteins/*genetics/metabolism ; Phylogeny ; Receptors, Transforming Growth Factor beta/genetics/metabolism ; *Signal Transduction ; Smad4 Protein/genetics/metabolism ; Tilapia/classification/*genetics/metabolism ; Transforming Growth Factor beta/*genetics/metabolism ; }, abstract = {Transforming growth factor β (TGF-β) signaling controls diverse cellular processes during embryogenesis as well as in mature tissues of multicellular animals. Here we carried out a comprehensive analysis of TGF-β pathway members in 24 representative animal species. The appearance of the TGF-β pathway was intrinsically linked to the emergence of metazoan. The total number of TGF-β ligands, receptors, and smads changed slightly in all invertebrates and jawless vertebrates analyzed. In contrast, expansion of the pathway members, especially ligands, was observed in jawed vertebrates most likely due to the second round of whole genome duplication (2R) and additional rounds in teleosts. Duplications of TGFB2, TGFBR2, ACVR1, SMAD4 and SMAD6, which were resulted from 2R, were first isolated. Type II receptors may be originated from the ACVR2-like ancestor. Interestingly, AMHR2 was not identified in Chimaeriformes and Cypriniformes even though they had the ligand AMH. Based on transcriptome data, TGF-β ligands exhibited a tissue-specific expression especially in the heart and gonads. However, most receptors and smads were expressed in multiple tissues indicating they were shared by different ligands. Spatial and temporal expression profiles of 8 genes in gonads of different developmental stages provided a fundamental clue for understanding their important roles in sex determination and reproduction. Taken together, our findings provided a global insight into the phylogeny and expression patterns of the TGF-β pathway genes, and hence contribute to the greater understanding of their biological roles in the organism especially in teleosts.}, }
@article {pmid29632050, year = {2018}, author = {Fidler, AL and Boudko, SP and Rokas, A and Hudson, BG}, title = {The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.}, journal = {Journal of cell science}, volume = {131}, number = {7}, pages = {}, doi = {10.1242/jcs.203950}, pmid = {29632050}, issn = {1477-9137}, support = {R01 DK018381/DK/NIDDK NIH HHS/United States ; R37 DK018381/DK/NIDDK NIH HHS/United States ; }, abstract = {The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution.}, }
@article {pmid29625658, year = {2018}, author = {Padder, SA and Prasad, R and Shah, AH}, title = {Quorum sensing: A less known mode of communication among fungi.}, journal = {Microbiological research}, volume = {210}, number = {}, pages = {51-58}, doi = {10.1016/j.micres.2018.03.007}, pmid = {29625658}, issn = {1618-0623}, mesh = {Anti-Infective Agents/pharmacology ; Bacteria/drug effects/genetics ; Bacterial Physiological Phenomena ; Candida albicans/physiology ; Drug Resistance, Multiple/genetics ; Farnesol/metabolism ; Fungi/*drug effects/*physiology ; Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Fungal ; Phenylethyl Alcohol/analogs &amp; derivatives/metabolism ; Pheromones/metabolism ; Quorum Sensing/*drug effects/genetics/*physiology ; Virulence/genetics ; Volatile Organic Compounds/metabolism ; }, abstract = {Quorum sensing (QS), a density-dependent signaling mechanism of microbial cells, involves an exchange and sense of low molecular weight signaling compounds called autoinducers. With the increase in population density, the autoinducers accumulate in the extracellular environment and once their concentration reaches a threshold, many genes are either expressed or repressed. This cell density-dependent signaling mechanism enables single cells to behave as multicellular organisms and regulates different microbial behaviors like morphogenesis, pathogenesis, competence, biofilm formation, bioluminescence, etc guided by environmental cues. Initially, QS was regarded to be a specialized system of certain bacteria. The discovery of filamentation control in pathogenic polymorphic fungus Candida albicans by farnesol revealed the phenomenon of QS in fungi as well. Pathogenic microorganisms primarily regulate the expression of virulence genes using QS systems. The indirect role of QS in the emergence of multiple drug resistance (MDR) in microbial pathogens necessitates the finding of alternative antimicrobial therapies that target QS and inhibit the same. A related phenomenon of quorum sensing inhibition (QSI) performed by small inhibitor molecules called quorum sensing inhibitors (QSIs) has an ability for efficient reduction of gene expression regulated by quorum sensing. In the present review, recent advancements in the study of different fungal quorum sensing molecules (QSMs) and quorum sensing inhibitors (QSIs) of fungal origin along with their mechanism of action and/or role/s are discussed.}, }
@article {pmid29619014, year = {2018}, author = {Jani, AJ and Briggs, CJ}, title = {Host and Aquatic Environment Shape the Amphibian Skin Microbiome but Effects on Downstream Resistance to the Pathogen Batrachochytrium dendrobatidis Are Variable.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {487}, doi = {10.3389/fmicb.2018.00487}, pmid = {29619014}, issn = {1664-302X}, abstract = {Symbiotic microbial communities play key roles in the health and development of their multicellular hosts. Understanding why microbial communities vary among different host species or individuals is an important step toward understanding the diversity and function of the microbiome. The amphibian skin microbiome may affect resistance to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Still, the factors that determine the diversity and composition of the amphibian skin microbiome, and therefore may ultimately contribute to disease resistance, are not well understood. We conducted a two-phase experiment to first test how host and environment shape the amphibian skin microbiome, and then test if the microbiome affects or is affected by Bd infection. Most lab experiments testing assembly of the amphibian skin microbiome so far have compared sterile to non-sterile environments or heavily augmented to non-augmented frogs. A goal of this study was to evaluate, in an experimental setting, realistic potential drivers of microbiome assembly that would be relevant to patterns observed in nature. We tested effects of frog genetic background (2 source populations) and 6 natural lake water sources in shaping the microbiome of the frog Rana sierrae. Water in which frogs were housed affected the microbiome in a manner that partially mimicked patterns observed in natural populations. In particular, frogs housed in water from disease-resistant populations had greater bacterial richness than frogs housed in water from populations that died out due to Bd. However, in the experiment this difference in microbiomes did not lead to differences in host mortality or rates of pathogen load increase. Frog source population also affected the microbiome and, although none of the frogs in this study showed true resistance to infection, host source population had a small effect on the rate of pathogen load increase. This difference in infection trajectories could be due to the observed differences in the microbiome, but could also be due to other traits that differ between frogs from the two populations. In addition to examining effects of the microbiome on Bd, we tested the effect of Bd infection severity on the microbiome. Specifically, we studied a time series of the microbiome over the course of infection to test if the effects of Bd on the microbiome are dependent on Bd infection severity. Although limited to a small subset of frogs, time series analysis suggested that relative abundances of several bacterial phylotypes changed as Bd loads increased through time, indicating that Bd-induced disturbance of the R. sierrae microbiome is not a binary effect but instead is dependent on infection severity. We conclude that both host and aquatic environment help shape the R. sierrae skin microbiome, with links to small changes in disease resistance in some cases, but in this study the effect of Bd on the microbiome was greater than the effect of the microbiome on Bd. Assessment of the microbiome differences between more distantly related populations than those studied here is needed to fully understand the role of the microbiome in resistance to Bd.}, }
@article {pmid29616867, year = {2018}, author = {Gaiti, F and Degnan, BM and Tanurdžić, M}, title = {Long non-coding regulatory RNAs in sponges and insights into the origin of animal multicellularity.}, journal = {RNA biology}, volume = {15}, number = {6}, pages = {696-702}, doi = {10.1080/15476286.2018.1460166}, pmid = {29616867}, issn = {1555-8584}, abstract = {How animals evolved from a single-celled ancestor over 700 million years ago is poorly understood. Recent transcriptomic and chromatin analyses in the sponge Amphimedon queenslandica, a morphologically-simple representative of one of the oldest animal phyletic lineages, have shed light on what innovations in the genome and its regulation underlie the emergence of animal multicellularity. Comparisons of the regulatory genome of this sponge with those of more complex bilaterian model species and even simpler unicellular relatives have revealed that fundamental changes in genome regulatory complexity accompanied the evolution of animal multicellularity. Here, we review and discuss the results of these recent investigations by specifically focusing on the contribution of long non-coding RNAs to the evolution of the animal regulatory genome.}, }
@article {pmid29614268, year = {2018}, author = {Park, B and Kim, H and Jeon, TJ}, title = {Loss of RapC causes defects in cytokinesis, cell migration, and multicellular development of Dictyostelium.}, journal = {Biochemical and biophysical research communications}, volume = {499}, number = {4}, pages = {783-789}, doi = {10.1016/j.bbrc.2018.03.223}, pmid = {29614268}, issn = {1090-2104}, mesh = {Cell Adhesion ; *Cell Movement ; Cell Shape ; *Cytokinesis ; Dictyostelium/*cytology/*growth &amp; development/metabolism ; Phenotype ; Phylogeny ; Protozoan Proteins/chemistry/*metabolism ; Sequence Homology, Amino Acid ; rap1 GTP-Binding Proteins/chemistry ; }, abstract = {The small GTPase Ras proteins are involved in diverse cellular processes. We investigated the functions of RapC, one of 15 Ras subfamily GTPases in Dictyostelium. Loss of RapC resulted in a spread shape of cells; severe defects in cytokinesis leading to multinucleation; decrease of migration speed in chemoattractant-mediated cell migration, likely through increased cell adhesion; and aberrations in multicellular development producing abnormal multiple tips from one mound and multi-branched developmental structures. Defects in cells lacking RapC were rescued by expressing GFP-RapC in rapC null cells. Our results demonstrate that RapC, despite its high sequence homology with Rap1, plays a negative role in cell spreading and cell adhesion, in contrast to Rap1, which is a key regulator of cell adhesion and cytoskeleton rearrangement. In addition, RapC appears to have a unique function in multicellular development and is involved in tip formation from mounds. This study contributes to the understanding of Ras-mediated cellular processes.}, }
@article {pmid29608173, year = {2018}, author = {Clarke, EK and Rivera Gomez, KA and Mustachi, Z and Murph, MC and Schvarzstein, M}, title = {Manipulation of Ploidy in Caenorhabditis elegans.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {133}, pages = {}, doi = {10.3791/57296}, pmid = {29608173}, issn = {1940-087X}, support = {P40 OD010440/OD/NIH HHS/United States ; //CIHR/Canada ; }, mesh = {Animals ; Caenorhabditis elegans/*genetics ; Male ; *Ploidies ; }, abstract = {Mechanisms that involve whole genome polyploidy play important roles in development and evolution; also, an abnormal generation of tetraploid cells has been associated with both the progression of cancer and the development of drug resistance. Until now, it has not been feasible to easily manipulate the ploidy of a multicellular animal without generating mostly sterile progeny. Presented here is a simple and rapid protocol for generating tetraploid Caenorhabditis elegans animals from any diploid strain. This method allows the user to create a bias in chromosome segregation during meiosis, ultimately increasing ploidy in C. elegans. This strategy relies on the transient reduction of expression of the rec-8 gene to generate diploid gametes. A rec-8 mutant produces diploid gametes that can potentially produce tetraploids upon fertilization. This tractable scheme has been used to generate tetraploid strains carrying mutations and chromosome rearrangements to gain insight into chromosomal dynamics and interactions during pairing and synapsis in meiosis. This method is efficient for generating stable tetraploid strains without genetic markers, can be applied to any diploid strain, and can be used to derive triploid C. elegans. This straightforward method is useful for investigating other fundamental biological questions relevant to genome instability, gene dosage, biological scaling, extracellular signaling, adaptation to stress, development of resistance to drugs, and mechanisms of speciation.}, }
@article {pmid29606595, year = {2018}, author = {Lherminier, P}, title = {[Informative predation: Towards a new species concept].}, journal = {Comptes rendus biologies}, volume = {341}, number = {4}, pages = {209-218}, doi = {10.1016/j.crvi.2018.02.004}, pmid = {29606595}, issn = {1768-3238}, mesh = {*Adaptation, Physiological ; Animals ; Biological Evolution ; Child ; Courtship ; Diploidy ; Female ; Fertility ; Genome ; Humans ; Male ; *Predatory Behavior ; Pregnancy ; Reproduction/genetics ; *Selection, Genetic ; }, abstract = {We distinguish two types of predations: the predation of matter-energy equals the food chain, and the informative predation is the capture of the information brought by the sexual partners. The cell or parent consumes energy and matter to grow, multiply and produce offspring. A fixed amount of resources is divided by the number of organisms, so individual growth and numerical multiplication are limited by depletion resources of the environment. Inversely, fertilization does not destroy information, but instead produces news. The information is multiplied by the number of partners and children, since each fertilization gives rise to a new genome following a combinatorial process that continues without exhaustion. The egg does not swallow the sperm to feed, but exchange good food for quality information. With the discovery of sex, that is, 1.5 Ga ago, life added soft predation to hard predation, i.e. information production within each species to matter-energy flow between species. Replicative and informative structures are subject to two competing biological constraints: replicative fidelity promotes proliferation, but limits adaptive evolution. On the contrary, the offspring of a couple obviously cannot be a copy of both partners, they are a new production, a re-production. Sexual recombination allows the exponential enrichment of the genetic diversity, thus promoting indefinite adaptive and evolutionary capacities. Evolutionary history illustrates this: the bacteria proliferate but have remained at the first purely nutritive stage in which most of the sensory functions, mobility, defense, and feeding have experienced almost no significant novelty in three billion years. Another world appeared with the sexual management of information. Sexual reproduction actually combines two functions: multiplicative by &quot;vertical transfer&quot; and informative by &quot;horizontal transfer&quot;. This distinction is very common: polypus - medusa alternations, parasite multiplication cycles, the lytochal and deuterotochal parthenogenesis of aphids, and the innumerable para- and pseudo-sexual strategies of plants opportunistically combine the two modes of asexual replication and sexual combination. However, for the majority of animals and multicellular plants that produce many gametes, numerical proliferation by descendants and informative diversity by sexuality are mutually implicated, for example in the seed. The true discovery of eukaryotes may not be the &quot;true nucleus&quot;, as their name implies, but an orderly informative function. The field of recombinations circumscribes a class of partners genetically compatible with each other, each simultaneously prey and predator of the DNA of the other. The mythical Maxwell demon capable of tracing entropy by sorting molecules according to their state does exist: each mate is the other's Maxwell's demon. While a sexless bacterium is simply divided into two cells, two sexual parents work together to produce a single offspring a time. Added to this are the burdens involved in meiosis and crossing-over, cellular diploidy, and mating. Sex produces an information gain that is paid for by a cost of energy-material, and this barter must be fair to survive. The domains of sexual intercourse are very diverse: uniparental reproduction, alternation of asexual proliferation and sexual information, self-fertilization, endogamy, exogamy, panmixis, diffuse or structured polymorphism, fertile or sterile hybridization, horizontal transfers. Each species is a recombination field between two domains, cloning and hybridization. Multiplicative descent and informative fertilization are organically distinct, but selectively associated: the information produced by the parents' sexuality favors the predation of matter-energy and therefore the proliferation of offspring, and this proliferation in turn favors the sexed producers of information. The equation specific to each species is: enough energy to proliferate, enough information to diversify. Alternatively, two other reproductive modes obtain or transmit less information at lower cost: not enough recombinations=repetitive clonal proliferation, and too many recombinations=disordered hybridization. But these marginal modes have poor prospects, as the model of the species is successfully attractive. Better discriminate to better inform. In bacteria, the exchanged and incorporated DNA segments are directly identified by the parity of the complementary strands, which determines simultaneously the similarity, the offspring, and the pairing. In eukaryotes, on the contrary, somatic growth and germinal information are segregated. During speciation, adaptive information is compacted, delocalized, codified and published to inform the species about its own state: the prezygotic relationship governs viable mating. Under the effect of sexual selection, the runaway and the reinforcement of the characters related to courtship testifies to their identifying function, which explains the paradox of the singularity and luxuriance of the sexual hypertrophies. The speciation discretizes a balanced recombination field and validates the informative relations. The species is without degree. Mates of a species recognize each other quickly and well because the logic of coding disengages from the ecological game of adaptations. The system of mate recognition has a function of cohesion and its regularity allows the adaptations of the less regular being, it is neither elitist nor normative, it is subjected neither to a level of aptitudes, nor to sexual performances, but permissive; it protects the variability and polymorphism. Two mutually irreducible relationships triggered the debate between the taxonomists who support the phyletic definition of the species by the descendance, and the proponents of the definition by interfertility. Such a taxonomic disagreement is not insurmountable, but the issue is deeper than taxonomic concepts, because these concepts relate to two different modes of evolution. According to the phyletic model, each species is a lineage passively isolated by external circumstances; on the contrary, in the sexual model each species is actively produced by an internal process of adjustment between replicative costs and informative gains. Each species develops a solution of the equation that matches material-energy expenditures with informative gains. A species concept based on a lasting relationship between these two quantities or on the limits of certain values or their equilibrium is therefore legitimate. It is this equilibrium that all couples resolve, without our formulation being as clearly as biology desires and as physics demands. Energy expenditures and informative gains in sexuality are almost impossible to measure, yet observation and experience allow an approximate ranking of the energy/information ratio. For example, endogamy is more economical, but less diversifying than exogamy, polymorphism increases information, the reinforcement of sexual isolation limits the rate of unproductive fertilization, between neighboring species hybridization allows certain genetic contributions, etc. A closed species evolves naturally towards another just as closed. On the contrary, the artificial transfer of DNA opens the species. The natural boundaries that isolate the species are easily trespassed as energy costs and constraints of sexual recognition are easily controlled; and the perspectives of manipulations are visible, whereas natural selection never anticipates and thus works blindly. Informative, artificially directed predation stimulates the evolution of species.}, }
@article {pmid29602367, year = {2018}, author = {Shingleton, AW and Frankino, WA}, title = {The (ongoing) problem of relative growth.}, journal = {Current opinion in insect science}, volume = {25}, number = {}, pages = {9-19}, doi = {10.1016/j.cois.2017.10.001}, pmid = {29602367}, issn = {2214-5753}, abstract = {Differential growth, the phenomenon where parts of the body grow at different rates, is necessary to generate the complex morphologies of most multicellular organisms. Despite this central importance, how differential growth is regulated remains largely unknown. Recent discoveries, particularly in insects, have started to uncover the molecular-genetic and physiological mechanisms that coordinate growth among different tissues throughout the body and regulate relative growth. These discoveries suggest that growth is coordinated by a network of signals that emanate from growing tissues and central endocrine organs. Here we review these findings and discuss their implications for understanding the regulation of relative growth and the evolution of morphology.}, }
@article {pmid29599012, year = {2018}, author = {Bang, C and Dagan, T and Deines, P and Dubilier, N and Duschl, WJ and Fraune, S and Hentschel, U and Hirt, H and Hülter, N and Lachnit, T and Picazo, D and Pita, L and Pogoreutz, C and Rädecker, N and Saad, MM and Schmitz, RA and Schulenburg, H and Voolstra, CR and Weiland-Bräuer, N and Ziegler, M and Bosch, TCG}, title = {Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?.}, journal = {Zoology (Jena, Germany)}, volume = {127}, number = {}, pages = {1-19}, doi = {10.1016/j.zool.2018.02.004}, pmid = {29599012}, issn = {1873-2720}, mesh = {*Adaptation, Physiological/physiology ; Animals ; Ecosystem ; *Extreme Environments ; Microbiota/genetics/*physiology ; Phylogeny ; Symbiosis/physiology ; }, abstract = {From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host-microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.}, }
@article {pmid29593113, year = {2018}, author = {Nair, RR and Fiegna, F and Velicer, GJ}, title = {Indirect evolution of social fitness inequalities and facultative social exploitation.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1875}, pages = {}, doi = {10.1098/rspb.2018.0054}, pmid = {29593113}, issn = {1471-2954}, abstract = {Microbial genotypes with similarly high proficiency at a cooperative behaviour in genetically pure groups often exhibit fitness inequalities caused by social interaction in mixed groups. Winning competitors in this scenario have been referred to as 'cheaters' in some studies. Such interaction-specific fitness inequalities, as well as social exploitation (in which interaction between genotypes increases absolute fitness), might evolve due to selection for competitiveness at the focal behaviour or might arise non-adaptively due to pleiotropy, hitchhiking or genetic drift. The bacterium Myxococcus xanthus sporulates during cooperative development of multicellular fruiting bodies. Using M. xanthus lineages that underwent experimental evolution in allopatry without selection on sporulation, we demonstrate that interaction-specific fitness inequalities and facultative social exploitation during development readily evolved indirectly among descendant lineages. Fitness inequalities between evolved genotypes were not caused by divergence in developmental speed, as faster-developing strains were not over-represented among competition winners. In competitions between ancestors and several evolved strains, all evolved genotypes produced more spores than the ancestors, including losers of evolved-versus-evolved competitions, indicating that adaptation in non-developmental contexts pleiotropically increased competitiveness for spore production. Overall, our results suggest that fitness inequalities caused by social interaction during cooperative processes may often evolve non-adaptively in natural populations.}, }
@article {pmid29590089, year = {2018}, author = {Alemany, A and Florescu, M and Baron, CS and Peterson-Maduro, J and van Oudenaarden, A}, title = {Whole-organism clone tracing using single-cell sequencing.}, journal = {Nature}, volume = {556}, number = {7699}, pages = {108-112}, doi = {10.1038/nature25969}, pmid = {29590089}, issn = {1476-4687}, mesh = {Animal Fins/cytology ; Animals ; Brain/cytology ; CRISPR-Cas Systems/genetics ; *Cell Lineage/genetics ; Cell Tracking/*methods ; Clone Cells/*cytology/*metabolism ; Embryonic Stem Cells/cytology/metabolism ; Eye/cytology ; Female ; Genes, Reporter/genetics ; Hematopoietic Stem Cells/cytology/metabolism ; Male ; Multipotent Stem Cells/cytology/metabolism ; Organ Specificity ; Regeneration ; Sequence Analysis/*methods ; *Single-Cell Analysis ; Transcriptome ; Whole Body Imaging ; Zebrafish/*anatomy &amp; histology/embryology/genetics ; }, abstract = {Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination. Single-cell transcriptomics provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.}, }
@article {pmid29587819, year = {2018}, author = {Dickson, LB and Ghozlane, A and Volant, S and Bouchier, C and Ma, L and Vega-Rúa, A and Dusfour, I and Jiolle, D and Paupy, C and Mayanja, MN and Kohl, A and Lutwama, JJ and Duong, V and Lambrechts, L}, title = {Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {207}, doi = {10.1186/s13071-018-2780-1}, pmid = {29587819}, issn = {1756-3305}, support = {ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/International ; MC_UU_12014//Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; }, mesh = {Aedes/*microbiology ; Animals ; Bacteria/*classification/*genetics ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Host-associated microbes, collectively known as the microbiota, play an important role in the biology of multicellular organisms. In mosquito vectors of human pathogens, the gut bacterial microbiota influences vectorial capacity and has become the subject of intense study. In laboratory studies of vector biology, genetic effects are often inferred from differences between geographically and genetically diverse colonies of mosquitoes that are reared in the same insectary. It is unclear, however, to what extent genetic effects can be confounded by uncontrolled differences in the microbiota composition among mosquito colonies. To address this question, we used 16S metagenomics to compare the midgut bacterial microbiome of six laboratory colonies of Aedes aegypti recently derived from wild populations representing the geographical range and genetic diversity of the species.<br><br>RESULTS: We found that the diversity, abundance, and community structure of the midgut bacterial microbiome was remarkably similar among the six different colonies of Ae. aegypti, regardless of their geographical origin. We also confirmed the relatively low complexity of bacterial communities inhabiting the mosquito midgut.<br><br>CONCLUSIONS: Our finding that geographically diverse colonies of Ae. aegypti reared in the same insectary harbor a similar gut bacterial microbiome supports the conclusion that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype. Thus, uncontrolled differences in microbiota composition are unlikely to represent a significant confounding factor in genetic studies of vector biology.}, }
@article {pmid29581530, year = {2018}, author = {Lin, W and Zhang, W and Zhao, X and Roberts, AP and Paterson, GA and Bazylinski, DA and Pan, Y}, title = {Genomic expansion of magnetotactic bacteria reveals an early common origin of magnetotaxis with lineage-specific evolution.}, journal = {The ISME journal}, volume = {12}, number = {6}, pages = {1508-1519}, doi = {10.1038/s41396-018-0098-9}, pmid = {29581530}, issn = {1751-7370}, abstract = {The origin and evolution of magnetoreception, which in diverse prokaryotes and protozoa is known as magnetotaxis and enables these microorganisms to detect Earth's magnetic field for orientation and navigation, is not well understood in evolutionary biology. The only known prokaryotes capable of sensing the geomagnetic field are magnetotactic bacteria (MTB), motile microorganisms that biomineralize intracellular, membrane-bounded magnetic single-domain crystals of either magnetite (Fe3O4) or greigite (Fe3S4) called magnetosomes. Magnetosomes are responsible for magnetotaxis in MTB. Here we report the first large-scale metagenomic survey of MTB from both northern and southern hemispheres combined with 28 genomes from uncultivated MTB. These genomes expand greatly the coverage of MTB in the Proteobacteria, Nitrospirae, and Omnitrophica phyla, and provide the first genomic evidence of MTB belonging to the Zetaproteobacteria and &quot;Candidatus Lambdaproteobacteria&quot; classes. The gene content and organization of magnetosome gene clusters, which are physically grouped genes that encode proteins for magnetosome biosynthesis and organization, are more conserved within phylogenetically similar groups than between different taxonomic lineages. Moreover, the phylogenies of core magnetosome proteins form monophyletic clades. Together, these results suggest a common ancient origin of iron-based (Fe3O4 and Fe3S4) magnetotaxis in the domain Bacteria that underwent lineage-specific evolution, shedding new light on the origin and evolution of biomineralization and magnetotaxis, and expanding significantly the phylogenomic representation of MTB.}, }
@article {pmid29579574, year = {2018}, author = {Lower, SS and McGurk, MP and Clark, AG and Barbash, DA}, title = {Satellite DNA evolution: old ideas, new approaches.}, journal = {Current opinion in genetics &amp; development}, volume = {49}, number = {}, pages = {70-78}, doi = {10.1016/j.gde.2018.03.003}, pmid = {29579574}, issn = {1879-0380}, support = {F32 GM126736/GM/NIGMS NIH HHS/United States ; R01 GM119125/GM/NIGMS NIH HHS/United States ; }, abstract = {A substantial portion of the genomes of most multicellular eukaryotes consists of large arrays of tandemly repeated sequence, collectively called satellite DNA. The processes generating and maintaining different satellite DNA abundances across lineages are important to understand as satellites have been linked to chromosome mis-segregation, disease phenotypes, and reproductive isolation between species. While much theory has been developed to describe satellite evolution, empirical tests of these models have fallen short because of the challenges in assessing satellite repeat regions of the genome. Advances in computational tools and sequencing technologies now enable identification and quantification of satellite sequences genome-wide. Here, we describe some of these tools and how their applications are furthering our knowledge of satellite evolution and function.}, }
@article {pmid29575407, year = {2018}, author = {Radzvilavicius, AL and Blackstone, NW}, title = {The evolution of individuality revisited.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {3}, pages = {1620-1633}, doi = {10.1111/brv.12412}, pmid = {29575407}, issn = {1469-185X}, abstract = {Evolutionary theory is formulated in terms of individuals that carry heritable information and are subject to selective pressures. However, individuality itself is a trait that had to evolve - an individual is not an indivisible entity, but a result of evolutionary processes that necessarily begin at the lower level of hierarchical organisation. Traditional approaches to biological individuality focus on cooperation and relatedness within a group, division of labour, policing mechanisms and strong selection at the higher level. Nevertheless, despite considerable theoretical progress in these areas, a full dynamical first-principles account of how new types of individuals arise is missing. To the extent that individuality is an emergent trait, the problem can be approached by recognising the importance of individuating mechanisms that are present from the very beginning of the transition, when only lower-level selection is acting. Here we review some of the most influential theoretical work on the role of individuating mechanisms in these transitions, and demonstrate how a lower-level, bottom-up evolutionary framework can be used to understand biological complexity involved in the origin of cellular life, early eukaryotic evolution, sexual life cycles and multicellular development. Some of these mechanisms inevitably stem from environmental constraints, population structure and ancestral life cycles. Others are unique to specific transitions - features of the natural history and biochemistry that are co-opted into conflict mediation. Identifying mechanisms of individuation that provide a coarse-grained description of the system's evolutionary dynamics is an important step towards understanding how biological complexity and hierarchical organisation evolves. In this way, individuality can be reconceptualised as an approximate model that with varying degrees of precision applies to a wide range of biological systems.}, }
@article {pmid29575018, year = {2018}, author = {Revilla-I-Domingo, R and Simakov, O}, title = {The Diversification of Early Emerging Metazoans: A Window into the Evolution of Animal Multicellularity.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {5}, pages = {e1800029}, doi = {10.1002/bies.201800029}, pmid = {29575018}, issn = {1521-1878}, abstract = {The biannual international workshop entitled &quot;The diversification of early emerging metazoans: A window into animal evolution?&quot; took place at the Evangelische Akademie Tutzing, Germany, 11-14. September 2017. It was organized by Thomas Bosch (Kiel), Thomas Holstein (Heidelberg), and Ulrich Technau (Vienna), and it was sponsored by the Deutsche Forschungsgemeinschaft (DFG). The meeting gathered over 140 researchers to discuss the contribution of non-bilaterian metazoan models (Porifera, Ctenophora, Placozoa, and Cnidaria) to our understanding of: a. The evolution of metazoan developmental processes; b. Fundamental molecular mechanisms underlying metazoan features; and c. The complex interactions that animals establish with their environment.}, }
@article {pmid29573204, year = {2018}, author = {Preisner, H and Habicht, J and Garg, SG and Gould, SB}, title = {Intermediate filament protein evolution and protists.}, journal = {Cytoskeleton (Hoboken, N.J.)}, volume = {75}, number = {6}, pages = {231-243}, doi = {10.1002/cm.21443}, pmid = {29573204}, issn = {1949-3592}, abstract = {Metazoans evolved from a single protist lineage. While all eukaryotes share a conserved actin and tubulin-based cytoskeleton, it is commonly perceived that intermediate filaments (IFs), including lamin, vimentin or keratin among many others, are restricted to metazoans. Actin and tubulin proteins are conserved enough to be detectable across all eukaryotic genomes using standard phylogenetic methods, but IF proteins, in contrast, are notoriously difficult to identify by such means. Since the 1950s, dozens of cytoskeletal proteins in protists have been identified that seemingly do not belong to any of the IF families described for metazoans, yet, from a structural and functional perspective fit criteria that define metazoan IF proteins. Here, we briefly review IF protein discovery in metazoans and the implications this had for the definition of this protein family. We argue that the many cytoskeletal and filament-forming proteins of protists should be incorporated into a more comprehensive picture of IF evolution by aligning it with the recent identification of lamins across the phylogenetic diversity of eukaryotic supergroups. This then brings forth the question of how the diversity of IF proteins has unfolded. The evolution of IF proteins likely represents an example of convergent evolution, which, in combination with the speed with which these cytoskeletal proteins are evolving, generated their current diversity. IF proteins did not first emerge in metazoa, but in protists. Only the emergence of cytosolic IF proteins that appear to stem from a nuclear lamin is unique to animals and coincided with the emergence of true animal multicellularity.}, }
@article {pmid29564400, year = {2018}, author = {Qin, X and Zhou, C and Zerr, DM and Adler, A and Addetia, A and Yuan, S and Greninger, AL}, title = {Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients.}, journal = {mSphere}, volume = {3}, number = {2}, pages = {}, doi = {10.1128/mSphere.00615-17}, pmid = {29564400}, issn = {2379-5042}, abstract = {Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability. Pseudomonas aeruginosa isolates from CF patients have long been recognized for their overall reduced rate of antimicrobial susceptibility, but their intraclonal MIC heterogeneity has long been overlooked. Using two distinct cohorts of clinical strains (n = 224 from 56 CF patients, n = 130 from 68 non-CF patients) isolated in 2013, we demonstrated profound Etest MIC heterogeneity in CF P. aeruginosa isolates in comparison to non-CF P. aeruginosa isolates. On the basis of whole-genome sequencing of 19 CF P. aeruginosa isolates from 9 patients with heterogeneous MICs, the core genome phylogenetic tree confirmed the within-patient CF P. aeruginosa clonal lineage along with considerable coding sequence variability. No extrachromosomal DNA elements or previously characterized antibiotic resistance mutations could account for the wide divergence in antimicrobial MICs between P. aeruginosa coisolates, though many heterogeneous mutations in efflux and porin genes and their regulators were present. A unique OprD sequence was conserved among the majority of isolates of CF P. aeruginosa analyzed, suggesting a pseudomonal response to selective pressure that is common to the isolates. Genomic sequence data also suggested that CF pseudomonal hypermutability was not entirely due to mutations in mutL, mutS, and uvr. We conclude that the net effect of hundreds of adaptive mutations, both shared between clonally related isolate pairs and unshared, accounts for their highly heterogeneous MIC variances. We hypothesize that this heterogeneity is indicative of the pseudomonal syntrophic-like lifestyle under conditions of being &quot;locked&quot; inside a host focal airway environment for prolonged periods. IMPORTANCE Patients with cystic fibrosis endure &quot;chronic focal infections&quot; with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P. aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P. aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents-a phenomenon we define as &quot;heterogeneous MICs.&quot; By sequencing pairs of P. aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair machinery, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications.}, }
@article {pmid29563281, year = {2018}, author = {Rodríguez-Rojas, A and Moreno-Morales, J and Mason, AJ and Rolff, J}, title = {Cationic antimicrobial peptides do not change recombination frequency in Escherichia coli.}, journal = {Biology letters}, volume = {14}, number = {3}, pages = {}, doi = {10.1098/rsbl.2018.0006}, pmid = {29563281}, issn = {1744-957X}, abstract = {Cationic antimicrobial peptides are ubiquitous immune effectors of multicellular organisms. We previously reported, that in contrast to most of the classic antibiotics, cationic antimicrobial peptides (AMPs) do not increase mutation rates in E. coli Here, we provide new evidence showing that AMPs do not stimulate or enhance bacterial DNA recombination in the surviving fractions. Recombination accelerates evolution of antibiotic resistance. Our findings have implications for our understanding of host-microbe interactions, the evolution of innate immune defences, and shed new light on the dynamic of antimicrobial-resistance evolution.}, }
@article {pmid29559848, year = {2018}, author = {Shabardina, V and Kischka, T and Kmita, H and Suzuki, Y and Makałowski, W}, title = {Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by comparative genomic analysis.}, journal = {International journal of biological sciences}, volume = {14}, number = {3}, pages = {306-320}, doi = {10.7150/ijbs.23869}, pmid = {29559848}, issn = {1449-2288}, abstract = {Amoebozoans are in many aspects interesting research objects, as they combine features of single-cell organisms with complex signaling and defense systems, comparable to multicellular organisms. Acanthamoeba castellanii is a cosmopolitan species and developed diverged feeding abilities and strong anti-bacterial resistance; Entamoeba histolytica is a parasitic amoeba, who underwent massive gene loss and its genome is almost twice smaller than that of A. castellanii. Nevertheless, both species prosper, demonstrating fitness to their specific environments. Here we compare transcriptomes of A. castellanii and E. histolytica with application of orthologs' search and gene ontology to learn how different life strategies influence genome evolution and restructuring of physiology. A. castellanii demonstrates great metabolic activity and plasticity, while E. histolytica reveals several interesting features in its translational machinery, cytoskeleton, antioxidant protection, and nutritional behavior. In addition, we suggest new features in E. histolytica physiology that may explain its successful colonization of human colon and may facilitate medical research.}, }
@article {pmid29556540, year = {2018}, author = {Hynson, NA and Frank, KL and Alegado, RA and Amend, AS and Arif, M and Bennett, GM and Jani, AJ and Medeiros, MCI and Mileyko, Y and Nelson, CE and Nguyen, NH and Nigro, OD and Prisic, S and Shin, S and Takagi, D and Wilson, ST and Yew, JY}, title = {Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, doi = {10.1128/mSystems.00159-17}, pmid = {29556540}, issn = {2379-5077}, support = {P30 GM114737/GM/NIGMS NIH HHS/United States ; R21 AI109293/AI/NIAID NIH HHS/United States ; }, abstract = {Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and molecular biology from the University of Hawai'i at Mānoa aims to fill this gap. We are united in our mutual interest in advancing a new paradigm for biology that incorporates our modern understanding of the importance of microorganisms. As our first concerted research effort, we will assess the diversity and function of microbes across an entire watershed on the island of Oahu, Hawai'i. Due to its high ecological diversity across tractable areas of land and sea, Hawai'i provides a model system for the study of complex microbial communities and the processes they mediate. Owing to our diverse expertise, we will leverage this study system to advance the field of biology.}, }
@article {pmid29547664, year = {2018}, author = {Zielich, J and Tzima, E and Schröder, EA and Jemel, F and Conradt, B and Lambie, EJ}, title = {Overlapping expression patterns and functions of three paralogous P5B ATPases in Caenorhabditis elegans.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194451}, doi = {10.1371/journal.pone.0194451}, pmid = {29547664}, issn = {1932-6203}, support = {P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/classification/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Caenorhabditis elegans/cytology/enzymology/*genetics ; Caenorhabditis elegans Proteins/*genetics/metabolism ; Cell Movement/genetics ; *Gene Expression Profiling ; *Gene Expression Regulation, Enzymologic ; Luminescent Proteins/genetics/metabolism ; Membrane Proteins/genetics/metabolism ; Mutation ; Organelles/enzymology ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {P5B ATPases are present in the genomes of diverse unicellular and multicellular eukaryotes, indicating that they have an ancient origin, and that they are important for cellular fitness. Inactivation of ATP13A2, one of the four human P5B ATPases, leads to early-onset Parkinson's disease (Kufor-Rakeb Syndrome). The presence of an invariant PPALP motif within the putative substrate interaction pocket of transmembrane segment M4 suggests that all P5B ATPases might have similar transport specificity; however, the identity of the transport substrate(s) remains unknown. Nematodes of the genus Caenorhabditis possess three paralogous P5B ATPase genes, catp-5, catp-6 and catp-7, which probably originated from a single ancestral gene around the time of origin of the Caenorhabditid clade. By using CRISPR/Cas9, we have systematically investigated the expression patterns, subcellular localization and biological functions of each of the P5B ATPases of C. elegans. We find that each gene has a unique expression pattern, and that some tissues express more than one P5B. In some tissues where their expression patterns overlap, different P5Bs are targeted to different subcellular compartments (e.g., early endosomes vs. plasma membrane), whereas in other tissues they localize to the same compartment (plasma membrane). We observed lysosomal co-localization between CATP-6::GFP and LMP-1::RFP in transgenic animals; however, this was an artifact of the tagged LMP-1 protein, since anti-LMP-1 antibody staining of native protein revealed that LMP-1 and CATP-6::GFP occupy different compartments. The nematode P5Bs are at least partially redundant, since we observed synthetic sterility in catp-5(0); catp-6(0) and catp-6(0) catp-7(0) double mutants. The double mutants exhibit defects in distal tip cell migration that resemble those of ina-1 (alpha integrin ortholog) and vab-3 (Pax6 ortholog) mutants, suggesting that the nematode P5Bs are required for ina-1and/or vab-3 function. This is potentially a conserved regulatory interaction, since mammalian ATP13A2, alpha integrin and Pax6 are all required for proper dopaminergic neuron function.}, }
@article {pmid29546464, year = {2018}, author = {Zhang, H and Yang, X and Feng, X and Xu, H and Yang, Q and Zou, L and Yan, M and Liu, D and Su, X and Jiao, B}, title = {Chromosome-wide gene dosage rebalance may benefit tumor progression.}, journal = {Molecular genetics and genomics : MGG}, volume = {293}, number = {4}, pages = {895-906}, doi = {10.1007/s00438-018-1429-2}, pmid = {29546464}, issn = {1617-4623}, support = {XDB13030400//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; No.2016FB038//Applied Basic Research Foundation of Yunnan Province/ ; No.31371502//National Natural Science Foundation of China/ ; No. GREKF15-11//Open Project from state Key Laboratory of Genetic Resources and Evolution/ ; No.GREKF14-05//Open Project from State Key Laboratory of Genetic Resources and Evolution/ ; }, mesh = {Breast Neoplasms/*genetics ; Chromosomes, Human, X/*genetics ; Female ; *Gene Dosage ; *Gene Expression Regulation, Neoplastic ; *Gene Ontology ; Humans ; MCF-7 Cells ; }, abstract = {The high-risk of tumor initiation in patients with Turner syndrome (TS) characterized by X chromosome monosomy in women has been well established and aneuploidy, defined as an abnormal number of chromosomes, is a common feature in human cancer. However, the underlying mechanisms of X chromosome aneuploidy promoting tumorigenesis remain obscure. We propose that chromosome-wide gene dosage imbalance (CDI) may serve as an important mechanism. Here, we assess the relative expression ratios of X chromosome and autosomes (expression ratios of X:AA) between tumor samples and adjacent normal samples across 16 tumor types using expression datasets from The Cancer Genome Atlas (TCGA) project. Our results show that the expression ratios of X:AA in tumor samples are frequently rebalanced to a lower level compared to those in adjacent normal samples, which is termed chromosome-wide gene dosage rebalance (CDR) thereafter. Gene ontology (GO) analysis of differentially expression genes from X chromosome reveals that downregulation of multicellularity-related genes and upregulation of unicellularity-related genes in tumors form a distinctive feature and enrichment analysis shows that downregulated genes are enriched in tumor suppressor genes, which indicate that CDR benefits tumor progression. Further experimental results prove that disturbance of X chromosome expression by knocking down of XIST in breast cancer cells, which functions in initiation phase of X chromosome inactivation (XCI), inhibits tumor progression. Our results demonstrate that the prevalent CDRs across tumor types serve as an important mechanism in promoting tumor progression, which partially explains the high risk of tumor in patients with TS and also provides a new cancer therapy from the CDR perspective.}, }
@article {pmid29546391, year = {2018}, author = {Kritzer, JA and Freyzon, Y and Lindquist, S}, title = {Yeast can accommodate phosphotyrosine: v-Src toxicity in yeast arises from a single disrupted pathway.}, journal = {FEMS yeast research}, volume = {18}, number = {3}, pages = {}, doi = {10.1093/femsyr/foy027}, pmid = {29546391}, issn = {1567-1364}, abstract = {Tyrosine phosphorylation is a key biochemical signal that controls growth and differentiation in multicellular organisms. Saccharomyces cerevisiae and nearly all other unicellular eukaryotes lack intact phosphotyrosine signaling pathways. However, many of these organisms have primitive phosphotyrosine-binding proteins and tyrosine phosphatases, leading to the assumption that the major barrier for emergence of phosphotyrosine signaling was the negative consequences of promiscuous tyrosine kinase activity. In this work, we reveal that the classic oncogene v-Src, which phosphorylates many dozens of proteins in yeast, is toxic because it disrupts a specific spore wall remodeling pathway. Using genetic selections, we find that expression of a specific cyclic peptide, or overexpression of SMK1, a MAP kinase that controls spore wall assembly, both lead to robust growth despite a continuous high level of phosphotyrosine in the yeast proteome. Thus, minimal genetic manipulations allow yeast to tolerate high levels of phosphotyrosine. These results indicate that the introduction of tyrosine kinases within single-celled organisms may not have been a major obstacle to the evolution of phosphotyrosine signaling.}, }
@article {pmid29545511, year = {2018}, author = {Rosenberg, AB and Roco, CM and Muscat, RA and Kuchina, A and Sample, P and Yao, Z and Graybuck, LT and Peeler, DJ and Mukherjee, S and Chen, W and Pun, SH and Sellers, DL and Tasic, B and Seelig, G}, title = {Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.}, journal = {Science (New York, N.Y.)}, volume = {360}, number = {6385}, pages = {176-182}, doi = {10.1126/science.aam8999}, pmid = {29545511}, issn = {1095-9203}, support = {R01 CA207029/CA/NCI NIH HHS/United States ; R01 NS064404/NS/NINDS NIH HHS/United States ; R21 NS086500/NS/NINDS NIH HHS/United States ; TL1 TR002318/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Brain/*growth &amp; development ; Cell Nucleus/genetics ; Gene Expression Profiling/*methods ; *Gene Expression Regulation, Developmental ; HEK293 Cells ; Humans ; Mice ; NIH 3T3 Cells ; Neurons/metabolism ; Sequence Analysis, RNA ; Single-Cell Analysis/*methods ; Spinal Cord/*growth &amp; development ; *Transcriptome ; }, abstract = {To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing, and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. More than 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation. Pseudotime analysis revealed transcriptional programs driving four developmental lineages, providing a snapshot of early postnatal development in the murine central nervous system. SPLiT-seq provides a path toward comprehensive single-cell transcriptomic analysis of other similarly complex multicellular systems.}, }
@article {pmid29540517, year = {2018}, author = {Yu, G and Baeder, DY and Regoes, RR and Rolff, J}, title = {Predicting drug resistance evolution: insights from antimicrobial peptides and antibiotics.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1874}, pages = {}, doi = {10.1098/rspb.2017.2687}, pmid = {29540517}, issn = {1471-2954}, abstract = {Antibiotic resistance constitutes one of the most pressing public health concerns. Antimicrobial peptides (AMPs) of multicellular organisms are considered part of a solution to this problem, and AMPs produced by bacteria such as colistin are last-resort drugs. Importantly, AMPs differ from many antibiotics in their pharmacodynamic characteristics. Here we implement these differences within a theoretical framework to predict the evolution of resistance against AMPs and compare it to antibiotic resistance. Our analysis of resistance evolution finds that pharmacodynamic differences all combine to produce a much lower probability that resistance will evolve against AMPs. The finding can be generalized to all drugs with pharmacodynamics similar to AMPs. Pharmacodynamic concepts are familiar to most practitioners of medical microbiology, and data can be easily obtained for any drug or drug combination. Our theoretical and conceptual framework is, therefore, widely applicable and can help avoid resistance evolution if implemented in antibiotic stewardship schemes or the rational choice of new drug candidates.}, }
@article {pmid29535324, year = {2018}, author = {Mukherjee, I and Large, RR and Corkrey, R and Danyushevsky, LV}, title = {The Boring Billion, a slingshot for Complex Life on Earth.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4432}, doi = {10.1038/s41598-018-22695-x}, pmid = {29535324}, issn = {2045-2322}, abstract = {The period 1800 to 800 Ma (&quot;Boring Billion&quot;) is believed to mark a delay in the evolution of complex life, primarily due to low levels of oxygen in the atmosphere. Earlier studies highlight the remarkably flat C, Cr isotopes and low trace element trends during the so-called stasis, caused by prolonged nutrient, climatic, atmospheric and tectonic stability. In contrast, we suggest a first-order variability of bio-essential trace element availability in the oceans by combining systematic sampling of the Proterozoic rock record with sensitive geochemical analyses of marine pyrite by LA-ICP-MS technique. We also recall that several critical biological evolutionary events, such as the appearance of eukaryotes, origin of multicellularity &amp; sexual reproduction, and the first major diversification of eukaryotes (crown group) occurred during this period. Therefore, it appears possible that the period of low nutrient trace elements (1800-1400 Ma) caused evolutionary pressures which became an essential trigger for promoting biological innovations in the eukaryotic domain. Later periods of stress-free conditions, with relatively high nutrient trace element concentration, facilitated diversification. We propose that the &quot;Boring Billion&quot; was a period of sequential stepwise evolution and diversification of complex eukaryotes, triggering evolutionary pathways that made possible the later rise of micro-metazoans and their macroscopic counterparts.}, }
@article {pmid29533392, year = {2018}, author = {Bennett, JM and Calosi, P and Clusella-Trullas, S and Martínez, B and Sunday, J and Algar, AC and Araújo, MB and Hawkins, BA and Keith, S and Kühn, I and Rahbek, C and Rodríguez, L and Singer, A and Villalobos, F and Ángel Olalla-Tárraga, M and Morales-Castilla, I}, title = {GlobTherm, a global database on thermal tolerances for aquatic and terrestrial organisms.}, journal = {Scientific data}, volume = {5}, number = {}, pages = {180022}, doi = {10.1038/sdata.2018.22}, pmid = {29533392}, issn = {2052-4463}, abstract = {How climate affects species distributions is a longstanding question receiving renewed interest owing to the need to predict the impacts of global warming on biodiversity. Is climate change forcing species to live near their critical thermal limits? Are these limits likely to change through natural selection? These and other important questions can be addressed with models relating geographical distributions of species with climate data, but inferences made with these models are highly contingent on non-climatic factors such as biotic interactions. Improved understanding of climate change effects on species will require extensive analysis of thermal physiological traits, but such data are both scarce and scattered. To overcome current limitations, we created the GlobTherm database. The database contains experimentally derived species' thermal tolerance data currently comprising over 2,000 species of terrestrial, freshwater, intertidal and marine multicellular algae, plants, fungi, and animals. The GlobTherm database will be maintained and curated by iDiv with the aim to keep expanding it, and enable further investigations on the effects of climate on the distribution of life on Earth.}, }
@article {pmid29524586, year = {2018}, author = {Heber-Katz, E and Messersmith, P}, title = {Drug delivery and epimorphic salamander-type mouse regeneration: A full parts and labor plan.}, journal = {Advanced drug delivery reviews}, volume = {129}, number = {}, pages = {254-261}, doi = {10.1016/j.addr.2018.02.006}, pmid = {29524586}, issn = {1872-8294}, support = {R01 CA180070/CA/NCI NIH HHS/United States ; R01 DE021104/DE/NIDCR NIH HHS/United States ; R01 DE021215/DE/NIDCR NIH HHS/United States ; }, abstract = {The capacity to regenerate entire body parts, tissues, and organs had generally been thought to be lost in evolution with very few exceptions (e.g. the liver) surviving in mammals. The discovery of the MRL mouse and the elucidation of the underlying molecular pathway centering around hypoxia inducible factor, HIF-1α, has allowed a drug and materials approach to regeneration in mice and hopefully humans. The HIF-1α pathway is ancient and permitted the transition from unicellular to multicellular organisms. Furthermore, HIF-1α and its regulation by PHDs, important oxygen sensors in the cell, provides a perfect drug target. We review the historical background of regeneration biology, the discovery of the MRL mouse, and its underlying biology, and novel approaches to drugs, targets, and delivery systems (see Fig. 1).}, }
@article {pmid29520890, year = {2018}, author = {Deevi, RK and Javadi, A and McClements, J and Vohhodina, J and Savage, K and Loughrey, MB and Evergren, E and Campbell, FC}, title = {Protein kinase C zeta suppresses low- or high-grade colorectal cancer (CRC) phenotypes by interphase centrosome anchoring.}, journal = {The Journal of pathology}, volume = {244}, number = {4}, pages = {445-459}, doi = {10.1002/path.5035}, pmid = {29520890}, issn = {1096-9896}, abstract = {Histological grading provides prognostic stratification of colorectal cancer (CRC) by scoring heterogeneous phenotypes. Features of aggressiveness include aberrant mitotic spindle configurations, chromosomal breakage, and bizarre multicellular morphology, but pathobiology is poorly understood. Protein kinase C zeta (PKCz) controls mitotic spindle dynamics, chromosome segregation, and multicellular patterns, but its role in CRC phenotype evolution remains unclear. Here, we show that PKCz couples genome segregation to multicellular morphology through control of interphase centrosome anchoring. PKCz regulates interdependent processes that control centrosome positioning. Among these, interaction between the cytoskeletal linker protein ezrin and its binding partner NHERF1 promotes the formation of a localized cue for anchoring interphase centrosomes to the cell cortex. Perturbation of these phenomena induced different outcomes in cells with single or extra centrosomes. Defective anchoring of a single centrosome promoted bipolar spindle misorientation, multi-lumen formation, and aberrant epithelial stratification. Collectively, these disturbances induce cribriform multicellular morphology that is typical of some categories of low-grade CRC. By contrast, defective anchoring of extra centrosomes promoted multipolar spindle formation, chromosomal instability (CIN), disruption of glandular morphology, and cell outgrowth across the extracellular matrix interface characteristic of aggressive, high-grade CRC. Because PKCz enhances apical NHERF1 intensity in 3D epithelial cultures, we used an immunohistochemical (IHC) assay of apical NHERF1 intensity as an indirect readout of PKCz activity in translational studies. We show that apical NHERF1 IHC intensity is inversely associated with multipolar spindle frequency and high-grade morphology in formalin-fixed human CRC samples. To conclude, defective PKCz control of interphase centrosome anchoring may underlie distinct categories of mitotic slippage that shape the development of low- or high-grade CRC phenotypes. © 2018 The Authors. The Journal of Pathology published by John Wiley &amp; Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.}, }
@article {pmid29512128, year = {2018}, author = {Flamier, A and Singh, S and Rasmussen, TP}, title = {Use of Human Embryoid Bodies for Teratology.}, journal = {Current protocols in toxicology}, volume = {75}, number = {}, pages = {13.13.1-13.13.14}, doi = {10.1002/cptx.38}, pmid = {29512128}, issn = {1934-9262}, abstract = {Human birth defects are relatively common and can be caused by exposure to environmental teratogens or to pharmaceuticals with teratogenic activities. Human embryonic stem cells (hESCs), by virtue of their pluripotent nature, provide an excellent cellular platform for teratogen detection and risk assessment. This unit describes detailed protocols for the preparation and validation of highly pluripotent hESCs, the production of large quantities of aggregated multicellular spheroids composed of hESCs, and these spheroids' differentiation into embryoid bodies (EBs). EBs contain a variety of cells of endodermal, ectodermal, and mesodermal origin and can be subjected to compound exposure in vitro. Hence, they are useful for the detection of chemicals with teratogenic activities. Beyond describing protocols to assemble and culture EBs, this unit details methods to exploit the EB system for teratological assessment. In addition, strategies to distinguish compounds with bona fide teratogenic activity versus simple toxicity are discussed. © 2018 by John Wiley &amp; Sons, Inc.}, }
@article {pmid29507840, year = {2018}, author = {Brüwer, JD and Voolstra, CR}, title = {First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4449}, doi = {10.7717/peerj.4449}, pmid = {29507840}, issn = {2167-8359}, abstract = {Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes. Despite the non-random selection of viral genetic material due to the nature of the sequencing data analyzed, our study provides a first insight into the viral community associated with Aiptasia. Similarities of the Aiptasia viral community with those of corals corroborate the application of Aiptasia as a model system to study coral holobionts. Further, the change in abundance of certain viral taxa across different symbiotic states suggests a role of viruses in the algal endosymbiosis, but the functional significance of this remains to be determined.}, }
@article {pmid29499253, year = {2018}, author = {Wood, KE and Komarova, NL}, title = {Cooperation-based branching as a mechanism of evolutionary speciation.}, journal = {Journal of theoretical biology}, volume = {445}, number = {}, pages = {166-186}, doi = {10.1016/j.jtbi.2018.02.033}, pmid = {29499253}, issn = {1095-8541}, abstract = {When performing complex tasks, coexistence of organisms in a shared environment can be achieved by means of different strategies. For example, individuals can evolve to complete all parts of the complex task, choosing self-sufficiency over cooperation. On the other hand, they may choose to split parts of the task and share the products for mutual benefit, such that distinct groups of the organisms specialize on a subset of elementary tasks. In contrast to the existing theory of specialization and task sharing for cells in multicellular organisms (or colonies of social insects), here we describe a mechanism of evolutionary branching which is based on cooperation and division of labor, and where selection happens at the individual level. Using a class of mathematical models and the methodology of adaptive dynamics, we investigate the conditions for such branching into distinct cooperating subgroups to occur. We show that, as long as performing multiple tasks is associated with additional cost, branching occurs for a wide parameter range, and this scenario is stable against the invasion of cheaters. We hypothesize that over time, this can lead to evolutionary speciation. Examples from bacterial evolution and the connection with the Black Queen Hypothesis are discussed. It is our hope that the theory of diversification rooted in cooperation may inspire further ecological research to identify more evolutionary examples consistent with this speciation mechanism.}, }
@article {pmid29487592, year = {2018}, author = {Muraille, E}, title = {Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {223}, doi = {10.3389/fmicb.2018.00223}, pmid = {29487592}, issn = {1664-302X}, abstract = {Diversity is widely known to fuel adaptation and evolutionary processes and increase robustness at the population, species and ecosystem levels. The Neo-Darwinian paradigm proposes that the diversity of biological entities is the consequence of genetic changes arising spontaneously and randomly, without regard for their usefulness. However, a growing body of evidence demonstrates that the evolutionary process has shaped mechanisms, such as horizontal gene transfer mechanisms, meiosis and the adaptive immune system, which has resulted in the regulated generation of diversity among populations. Though their origins are unrelated, these diversity generator (DG) mechanisms share common functional properties. They (i) contribute to the great unpredictability of the composition and/or behavior of biological systems, (ii) favor robustness and collectivism among populations and (iii) operate mainly by manipulating the systems that control the interaction of living beings with their environment. The definition proposed here for DGs is based on these properties and can be used to identify them according to function. Interestingly, prokaryotic DGs appear to be mainly reactive, as they generate diversity in response to environmental stress. They are involved in the widely described Red Queen/arms race/Cairnsian dynamic. The emergence of multicellular organisms harboring K selection traits (longer reproductive life cycle and smaller population size) has led to the acquisition of a new class of DGs that act anticipatively to stress pressures and generate a distinct dynamic called the &quot;White Queen&quot; here. The existence of DGs leads to the view of evolution as a more &quot;intelligent&quot; and Lamarckian-like process. Their repeated selection during evolution could be a neglected example of convergent evolution and suggests that some parts of the evolutionary process are tightly constrained by ecological factors, such as the population size, the generation time and the intensity of selective pressure. The ubiquity of DGs also suggests that regulated auto-generation of diversity is a fundamental property of life.}, }
@article {pmid29473286, year = {2018}, author = {Xiao, M and Li, M and Reynolds, CS}, title = {Colony formation in the cyanobacterium Microcystis.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {3}, pages = {1399-1420}, doi = {10.1111/brv.12401}, pmid = {29473286}, issn = {1469-185X}, abstract = {Morphological evolution from a unicellular to multicellular state provides greater opportunities for organisms to attain larger and more complex living forms. As the most common freshwater cyanobacterial genus, Microcystis is a unicellular microorganism, with high phenotypic plasticity, which forms colonies and blooms in lakes and reservoirs worldwide. We conducted a systematic review of field studies from the 1990s to 2017 where Microcystis was dominant. Microcystis was detected as the dominant genus in waterbodies from temperate to subtropical and tropical zones. Unicellular Microcystis spp. can be induced to form colonies by adjusting biotic and abiotic factors in laboratory. Colony formation by cell division has been induced by zooplankton filtrate, high Pb2+ concentration, the presence of another cyanobacterium (Cylindrospermopsis raciborskii), heterotrophic bacteria, and by low temperature and light intensity. Colony formation by cell adhesion can be induced by zooplankton grazing, high Ca2+ concentration, and microcystins. We hypothesise that single cells of all Microcystis morphospecies initially form colonies with a similar morphology to those found in the early spring. These colonies gradually change their morphology to that of M. ichthyoblabe, M. wesenbergii and M. aeruginosa with changing environmental conditions. Colony formation provides Microcystis with many ecological advantages, including adaption to varying light, sustained growth under poor nutrient supply, protection from chemical stressors and protection from grazing. These benefits represent passive tactics responding to environmental stress. Microcystis colonies form at the cost of decreased specific growth rates compared with a unicellular habit. Large colony size allows Microcystis to attain rapid floating velocities (maximum recorded for a single colony, ∼ 10.08 m h-1) that enable them to develop and maintain a large biomass near the surface of eutrophic lakes, where they may shade and inhibit the growth of less-buoyant species in deeper layers. Over time, accompanying species may fail to maintain viable populations, allowing Microcystis to dominate. Microcystis blooms can be controlled by artificial mixing. Microcystis colonies and non-buoyant phytoplankton will be exposed to identical light conditions if they are evenly distributed over the water column. In that case, green algae and diatoms, which generally have a higher growth rate than Microcystis, will be more successful. Under such mixing conditions, other phytoplankton taxa could recover and the dominance of Microcystis would be reduced. This review advances our understanding of the factors and mechanisms affecting Microcystis colony formation and size in the field and laboratory through synthesis of current knowledge. The main transition pathways of morphological changes in Microcystis provide an example of the phenotypic plasticity of organisms during morphological evolution from a unicellular to multicellular state. We emphasise that the mechanisms and factors influencing competition among various close morphospecies are sometimes paradoxical because these morphospecies are potentially a single species. Further work is required to clarify the colony-forming process in different Microcystis morphospecies and the seasonal variation in this process. This will allow researchers to grow laboratory cultures that more closely reflect field morphologies and to optimise artificial mixing to manage blooms more effectively.}, }
@article {pmid29472284, year = {2018}, author = {Raina, JB and Eme, L and Pollock, FJ and Spang, A and Archibald, JM and Williams, TA}, title = {Symbiosis in the microbial world: from ecology to genome evolution.}, journal = {Biology open}, volume = {7}, number = {2}, pages = {}, doi = {10.1242/bio.032524}, pmid = {29472284}, issn = {2046-6390}, abstract = {The concept of symbiosis - defined in 1879 by de Bary as 'the living together of unlike organisms' - has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists' workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.}, }
@article {pmid29461501, year = {2018}, author = {Żółtowska-Aksamitowska, S and Shaala, LA and Youssef, DTA and Elhady, SS and Tsurkan, MV and Petrenko, I and Wysokowski, M and Tabachnick, K and Meissner, H and Ivanenko, VN and Bechmann, N and Joseph, Y and Jesionowski, T and Ehrlich, H}, title = {First Report on Chitin in a Non-Verongiid Marine Demosponge: The Mycale euplectellioides Case.}, journal = {Marine drugs}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/md16020068}, pmid = {29461501}, issn = {1660-3397}, mesh = {Animals ; Aquatic Organisms/chemistry/*metabolism ; Biocompatible Materials/chemistry ; Biomimetics/methods ; Chitin/*chemistry/*metabolism ; Chitinases/metabolism ; Microscopy, Electron, Scanning/methods ; Porifera/*chemistry/*metabolism ; Skeleton/chemistry/metabolism ; Spectroscopy, Fourier Transform Infrared/methods ; Spectrum Analysis, Raman/methods ; Tissue Engineering/methods ; }, abstract = {Sponges (Porifera) are recognized as aquatic multicellular organisms which developed an effective biochemical pathway over millions of years of evolution to produce both biologically active secondary metabolites and biopolymer-based skeletal structures. Among marine demosponges, only representatives of the Verongiida order are known to synthetize biologically active substances as well as skeletons made of structural polysaccharide chitin. The unique three-dimensional (3D) architecture of such chitinous skeletons opens the widow for their recent applications as adsorbents, as well as scaffolds for tissue engineering and biomimetics. This study has the ambitious goal of monitoring other orders beyond Verongiida demosponges and finding alternative sources of naturally prestructured chitinous scaffolds; especially in those demosponge species which can be cultivated at large scales using marine farming conditions. Special attention has been paid to the demosponge Mycale euplectellioides(Heteroscleromorpha: Poecilosclerida: Mycalidae) collected in the Red Sea. For the first time, we present here a detailed study of the isolation of chitin from the skeleton of this sponge, as well as its identification using diverse bioanalytical tools. Calcofluor white staining, Fourier-transform Infrared Spcetcroscopy (FTIR), electrospray ionization mass spectrometry (ESI-MS), scanning electron microscopy (SEM), and fluorescence microscopy, as well as a chitinase digestion assay were applied in order to confirm with strong evidence the finding of a-chitin in the skeleton of M. euplectellioides. We suggest that the discovery of chitin within representatives of the Mycale genus is a promising step in their evaluation of these globally distributed sponges as new renewable sources for both biologically active metabolites and chitin, which are of prospective use for pharmacology and biomaterials oriented biomedicine, respectively.}, }
@article {pmid29442314, year = {2018}, author = {Aruga, J and Hatayama, M}, title = {Comparative Genomics of the Zic Family Genes.}, journal = {Advances in experimental medicine and biology}, volume = {1046}, number = {}, pages = {3-26}, doi = {10.1007/978-981-10-7311-3_1}, pmid = {29442314}, issn = {0065-2598}, mesh = {Animals ; *Evolution, Molecular ; Humans ; Multigene Family/*physiology ; *Phylogeny ; Protein Domains ; Species Specificity ; *Transcription Factors/genetics/metabolism ; Zinc Fingers/*physiology ; }, abstract = {Zic family genes encode five C2H2-type zinc finger domain-containing proteins that have many roles in animal development and maintenance. Recent phylogenetic analyses showed that Zic family genes are distributed in metazoans (multicellular animals), except Porifera (sponges) and Ctenophora (comb jellies). The sequence comparisons revealed that the zinc finger domains were absolutely conserved among the Zic family genes. Zic zinc finger domains are similar to, but distinct from those of the Gli, Glis, and Nkl gene family, and these zinc finger protein families are proposed to have been derived from a common ancestor gene. The Gli-Glis-Nkl-Zic superfamily and some other eukaryotic zinc finger proteins share a tandem CWCH2 (tCWCH2) motif, a hallmark for inter-zinc finger interaction between two adjacent C2H2 zinc fingers. In Zic family proteins, there exist additional evolutionally conserved domains known as ZOC and ZFNC, both of which may have appeared before cnidarian-bilaterian divergence. Comparison of the exon-intron boundaries in the Zic zinc finger domains revealed an intron (A-intron) that was absolutely conserved in bilaterians (metazoans with bilateral symmetry) and a placozoan (a simple nonparasitic metazoan). In vertebrates, there are five to seven Zic paralogs among which Zic1, Zic2, and Zic3 are generated through a tandem gene duplication and carboxy-terminal truncation in a vertebrate common ancestor, sharing a conserved carboxy-terminal sequence. Several hypotheses have been proposed to explain the Zic family phylogeny, including their origin, unique features in the first and second zinc finger motif, evolution of the nuclear localization signal, significance of the animal taxa-selective degeneration, gene multiplication in the vertebrate lineage, and involvement in the evolutionary alteration of the animal body plan.}, }
@article {pmid29440299, year = {2018}, author = {Simonini, S and Stephenson, P and Østergaard, L}, title = {A molecular framework controlling style morphology in Brassicaceae.}, journal = {Development (Cambridge, England)}, volume = {145}, number = {5}, pages = {}, doi = {10.1242/dev.158105}, pmid = {29440299}, issn = {1477-9129}, support = {BBS/E/J/00000613//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M004112/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004588/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P013511/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Brassicaceae/*genetics/*growth &amp; development ; Flowers/anatomy &amp; histology/*genetics/*growth &amp; development ; Gene Expression Regulation, Developmental/drug effects ; Gene Expression Regulation, Plant/drug effects ; Indoleacetic Acids/pharmacology ; Phenotype ; Plant Development/drug effects/*genetics ; Plant Growth Regulators/pharmacology ; Plants, Genetically Modified ; Transcription Factors/physiology ; }, abstract = {Organ formation in multicellular organisms depends on the coordinated activities of regulatory components that integrate developmental and hormonal cues to control gene expression and mediate cell-type specification. For example, development of the Arabidopsis gynoecium is tightly controlled by distribution and synthesis of the plant hormone auxin. The functions of several transcription factors (TFs) have been linked with auxin dynamics during gynoecium development; yet how their activities are coordinated is not known. Here, we show that five such TFs function together to ensure polarity establishment at the gynoecium apex. The auxin response factor ETTIN (ARF3; herein, ETT) is a central component of this framework. Interaction of ETT with TF partners is sensitive to the presence of auxin and our results suggest that ETT forms part of a repressive gene-regulatory complex. We show that this function is conserved between members of the Brassicaceae family and that variation in an ETT subdomain affects interaction strengths and gynoecium morphology. These results suggest that variation in affinities between conserved TFs can lead to morphological differences and thus contribute to the evolution of diverse organ shapes.}, }
@article {pmid29439555, year = {2018}, author = {Kapellos, GE and Paraskeva, CA and Kalogerakis, N and Doyle, PS}, title = {Theoretical Insight into the Biodegradation of Solitary Oil Microdroplets Moving through a Water Column.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {5}, number = {1}, pages = {}, doi = {10.3390/bioengineering5010015}, pmid = {29439555}, issn = {2306-5354}, abstract = {In the aftermath of oil spills in the sea, clouds of droplets drift into the seawater column and are carried away by sea currents. The fate of the drifting droplets is determined by natural attenuation processes, mainly dissolution into the seawater and biodegradation by oil-degrading microbial communities. Specifically, microbes have developed three fundamental strategies for accessing and assimilating oily substrates. Depending on their affinity for the oily phase and ability to proliferate in multicellular structures, microbes might either attach to the oil surface and directly uptake compounds from the oily phase, or grow suspended in the aqueous phase consuming solubilized oil, or form three-dimensional biofilms over the oil-water interface. In this work, a compound particle model that accounts for all three microbial strategies is developed for the biodegradation of solitary oil microdroplets moving through a water column. Under a set of educated hypotheses, the hydrodynamics and solute transport problems are amenable to analytical solutions and a closed-form correlation is established for the overall dissolution rate as a function of the Thiele modulus, the Biot number and other key parameters. Moreover, two coupled ordinary differential equations are formulated for the evolution of the particle size and used to investigate the impact of the dissolution and biodegradation processes on the droplet shrinking rate.}, }
@article {pmid29436502, year = {2018}, author = {Hörandl, E and Speijer, D}, title = {How oxygen gave rise to eukaryotic sex.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1872}, pages = {}, doi = {10.1098/rspb.2017.2706}, pmid = {29436502}, issn = {1471-2954}, abstract = {How did full meiotic eukaryotic sex evolve and what was the immediate advantage allowing it to develop? We propose that the crucial determinant can be found in internal reactive oxygen species (ROS) formation at the start of eukaryotic evolution approximately 2 × 109 years ago. The large amount of ROS coming from a bacterial endosymbiont gave rise to DNA damage and vast increases in host genome mutation rates. Eukaryogenesis and chromosome evolution represent adaptations to oxidative stress. The host, an archaeon, most probably already had repair mechanisms based on DNA pairing and recombination, and possibly some kind of primitive cell fusion mechanism. The detrimental effects of internal ROS formation on host genome integrity set the stage allowing evolution of meiotic sex from these humble beginnings. Basic meiotic mechanisms thus probably evolved in response to endogenous ROS production by the 'pre-mitochondrion'. This alternative to mitosis is crucial under novel, ROS-producing stress situations, like extensive motility or phagotrophy in heterotrophs and endosymbiontic photosynthesis in autotrophs. In multicellular eukaryotes with a germline-soma differentiation, meiotic sex with diploid-haploid cycles improved efficient purging of deleterious mutations. Constant pressure of endogenous ROS explains the ubiquitous maintenance of meiotic sex in practically all eukaryotic kingdoms. Here, we discuss the relevant observations underpinning this model.}, }
@article {pmid29435031, year = {2018}, author = {Al-Ramadan, A and Mortensen, AC and Carlsson, J and Nestor, MV}, title = {Analysis of radiation effects in two irradiated tumor spheroid models.}, journal = {Oncology letters}, volume = {15}, number = {3}, pages = {3008-3016}, doi = {10.3892/ol.2017.7716}, pmid = {29435031}, issn = {1792-1074}, abstract = {Multicellular spheroids have proven suitable as three-dimensional in vivo-like models of non-vascularized micrometastases. Unlike monolayer-based models, spheroids mirror the cellular milieu and the pathophysiological gradients inside tumor nodules. However, there is limited knowledge of the radiation effects at the molecular level in spheroids of human origin. The present study is a presentation of selected cell biological processes that may easily be analyzed with methods available at routine pathology laboratories. Using gamma irradiated pancreatic neuroendocrine BON1 and colonic adenocarcinoma HCT116 spheroids as model systems, the present study assessed the radiobiological response in these models. Spheroid growth after irradiation was followed over time and molecular responses were subsequently assessed with immunohistochemistry (IHC) staining for descriptive analyses and semi-automatic grading of apoptosis, G2-phase and senescence in thin sections of the spheroids. Growth studies demonstrated the BON1 spheroids were slower growing and less sensitive to radiation compared with the HCT116 spheroids. IHC staining for G2-phase was primarily observed in the outer viable P-cell layers of the spheroids, with the 6 Gy irradiated HCT116 spheroids demonstrating a very clear increase in staining intensity compared with unirradiated spheroids. Apoptosis staining results indicated increased apoptosis with increasing radiation doses. No clear association between senescence and radiation exposure in the spheroids were observed. The present results demonstrate the feasibility of the use of multicellular spheroids of human origin in combination with IHC analyses to unravel radiobiological responses at a molecular level. The present findings inspire further investigations, including other relevant IHC-detectable molecular processes in time- and radiation dose-dependent settings.}, }
@article {pmid29432421, year = {2018}, author = {Exposito-Alonso, M and Becker, C and Schuenemann, VJ and Reiter, E and Setzer, C and Slovak, R and Brachi, B and Hagmann, J and Grimm, DG and Chen, J and Busch, W and Bergelson, J and Ness, RW and Krause, J and Burbano, HA and Weigel, D}, title = {The rate and potential relevance of new mutations in a colonizing plant lineage.}, journal = {PLoS genetics}, volume = {14}, number = {2}, pages = {e1007155}, doi = {10.1371/journal.pgen.1007155}, pmid = {29432421}, issn = {1553-7404}, mesh = {Arabidopsis/genetics/growth &amp; development ; Crosses, Genetic ; Directed Molecular Evolution ; Evolution, Molecular ; Gene Flow/physiology ; *Genome, Plant ; Introduced Species ; Mutation/*physiology ; *Mutation Rate ; Phenotype ; Phylogeny ; Plant Development/*genetics ; Plant Weeds/genetics/growth &amp; development ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by &quot;natural evolution experiments&quot; that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions-the subset of mutations that survived natural selection and drift-, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance.}, }
@article {pmid29425731, year = {2018}, author = {Israel, MR and Morgan, M and Tay, B and Deuis, JR}, title = {Toxins as tools: Fingerprinting neuronal pharmacology.}, journal = {Neuroscience letters}, volume = {679}, number = {}, pages = {4-14}, doi = {10.1016/j.neulet.2018.02.001}, pmid = {29425731}, issn = {1872-7972}, abstract = {Toxins have been used as tools for decades to study the structure and function of neuronal ion channels and receptors. The biological origin of these toxins varies from single cell organisms, including bacteria and algae, to complex multicellular organisms, including a wide variety of plants and venomous animals. Toxins are a structurally and functionally diverse group of compounds that often modulate neuronal function by interacting with an ion channel or receptor. Many of these toxins display high affinity and exquisite selectivity, making them valuable tools to probe the structure and function of neuronal ion channels and receptors. This review article provides an overview of the experimental techniques used to assess the effects that toxins have on neuronal function, as well as discussion on toxins that have been used as tools, with a focus on toxins that target voltage-gated and ligand-gated ion channels.}, }
@article {pmid29424391, year = {2018}, author = {Cipriano, JLD and Cruz, ACF and Mancini, KC and Schmildt, ER and Lopes, JC and Otoni, WC and Alexandre, RS}, title = {Somatic embryogenesis in Carica papaya as affected by auxins and explants, and morphoanatomical-related aspects.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {90}, number = {1}, pages = {385-400}, doi = {10.1590/0001-3765201820160252}, pmid = {29424391}, issn = {1678-2690}, mesh = {Abscisic Acid/pharmacology ; Carica/anatomy &amp; histology/drug effects/*embryology/*physiology ; Culture Media ; Germination/drug effects/physiology ; Indoleacetic Acids/*analysis ; Microscopy, Electron, Scanning ; Plant Growth Regulators/pharmacology ; Plant Leaves/drug effects/physiology ; Plant Shoots/drug effects/*physiology ; Plant Somatic Embryogenesis Techniques/*methods ; Reference Values ; Reproducibility of Results ; Time Factors ; }, abstract = {The aim of this study was to evaluate somatic embryogenesis in juvenile explants of the THB papaya cultivar. Apical shoots and cotyledonary leaves were inoculated in an induction medium composed of different concentrations of 2,4-D (6, 9, 12, 15 and 18 µM) or 4-CPA (19, 22, 25, 28 and 31 µM). The embryogenic calluses were transferred to a maturation medium for 30 days. Histological analysis were done during the induction and scanning electron microscopy after maturing. For both types of auxin, embryogenesis was achieved at higher frequencies with cotyledonary leaves incubated in induction medium than with apical shoots; except for callogenesis. The early-stage embryos (e.g., globular or heart-shape) predominated. Among the auxins, best results were observed in cotyledonary leaves induced with 4-CPA (25 µM). Histological analyses of the cotyledonary leaf-derived calluses confirmed that the somatic embryos (SEs) formed from parenchyma cells, predominantly differentiated via indirect and multicellular origin and infrequently via synchronized embryogenesis. The secondary embryogenesis was observed during induction and maturation phases in papaya THB cultivar. The combination of ABA (0.5 µM) and AC (15 g L-1) in maturation medium resulted in the highest somatic embryogenesis induction frequency (70 SEs callus-1) and the lowest percentage of early germination (4%).}, }
@article {pmid29422410, year = {2018}, author = {Potjewyd, G and Moxon, S and Wang, T and Domingos, M and Hooper, NM}, title = {Tissue Engineering 3D Neurovascular Units: A Biomaterials and Bioprinting Perspective.}, journal = {Trends in biotechnology}, volume = {36}, number = {4}, pages = {457-472}, doi = {10.1016/j.tibtech.2018.01.003}, pmid = {29422410}, issn = {1879-3096}, abstract = {Neurovascular dysfunction is a central process in the pathogenesis of stroke and most neurodegenerative diseases, including Alzheimer's disease. The multicellular neurovascular unit (NVU) combines the neural, vascular and extracellular matrix (ECM) components in an important interface whose correct functioning is critical to maintain brain health. Tissue engineering is now offering new tools and insights to advance our understanding of NVU function. Here, we review how the use of novel biomaterials to mimic the mechanical and functional cues of the ECM, coupled with precisely layered deposition of the different cells of the NVU through 3D bioprinting, is revolutionising the study of neurovascular function and dysfunction.}, }
@article {pmid29415511, year = {2018}, author = {Henderson, SW and Wege, S and Gilliham, M}, title = {Plant Cation-Chloride Cotransporters (CCC): Evolutionary Origins and Functional Insights.}, journal = {International journal of molecular sciences}, volume = {19}, number = {2}, pages = {}, doi = {10.3390/ijms19020492}, pmid = {29415511}, issn = {1422-0067}, mesh = {Biological Evolution ; Gene Expression ; Homeostasis ; Ions/metabolism ; Phenotype ; Plant Development/genetics ; Plant Proteins/genetics/*metabolism ; Plants/classification/drug effects/genetics/*metabolism ; Sodium-Potassium-Chloride Symporters/genetics/*metabolism ; Water/metabolism ; }, abstract = {Genomes of unicellular and multicellular green algae, mosses, grasses and dicots harbor genes encoding cation-chloride cotransporters (CCC). CCC proteins from the plant kingdom have been comparatively less well investigated than their animal counterparts, but proteins from both plants and animals have been shown to mediate ion fluxes, and are involved in regulation of osmotic processes. In this review, we show that CCC proteins from plants form two distinct phylogenetic clades (CCC1 and CCC2). Some lycophytes and bryophytes possess members from each clade, most land plants only have members of the CCC1 clade, and green algae possess only the CCC2 clade. It is currently unknown whether CCC1 and CCC2 proteins have similar or distinct functions, however they are both more closely related to animal KCC proteins compared to NKCCs. Existing heterologous expression systems that have been used to functionally characterize plant CCC proteins, namely yeast and Xenopus laevis oocytes, have limitations that are discussed. Studies from plants exposed to chemical inhibitors of animal CCC protein function are reviewed for their potential to discern CCC function in planta. Thus far, mutations in plant CCC genes have been evaluated only in two species of angiosperms, and such mutations cause a diverse array of phenotypes-seemingly more than could simply be explained by localized disruption of ion transport alone. We evaluate the putative roles of plant CCC proteins and suggest areas for future investigation.}, }
@article {pmid29411901, year = {2018}, author = {Taverne, YJ and Merkus, D and Bogers, AJ and Halliwell, B and Duncker, DJ and Lyons, TW}, title = {Reactive Oxygen Species: Radical Factors in the Evolution of Animal Life: A molecular timescale from Earth's earliest history to the rise of complex life.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {3}, pages = {}, doi = {10.1002/bies.201700158}, pmid = {29411901}, issn = {1521-1878}, abstract = {Introduction of O2 to Earth's early biosphere stimulated remarkable evolutionary adaptations, and a wide range of electron acceptors allowed diverse, energy-yielding metabolic pathways. Enzymatic reduction of O2 yielded a several-fold increase in energy production, enabling evolution of multi-cellular animal life. However, utilization of O2 also presented major challenges as O2 and many of its derived reactive oxygen species (ROS) are highly toxic, possibly impeding multicellular evolution after the Great Oxidation Event. Remarkably, ROS, and especially hydrogen peroxide, seem to play a major part in early diversification and further development of cellular respiration and other oxygenic pathways, thus becoming an intricate part of evolution of complex life. Hence, although harnessing of chemical and thermo-dynamic properties of O2 for aerobic metabolism is generally considered to be an evolutionary milestone, the ability to use ROS for cell signaling and regulation may have been the first true breakthrough in development of complex life.}, }
@article {pmid29405978, year = {2018}, author = {Wechman, SL and Pradhan, AK and DeSalle, R and Das, SK and Emdad, L and Sarkar, D and Fisher, PB}, title = {New Insights Into Beclin-1: Evolution and Pan-Malignancy Inhibitor Activity.}, journal = {Advances in cancer research}, volume = {137}, number = {}, pages = {77-114}, doi = {10.1016/bs.acr.2017.11.002}, pmid = {29405978}, issn = {2162-5557}, abstract = {Autophagy is a functionally conserved self-degradation process that facilitates the survival of eukaryotic life via the management of cellular bioenergetics and maintenance of the fidelity of genomic DNA. The first known autophagy inducer was Beclin-1. Beclin-1 is expressed in multicellular eukaryotes ranging throughout plants to animals, comprising a nonmonophyllic group, as shown in this report via aggressive BLAST searches. In humans, Beclin-1 is a haploinsuffient tumor suppressor as biallelic deletions have not been observed in patient tumors clinically. Therefore, Beclin-1 fails the Knudson hypothesis, implicating expression of at least one Beclin-1 allele is essential for cancer cell survival. However, Beclin-1 is frequently monoallelically deleted in advanced human cancers and the expression of two Beclin-1 allelles is associated with greater anticancer effects. Overall, experimental evidence suggests that Beclin-1 inhibits tumor formation, angiogenesis, and metastasis alone and in cooperation with the tumor suppressive molecules UVRAG, Bif-1, Ambra1, and MDA-7/IL-24 via diverse mechanisms of action. Conversely, Beclin-1 is upregulated in cancer stem cells (CSCs), portending a role in cancer recurrence, and highlighting this molecule as an intriguing molecular target for the treatment of CSCs. Many aspects of Beclin-1's biological effects remain to be studied. The consequences of these BLAST searches on the molecular evolution of Beclin-1, and the eukaryotic branches of the tree of life, are discussed here in greater detail with future inquiry focused upon protist taxa. Also in this review, the effects of Beclin-1 on tumor suppression and cancer malignancy are discussed. Beclin-1 holds significant promise for the development of novel targeted cancer therapeutics and is anticipated to lead to a many advances in our understanding of eukaryotic evolution, multicellularity, and even the treatment of CSCs in the coming decades.}, }
@article {pmid29400699, year = {2018}, author = {Ćetković, H and Bosnar, MH and Perina, D and Mikoč, A and Deželjin, M and Belužić, R and Bilandžija, H and Ruiz-Trillo, I and Harcet, M}, title = {Characterization of a group I Nme protein of Capsaspora owczarzaki-a close unicellular relative of animals.}, journal = {Laboratory investigation; a journal of technical methods and pathology}, volume = {98}, number = {3}, pages = {304-314}, doi = {10.1038/labinvest.2017.134}, pmid = {29400699}, issn = {1530-0307}, abstract = {Nucleoside diphosphate kinases are enzymes present in all domains of life. In animals, they are called Nme or Nm23 proteins, and are divided into group I and II. Human Nme1 was the first protein identified as a metastasis suppressor. Because of its medical importance, it has been extensively studied. In spite of the large research effort, the exact mechanism of metastasis suppression remains unclear. It is unknown which of the biochemical properties or biological functions are responsible for the antimetastatic role of the mammalian Nme1. Furthermore, it is not clear at which point in the evolution of life group I Nme proteins acquired the potential to suppress metastasis, a process that is usually associated with complex animals. In this study we performed a series of tests and assays on a group I Nme protein from filasterean Capsaspora owczarzaki, a close unicellular relative of animals. The aim was to compare the protein to the well-known human Nme1 and Nme2 homologs, as well as with the homolog from a simple animal-sponge (Porifera), in order to see how the proteins changed with the transition to multicellularity, and subsequently in the evolution of complex animals. We found that premetazoan-type protein is highly similar to the homologs from sponge and human, in terms of biochemical characteristics and potential biological functions. Like the human Nme1 and Nme2, it is able to diminish the migratory potential of human cancer cells in culture.}, }
@article {pmid29398221, year = {2018}, author = {Pang, K and Tang, Q and Chen, L and Wan, B and Niu, C and Yuan, X and Xiao, S}, title = {Nitrogen-Fixing Heterocystous Cyanobacteria in the Tonian Period.}, journal = {Current biology : CB}, volume = {28}, number = {4}, pages = {616-622.e1}, doi = {10.1016/j.cub.2018.01.008}, pmid = {29398221}, issn = {1879-0445}, abstract = {Cyanobacteria were the ultimate ancestor of all plastids and, for much of Earth's history, the only source of biogenic oxygen and a major source of fixed carbon and nitrogen. One cyanobacterial clade, subsections IV+V, is characterized by multicellularity and cell differentiation, with many members bearing specialized nitrogen-fixing (or diazotrophic) heterocysts and encysting akinetes [1-3]. Molecular clock estimates of the divergence time of this clade are highly variable, ranging from ∼2,000 Ma (mega-annum) [4-9] to ∼500 Ma [10]. The older estimates are invariably calibrated by putative akinete fossils from Paleoproterozoic-Mesoproterozoic rocks around 2,100-1,400 Ma [3, 11, 12]. However, the interpretation of these fossils as akinetes has been questioned [13], and the next oldest akinete and heterocyst fossils are ∼410 Ma [14]. Thus, the scarcity of reliable heterocystous cyanobacterial fossils significantly hampers our understanding of the evolution of complex multicellularity among cyanobacteria, their role in regulating geochemical cycles in the geological past, and our ability to calibrate cyanobacterial molecular clocks. Here, we report Tonian (∼1,000-720 Ma) filamentous cyanobacteria that are characterized by large cells, binary fission (for filament elongation), hormogonia (for asexual reproduction and dispersal), probable akinetes (for survival in adverse conditions), and by implication, diazotrophic heterocysts. The new fossils provide a minimum age calibration on the divergence of subsections IV+V and place a firm constraint on the evolution of akinetes and heterocysts.}, }
@article {pmid29395928, year = {2018}, author = {Yamaoka, S and Nishihama, R and Yoshitake, Y and Ishida, S and Inoue, K and Saito, M and Okahashi, K and Bao, H and Nishida, H and Yamaguchi, K and Shigenobu, S and Ishizaki, K and Yamato, KT and Kohchi, T}, title = {Generative Cell Specification Requires Transcription Factors Evolutionarily Conserved in Land Plants.}, journal = {Current biology : CB}, volume = {28}, number = {3}, pages = {479-486.e5}, doi = {10.1016/j.cub.2017.12.053}, pmid = {29395928}, issn = {1879-0445}, abstract = {Land plants differentiate germ cells in the haploid gametophyte. In flowering plants, a generative cell is specified as a precursor that subsequently divides into two sperm cells in the developing male gametophyte, pollen. Generative cell specification requires cell-cycle control and microtubule-dependent nuclear relocation (reviewed in [1-3]). However, the generative cell fate determinant and its evolutionary origin are still unknown. In bryophytes, gametophytes produce eggs and sperm in multicellular reproductive organs called archegonia and antheridia, respectively, or collectively called gametangia. Given the monophyletic origin of land plants [4-6], evolutionarily conserved mechanisms may play key roles in these diverse reproductive processes. Here, we showed that a single member of the subfamily VIIIa of basic helix-loop-helix (bHLH) transcription factors in the liverwort Marchantia polymorpha primarily accumulated in the initial cells and controlled their development into gametangia. We then demonstrated that an Arabidopsis thaliana VIIIa bHLH transiently accumulated in the smaller daughter cell after an asymmetric division of the meiosis-derived microspore and was required for generative cell specification redundantly with its paralog. Furthermore, these A. thaliana VIIIa bHLHs were functionally replaceable by the M. polymorpha VIIIa bHLH. These findings suggest the VIIIa bHLH proteins as core regulators for reproductive development, including germ cell differentiation, since an early stage of land plant evolution.}, }
@article {pmid29394379, year = {2018}, author = {Niklas, KJ and Dunker, AK and Yruela, I}, title = {The evolutionary origins of cell type diversification and the role of intrinsically disordered proteins.}, journal = {Journal of experimental botany}, volume = {69}, number = {7}, pages = {1437-1446}, doi = {10.1093/jxb/erx493}, pmid = {29394379}, issn = {1460-2431}, abstract = {The evolution of complex multicellular life forms occurred multiple times and was attended by cell type specialization. We review seven lines of evidence indicating that intrinsically disordered/ductile proteins (IDPs) played a significant role in the evolution of multicellularity and cell type specification: (i) most eukaryotic transcription factors (TFs) and multifunctional enzymes contain disproportionately long IDP sequences (≥30 residues in length), whereas highly conserved enzymes are normally IDP region poor; (ii) ~80% of the proteome involved in development are IDPs; (iii) the majority of proteins undergoing alternative splicing (AS) of pre-mRNA contain significant IDP regions; (iv) proteins encoded by DNA regions flanking crossing-over 'hot spots' are significantly enriched in IDP regions; (v) IDP regions are disproportionately subject to combinatorial post-translational modifications (PTMs) as well as AS; (vi) proteins involved in transcription and RNA processing are enriched in IDP regions; and (vii) a strong positive correlation exists between the number of different cell types and the IDP proteome fraction across a broad spectrum of uni- and multicellular algae, plants, and animals. We argue that the multifunctionalities conferred by IDPs and the disproportionate involvement of IDPs with AS and PTMs provided a IDP-AS-PTM 'motif' that significantly contributed to the evolution of multicellularity in all major eukaryotic lineages.}, }
@article {pmid29385672, year = {2018}, author = {Park, B and Shin, DY and Jeon, TJ}, title = {CBP7 Interferes with the Multicellular Development of Dictyostelium Cells by Inhibiting Chemoattractant-Mediated Cell Aggregation.}, journal = {Molecules and cells}, volume = {41}, number = {2}, pages = {103-109}, doi = {10.14348/molcells.2018.2170}, pmid = {29385672}, issn = {0219-1032}, mesh = {Calcium/metabolism ; Calcium-Binding Proteins/classification/genetics/*metabolism ; Chemotactic Factors/genetics/metabolism ; *Chemotaxis ; Cyclic AMP/metabolism ; Dictyostelium/cytology/genetics/*metabolism ; Movement ; Phylogeny ; *Signal Transduction ; }, abstract = {Calcium ions are involved in the regulation of diverse cellular processes. Fourteen genes encoding calcium binding proteins have been identified in Dictyostelium. CBP7, one of the 14 CBPs, is composed of 169 amino acids and contains four EF-hand motifs. Here, we investigated the roles of CBP7 in the development and cell migration of Dictyostelium cells and found that high levels of CBP7 exerted a negative effect on cells aggregation during development, possibly by inhibiting chemoattractant-directed cell migration. While cells lacking CBP7 exhibited normal development and chemotaxis similar that of wild-type cells, CBP7 overexpressing cells completely lost their chemotactic abilities to move toward increasing cAMP concentrations. This resulted in inhibition of cellular aggregation, a process required for forming multicellular organisms during development. Low levels of cytosolic free calcium were observed in CBP7 overexpressing cells, which was likely the underlying cause of their lack of chemotaxis. Our results demonstrate that CBP7 plays an important role in cell spreading and cell-substrate adhesion. cbp7 null cells showed decreased cell size and cell-substrate adhesion. The present study contributes to further understanding the role of calcium signaling in regulation of cell migration and development.}, }
@article {pmid29381766, year = {2018}, author = {Boyd, M and Rosenzweig, F and Herron, MD}, title = {Analysis of motility in multicellular Chlamydomonas reinhardtii evolved under predation.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0192184}, doi = {10.1371/journal.pone.0192184}, pmid = {29381766}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/*physiology ; *Predatory Behavior ; }, abstract = {The advent of multicellularity was a watershed event in the history of life, yet the transition from unicellularity to multicellularity is not well understood. Multicellularity opens up opportunities for innovations in intercellular communication, cooperation, and specialization, which can provide selective advantages under certain ecological conditions. The unicellular alga Chlamydomonas reinhardtii has never had a multicellular ancestor yet it is closely related to the volvocine algae, a clade containing taxa that range from simple unicells to large, specialized multicellular colonies. Simple multicellular structures have been observed to evolve in C. reinhardtii in response to predation or to settling rate-based selection. Structures formed in response to predation consist of individual cells confined within a shared transparent extracellular matrix. Evolved isolates form such structures obligately under culture conditions in which their wild type ancestors do not, indicating that newly-evolved multicellularity is heritable. C. reinhardtii is capable of photosynthesis, and possesses an eyespot and two flagella with which it moves towards or away from light in order to optimize input of radiant energy. Motility contributes to C. reinhardtii fitness because it allows cells or colonies to achieve this optimum. Utilizing phototaxis to assay motility, we determined that newly evolved multicellular strains do not exhibit significant directional movement, even though the flagellae of their constituent unicells are present and active. In C. reinhardtii the first steps towards multicellularity in response to predation appear to result in a trade-off between motility and differential survivorship, a trade-off that must be overcome by further genetic change to ensure long-term success of the new multicellular organism.}, }
@article {pmid29381236, year = {2018}, author = {Li, Y and Zuo, S and Zhang, Z and Li, Z and Han, J and Chu, Z and Hasterok, R and Wang, K}, title = {Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus.}, journal = {The Plant journal : for cell and molecular biology}, volume = {93}, number = {6}, pages = {1088-1101}, doi = {10.1111/tpj.13832}, pmid = {29381236}, issn = {1365-313X}, abstract = {Brachypodium distachyon is a well-established model monocot plant, and its small and compact genome has been used as an accurate reference for the much larger and often polyploid genomes of cereals such as Avena sativa (oats), Hordeum vulgare (barley) and Triticum aestivum (wheat). Centromeres are indispensable functional units of chromosomes and they play a core role in genome polyploidization events during evolution. As the Brachypodium genus contains about 20 species that differ significantly in terms of their basic chromosome numbers, genome size, ploidy levels and life strategies, studying their centromeres may provide important insight into the structure and evolution of the genome in this interesting and important genus. In this study, we isolated the centromeric DNA of the B. distachyon reference line Bd21 and characterized its composition via the chromatin immunoprecipitation of the nucleosomes that contain the centromere-specific histone CENH3. We revealed that the centromeres of Bd21 have the features of typical multicellular eukaryotic centromeres. Strikingly, these centromeres contain relatively few centromeric satellite DNAs; in particular, the centromere of chromosome 5 (Bd5) consists of only ~40 kb. Moreover, the centromeric retrotransposons in B. distachyon (CRBds) are evolutionarily young. These transposable elements are located both within and adjacent to the CENH3 binding domains, and have similar compositions. Moreover, based on the presence of CRBds in the centromeres, the species in this study can be grouped into two distinct lineages. This may provide new evidence regarding the phylogenetic relationships within the Brachypodium genus.}, }
@article {pmid29378020, year = {2018}, author = {Hillmann, F and Forbes, G and Novohradská, S and Ferling, I and Riege, K and Groth, M and Westermann, M and Marz, M and Spaller, T and Winckler, T and Schaap, P and Glöckner, G}, title = {Multiple Roots of Fruiting Body Formation in Amoebozoa.}, journal = {Genome biology and evolution}, volume = {10}, number = {2}, pages = {591-606}, doi = {10.1093/gbe/evy011}, pmid = {29378020}, issn = {1759-6653}, mesh = {Amoebozoa/cytology/*genetics/*growth &amp; development ; Cell Communication ; Dictyostelium/cytology/genetics/growth &amp; development ; Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Phylogeny ; Protozoan Proteins/genetics ; Transcriptome ; }, abstract = {Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree, differ by producing only one or few single stalked spores. Thus, one obvious difference in the developmental cycle of protosteliids and dictyosteliids seems to be the establishment of multicellularity. To separate spore development from multicellular interactions, we compared the genome and transcriptome of a Protostelium species (Protostelium aurantium var. fungivorum) with those of social and solitary members of the Amoebozoa. During fruiting body formation nearly 4,000 genes, corresponding to specific pathways required for differentiation processes, are upregulated. A comparison with genes involved in the development of dictyosteliids revealed conservation of >500 genes, but most of them are also present in Acanthamoeba castellanii for which fruiting bodies have not been documented. Moreover, expression regulation of those genes differs between P. aurantium and Dictyostelium discoideum. Within Amoebozoa differentiation to fruiting bodies is common, but our current genome analysis suggests that protosteliids and dictyosteliids used different routes to achieve this. Most remarkable is both the large repertoire and diversity between species in genes that mediate environmental sensing and signal processing. This likely reflects an immense adaptability of the single cell stage to varying environmental conditions. We surmise that this signaling repertoire provided sufficient building blocks to accommodate the relatively simple demands for cell-cell communication in the early multicellular forms.}, }
@article {pmid29375513, year = {2017}, author = {Yin, QJ and Zhang, WJ and Qi, XQ and Zhang, SD and Jiang, T and Li, XG and Chen, Y and Santini, CL and Zhou, H and Chou, IM and Wu, LF}, title = {High Hydrostatic Pressure Inducible Trimethylamine N-Oxide Reductase Improves the Pressure Tolerance of Piezosensitive Bacteria Vibrio fluvialis.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2646}, doi = {10.3389/fmicb.2017.02646}, pmid = {29375513}, issn = {1664-302X}, abstract = {High hydrostatic pressure (HHP) exerts severe effects on cellular processes including impaired cell division, abolished motility and affected enzymatic activities. Transcriptomic and proteomic analyses showed that bacteria switch the expression of genes involved in multiple energy metabolism pathways to cope with HHP. We sought evidence of a changing bacterial metabolism by supplying appropriate substrates that might have beneficial effects on the bacterial lifestyle at elevated pressure. We isolated a piezosensitive marine bacterium Vibrio fluvialis strain QY27 from the South China Sea. When trimethylamine N-oxide (TMAO) was used as an electron acceptor for energy metabolism, QY27 exhibited a piezophilic-like phenotype with an optimal growth at 30 MPa. Raman spectrometry and biochemistry analyses revealed that both the efficiency of the TMAO metabolism and the activity of the TMAO reductase increased under high pressure conditions. Among the two genes coding for TMAO reductase catalytic subunits, the expression level and enzymatic activity of TorA was up-regulated by elevated pressure. Furthermore, a genetic interference assay with the CRISPR-dCas9 system demonstrated that TorA is essential for underpinning the improved pressure tolerance of QY27. We extended the study to Vibrio fluvialis type strain ATCC33809 and observed the same phenotype of TMAO-metabolism improved the pressure tolerance. These results provide compelling evidence for the determinant role of metabolism in the adaption of bacteria to the deep-sea ecosystems with HHP.}, }
@article {pmid29361519, year = {2018}, author = {Cocorocchio, M and Baldwin, AJ and Stewart, B and Kim, L and Harwood, AJ and Thompson, CRL and Andrews, PLR and Williams, RSB}, title = {Curcumin and derivatives function through protein phosphatase 2A and presenilin orthologues in Dictyostelium discoideum.}, journal = {Disease models &amp; mechanisms}, volume = {11}, number = {1}, pages = {}, doi = {10.1242/dmm.032375}, pmid = {29361519}, issn = {1754-8411}, support = {101582Z/13/Z//Wellcome Trust/United Kingdom ; }, mesh = {Antioxidants/pharmacology ; Curcumin/analogs &amp; derivatives/chemistry/*pharmacology ; Dictyostelium/drug effects/growth &amp; development/*metabolism ; Ligands ; Molecular Docking Simulation ; Presenilin-1/*metabolism ; Protein Phosphatase 2/*metabolism ; *Sequence Homology, Amino Acid ; }, abstract = {Natural compounds often have complex molecular structures and unknown molecular targets. These characteristics make them difficult to analyse using a classical pharmacological approach. Curcumin, the main curcuminoid of turmeric, is a complex molecule possessing wide-ranging biological activities, cellular mechanisms and roles in potential therapeutic treatment, including Alzheimer's disease and cancer. Here, we investigate the physiological effects and molecular targets of curcumin in Dictyostelium discoideum We show that curcumin exerts acute effects on cell behaviour, reduces cell growth and slows multicellular development. We employed a range of structurally related compounds to show the distinct role of different structural groups in curcumin's effects on cell behaviour, growth and development, highlighting active moieties in cell function, and showing that these cellular effects are unrelated to the well-known antioxidant activity of curcumin. Molecular mechanisms underlying the effect of curcumin and one synthetic analogue (EF24) were then investigated to identify a curcumin-resistant mutant lacking the protein phosphatase 2A regulatory subunit (PsrA) and an EF24-resistant mutant lacking the presenilin 1 orthologue (PsenB). Using in silico docking analysis, we then showed that curcumin might function through direct binding to a key regulatory region of PsrA. These findings reveal novel cellular and molecular mechanisms for the function of curcumin and related compounds.}, }
@article {pmid29348641, year = {2018}, author = {Hammarlund, EU and von Stedingk, K and Påhlman, S}, title = {Refined control of cell stemness allowed animal evolution in the oxic realm.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {2}, pages = {220-228}, doi = {10.1038/s41559-017-0410-5}, pmid = {29348641}, issn = {2397-334X}, abstract = {Animal diversification on Earth has long been presumed to be associated with the increasing extent of oxic niches. Here, we challenge that view. We start with the fact that hypoxia (<1-3% O2) maintains cellular immaturity (stemness), whereas adult stem cells continuously-and paradoxically-regenerate animal tissue in oxygenated settings. Novel insights from tumour biology illuminate how cell stemness nevertheless can be achieved through the action of oxygen-sensing transcription factors in oxygenated, regenerating tissue. We suggest that these hypoxia-inducible transcription factors provided animals with unprecedented control over cell stemness that allowed them to cope with fluctuating oxygen concentrations. Thus, a refinement of the cellular hypoxia-response machinery enabled cell stemness at oxic conditions and, then, animals to evolve into the oxic realm. This view on the onset of animal diversification is consistent with geological evidence and provides a new perspective on the challenges and evolution of multicellular life.}, }
@article {pmid29348455, year = {2018}, author = {Libby, E and Driscoll, WW and Ratcliff, WC}, title = {Programmed cell death can increase the efficacy of microbial bet -hedging.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1120}, doi = {10.1038/s41598-017-18687-y}, pmid = {29348455}, issn = {2045-2322}, abstract = {Programmed cell death (PCD) occurs in both unicellular and multicellular organisms. While PCD plays a key role in the development and maintenance of multicellular organisms, explaining why single-celled organisms would evolve to actively commit suicide has been far more challenging. Here, we explore the potential for PCD to act as an accessory to microbial bet-hedging strategies that utilize stochastic phenotype switching. We consider organisms that face unpredictable and recurring disasters, in which fitness depends on effective phenotypic diversification. We show that when reproductive opportunities are limited by carrying capacity, PCD drives population turnover, providing increased opportunities for phenotypic diversification through stochastic phenotype switching. The main cost of PCD, providing resources for growth to a PCD(-) competitor, is ameliorated by genetic assortment in spatially structured populations. Using agent -based simulations, we explore how basic demographic factors, namely bottlenecks and local dispersal, can generate sufficient spatial structure to favor the evolution of high PCD rates.}, }
@article {pmid29340409, year = {2018}, author = {Ray, A and Morford, RK and Ghaderi, N and Odde, DJ and Provenzano, PP}, title = {Dynamics of 3D carcinoma cell invasion into aligned collagen.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {10}, number = {2}, pages = {100-112}, doi = {10.1039/c7ib00152e}, pmid = {29340409}, issn = {1757-9708}, support = {R01 CA172986/CA/NCI NIH HHS/United States ; R01 CA181385/CA/NCI NIH HHS/United States ; U54 CA210190/CA/NCI NIH HHS/United States ; }, abstract = {Carcinoma cells frequently expand and invade from a confined lesion, or multicellular clusters, into and through the stroma on the path to metastasis, often with an efficiency dictated by the architecture and composition of the microenvironment. Specifically, in desmoplastic carcinomas such as those of the breast, aligned collagen tracks provide contact guidance cues for directed cancer cell invasion. Yet, the evolving dynamics of this process of invasion remains poorly understood, in part due to difficulties in continuously capturing both spatial and temporal heterogeneity and progression to invasion in experimental systems. Therefore, to study the local invasion process from cell dense clusters into aligned collagen architectures found in solid tumors, we developed a novel engineered 3D invasion platform that integrates an aligned collagen matrix with a cell dense tumor-like plug. Using multiphoton microscopy and quantitative analysis of cell motility, we track the invasion of cancer cells from cell-dense bulk clusters into the pre-aligned 3D matrix, and define the temporal evolution of the advancing invasion fronts over several days. This enables us to identify and probe cell dynamics in key regions of interest: behind, at, and beyond the edge of the invading lesion at distinct time points. Analysis of single cell migration identifies significant spatial heterogeneity in migration behavior between cells in the highly cell-dense region behind the leading edge of the invasion front and cells at and beyond the leading edge. Moreover, temporal variations in motility and directionality are also observed between cells within the cell-dense tumor-like plug and the leading invasive edge as its boundary extends into the anisotropic collagen over time. Furthermore, experimental results combined with mathematical modeling demonstrate that in addition to contact guidance, physical crowding of cells is a key regulating factor orchestrating variability in single cell migration during invasion into anisotropic ECM. Thus, our novel platform enables us to capture spatio-temporal dynamics of cell behavior behind, at, and beyond the invasive front and reveals heterogeneous, local interactions that lead to the emergence and maintenance of the advancing front.}, }
@article {pmid29337961, year = {2018}, author = {Trigos, AS and Pearson, RB and Papenfuss, AT and Goode, DL}, title = {How the evolution of multicellularity set the stage for cancer.}, journal = {British journal of cancer}, volume = {118}, number = {2}, pages = {145-152}, doi = {10.1038/bjc.2017.398}, pmid = {29337961}, issn = {1532-1827}, abstract = {Neoplastic growth and many of the hallmark properties of cancer are driven by the disruption of molecular networks established during the emergence of multicellularity. Regulatory pathways and molecules that evolved to impose regulatory constraints upon networks established in earlier unicellular organisms enabled greater communication and coordination between the diverse cell types required for multicellularity, but also created liabilities in the form of points of vulnerability in the network that when mutated or dysregulated facilitate the development of cancer. These factors are usually overlooked in genomic analyses of cancer, but understanding where vulnerabilities to cancer lie in the networks of multicellular species would provide important new insights into how core molecular processes and gene regulation change during tumourigenesis. We describe how the evolutionary origins of genes influence their roles in cancer, and how connections formed between unicellular and multicellular genes that act as key regulatory hubs for normal tissue homeostasis can also contribute to malignant transformation when disrupted. Tumours in general are characterised by increased dependence on unicellular processes for survival, and major dysregulation of the control structures imposed on these processes during the evolution of multicellularity. Mounting molecular evidence suggests altered interactions at the interface between unicellular and multicellular genes play key roles in the initiation and progression of cancer. Furthermore, unicellular network regions activated in cancer show high degrees of robustness and plasticity, conferring increased adaptability to tumour cells by supporting effective responses to environmental pressures such as drug exposure. Examining how the links between multicellular and unicellular regions get disrupted in tumours has great potential to identify novel drivers of cancer, and to guide improvements to cancer treatment by identifying more effective therapeutic strategies. Recent successes in targeting unicellular processes by novel compounds underscore the logic of such approaches. Further gains could come from identifying genes at the interface between unicellular and multicellular processes and manipulating the communication between network regions of different evolutionary ages.}, }
@article {pmid29326726, year = {2017}, author = {Zheng, Q and Ma, A and Yuan, L and Gao, N and Feng, Q and Franc, NC and Xiao, H}, title = {Apoptotic Cell Clearance in Drosophila melanogaster.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {1881}, doi = {10.3389/fimmu.2017.01881}, pmid = {29326726}, issn = {1664-3224}, abstract = {The swift clearance of apoptotic cells (ACs) (efferocytosis) by phagocytes is a critical event during development of all multicellular organisms. It is achieved through phagocytosis by professional or amateur phagocytes. Failure in this process can lead to the development of inflammatory autoimmune or neurodegenerative diseases. AC clearance has been conserved throughout evolution, although many details in its mechanisms remain to be explored. It has been studied in the context of mammalian macrophages, and in the nematode Caenorhabditis elegans, which lacks &quot;professional&quot; phagocytes such as macrophages, but in which other cell types can engulf apoptotic corpses. In Drosophila melanogaster, ACs are engulfed by macrophages, glial, and epithelial cells. Drosophila macrophages perform similar functions to those of mammalian macrophages. They are professional phagocytes that participate in phagocytosis of ACs and pathogens. Study of AC clearance in Drosophila has identified some key elements, like the receptors Croquemort and Draper, promoting Drosophila as a suitable model to genetically dissect this process. In this review, we survey recent works of AC clearance pathways in Drosophila, and discuss the physiological outcomes and consequences of this process.}, }
@article {pmid29322818, year = {2018}, author = {Baig, AM and Zohaib, R and Tariq, S and Ahmad, HR}, title = {Evolution of pH buffers and water homeostasis in eukaryotes: homology between humans and Acanthamoeba proteins.}, journal = {Future microbiology}, volume = {13}, number = {}, pages = {195-207}, doi = {10.2217/fmb-2017-0116}, pmid = {29322818}, issn = {1746-0921}, abstract = {AIM: This study intended to trace the evolution of acid-base buffers and water homeostasis in eukaryotes. Acanthamoeba castellanii was selected as a model unicellular eukaryote for this purpose. Homologies of proteins involved in pH and water regulatory mechanisms at cellular levels were compared between humans and A. castellanii.<br><br>MATERIALS &amp; METHODS: Amino acid sequence homology, structural homology, 3D modeling and docking prediction were done to show the extent of similarities between carbonic anhydrase 1 (CA1), aquaporin (AQP), band-3 protein and H+ pump. Experimental assays were done with acetazolamide (AZM), brinzolamide and mannitol to observe their effects on the trophozoites of A. castellanii.<br><br>RESULTS: The human CA1, AQP, band-3 protein and H+-transport proteins revealed similar proteins in Acanthamoeba. Docking showed the binding of AZM on amoebal AQP-like proteins. Acanthamoeba showed transient shape changes and encystation at differential doses of brinzolamide, mannitol and AZM. Conclusion: Water and pH regulating adapter proteins in Acanthamoeba and humans show significant homology, these mechanisms evolved early in the primitive unicellular eukaryotes and have remained conserved in multicellular eukaryotes.}, }
@article {pmid29320478, year = {2018}, author = {Smakowska-Luzan, E and Mott, GA and Parys, K and Stegmann, M and Howton, TC and Layeghifard, M and Neuhold, J and Lehner, A and Kong, J and Grünwald, K and Weinberger, N and Satbhai, SB and Mayer, D and Busch, W and Madalinski, M and Stolt-Bergner, P and Provart, NJ and Mukhtar, MS and Zipfel, C and Desveaux, D and Guttman, DS and Belkhadir, Y}, title = {An extracellular network of Arabidopsis leucine-rich repeat receptor kinases.}, journal = {Nature}, volume = {553}, number = {7688}, pages = {342-346}, doi = {10.1038/nature25184}, pmid = {29320478}, issn = {1476-4687}, mesh = {Arabidopsis/cytology/*enzymology/immunology/microbiology ; Arabidopsis Proteins/*chemistry/*metabolism ; Leucine/*metabolism ; Protein Binding ; Protein Domains ; Protein Kinases/*chemistry/*metabolism ; Protein-Serine-Threonine Kinases/chemistry/metabolism ; Receptors, Cell Surface/chemistry/metabolism ; Reproducibility of Results ; Signal Transduction ; }, abstract = {The cells of multicellular organisms receive extracellular signals using surface receptors. The extracellular domains (ECDs) of cell surface receptors function as interaction platforms, and as regulatory modules of receptor activation. Understanding how interactions between ECDs produce signal-competent receptor complexes is challenging because of their low biochemical tractability. In plants, the discovery of ECD interactions is complicated by the massive expansion of receptor families, which creates tremendous potential for changeover in receptor interactions. The largest of these families in Arabidopsis thaliana consists of 225 evolutionarily related leucine-rich repeat receptor kinases (LRR-RKs), which function in the sensing of microorganisms, cell expansion, stomata development and stem-cell maintenance. Although the principles that govern LRR-RK signalling activation are emerging, the systems-level organization of this family of proteins is unknown. Here, to address this, we investigated 40,000 potential ECD interactions using a sensitized high-throughput interaction assay, and produced an LRR-based cell surface interaction network (CSILRR) that consists of 567 interactions. To demonstrate the power of CSILRR for detecting biologically relevant interactions, we predicted and validated the functions of uncharacterized LRR-RKs in plant growth and immunity. In addition, we show that CSILRR operates as a unified regulatory network in which the LRR-RKs most crucial for its overall structure are required to prevent the aberrant signalling of receptors that are several network-steps away. Thus, plants have evolved LRR-RK networks to process extracellular signals into carefully balanced responses.}, }
@article {pmid29320389, year = {2018}, author = {Ćetković, H and Halasz, M and Herak Bosnar, M}, title = {Sponges: A Reservoir of Genes Implicated in Human Cancer.}, journal = {Marine drugs}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/md16010020}, pmid = {29320389}, issn = {1660-3397}, mesh = {Animals ; Evolution, Molecular ; Genome/genetics ; Humans ; Neoplasms/*genetics ; Porifera/*genetics ; Proteome/genetics ; Signal Transduction/genetics ; }, abstract = {Recently, it was shown that the majority of genes linked to human diseases, such as cancer genes, evolved in two major evolutionary transitions-the emergence of unicellular organisms and the transition to multicellularity. Therefore, it has been widely accepted that the majority of disease-related genes has already been present in species distantly related to humans. An original way of studying human diseases relies on analyzing genes and proteins that cause a certain disease using model organisms that belong to the evolutionary level at which these genes have emerged. This kind of approach is supported by the simplicity of the genome/proteome, body plan, and physiology of such model organisms. It has been established for quite some time that sponges are an ideal model system for such studies, having a vast variety of genes known to be engaged in sophisticated processes and signalling pathways associated with higher animals. Sponges are considered to be the simplest multicellular animals and have changed little during evolution. Therefore, they provide an insight into the metazoan ancestor genome/proteome features. This review compiles current knowledge of cancer-related genes/proteins in marine sponges.}, }
@article {pmid29301490, year = {2018}, author = {Strader, ME and Aglyamova, GV and Matz, MV}, title = {Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {17}, doi = {10.1186/s12864-017-4392-0}, pmid = {29301490}, issn = {1471-2164}, support = {DEB-1501463//National Science Foundation/International ; }, mesh = {Animals ; Anthozoa/anatomy &amp; histology/embryology/*genetics/*growth &amp; development ; Behavior, Animal/drug effects ; Fertilization ; Larva/genetics/growth &amp; development/metabolism ; Luminescent Proteins/metabolism ; Metamorphosis, Biological/genetics ; Transcriptome ; }, abstract = {BACKGROUND: Molecular mechanisms underlying coral larval competence, the ability of larvae to respond to settlement cues, determine their dispersal potential and are potential targets of natural selection. Here, we profiled competence, fluorescence and genome-wide gene expression in embryos and larvae of the reef-building coral Acropora millepora daily throughout 12 days post-fertilization.<br><br>RESULTS: Gene expression associated with competence was positively correlated with transcriptomic response to the natural settlement cue, confirming that mature coral larvae are &quot;primed&quot; for settlement. Rise of competence through development was accompanied by up-regulation of sensory and signal transduction genes such as ion channels, genes involved in neuropeptide signaling, and G-protein coupled receptor (GPCRs). A drug screen targeting components of GPCR signaling pathways confirmed a role in larval settlement behavior and metamorphosis.<br><br>CONCLUSIONS: These results gives insight into the molecular complexity underlying these transitions and reveals receptors and pathways that, if altered by changing environments, could affect dispersal capabilities of reef-building corals. In addition, this dataset provides a toolkit for asking broad questions about sensory capacity in multicellular animals and the evolution of development.}, }
@article {pmid29294063, year = {2018}, author = {Featherston, J and Arakaki, Y and Hanschen, ER and Ferris, PJ and Michod, RE and Olson, BJSC and Nozaki, H and Durand, PM}, title = {The 4-Celled Tetrabaena socialis Nuclear Genome Reveals the Essential Components for Genetic Control of Cell Number at the Origin of Multicellularity in the Volvocine Lineage.}, journal = {Molecular biology and evolution}, volume = {35}, number = {4}, pages = {855-870}, doi = {10.1093/molbev/msx332}, pmid = {29294063}, issn = {1537-1719}, abstract = {Multicellularity is the premier example of a major evolutionary transition in individuality and was a foundational event in the evolution of macroscopic biodiversity. The volvocine chlorophyte lineage is well suited for studying this process. Extant members span unicellular, simple colonial, and obligate multicellular taxa with germ-soma differentiation. Here, we report the nuclear genome sequence of one of the most morphologically simple organisms in this lineage-the 4-celled colonial Tetrabaena socialis and compare this to the three other complete volvocine nuclear genomes. Using conservative estimates of gene family expansions a minimal set of expanded gene families was identified that associate with the origin of multicellularity. These families are rich in genes related to developmental processes. A subset of these families is lineage specific, which suggests that at a genomic level the evolution of multicellularity also includes lineage-specific molecular developments. Multiple points of evidence associate modifications to the ubiquitin proteasomal pathway (UPP) with the beginning of coloniality. Genes undergoing positive or accelerating selection in the multicellular volvocines were found to be enriched in components of the UPP and gene families gained at the origin of multicellularity include components of the UPP. A defining feature of colonial/multicellular life cycles is the genetic control of cell number. The genomic data presented here, which includes diversification of cell cycle genes and modifications to the UPP, align the genetic components with the evolution of this trait.}, }
@article {pmid29293210, year = {2017}, author = {Wade, J and Dyck, B and Palin, RM and Moore, JDP and Smye, AJ}, title = {The divergent fates of primitive hydrospheric water on Earth and Mars.}, journal = {Nature}, volume = {552}, number = {7685}, pages = {391-394}, doi = {10.1038/nature25031}, pmid = {29293210}, issn = {1476-4687}, mesh = {Convection ; *Earth (Planet) ; Extraterrestrial Environment/*chemistry ; Ferrous Compounds/analysis/chemistry ; Geologic Sediments/*chemistry ; Hot Temperature ; Magnetic Fields ; *Mars ; Origin of Life ; Photolysis ; Pressure ; Silicates/analysis/chemistry ; Water/*analysis/*chemistry ; }, abstract = {Despite active transport into Earth's mantle, water has been present on our planet's surface for most of geological time. Yet water disappeared from the Martian surface soon after its formation. Although some of the water on Mars was lost to space via photolysis following the collapse of the planet's magnetic field, the widespread serpentinization of Martian crust suggests that metamorphic hydration reactions played a critical part in the sequestration of the crust. Here we quantify the relative volumes of water that could be removed from each planet's surface via the burial and metamorphism of hydrated mafic crusts, and calculate mineral transition-induced bulk-density changes at conditions of elevated pressure and temperature for each. The metamorphic mineral assemblages in relatively FeO-rich Martian lavas can hold about 25 per cent more structurally bound water than those in metamorphosed terrestrial basalts, and can retain it at greater depths within Mars. Our calculations suggest that in excess of 9 per cent by volume of the Martian mantle may contain hydrous mineral species as a consequence of surface reactions, compared to about 4 per cent by volume of Earth's mantle. Furthermore, neither primitive nor evolved hydrated Martian crust show noticeably different bulk densities compared to their anhydrous equivalents, in contrast to hydrous mafic terrestrial crust, which transforms to denser eclogite upon dehydration. This would have allowed efficient overplating and burial of early Martian crust in a stagnant-lid tectonic regime, in which the lithosphere comprised a single tectonic plate, with only the warmer, lower crust involved in mantle convection. This provided an important sink for hydrospheric water and a mechanism for oxidizing the Martian mantle. Conversely, relatively buoyant mafic crust and hotter geothermal gradients on Earth reduced the potential for upper-mantle hydration early in its geological history, leading to water being retained close to its surface, and thus creating conditions conducive for the evolution of complex multicellular life.}, }
@article {pmid29292130, year = {2018}, author = {López, JL and Alvarez, F and Príncipe, A and Salas, ME and Lozano, MJ and Draghi, WO and Jofré, E and Lagares, A}, title = {Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds.}, journal = {Journal of biotechnology}, volume = {267}, number = {}, pages = {55-62}, doi = {10.1016/j.jbiotec.2017.12.020}, pmid = {29292130}, issn = {1873-4863}, mesh = {Actinobacteria/genetics/isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification ; Endophytes/classification/*genetics ; Firmicutes/genetics/isolation &amp; purification ; Medicago sativa/genetics/*microbiology ; Microbiota/*genetics ; *Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seedlings/microbiology ; Seeds/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {A growing body of evidence has reinforced the central role of microbiomes in the life of sound multicellular eukaryotes, thus more properly described as true holobionts. Though soil was considered a main source of plant microbiomes, seeds have been shown to be endophytically colonized by microorganisms thus representing natural carriers of a selected microbial inoculum to the young seedlings. In this work we have investigated the type of culturable endophytic bacteria that are carried within surface-sterilized alfalfa seeds. MALDI-TOF analysis revealed the presence of bacteria that belonged to 40 separate genera, distributed within four taxa (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes). Nonsymbiotic members of the Rhizobiaceae family were also found. The evaluation of nine different in-vitro biochemical activities demonstrated isolates with complex combinations of traits that, upon a Principal-Component-Analysis, could be classified into four phenotypic groups. That isolates from nearly half of the genera identified had been able to colonize alfalfa plants grown under axenic conditions was remarkable. Further analyses should be addressed to investigating the colonization mechanisms of the alfalfa seeds, the evolutionary significance of the alfalfa-seed endophytes, and also how after germination the seed microbiome competes with spermospheric and rhizospheric soil bacteria to colonize newly emerging seedlings.}, }
@article {pmid29283188, year = {2018}, author = {Peccoud, J and Cordaux, R and Gilbert, C}, title = {Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {2}, pages = {}, doi = {10.1002/bies.201700177}, pmid = {29283188}, issn = {1521-1878}, abstract = {Whoever compares the genomes of distantly related species might find aberrantly high sequence similarity at certain loci. Such anomaly can only be explained by genetic material being transferred through other means than reproduction, that is, a horizontal transfer (HT). Between multicellular organisms, the transferred material will likely turn out to be a transposable element (TE). Because TEs can move between loci and invade chromosomes by replicating themselves, HT of TEs (HTT) profoundly impacts genome evolution. Yet, very few studies have quantified HTT at large taxonomic scales. Indeed, this task currently faces difficulties that range from the variable quality of available genome sequences to limitations of analytical procedures, some of which have been overlooked. Here we review the many challenges that an extensive analysis of HTT must overcome, we expose biases and limits of current methods, suggest solutions or workarounds, and reflect upon approaches that could be developed to better quantify this phenomenon.}, }
@article {pmid29279310, year = {2018}, author = {Hesp, ZC and Yoseph, RY and Suzuki, R and Jukkola, P and Wilson, C and Nishiyama, A and McTigue, DM}, title = {Proliferating NG2-Cell-Dependent Angiogenesis and Scar Formation Alter Axon Growth and Functional Recovery After Spinal Cord Injury in Mice.}, journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience}, volume = {38}, number = {6}, pages = {1366-1382}, doi = {10.1523/JNEUROSCI.3953-16.2017}, pmid = {29279310}, issn = {1529-2401}, support = {R01 NS074870/NS/NINDS NIH HHS/United States ; P30 NS045758/NS/NINDS NIH HHS/United States ; F31 NS095606/NS/NINDS NIH HHS/United States ; P30 NS104177/NS/NINDS NIH HHS/United States ; R01 NS073425/NS/NINDS NIH HHS/United States ; R01 NS049267/NS/NINDS NIH HHS/United States ; R01 NS043246/NS/NINDS NIH HHS/United States ; }, abstract = {Spinal cord injury (SCI) induces a centralized fibrotic scar surrounded by a reactive glial scar at the lesion site. The origin of these scars is thought to be perivascular cells entering lesions on ingrowing blood vessels and reactive astrocytes, respectively. However, two NG2-expressing cell populations, pericytes and glia, may also influence scar formation. In the periphery, new blood vessel growth requires proliferating NG2+ pericytes; if this were also true in the CNS, then the fibrotic scar would depend on dividing NG2+ pericytes. NG2+ glial cells (also called oligodendrocyte progenitors or polydendrocytes) also proliferate after SCI and accumulate in large numbers among astrocytes in the glial scar. Their effect there, if any, is unknown. We show that proliferating NG2+ pericytes and glia largely segregate into the fibrotic and glial scars, respectively; therefore, we used a thymidine kinase/ganciclovir paradigm to ablate both dividing NG2+ cell populations to determine whether either scar was altered. Results reveal that loss of proliferating NG2+ pericytes in the lesion prevented intralesion angiogenesis and completely abolished the fibrotic scar. The glial scar was also altered in the absence of acutely dividing NG2+ cells, displaying discontinuous borders and significantly reduced GFAP density. Collectively, these changes enhanced edema, prolonged hemorrhage, and impaired forelimb functional recovery. Interestingly, after halting GCV at 14 d postinjury, scar elements and vessels entered the lesions over the next 7 d, as did large numbers of axons that were not present in controls. Collectively, these data reveal that acutely dividing NG2+ pericytes and glia play fundamental roles in post-SCI tissue remodeling.SIGNIFICANCE STATEMENT Spinal cord injury (SCI) is characterized by formation of astrocytic and fibrotic scars, both of which are necessary for lesion repair. NG2+ cells may influence both scar-forming processes. This study used a novel transgenic mouse paradigm to ablate proliferating NG2+ cells after SCI to better understand their role in repair. For the first time, our data show that dividing NG2+ pericytes are required for post-SCI angiogenesis, which in turn is needed for fibrotic scar formation. Moreover, loss of cycling NG2+ glia and pericytes caused significant multicellular tissue changes, including altered astrocyte responses and impaired functional recovery. This work reveals previously unknown ways in which proliferating NG2+ cells contribute to endogenous repair after SCI.}, }
@article {pmid29276774, year = {2017}, author = {Vasemägi, A and Visse, M and Kisand, V}, title = {Effect of Environmental Factors and an Emerging Parasitic Disease on Gut Microbiome of Wild Salmonid Fish.}, journal = {mSphere}, volume = {2}, number = {6}, pages = {}, doi = {10.1128/mSphere.00418-17}, pmid = {29276774}, issn = {2379-5042}, abstract = {The gastrointestinal tract (GIT) of fish supports a dynamic microbial ecosystem that is intimately linked to host nutrient acquisition, epithelial development, immune system priming, and disease prevention, and we are far from understanding the complex interactions among parasites, symbiotic gut bacteria, and host fitness. Here, we analyzed the effects of environmental factors and parasitic burdens on the microbial composition and diversity within the GIT of the brown trout (Salmo trutta). We focused on the emerging dangerous salmonid myxozoan parasite Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, to demonstrate the potential role of GIT micobiomes in the modulation of host-parasite relationships. The microbial diversity in the GIT displayed clear clustering according to the river of origin, while considerable variation was also found among fish from the same river. Environmental variables such as oxygen concentration, water temperature, and river morphometry strongly associated with both the river microbial community and the GIT microbiome, supporting the role of the environment in microbial assemblage and the relative insignificance of the host genotype and gender. Contrary to expectations, the parasite load exhibited a significant positive relationship with the richness of the GIT microbiome. Many operational taxonomic units (OTUs; n = 202) are more abundant in T. bryosalmonae-infected fish, suggesting that brown trout with large parasite burdens are prone to lose their GIT microbiome homeostasis. The OTUs with the strongest increase in infected trout are mostly nonpathogenic aquatic, anaerobic sediment/sludge, or ruminant bacteria. Our results underscore the significance of the interactions among parasitic disease, abiotic factors, and the GIT microbiome in disease etiology. IMPORTANCE Cohabiting microorganisms play diverse and important roles in the biology of multicellular hosts, but their diversity and interactions with abiotic and biotic factors remain largely unsurveyed. Nevertheless, it is becoming increasingly clear that many properties of host phenotypes reflect contributions from the associated microbiome. We focus on a question of how parasites, the host genetic background, and abiotic factors influence the microbiome in salmonid hosts by using a host-parasite model consisting of wild brown trout (Salmo trutta) and the myxozoan Tetracapsuloides bryosalmonae, which causes widely distributed proliferative kidney disease. We show that parasite infection increases the frequency of bacteria from the surrounding river water community, reflecting impaired homeostasis in the fish gut. Our results also demonstrate the importance of abiotic environmental factors and host size in the assemblage of the gut microbiome of fish and the relative insignificance of the host genotype and gender.}, }
@article {pmid29269894, year = {2017}, author = {Liu, J and Zhang, W and Li, X and Li, X and Chen, X and Li, JH and Teng, Z and Xu, C and Santini, CL and Zhao, L and Zhao, Y and Zhang, H and Zhang, WJ and Xu, K and Li, C and Pan, Y and Xiao, T and Pan, H and Wu, LF}, title = {Bacterial community structure and novel species of magnetotactic bacteria in sediments from a seamount in the Mariana volcanic arc.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {17964}, doi = {10.1038/s41598-017-17445-4}, pmid = {29269894}, issn = {2045-2322}, abstract = {Seamounts are undersea mountains rising abruptly from the sea floor and interacting dynamically with underwater currents. They represent unique biological habitats with various microbial community structures. Certain seamount bacteria form conspicuous extracellular iron oxide structures, including encrusted stalks, flattened bifurcating tubes, and filamentous sheaths. To extend our knowledge of seamount ecosystems, we performed an integrated study on population structure and the occurrence of magnetotactic bacteria (MTB) that synthesize intracellular iron oxide nanocrystals in sediments of a seamount in the Mariana volcanic arc. We found Proteobacteria dominant at 13 of 14 stations, but ranked second in abundance to members of the phylum Firmicutes at the deep-water station located on a steep slope facing the Mariana-Yap Trench. Live MTB dwell in biogenic sediments from all 14 stations ranging in depth from 238 to 2,023 m. Some magnetotactic cocci possess the most complex flagellar apparatus yet reported; 19 flagella are arranged in a 3:4:5:4:3 array within a flagellar bundle. Phylogenetic analysis of 16S rRNA gene sequences identified 16 novel species of MTB specific to this seamount. Together the results obtained indicate that geographic properties of the seamount stations are important in shaping the bacterial community structure and the MTB composition.}, }
@article {pmid29260254, year = {2018}, author = {Böttcher, T}, title = {From Molecules to Life: Quantifying the Complexity of Chemical and Biological Systems in the Universe.}, journal = {Journal of molecular evolution}, volume = {86}, number = {1}, pages = {1-10}, doi = {10.1007/s00239-017-9824-6}, pmid = {29260254}, issn = {1432-1432}, support = {Emmy Noether//DFG/ ; Marie Curie Zukunftskolleg Incoming Fellowship//EU FP7/ ; }, abstract = {Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms. Entities with a certain level of information complexity directly require a functionally complex mechanism for their production or replication and are hence indicative for life-like systems. In order to describe entities combining molecular and information complexity, the term biogenic unit was introduced. Exemplified biogenic unit complexities were calculated for ribozymes, protein enzymes, multimeric protein complexes, and even an entire virus particle. Complexities of prokaryotic and eukaryotic cells, as well as multicellular organisms, were estimated. Thereby distinct evolutionary stages in complexity space were identified. The here developed approach to compare the complexity of biogenic units allows for the first time to address the gradual characteristics of prebiotic and life-like systems without the need for a definition of life. This operational concept may guide our search for life in the Universe, and it may direct the investigations of prebiotic trajectories that lead towards the evolution of complexity at the origins of life.}, }
@article {pmid29259597, year = {2017}, author = {Iakobachvili, N and Peters, PJ}, title = {Humans in a Dish: The Potential of Organoids in Modeling Immunity and Infectious Diseases.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2402}, doi = {10.3389/fmicb.2017.02402}, pmid = {29259597}, issn = {1664-302X}, abstract = {For many decades, human infectious diseases have been studied in immortalized cell lines, isolated primary cells from blood and a range of animal hosts. This research has been of fundamental importance in advancing our understanding of host and pathogen responses but remains limited by the absence of multicellular context and inherent differences in animal immune systems that result in altered immune responses. Recent developments in stem cell biology have led to the in vitro growth of organoids that faithfully recapitulate a variety of human tissues including lung, intestine and brain amongst many others. Organoids are derived from human stem cells and retain the genomic background, cellular organization and functionality of their tissue of origin. Thus they have been widely used to characterize stem cell development, numerous cancers and genetic diseases. We believe organoid technology can be harnessed to study host-pathogen interactions resulting in a more physiologically relevant model that yields more predictive data of human infectious diseases than current systems. Here, we highlight recent work and discuss the potential of human stem cell-derived organoids in studying infectious diseases and immunity.}, }
@article {pmid29251593, year = {2017}, author = {Molaro, A and Malik, HS}, title = {Culture shock.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, doi = {10.7554/eLife.33312}, pmid = {29251593}, issn = {2050-084X}, abstract = {Many different human cell lines, including both normal and cancer cells, appear to converge to a state that contains an unusual number of chromosomes when they are grown in culture.}, }
@article {pmid29245010, year = {2017}, author = {Kundu, P and Blacher, E and Elinav, E and Pettersson, S}, title = {Our Gut Microbiome: The Evolving Inner Self.}, journal = {Cell}, volume = {171}, number = {7}, pages = {1481-1493}, doi = {10.1016/j.cell.2017.11.024}, pmid = {29245010}, issn = {1097-4172}, mesh = {Aging ; Animals ; Bacteria/classification/*growth &amp; development/metabolism ; Biological Evolution ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Organ Specificity ; Puberty ; Symbiosis ; }, abstract = {The &quot;holobiont&quot; concept, defined as the collective contribution of the eukaryotic and prokaryotic counterparts to the multicellular organism, introduces a complex definition of individuality enabling a new comprehensive view of human evolution and personalized characteristics. Here, we provide snapshots of the evolving microbial-host associations and relations during distinct milestones across the lifespan of a human being. We discuss the current knowledge of biological symbiosis between the microbiome and its host and portray the challenges in understanding these interactions and their potential effects on human physiology, including microbiome-nervous system inter-relationship and its relevance to human variation and individuality.}, }
@article {pmid29225309, year = {2017}, author = {Jong, LW and Fujiwara, T and Nozaki, H and Miyagishima, SY}, title = {Cell size for commitment to cell division and number of successive cell divisions in multicellular volvocine green algae Tetrabaena socialis and Gonium pectorale.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {93}, number = {10}, pages = {832-840}, doi = {10.2183/pjab.93.052}, pmid = {29225309}, issn = {1349-2896}, abstract = {Volvocine algae constitute a green algal lineage comprising unicellular Chlamydomonas, four-celled Tetrabaena, eight to 32-celled Gonium, and others up to Volvox spp., which consist of up to 50,000 cells. These algae proliferate by multiple fissions with cellular growth up to several fold in size and subsequent successive cell divisions. Chlamydomonas reinhardtii cells produce two to 32 daughter cells by one to five divisions, depending on cellular growth in the G1 phase. By contrast, in this study, we found that Tetrabaena socialis and Gonium pectorale cells mostly produced four and eight daughter cells by two and three successive divisions, respectively. In contrast to C. reinhardtii, which is committed to cell division when the cell has grown two-fold, T. socialis and G. pectorale are committed only when the cells have grown four- and eight-fold, respectively. Thus, our results suggest that evolutionary changes in cellular size for commitment largely contributes to the emergence and evolution of multicellularity in volvocine algae.}, }
@article {pmid29212441, year = {2017}, author = {Arakaki, Y and Fujiwara, T and Kawai-Toyooka, H and Kawafune, K and Featherston, J and Durand, PM and Miyagishima, SY and Nozaki, H}, title = {Evolution of cytokinesis-related protein localization during the emergence of multicellularity in volvocine green algae.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {243}, doi = {10.1186/s12862-017-1091-z}, pmid = {29212441}, issn = {1471-2148}, support = {2016-B//NIG-JOINT/International ; 25-9234//Japan Society for the Promotion of Science/International ; 16H02518//Japan Society for the Promotion of Science/International ; RA151217156515//National Research Foundation/International ; }, mesh = {Algal Proteins/*genetics ; Cytokinesis/*genetics ; *Evolution, Molecular ; Likelihood Functions ; Models, Biological ; Phylogeny ; Protein Transport ; Species Specificity ; Subcellular Fractions/metabolism ; Volvox/*cytology/*genetics ; }, abstract = {BACKGROUND: The volvocine lineage, containing unicellular Chlamydomonas reinhardtii and differentiated multicellular Volvox carteri, is a powerful model for comparative studies aiming at understanding emergence of multicellularity. Tetrabaena socialis is the simplest multicellular volvocine alga and belongs to the family Tetrabaenaceae that is sister to more complex multicellular volvocine families, Goniaceae and Volvocaceae. Thus, T. socialis is a key species to elucidate the initial steps in the evolution of multicellularity. In the asexual life cycle of C. reinhardtii and multicellular volvocine species, reproductive cells form daughter cells/colonies by multiple fission. In embryogenesis of the multicellular species, daughter protoplasts are connected to one another by cytoplasmic bridges formed by incomplete cytokinesis during multiple fission. These bridges are important for arranging the daughter protoplasts in appropriate positions such that species-specific integrated multicellular individuals are shaped. Detailed comparative studies of cytokinesis between unicellular and simple multicellular volvocine species will help to elucidate the emergence of multicellularity from the unicellular ancestor. However, the cytokinesis-related genes between closely related unicellular and multicellular species have not been subjected to a comparative analysis.<br><br>RESULTS: Here we focused on dynamin-related protein 1 (DRP1), which is known for its role in cytokinesis in land plants. Immunofluorescence microscopy using an antibody against T. socialis DRP1 revealed that volvocine DRP1 was localized to division planes during cytokinesis in unicellular C. reinhardtii and two simple multicellular volvocine species T. socialis and Gonium pectorale. DRP1 signals were mainly observed in the newly formed division planes of unicellular C. reinhardtii during multiple fission, whereas in multicellular T. socialis and G. pectorale, DRP1 signals were observed in all division planes during embryogenesis.<br><br>CONCLUSIONS: These results indicate that the molecular mechanisms of cytokinesis may be different in unicellular and multicellular volvocine algae. The localization of DRP1 during multiple fission might have been modified in the common ancestor of multicellular volvocine algae. This modification may have been essential for the re-orientation of cells and shaping colonies during the emergence of multicellularity in this lineage.}, }
@article {pmid29208647, year = {2018}, author = {Matt, GY and Umen, JG}, title = {Cell-Type Transcriptomes of the Multicellular Green Alga Volvox carteri Yield Insights into the Evolutionary Origins of Germ and Somatic Differentiation Programs.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {2}, pages = {531-550}, doi = {10.1534/g3.117.300253}, pmid = {29208647}, issn = {2160-1836}, support = {P30 CA091842/CA/NCI NIH HHS/United States ; R01 GM078376/GM/NIGMS NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Algal Proteins/classification/genetics ; Cell Differentiation/*genetics ; Energy Metabolism/genetics ; *Evolution, Molecular ; *Gene Expression Profiling ; Gene Ontology ; Light-Harvesting Protein Complexes/classification/genetics ; Phylogeny ; Volvox/cytology/*genetics/metabolism ; }, abstract = {Germ-soma differentiation is a hallmark of complex multicellular organisms, yet its origins are not well understood. Volvox carteri is a simple multicellular green alga that has recently evolved a simple germ-soma dichotomy with only two cell-types: large germ cells called gonidia and small terminally differentiated somatic cells. Here, we provide a comprehensive characterization of the gonidial and somatic transcriptomes of V. carteri to uncover fundamental differences between the molecular and metabolic programming of these cell-types. We found extensive transcriptome differentiation between cell-types, with somatic cells expressing a more specialized program overrepresented in younger, lineage-specific genes, and gonidial cells expressing a more generalist program overrepresented in more ancient genes that shared striking overlap with stem cell-specific genes from animals and land plants. Directed analyses of different pathways revealed a strong dichotomy between cell-types with gonidial cells expressing growth-related genes and somatic cells expressing an altruistic metabolic program geared toward the assembly of flagella, which support organismal motility, and the conversion of storage carbon to sugars, which act as donors for production of extracellular matrix (ECM) glycoproteins whose secretion enables massive organismal expansion. V. carteri orthologs of diurnally controlled genes from C. reinhardtii, a single-celled relative, were analyzed for cell-type distribution and found to be strongly partitioned, with expression of dark-phase genes overrepresented in somatic cells and light-phase genes overrepresented in gonidial cells- a result that is consistent with cell-type programs in V. carteri arising by cooption of temporal regulons in a unicellular ancestor. Together, our findings reveal fundamental molecular, metabolic, and evolutionary mechanisms that underlie the origins of germ-soma differentiation in V. carteri and provide a template for understanding the acquisition of germ-soma differentiation in other multicellular lineages.}, }
@article {pmid29198427, year = {2018}, author = {Kenny, NJ and de Goeij, JM and de Bakker, DM and Whalen, CG and Berezikov, E and Riesgo, A}, title = {Towards the identification of ancestrally shared regenerative mechanisms across the Metazoa: A Transcriptomic case study in the Demosponge Halisarca caerulea.}, journal = {Marine genomics}, volume = {37}, number = {}, pages = {135-147}, doi = {10.1016/j.margen.2017.11.001}, pmid = {29198427}, issn = {1876-7478}, mesh = {Animals ; *Evolution, Molecular ; Porifera/genetics/*physiology ; Regeneration/*genetics ; Time Factors ; *Transcriptome ; }, abstract = {Regeneration is an essential process for all multicellular organisms, allowing them to recover effectively from internal and external injury. This process has been studied extensively in a medical context in vertebrates, with pathways often investigated mechanistically, both to derive increased understanding and as potential drug targets for therapy. Several species from other parts of the metazoan tree of life, including Hydra, planarians and echinoderms, noted for their regenerative capabilities, have previously been targeted for study. Less well-documented for their regenerative abilities are sponges. This is surprising, as they are both one of the earliest-branching extant metazoan phyla on Earth, and are rapidly able to respond to injury. Their sessile lifestyle, lack of an external protective layer, inability to respond to predation and filter-feeding strategy all mean that regeneration is often required. In particular the demosponge genus Halisarca has been noted for its fast cell turnover and ability to quickly adjust its cell kinetic properties to repair damage through regeneration. However, while the rate and structure of regeneration in sponges has begun to be investigated, the molecular mechanisms behind this ability are yet to be catalogued. Here we describe the assembly of a reference transcriptome for Halisarca caerulea, along with additional transcriptomes noting response to injury before, shortly following (2h post-), and 12h after trauma. RNAseq reads were assembled using Trinity, annotated, and samples compared, to allow initial insight into the transcriptomic basis of sponge regenerative processes. These resources are deep, with our reference assembly containing >92.6% of the BUSCO Metazoa set of genes, and well-assembled (N50s of 836, 957, 1688 and 2032 for untreated, 2h, 12h and reference transcriptomes respectively), and therefore represent excellent qualitative resources as a bedrock for future study. The generation of transcriptomic resources from sponges before and following deliberate damage has allowed us to study particular pathways within this species responsible for repairing damage. We note particularly the involvement of the Wnt cascades in this process in this species, and detail the contents of this cascade, along with cell cycle, extracellular matrix and apoptosis-linked genes in this work. This resource represents an initial starting point for the continued development of this knowledge, given H. caerulea's ability to regenerate and position as an outgroup for comparing the process of regeneration across metazoan lineages. With this resource in place, we can begin to infer the regenerative capacity of the common ancestor of all extant animal life, and unravel the elements of regeneration in an often-overlooked clade.}, }
@article {pmid29191225, year = {2017}, author = {Sanfilippo, P and Wen, J and Lai, EC}, title = {Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {229}, doi = {10.1186/s13059-017-1358-0}, pmid = {29191225}, issn = {1474-760X}, support = {R01-GM083300//National Institute of General Medical Sciences/ ; P30-CA008748//National Cancer Institute/ ; R01-NS083833//National Institute of Neurological Disorders and Stroke/ ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 NS083833/NS/NINDS NIH HHS/United States ; R01 GM083300/GM/NIGMS NIH HHS/United States ; }, mesh = {*3' Untranslated Regions ; Animals ; Cell Line ; Computational Biology/methods ; Drosophila/embryology/*genetics ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; Molecular Sequence Annotation ; Organ Specificity/genetics ; *Poly A ; Polyadenylation ; RNA Isoforms ; RNA-Binding Proteins/metabolism ; Species Specificity ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3'-sequencing data in this species precludes comprehensive assessment of alternative polyadenylation (APA), which is subject to broad tissue-specific control.<br><br>RESULTS: Here, we generate deep 3'-sequencing data from 23 developmental stages, tissues, and cell lines of D. melanogaster, yielding a comprehensive atlas of ~ 62,000 polyadenylated ends. These data broadly extend the annotated transcriptome, identify ~ 40,000 novel 3' termini, and reveal that two-thirds of Drosophila genes are subject to APA. Furthermore, we dramatically expand the numbers of genes known to be subject to tissue-specific APA, such as 3' untranslated region (UTR) lengthening in head and 3' UTR shortening in testis, and characterize new tissue and developmental 3' UTR patterns. Our thorough 3' UTR annotations permit reassessment of post-transcriptional regulatory networks, via conserved miRNA and RNA binding protein sites. To evaluate the evolutionary conservation and divergence of APA patterns, we generate developmental and tissue-specific 3'-seq libraries from Drosophila yakuba and Drosophila virilis. We document broadly analogous tissue-specific APA trends in these species, but also observe significant alterations in 3' end usage across orthologs. We exploit the population of functionally evolving poly(A) sites to gain clear evidence that evolutionary divergence in core polyadenylation signal (PAS) and downstream sequence element (DSE) motifs drive broad alterations in 3' UTR isoform expression across the Drosophila phylogeny.<br><br>CONCLUSIONS: These data provide a critical resource for the Drosophila community and offer many insights into the complex control of alternative tissue-specific 3' UTR formation and its consequences for post-transcriptional regulatory networks.}, }
@article {pmid29179763, year = {2017}, author = {Klein, B and Wibberg, D and Hallmann, A}, title = {Whole transcriptome RNA-Seq analysis reveals extensive cell type-specific compartmentalization in Volvox carteri.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {111}, doi = {10.1186/s12915-017-0450-y}, pmid = {29179763}, issn = {1741-7007}, mesh = {*Biological Evolution ; Computational Biology ; Gene Expression Profiling ; *Genome ; Sequence Analysis, RNA ; *Transcriptome ; Volvox/*genetics ; }, abstract = {BACKGROUND: One of evolution's most important achievements is the development and radiation of multicellular organisms with different types of cells. Complex multicellularity has evolved several times in eukaryotes; yet, in most lineages, an investigation of its molecular background is considerably challenging since the transition occurred too far in the past and, in addition, these lineages evolved a large number of cell types. However, for volvocine green algae, such as Volvox carteri, multicellularity is a relatively recent innovation. Furthermore, V. carteri shows a complete division of labor between only two cell types - small, flagellated somatic cells and large, immotile reproductive cells. Thus, V. carteri provides a unique opportunity to study multicellularity and cellular differentiation at the molecular level.<br><br>RESULTS: This study provides a whole transcriptome RNA-Seq analysis of separated cell types of the multicellular green alga V. carteri f. nagariensis to reveal cell type-specific components and functions. To this end, 246 million quality filtered reads were mapped to the genome and valid expression data were obtained for 93% of the 14,247 gene loci. In the subsequent search for protein domains with assigned molecular function, we identified 9435 previously classified domains in 44% of all gene loci. Furthermore, in 43% of all gene loci we identified 15,254 domains that are involved in biological processes. All identified domains were investigated regarding cell type-specific expression. Moreover, we provide further insight into the expression pattern of previously described gene families (e.g., pherophorin, extracellular matrix metalloprotease, and VARL families). Our results demonstrate an extensive compartmentalization of the transcriptome between cell types: More than half of all genes show a clear difference in expression between somatic and reproductive cells.<br><br>CONCLUSIONS: This study constitutes the first transcriptome-wide RNA-Seq analysis of separated cell types of V. carteri focusing on gene expression. The high degree of differential expression indicates a strong differentiation of cell types despite the fact that V. carteri diverged relatively recently from its unicellular relatives. Our expression dataset and the bioinformatic analyses provide the opportunity to further investigate and understand the mechanisms of cell type-specific expression and its transcriptional regulation.}, }
@article {pmid29175233, year = {2018}, author = {Miller, WB}, title = {Biological information systems: Evolution as cognition-based information management.}, journal = {Progress in biophysics and molecular biology}, volume = {134}, number = {}, pages = {1-26}, doi = {10.1016/j.pbiomolbio.2017.11.005}, pmid = {29175233}, issn = {1873-1732}, abstract = {An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.}, }
@article {pmid29170260, year = {2018}, author = {Swafford, AJM and Oakley, TH}, title = {Multimodal sensorimotor system in unicellular zoospores of a fungus.}, journal = {The Journal of experimental biology}, volume = {221}, number = {Pt 2}, pages = {}, doi = {10.1242/jeb.163196}, pmid = {29170260}, issn = {1477-9145}, abstract = {Complex sensory systems often underlie critical behaviors, including avoiding predators and locating prey, mates and shelter. Multisensory systems that control motor behavior even appear in unicellular eukaryotes, such as Chlamydomonas, which are important laboratory models for sensory biology. However, we know of no unicellular opisthokonts that control motor behavior using a multimodal sensory system. Therefore, existing single-celled models for multimodal sensorimotor integration are very distantly related to animals. Here, we describe a multisensory system that controls the motor function of unicellular fungal zoospores. We found that zoospores of Allomyces arbusculus exhibit both phototaxis and chemotaxis. Furthermore, we report that closely related Allomyces species respond to either the chemical or the light stimuli presented in this study, not both, and likely do not share this multisensory system. This diversity of sensory systems within Allomyces provides a rare example of a comparative framework that can be used to examine the evolution of sensory systems following the gain/loss of available sensory modalities. The tractability of Allomyces and related fungi as laboratory organisms will facilitate detailed mechanistic investigations into the genetic underpinnings of novel photosensory systems, and how multisensory systems may have functioned in early opisthokonts before multicellularity allowed for the evolution of specialized cell types.}, }
@article {pmid29166656, year = {2017}, author = {Pichugin, Y and Peña, J and Rainey, PB and Traulsen, A}, title = {Fragmentation modes and the evolution of life cycles.}, journal = {PLoS computational biology}, volume = {13}, number = {11}, pages = {e1005860}, doi = {10.1371/journal.pcbi.1005860}, pmid = {29166656}, issn = {1553-7358}, mesh = {Animals ; Bacteria/cytology ; *Biological Evolution ; Cell Physiological Phenomena/*physiology ; Computational Biology ; Life Cycle Stages/*physiology ; *Models, Biological ; Reproduction/physiology ; }, abstract = {Reproduction is a defining feature of living systems. To reproduce, aggregates of biological units (e.g., multicellular organisms or colonial bacteria) must fragment into smaller parts. Fragmentation modes in nature range from binary fission in bacteria to collective-level fragmentation and the production of unicellular propagules in multicellular organisms. Despite this apparent ubiquity, the adaptive significance of fragmentation modes has received little attention. Here, we develop a model in which groups arise from the division of single cells that do not separate but stay together until the moment of group fragmentation. We allow for all possible fragmentation patterns and calculate the population growth rate of each associated life cycle. Fragmentation modes that maximise growth rate comprise a restrictive set of patterns that include production of unicellular propagules and division into two similar size groups. Life cycles marked by single-cell bottlenecks maximise population growth rate under a wide range of conditions. This surprising result offers a new evolutionary explanation for the widespread occurrence of this mode of reproduction. All in all, our model provides a framework for exploring the adaptive significance of fragmentation modes and their associated life cycles.}, }
@article {pmid29162942, year = {2017}, author = {Lin, H and Kazlauskas, RJ and Travisano, M}, title = {Developmental evolution facilitates rapid adaptation.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15891}, doi = {10.1038/s41598-017-16229-0}, pmid = {29162942}, issn = {2045-2322}, abstract = {Developmental evolution has frequently been identified as a mode for rapid adaptation, but direct observations of the selective benefits and associated mechanisms of developmental evolution are necessarily challenging to obtain. Here we show rapid evolution of greatly increased rates of dispersal by developmental changes when populations experience stringent selection. Replicate populations of the filamentous fungus Trichoderma citrinoviride underwent 85 serial transfers, under conditions initially favoring growth but not dispersal. T. citrinoviride populations shifted away from multicellular growth toward increased dispersal by producing one thousand times more single-celled asexual conidial spores, three times sooner than the ancestral genotype. Conidia of selected lines also germinated fifty percent faster. Gene expression changed substantially between the ancestral and selected fungi, especially for spore production and growth, demonstrating rapid evolution of tight regulatory control for down-regulation of growth and up-regulation of conidia production between 18 and 24 hours of growth. These changes involved both developmentally fixed and plastic changes in gene expression, showing that complex developmental changes can serve as a mechanism for rapid adaptation.}, }
@article {pmid29152201, year = {2017}, author = {Witting, L}, title = {The natural selection of metabolism and mass selects lifeforms from viruses to multicellular animals.}, journal = {Ecology and evolution}, volume = {7}, number = {21}, pages = {9098-9118}, doi = {10.1002/ece3.3432}, pmid = {29152201}, issn = {2045-7758}, abstract = {I show that the natural selection of metabolism and mass can select for the major life-history and allometric transitions that define lifeforms from viruses, over prokaryotes and larger unicells, to multicellular animals. The proposed selection is driven by a mass-specific metabolism that is selected as the pace of the resource handling that generates net energy for self-replication. An initial selection of mass is given by a dependence of mass-specific metabolism on mass in replicators that are close to a lower size limit. A sublinear maximum dependence selects for virus-like replicators, with no intrinsic metabolism, no cell, and practically no mass. A superlinear dependence selects for prokaryote-like self-replicating cells, with asexual reproduction and incomplete metabolic pathways. These self-replicators have selection for increased net energy, and this generates a gradual unfolding of population-dynamic feed-back selection from interactive competition. The incomplete feed-back selects for larger unicells with more developed metabolic pathways, and the completely developed feed-back for multicellular animals with sexual reproduction. This model unifies the natural selection of lifeforms from viruses to multicellular animals, and it provides a parsimonious explanation where allometries and major life histories evolve from the natural selection of metabolism and mass.}, }
@article {pmid29149403, year = {2017}, author = {Xoconostle-Cázares, B and Ruiz-Medrano, R}, title = {Structure-Function Relationship of TCTP.}, journal = {Results and problems in cell differentiation}, volume = {64}, number = {}, pages = {47-68}, doi = {10.1007/978-3-319-67591-6_3}, pmid = {29149403}, issn = {0080-1844}, abstract = {The translationally controlled tumor protein (TCTP) is a small, multifunctional protein found in most, if not all, eukaryotic lineages, involved in a myriad of key regulatory processes. Among these, the control of proliferation and inhibition of cell death, as well as differentiation, are the most important, and it is probable that other responses are derived from the ability of TCTP to influence them in both unicellular and multicellular organisms. In the latter, an additional function for TCTP stems from its capacity to be secreted via a nonclassical pathway and function in a non-cell autonomous (paracrine) manner, thus affecting the responses of neighboring or distant cells to developmental or environmental stimuli (as in the case of serum TCTP/histamine-releasing factor in mammals and phloem TCTP in Arabidopsis). The additional ability to traverse membranes without a requirement for transmembrane receptors adds to its functional flexibility. The long-distance transport of TCTP mRNA and protein in plants via the vascular system supports the notion that an important aspect of TCTP function is its ability to influence the response of neighboring and distant cells to endogenous and exogenous signals in a supracellular manner. The predicted tridimensional structure of TCTPs indicates a high degree of conservation, more than its amino acid sequence similarity could suggest. However, subtle differences in structure could lead to different activities, as evidenced by TCTPs secreted by Plasmodium spp. Similar structural variations in animal and plant TCTPs, likely the result of convergent evolution, could lead to deviations from the canonical function of this group of proteins, which could have an impact from a biomedical and agricultural perspectives.}, }
@article {pmid29141015, year = {2017}, author = {Bozler, J and Kacsoh, BZ and Bosco, G}, title = {Nematocytes: Discovery and characterization of a novel anculeate hemocyte in Drosophila falleni and Drosophila phalerata.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0188133}, doi = {10.1371/journal.pone.0188133}, pmid = {29141015}, issn = {1932-6203}, support = {DP1 MH110234/MH/NIMH NIH HHS/United States ; P30 CA023108/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Drosophila/*classification/immunology ; *Hemocytes ; Immunity, Innate ; Microscopy, Fluorescence ; Phylogeny ; Species Specificity ; }, abstract = {Immune challenges, such as parasitism, can be so pervasive and deleterious that they constitute an existential threat to a species' survival. In response to these ecological pressures, organisms have developed a wide array of novel behavioral, cellular, and molecular adaptations. Research into these immune defenses in model systems has resulted in a revolutionary understanding of evolution and functional biology. As the field has expanded beyond the limited number of model organisms our appreciation of evolutionary innovation and unique biology has widened as well. With this in mind, we have surveyed the hemolymph of several non-model species of Drosophila. Here we identify and describe a novel hemocyte, type-II nematocytes, found in larval stages of numerous Drosophila species. Examined in detail in Drosophila falleni and Drosophila phalerata, we find that these remarkable cells are distinct from previously described hemocytes due to their anucleate state (lacking a nucleus) and unusual morphology. Type-II nematocytes are long, narrow cells with spindle-like projections extending from a cell body with high densities of mitochondria and microtubules, and exhibit the ability to synthesize proteins. These properties are unexpected for enucleated cells, and together with our additional characterization, we demonstrate that these type-II nematocytes represent a biological novelty. Surprisingly, despite the absence of a nucleus, we observe through live cell imaging that these cells remain motile with a highly dynamic cellular shape. Furthermore, these cells demonstrate the ability to form multicellular structures, which we suggest may be a component of the innate immune response to macro-parasites. In addition, live cell imaging points to a large nucleated hemocyte, type-I nematocyte, as the progenitor cell, leading to enucleation through a budding or asymmetrical division process rather than nuclear ejection: This study is the first to report such a process of enucleation. Here we describe these cells in detail for the first time and examine their evolutionary history in Drosophila.}, }
@article {pmid29134064, year = {2017}, author = {Bertolaso, M and Dieli, AM}, title = {Cancer and intercellular cooperation.}, journal = {Royal Society open science}, volume = {4}, number = {10}, pages = {170470}, doi = {10.1098/rsos.170470}, pmid = {29134064}, issn = {2054-5703}, abstract = {The major transitions approach in evolutionary biology has shown that the intercellular cooperation that characterizes multicellular organisms would never have emerged without some kind of multilevel selection. Relying on this view, the Evolutionary Somatic view of cancer considers cancer as a breakdown of intercellular cooperation and as a loss of the balance between selection processes that take place at different levels of organization (particularly single cell and individual organism). This seems an elegant unifying framework for healthy organism, carcinogenesis, tumour proliferation, metastasis and other phenomena such as ageing. However, the gene-centric version of Darwinian evolution, which is often adopted in cancer research, runs into empirical problems: proto-tumoural and tumoural features in precancerous cells that would undergo 'natural selection' have proved hard to demonstrate; cells are radically context-dependent, and some stages of cancer are poorly related to genetic change. Recent perspectives propose that breakdown of intercellular cooperation could depend on 'fields' and other higher-level phenomena, and could be even mutations independent. Indeed, the field would be the context, allowing (or preventing) genetic mutations to undergo an intra-organism process analogous to natural selection. The complexities surrounding somatic evolution call for integration between multiple incomplete frameworks for interpreting intercellular cooperation and its pathologies.}, }
@article {pmid29133828, year = {2017}, author = {Schenkelaars, Q and Pratlong, M and Kodjabachian, L and Fierro-Constain, L and Vacelet, J and Le Bivic, A and Renard, E and Borchiellini, C}, title = {Animal multicellularity and polarity without Wnt signaling.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15383}, doi = {10.1038/s41598-017-15557-5}, pmid = {29133828}, issn = {2045-2322}, abstract = {Acquisition of multicellularity is a central event in the evolution of Eukaryota. Strikingly, animal multicellularity coincides with the emergence of three intercellular communication pathways - Notch, TGF-β and Wnt - all considered as hallmarks of metazoan development. By investigating Oopsacas minuta and Aphrocallistes vastus, we show here that the emergence of a syncytium and plugged junctions in glass sponges coincides with the loss of essential components of the Wnt signaling (i.e. Wntless, Wnt ligands and Disheveled), whereas core components of the TGF-β and Notch modules appear unaffected. This suggests that Wnt signaling is not essential for cell differentiation, polarity and morphogenesis in glass sponges. Beyond providing a comparative study of key developmental toolkits, we define here the first case of a metazoan phylum that maintained a level of complexity similar to its relatives despite molecular degeneration of Wnt pathways.}, }
@article {pmid29133443, year = {2017}, author = {Kempes, CP and Wolpert, D and Cohen, Z and Pérez-Mercader, J}, title = {The thermodynamic efficiency of computations made in cells across the range of life.}, journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences}, volume = {375}, number = {2109}, pages = {}, doi = {10.1098/rsta.2016.0343}, pmid = {29133443}, issn = {1471-2962}, abstract = {Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems. Here we show that the computational efficiency of translation, defined as free energy expended per amino acid operation, outperforms the best supercomputers by several orders of magnitude, and is only about an order of magnitude worse than the Landauer bound. However, this efficiency depends strongly on the size and architecture of the cell in question. In particular, we show that the useful efficiency of an amino acid operation, defined as the bulk energy per amino acid polymerization, decreases for increasing bacterial size and converges to the polymerization cost of the ribosome. This cost of the largest bacteria does not change in cells as we progress through the major evolutionary shifts to both single- and multicellular eukaryotes. However, the rates of total computation per unit mass are non-monotonic in bacteria with increasing cell size, and also change across different biological architectures, including the shift from unicellular to multicellular eukaryotes.This article is part of the themed issue 'Reconceptualizing the origins of life'.}, }
@article {pmid29129605, year = {2018}, author = {Pogozheva, ID and Lomize, AL}, title = {Evolution and adaptation of single-pass transmembrane proteins.}, journal = {Biochimica et biophysica acta. Biomembranes}, volume = {1860}, number = {2}, pages = {364-377}, doi = {10.1016/j.bbamem.2017.11.002}, pmid = {29129605}, issn = {0005-2736}, mesh = {*Adaptation, Physiological ; Arabidopsis/genetics/metabolism ; Cell Membrane/*metabolism ; Databases, Protein ; Dictyostelium/genetics/metabolism ; Escherichia coli/genetics/metabolism ; *Evolution, Molecular ; Humans ; Membrane Proteins/chemistry/genetics/*metabolism ; Methanocaldococcus/genetics/metabolism ; Protein Conformation, alpha-Helical ; Protein Multimerization ; Proteome/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Species Specificity ; }, abstract = {A comparative analysis of 6039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the Membranome database. The observed repertoire of bitopic proteins is significantly enlarged in eukaryotic cells and especially in multicellular organisms due to the diversification of enzymes, emergence of proteins involved in vesicular trafficking, and expansion of receptors, structural, and adhesion proteins. The majority of bitopic proteins in multicellular organisms are located in the plasma membrane (PM) and involved in cell communication. Bitopic proteins from different membranes significantly diverge in terms of their biological functions, size, topology, domain architecture, physical properties of transmembrane (TM) helices and propensity to form homodimers. Most proteins from eukaryotic PM and endoplasmic reticulum (ER) have the N-out topology. The predicted lengths of TM helices and hydrophobic thicknesses, stabilities and hydrophobicities of TM α-helices are the highest for proteins from eukaryotic PM, intermediate for proteins from prokaryotic cells, ER and Golgi apparatus, and lowest for proteins from mitochondria, chloroplasts, and peroxisomes. Tyr and Phe residues accumulate at the cytoplasmic leaflet of PM and at the outer leaflet of membranes of bacteria, Golgi apparatus, and nucleus. The propensity for dimerization increases from unicellular to multicellular eukaryotes, from enzymes to receptors, and from intracellular membrane proteins to PM proteins. More than half of PM proteins form homodimers with a 2:1 ratio of right-handed to left-handed helix packing arrangements. The inverse ratio (1:2) was observed for dimers from the ER, Golgi and vesicles.}, }
@article {pmid29121339, year = {2017}, author = {Polychronopoulos, D and King, JWD and Nash, AJ and Tan, G and Lenhard, B}, title = {Conserved non-coding elements: developmental gene regulation meets genome organization.}, journal = {Nucleic acids research}, volume = {45}, number = {22}, pages = {12611-12624}, doi = {10.1093/nar/gkx1074}, pmid = {29121339}, issn = {1362-4962}, support = {MC_UP_1102/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Conserved Sequence/*genetics ; Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Genes, Developmental/genetics ; Genome/*genetics ; Humans ; Regulatory Sequences, Nucleic Acid/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks-dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.}, }
@article {pmid29120392, year = {2017}, author = {Drezen, JM and Josse, T and Bézier, A and Gauthier, J and Huguet, E and Herniou, EA}, title = {Impact of Lateral Transfers on the Genomes of Lepidoptera.}, journal = {Genes}, volume = {8}, number = {11}, pages = {}, doi = {10.3390/genes8110315}, pmid = {29120392}, issn = {2073-4425}, abstract = {Transfer of DNA sequences between species regardless of their evolutionary distance is very common in bacteria, but evidence that horizontal gene transfer (HGT) also occurs in multicellular organisms has been accumulating in the past few years. The actual extent of this phenomenon is underestimated due to frequent sequence filtering of &quot;alien&quot; DNA before genome assembly. However, recent studies based on genome sequencing have revealed, and experimentally verified, the presence of foreign DNA sequences in the genetic material of several species of Lepidoptera. Large DNA viruses, such as baculoviruses and the symbiotic viruses of parasitic wasps (bracoviruses), have the potential to mediate these transfers in Lepidoptera. In particular, using ultra-deep sequencing, newly integrated transposons have been identified within baculovirus genomes. Bacterial genes have also been acquired by genomes of Lepidoptera, as in other insects and nematodes. In addition, insertions of bracovirus sequences were present in the genomes of certain moth and butterfly lineages, that were likely corresponding to rearrangements of ancient integrations. The viral genes present in these sequences, sometimes of hymenopteran origin, have been co-opted by lepidopteran species to confer some protection against pathogens.}, }
@article {pmid29119267, year = {2018}, author = {Li, L and Aslam, M and Rabbi, F and Vanderwel, MC and Ashton, NW and Suh, DY}, title = {PpORS, an ancient type III polyketide synthase, is required for integrity of leaf cuticle and resistance to dehydration in the moss, Physcomitrella patens.}, journal = {Planta}, volume = {247}, number = {2}, pages = {527-541}, doi = {10.1007/s00425-017-2806-5}, pmid = {29119267}, issn = {1432-2048}, support = {262038-2013//Natural Sciences and Engineering Research Council of Canada/ ; 2982-2008//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Acyltransferases/genetics/*metabolism ; Biological Evolution ; Bryopsida/*enzymology/genetics/physiology ; Dehydration ; Gene Knockout Techniques ; Mutation ; Phenotype ; Phylogeny ; Plant Leaves/enzymology/genetics/physiology ; Plant Proteins/genetics/metabolism ; Water/physiology ; }, abstract = {MAIN CONCLUSION: PpORS knockout mutants produced abnormal leaves with increased dye permeability and were more susceptible to dehydration, consistent with PpORS products being constituents of a cuticular structure in the moss. Type III polyketide synthases (PKSs) have co-evolved with terrestrial plants such that each taxon can generate a characteristic collection of polyketides, fine-tuned to its needs. 2'-Oxoalkylresorcinol synthase from Physcomitrella patens (PpORS) is basal to all plant type III PKSs in phylogenetic trees and may closely resemble their most recent common ancestor. To gain insight into the roles that ancestral plant type III PKSs might have played during early land plant evolution, we constructed and phenotypically characterized targeted knockouts of PpORS. Ors gametophores, unless submerged in water while they were developing, displayed various leaf malformations that included grossly misshapen leaves, missing or abnormal midribs, multicellular protuberances and localized necrosis. Ors leaves, particularly abnormal ones, showed increased permeability to the hydrophilic dye, toluidine blue. Ors gametophores lost water faster and were more susceptible to dehydration than those of the control strain. Our findings are consistent with ors leaves possessing a partially defective cuticle and implicate PpORS in synthesis of the intact cuticle. PpORS orthologs are present in a few moss species but have not been found in other plants. However, conceivably an ancestral ORS in early land plants may have contributed to their protection from dehydration.}, }
@article {pmid29118134, year = {2017}, author = {Berger, D and Stångberg, J and Grieshop, K and Martinossi-Allibert, I and Arnqvist, G}, title = {Temperature effects on life-history trade-offs, germline maintenance and mutation rate under simulated climate warming.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1866}, pages = {}, doi = {10.1098/rspb.2017.1721}, pmid = {29118134}, issn = {1471-2954}, mesh = {Acclimatization ; Animals ; Climate Change ; Coleoptera/*physiology ; Female ; *Germ-Line Mutation ; *Life History Traits ; Longevity ; Male ; *Mutation Rate ; Reproduction ; }, abstract = {Mutation has a fundamental influence over evolutionary processes, but how evolutionary processes shape mutation rate remains less clear. In asexual unicellular organism, increased mutation rates have been observed in stressful environments and the reigning paradigm ascribes this increase to selection for evolvability. However, this explanation does not apply in sexually reproducing species, where little is known about how the environment affects mutation rate. Here we challenged experimental lines of seed beetle, evolved at ancestral temperature or under simulated climate warming, to repair induced mutations at ancestral and stressful temperature. Results show that temperature stress causes individuals to pass on a greater mutation load to their grand-offspring. This suggests that stress-induced mutation rates, in unicellular and multicellular organisms alike, can result from compromised germline DNA repair in low condition individuals. Moreover, lines adapted to simulated climate warming had evolved increased longevity at the cost of reproduction, and this allocation decision improved germline repair. These results suggest that mutation rates can be modulated by resource allocation trade-offs encompassing life-history traits and the germline and have important implications for rates of adaptation and extinction as well as our understanding of genetic diversity in multicellular organisms.}, }
@article {pmid29114025, year = {2017}, author = {Hajjar, C and Cherrier, MV and Dias Mirandela, G and Petit-Hartlein, I and Stasia, MJ and Fontecilla-Camps, JC and Fieschi, F and Dupuy, J}, title = {The NOX Family of Proteins Is Also Present in Bacteria.}, journal = {mBio}, volume = {8}, number = {6}, pages = {}, doi = {10.1128/mBio.01487-17}, pmid = {29114025}, issn = {2150-7511}, mesh = {Algorithms ; Bacterial Proteins/chemistry/*genetics/isolation &amp; purification/*metabolism ; Databases, Genetic ; Electron Transport ; Humans ; NADPH Oxidase 2/chemistry/genetics ; NADPH Oxidases/chemistry/*genetics/isolation &amp; purification/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Phagocytes/enzymology ; Phylogeny ; Reactive Oxygen Species/metabolism ; Signal Transduction ; Streptococcus pneumoniae/enzymology/*genetics ; }, abstract = {Transmembrane NADPH oxidase (NOX) enzymes have been so far only characterized in eukaryotes. In most of these organisms, they reduce molecular oxygen to superoxide and, depending on the presence of additional domains, are called NOX or dual oxidases (DUOX). Reactive oxygen species (ROS), including superoxide, have been traditionally considered accidental toxic by-products of aerobic metabolism. However, during the last decade it has become evident that both O2•- and H2O2 are key players in complex signaling networks and defense. A well-studied example is the production of O2•- during the bactericidal respiratory burst of phagocytes; this production is catalyzed by NOX2. Here, we devised and applied a novel algorithm to search for additional NOX genes in genomic databases. This procedure allowed us to discover approximately 23% new sequences from bacteria (in relation to the number of NOX-related sequences identified by the authors) that we have added to the existing eukaryotic NOX family and have used to build an expanded phylogenetic tree. We cloned and overexpressed the identified nox gene from Streptococcus pneumoniae and confirmed that it codes for an NADPH oxidase. The membrane of the S. pneumoniae NOX protein (SpNOX) shares many properties with its eukaryotic counterparts, such as affinity for NADPH and flavin adenine dinucleotide, superoxide dismutase and diphenylene iodonium inhibition, cyanide resistance, oxygen consumption, and superoxide production. Traditionally, NOX enzymes in eukaryotes are related to functions linked to multicellularity. Thus, the discovery of a large family of NOX-related enzymes in the bacterial world brings up fascinating questions regarding their role in this new biological context.IMPORTANCE NADPH oxidase (NOX) enzymes have not yet been reported in bacteria. Here, we carried out computational and experimental studies to provide the first characterization of a prokaryotic NOX. Out of 996 prokaryotic proteins showing NOX signatures, we initially selected, cloned, and overexpressed four of them. Subsequently, and based on preliminary testing, we concentrated our efforts on Streptococcus SpNOX, which shares many biochemical characteristics with NOX2, the referent model of NOX enzymes. Our work makes possible, for the first time, the study of pure forms of this important family of enzymes, allowing for biophysical and molecular characterization in an unprecedented way. Similar advances regarding other membrane protein families have led to new structures, further mechanistic studies, and the improvement of inhibitors. In addition, biological functions of these newly described bacterial enzymes will be certainly discovered in the near future.}, }
@article {pmid29109232, year = {2017}, author = {Stapley, J and Feulner, PGD and Johnston, SE and Santure, AW and Smadja, CM}, title = {Recombination: the good, the bad and the variable.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1736}, pages = {}, doi = {10.1098/rstb.2017.0279}, pmid = {29109232}, issn = {1471-2970}, mesh = {Genome ; Recombination, Genetic/genetics/*physiology ; Reproduction ; }, abstract = {Recombination, the process by which DNA strands are broken and repaired, producing new combinations of alleles, occurs in nearly all multicellular organisms and has important implications for many evolutionary processes. The effects of recombination can be good, as it can facilitate adaptation, but also bad when it breaks apart beneficial combinations of alleles, and recombination is highly variable between taxa, species, individuals and across the genome. Understanding how and why recombination rate varies is a major challenge in biology. Most theoretical and empirical work has been devoted to understanding the role of recombination in the evolution of sex-comparing between sexual and asexual species or populations. How recombination rate evolves and what impact this has on evolutionary processes within sexually reproducing organisms has received much less attention. This Theme Issue focusses on how and why recombination rate varies in sexual species, and aims to coalesce knowledge of the molecular mechanisms governing recombination with our understanding of the evolutionary processes driving variation in recombination within and between species. By integrating these fields, we can identify important knowledge gaps and areas for future research, and pave the way for a more comprehensive understanding of how and why recombination rate varies.}, }
@article {pmid29109219, year = {2017}, author = {Stapley, J and Feulner, PGD and Johnston, SE and Santure, AW and Smadja, CM}, title = {Variation in recombination frequency and distribution across eukaryotes: patterns and processes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1736}, pages = {}, doi = {10.1098/rstb.2016.0455}, pmid = {29109219}, issn = {1471-2970}, mesh = {Chromosome Mapping ; Eukaryota/*genetics ; *Genetic Linkage ; *Genome ; Recombination, Genetic/*genetics ; }, abstract = {Recombination, the exchange of DNA between maternal and paternal chromosomes during meiosis, is an essential feature of sexual reproduction in nearly all multicellular organisms. While the role of recombination in the evolution of sex has received theoretical and empirical attention, less is known about how recombination rate itself evolves and what influence this has on evolutionary processes within sexually reproducing organisms. Here, we explore the patterns of, and processes governing recombination in eukaryotes. We summarize patterns of variation, integrating current knowledge with an analysis of linkage map data in 353 organisms. We then discuss proximate and ultimate processes governing recombination rate variation and consider how these influence evolutionary processes. Genome-wide recombination rates (cM/Mb) can vary more than tenfold across eukaryotes, and there is large variation in the distribution of recombination events across closely related taxa, populations and individuals. We discuss how variation in rate and distribution relates to genome architecture, genetic and epigenetic mechanisms, sex, environmental perturbations and variable selective pressures. There has been great progress in determining the molecular mechanisms governing recombination, and with the continued development of new modelling and empirical approaches, there is now also great opportunity to further our understanding of how and why recombination rate varies.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.}, }
@article {pmid29104545, year = {2017}, author = {Dobson, GP and Arsyad, A and Letson, HL}, title = {The Adenosine Hypothesis Revisited: Modulation of Coupling between Myocardial Perfusion and Arterial Compliance.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {824}, doi = {10.3389/fphys.2017.00824}, pmid = {29104545}, issn = {1664-042X}, abstract = {For over four decades the thoracic aortic ring model has become one of the most widely used methods to study vascular reactivity and electromechanical coupling. A question that is rarely asked, however, is what function does a drug-mediated relaxation (or contraction) in this model serve in the intact system? The physiological significance of adenosine relaxation in rings isolated from large elastic conduit arteries from a wide range of species remains largely unknown. We propose that adenosine relaxation increases aortic compliance in acute stress states and facilitates ventricular-arterial (VA) coupling, and thereby links compliance and coronary artery perfusion to myocardial energy metabolism. In 1963 Berne argued that adenosine acts as a local negative feedback regulator between oxygen supply and demand in the heart during hypoxic/ischemic stress. The adenosine VA coupling hypothesis extends and enhances Berne's &quot;adenosine hypothesis&quot; from a local regulatory scheme in the heart to include conduit arterial function. In multicellular organisms, evolution may have selected adenosine, nitric oxide, and other vascular mediators, to modulate VA coupling for optimal transfer of oxygen (and nutrients) from the lung, heart, large conduit arteries, arterioles and capillaries to respiring mitochondria. Finally, a discussion of the potential clinical significance of adenosine modulation of VA coupling is extended to vascular aging and disease, including hypertension, diabetes, obesity, coronary artery disease and heart failure.}, }
@article {pmid29101312, year = {2017}, author = {Björnfot Holmström, S and Clark, R and Zwicker, S and Bureik, D and Kvedaraite, E and Bernasconi, E and Nguyen Hoang, AT and Johannsen, G and Marsland, BJ and Boström, EA and Svensson, M}, title = {Gingival Tissue Inflammation Promotes Increased Matrix Metalloproteinase-12 Production by CD200Rlow Monocyte-Derived Cells in Periodontitis.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {199}, number = {12}, pages = {4023-4035}, doi = {10.4049/jimmunol.1700672}, pmid = {29101312}, issn = {1550-6606}, mesh = {Adult ; Antigens, Surface/biosynthesis/genetics/*physiology ; Cell Division ; Cells, Cultured ; Coculture Techniques ; Cyclooxygenase Inhibitors/pharmacology ; Epithelial Cells/metabolism ; Fibroblasts/metabolism ; Flow Cytometry ; Gene Expression Regulation ; Gingiva/*enzymology/pathology ; Granulocyte-Macrophage Colony-Stimulating Factor/pharmacology ; Humans ; Inflammation ; Keratinocytes/metabolism ; Matrix Metalloproteinase 12/biosynthesis/genetics/*physiology ; Monocytes/*enzymology/pathology ; Periodontitis/*enzymology/pathology ; Pyrazoles/pharmacology ; Real-Time Polymerase Chain Reaction ; Receptors, Cell Surface/biosynthesis/genetics/*physiology ; }, abstract = {Irreversible tissue recession in chronic inflammatory diseases is associated with dysregulated immune activation and production of tissue degradative enzymes. In this study, we identified elevated levels of matrix metalloproteinase (MMP)-12 in gingival tissue of patients with the chronic inflammatory disease periodontitis (PD). The source of MMP12 was cells of monocyte origin as determined by the expression of CD14, CD68, and CD64. These MMP12-producing cells showed reduced surface levels of the coinhibitory molecule CD200R. Similarly, establishing a multicellular three-dimensional model of human oral mucosa with induced inflammation promoted MMP12 production and reduced CD200R surface expression by monocyte-derived cells. MMP12 production by monocyte-derived cells was induced by CSF2 rather than the cyclooxygenase-2 pathway, and treatment of monocyte-derived cells with a CD200R ligand reduced CSF2-induced MMP12 production. Further, MMP12-mediated degradation of the extracellular matrix proteins tropoelastin and fibronectin in the tissue model coincided with a loss of Ki-67, a protein strictly associated with cell proliferation. Reduced amounts of tropoelastin were confirmed in gingival tissue from PD patients. Thus, this novel association of the CD200/CD200R pathway with MMP12 production by monocyte-derived cells may play a key role in PD progression and will be important to take into consideration in the development of future strategies to diagnose, treat, and prevent PD.}, }
@article {pmid29099481, year = {2018}, author = {Strasser, A and Vaux, DL}, title = {Viewing BCL2 and cell death control from an evolutionary perspective.}, journal = {Cell death and differentiation}, volume = {25}, number = {1}, pages = {13-20}, doi = {10.1038/cdd.2017.145}, pmid = {29099481}, issn = {1476-5403}, mesh = {Animals ; *Apoptosis ; Biological Evolution ; Caenorhabditis elegans/genetics ; Humans ; Inflammation ; Neoplasms/drug therapy ; Proto-Oncogene Proteins c-bcl-2/genetics/*physiology ; Stress, Physiological ; }, abstract = {The last 30 years of studying BCL2 have brought cell death research into the molecular era, and revealed its relevance to human pathophysiology. Most, if not all metazoans use an evolutionarily conserved process for cellular self destruction that is controlled and implemented by proteins related to BCL2. We propose the anti-apoptotic BCL2-like and pro-apoptotic BH3-only members of the family arose through duplication and modification of genes for the pro-apoptotic multi-BH domain family members, such as BAX and BAK1. In that way, a cell suicide process that initially evolved as a mechanism for defense against intracellular parasites was then also used in multicellular organisms for morphogenesis and to maintain the correct number of cells in adults by balancing cell production by mitosis.}, }
@article {pmid29085064, year = {2017}, author = {Sipos, G and Prasanna, AN and Walter, MC and O'Connor, E and Bálint, B and Krizsán, K and Kiss, B and Hess, J and Varga, T and Slot, J and Riley, R and Bóka, B and Rigling, D and Barry, K and Lee, J and Mihaltcheva, S and LaButti, K and Lipzen, A and Waldron, R and Moloney, NM and Sperisen, C and Kredics, L and Vágvölgyi, C and Patrignani, A and Fitzpatrick, D and Nagy, I and Doyle, S and Anderson, JB and Grigoriev, IV and Güldener, U and Münsterkötter, M and Nagy, LG}, title = {Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {12}, pages = {1931-1941}, doi = {10.1038/s41559-017-0347-8}, pmid = {29085064}, issn = {2397-334X}, mesh = {Armillaria/*genetics ; Fungal Proteins/*genetics ; *Genome, Fungal ; Proteomics ; Sequence Analysis, RNA ; Species Specificity ; Transcriptome ; }, abstract = {Armillaria species are both devastating forest pathogens and some of the largest terrestrial organisms on Earth. They forage for hosts and achieve immense colony sizes via rhizomorphs, root-like multicellular structures of clonal dispersal. Here, we sequenced and analysed the genomes of four Armillaria species and performed RNA sequencing and quantitative proteomic analysis on the invasive and reproductive developmental stages of A. ostoyae. Comparison with 22 related fungi revealed a significant genome expansion in Armillaria, affecting several pathogenicity-related genes, lignocellulose-degrading enzymes and lineage-specific genes expressed during rhizomorph development. Rhizomorphs express an evolutionarily young transcriptome that shares features with the transcriptomes of both fruiting bodies and vegetative mycelia. Several genes show concomitant upregulation in rhizomorphs and fruiting bodies and share cis-regulatory signatures in their promoters, providing genetic and regulatory insights into complex multicellularity in fungi. Our results suggest that the evolution of the unique dispersal and pathogenicity mechanisms of Armillaria might have drawn upon ancestral genetic toolkits for wood-decay, morphogenesis and complex multicellularity.}, }
@article {pmid29070590, year = {2017}, author = {de Wiljes, OO and van Elburg, RAJ and Keijzer, FA}, title = {Modelling the effects of short and random proto-neural elongations.}, journal = {Journal of the Royal Society, Interface}, volume = {14}, number = {135}, pages = {}, doi = {10.1098/rsif.2017.0399}, pmid = {29070590}, issn = {1742-5662}, mesh = {Animals ; Axons/*physiology ; *Computer Simulation ; Dendrites/*physiology ; *Models, Biological ; }, abstract = {To understand how neurons and nervous systems first evolved, we need an account of the origins of neural elongations: why did neural elongations (axons and dendrites) first originate, such that they could become the central component of both neurons and nervous systems? Two contrasting conceptual accounts provide different answers to this question. Braitenberg's vehicles provide the iconic illustration of the dominant input-output (IO) view. Here, the basic role of neural elongations is to connect sensors to effectors, both situated at different positions within the body. For this function, neural elongations are thought of as comparatively long and specific connections, which require an articulated body involving substantial developmental processes to build. Internal coordination (IC) models stress a different function for early nervous systems. Here, the coordination of activity across extended parts of a multicellular body is held central, in particular, for the contractions of (muscle) tissue. An IC perspective allows the hypothesis that the earliest proto-neural elongations could have been functional even when they were initially simple, short and random connections, as long as they enhanced the patterning of contractile activity across a multicellular surface. The present computational study provides a proof of concept that such short and random neural elongations can play this role. While an excitable epithelium can generate basic forms of patterning for small body configurations, adding elongations allows such patterning to scale up to larger bodies. This result supports a new, more gradual evolutionary route towards the origins of the very first neurons and nervous systems.}, }
@article {pmid29069493, year = {2018}, author = {Gao, D and Chu, Y and Xia, H and Xu, C and Heyduk, K and Abernathy, B and Ozias-Akins, P and Leebens-Mack, JH and Jackson, SA}, title = {Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants.}, journal = {Molecular biology and evolution}, volume = {35}, number = {2}, pages = {354-364}, doi = {10.1093/molbev/msx275}, pmid = {29069493}, issn = {1537-1719}, abstract = {Even though lateral movements of transposons across families and even phyla within multicellular eukaryotic kingdoms have been found, little is known about transposon transfer between the kingdoms Animalia and Plantae. We discovered a novel non-LTR retrotransposon, AdLINE3, in a wild peanut species. Sequence comparisons and phylogenetic analyses indicated that AdLINE3 is a member of the RTE clade, originally identified in a nematode and rarely reported in plants. We identified RTE elements in 82 plants, spanning angiosperms to algae, including recently active elements in some flowering plants. RTE elements in flowering plants were likely derived from a single family we refer to as An-RTE. Interestingly, An-RTEs show significant DNA sequence identity with non-LTR retroelements from 42 animals belonging to four phyla. Moreover, the sequence identity of RTEs between two arthropods and two plants was higher than that of homologous genes. Phylogenetic and evolutionary analyses of RTEs from both animals and plants suggest that the An-RTE family was likely transferred horizontally into angiosperms from an ancient aphid(s) or ancestral arthropod(s). Notably, some An-RTEs were recruited as coding sequences of functional genes participating in metabolic or other biochemical processes in plants. This is the first potential example of horizontal transfer of transposons between animals and flowering plants. Our findings help to understand exchanges of genetic material between the kingdom Animalia and Plantae and suggest arthropods likely impacted on plant genome evolution.}, }
@article {pmid29065305, year = {2017}, author = {Brunet, T and King, N}, title = {The Origin of Animal Multicellularity and Cell Differentiation.}, journal = {Developmental cell}, volume = {43}, number = {2}, pages = {124-140}, doi = {10.1016/j.devcel.2017.09.016}, pmid = {29065305}, issn = {1878-1551}, support = {//Howard Hughes Medical Institute/United States ; R01 GM089977/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; *Cell Differentiation ; *Cell Lineage ; }, abstract = {Over 600 million years ago, animals evolved from a unicellular or colonial organism whose cell(s) captured bacteria with a collar complex, a flagellum surrounded by a microvillar collar. Using principles from evolutionary cell biology, we reason that the transition to multicellularity required modification of pre-existing mechanisms for extracellular matrix synthesis and cytokinesis. We discuss two hypotheses for the origin of animal cell types: division of labor from ancient plurifunctional cells and conversion of temporally alternating phenotypes into spatially juxtaposed cell types. Mechanistic studies in diverse animals and their relatives promise to deepen our understanding of animal origins and cell biology.}, }
@article {pmid29061899, year = {2017}, author = {Dukas, R}, title = {Cognitive innovations and the evolutionary biology of expertise.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1735}, pages = {}, doi = {10.1098/rstb.2016.0427}, pmid = {29061899}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; *Cognition ; *Learning ; Social Learning ; }, abstract = {Animal life can be perceived as the selective use of information for maximizing survival and reproduction. All organisms including bacteria and protists rely on genetic networks to build and modulate sophisticated structures and biochemical mechanisms for perceiving information and responding to environmental changes. Animals, however, have gone through a series of innovations that dramatically increased their capacity to acquire, retain and act upon information. Multicellularity was associated with the evolution of the nervous system, which took over many tasks of internal communication and coordination. This paved the way for the evolution of learning, initially based on individual experience and later also via social interactions. The increased importance of social learning also led to the evolution of language in a single lineage. Individuals' ability to dramatically increase performance via learning may have led to an evolutionary cycle of increased lifespan and greater investment in cognitive abilities, as well as in the time necessary for the development and refinement of expertise. We still know little, however, about the evolutionary biology, genetics and neurobiological mechanisms that underlie such expertise and its development.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.}, }
@article {pmid29061894, year = {2017}, author = {Aktipis, A and Maley, CC}, title = {Cooperation and cheating as innovation: insights from cellular societies.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1735}, pages = {}, doi = {10.1098/rstb.2016.0421}, pmid = {29061894}, issn = {1471-2970}, support = {P01 CA091955/CA/NCI NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; R01 CA185138/CA/NCI NIH HHS/United States ; }, mesh = {*Biological Evolution ; Cooperative Behavior ; *Eukaryota ; Microbial Interactions ; *Microbiota ; Models, Biological ; }, abstract = {The capacity to innovate is often considered a defining feature of human societies, but it is not a capacity that is unique to human societies: innovation occurs in cellular societies as well. Cellular societies such as multicellular bodies and microbial communities, including the human microbiome, are capable of innovation in response to novel opportunities and threats. Multicellularity represents a suite of innovations for cellular cooperation, but multicellularity also opened up novel opportunities for cells to cheat, exploiting the infrastructure and resources of the body. Multicellular bodies evolve less quickly than the cells within them, leaving them vulnerable to cellular innovations that can lead to cancer and infections. In order to counter these threats, multicellular bodies deploy additional innovations including the adaptive immune system and the development of partnerships with preferred microbial partners. What can we learn from examining these innovations in cooperation and cheating in cellular societies? First, innovation in social systems involves a constant tension between novel mechanisms that enable greater size and complexity of cooperative entities and novel ways of cheating. Second, cultivating cooperation with partners who can rapidly and effectively innovate (such as microbes) is important for large entities including multicellular bodies. And third, multicellularity enabled cells to manage risk socially, allowing organisms to survive in challenging environments where life would otherwise be impossible. Throughout, we ask how insights from cellular societies might be translated into new innovations in human health and medicine, promoting and protecting the cellular cooperation that makes us viable multicellular organisms.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.}, }
@article {pmid29061893, year = {2017}, author = {Ratcliff, WC and Herron, M and Conlin, PL and Libby, E}, title = {Nascent life cycles and the emergence of higher-level individuality.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1735}, pages = {}, doi = {10.1098/rstb.2016.0420}, pmid = {29061893}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Individuality ; *Life Cycle Stages ; *Life History Traits ; Models, Genetic ; Mutation ; }, abstract = {Evolutionary transitions in individuality (ETIs) occur when formerly autonomous organisms evolve to become parts of a new, 'higher-level' organism. One of the first major hurdles that must be overcome during an ETI is the emergence of Darwinian evolvability in the higher-level entity (e.g. a multicellular group), and the loss of Darwinian autonomy in the lower-level units (e.g. individual cells). Here, we examine how simple higher-level life cycles are a key innovation during an ETI, allowing this transfer of fitness to occur 'for free'. Specifically, we show how novel life cycles can arise and lead to the origin of higher-level individuals by (i) mitigating conflicts between levels of selection, (ii) engendering the expression of heritable higher-level traits and (iii) allowing selection to efficiently act on these emergent higher-level traits. Further, we compute how canonical early life cycles vary in their ability to fix beneficial mutations via mathematical modelling. Life cycles that lack a persistent lower-level stage and develop clonally are far more likely to fix 'ratcheting' mutations that limit evolutionary reversion to the pre-ETI state. By stabilizing the fragile first steps of an evolutionary transition in individuality, nascent higher-level life cycles may play a crucial role in the origin of complex life.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.}, }
@article {pmid29050666, year = {2017}, author = {Fortier, LC}, title = {The Contribution of Bacteriophages to the Biology and Virulence of Pathogenic Clostridia.}, journal = {Advances in applied microbiology}, volume = {101}, number = {}, pages = {169-200}, doi = {10.1016/bs.aambs.2017.05.002}, pmid = {29050666}, issn = {0065-2164}, mesh = {Bacteriophages/*physiology ; Clostridium difficile/pathogenicity/physiology/*virology ; Humans ; Prophages ; Virulence ; }, abstract = {Bacteriophages are key players in the evolution of most bacteria. Temperate phages have been associated with virulence of some of the deadliest pathogenic bacteria. Among the most notorious cases, the genes encoding the botulinum neurotoxin produced by Clostridium botulinum types C and D and the α-toxin (TcnA) produced by Clostridium novyi are both encoded within prophage genomes. Clostridium difficile is another important human pathogen and the recent identification of a complete binary toxin locus (CdtLoc) carried on a C. difficile prophage raises the potential for horizontal transfer of toxin genes by mobile genetic elements. Although the TcdA and TcdB toxins produced by C. difficile have never been found outside the pathogenicity locus (PaLoc), some prophages can still influence their production. Prophages can alter the expression of several metabolic and regulatory genes in C. difficile, as well as cell surface proteins such as CwpV, which confers phage resistance. Homologs of an Agr-like quorum sensing system have been identified in a C. difficile prophage, suggesting that it could possibly participate in cell-cell communication. Yet, other C. difficile prophages contain riboswitches predicted to recognize the secondary messenger molecule c-di-GMP involved in bacterial multicellular behaviors. Altogether, recent findings on clostridial phages underline the diversity of mechanisms and intricate relationship linking phages with their host. Here, milestone discoveries linking phages and virulence of some of the most pathogenic clostridial species will be retraced, with a focus on C. botulinum, C. novyi, C. difficile, and Clostridium perfringens phages, for which evidences are mostly available.}, }
@article {pmid29046735, year = {2017}, author = {Luebeck, EG and Curtius, K and Hazelton, WD and Maden, S and Yu, M and Thota, PN and Patil, DT and Chak, A and Willis, JE and Grady, WM}, title = {Identification of a key role of widespread epigenetic drift in Barrett's esophagus and esophageal adenocarcinoma.}, journal = {Clinical epigenetics}, volume = {9}, number = {}, pages = {113}, doi = {10.1186/s13148-017-0409-4}, pmid = {29046735}, issn = {1868-7083}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; P50 CA150964/CA/NCI NIH HHS/United States ; U01 CA086402/CA/NCI NIH HHS/United States ; U01 CA182940/CA/NCI NIH HHS/United States ; P30 CA043703/CA/NCI NIH HHS/United States ; U01 CA152756/CA/NCI NIH HHS/United States ; U54 CA163060/CA/NCI NIH HHS/United States ; }, mesh = {Adenocarcinoma/*genetics ; Aged ; Barrett Esophagus/*genetics ; CpG Islands ; *DNA Methylation ; Databases, Genetic ; Disease Progression ; Epigenesis, Genetic ; Esophageal Neoplasms/*genetics ; Female ; Gene Expression Regulation, Neoplastic ; *Genetic Drift ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; Models, Genetic ; }, abstract = {BACKGROUND: Recent studies have identified age-related changes in DNA methylation patterns in normal and cancer tissues in a process that is called epigenetic drift. However, the evolving patterns, functional consequences, and dynamics of epigenetic drift during carcinogenesis remain largely unexplored. Here we analyze the evolution of epigenetic drift patterns during progression from normal squamous esophagus tissue to Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) using 173 tissue samples from 100 (nonfamilial) BE patients, along with publically available datasets including The Cancer Genome Atlas (TCGA).<br><br>RESULTS: Our analysis reveals extensive methylomic drift between normal squamous esophagus and BE tissues in nonprogressed BE patients, with differential drift affecting 4024 (24%) of 16,984 normally hypomethylated cytosine-guanine dinucleotides (CpGs) occurring in CpG islands. The majority (63%) of islands that include drift CpGs are associated with gene promoter regions. Island CpGs that drift have stronger pairwise correlations than static islands, reflecting collective drift consistent with processive DNA methylation maintenance. Individual BE tissues are extremely heterogeneous in their distribution of methylomic drift and encompass unimodal low-drift to bimodal high-drift patterns, reflective of differences in BE tissue age. Further analysis of longitudinally collected biopsy samples from 20 BE patients confirm the time-dependent evolution of these drift patterns. Drift patterns in EAC are similar to those in BE, but frequently exhibit enhanced bimodality and advanced mode drift. To better understand the observed drift patterns, we developed a multicellular stochastic model at the CpG island level. Importantly, we find that nonlinear feedback in the model between mean island methylation and CpG methylation rates is able to explain the widely heterogeneous collective drift patterns. Using matched gene expression and DNA methylation data in EAC from TCGA and other publically available data, we also find that advanced methylomic drift is correlated with significant transcriptional repression of ~ 200 genes in important regulatory and developmental pathways, including several checkpoint and tumor suppressor-like genes.<br><br>CONCLUSIONS: Taken together, our findings suggest that epigenetic drift evolution acts to significantly reduce the expression of developmental genes that may alter tissue characteristics and improve functional adaptation during BE to EAC progression.}, }
@article {pmid29021161, year = {2017}, author = {Jackson, MDB and Duran-Nebreda, S and Bassel, GW}, title = {Network-based approaches to quantify multicellular development.}, journal = {Journal of the Royal Society, Interface}, volume = {14}, number = {135}, pages = {}, doi = {10.1098/rsif.2017.0484}, pmid = {29021161}, issn = {1742-5662}, mesh = {Animals ; Humans ; *Models, Biological ; }, abstract = {Multicellularity and cellular cooperation confer novel functions on organs following a structure-function relationship. How regulated cell migration, division and differentiation events generate cellular arrangements has been investigated, providing insight into the regulation of genetically encoded patterning processes. Much less is known about the higher-order properties of cellular organization within organs, and how their functional coordination through global spatial relations shape and constrain organ function. Key questions to be addressed include: why are cells organized in the way they are? What is the significance of the patterns of cellular organization selected for by evolution? What other configurations are possible? These may be addressed through a combination of global cellular interaction mapping and network science to uncover the relationship between organ structure and function. Using this approach, global cellular organization can be discretized and analysed, providing a quantitative framework to explore developmental processes. Each of the local and global properties of integrated multicellular systems can be analysed and compared across different tissues and models in discrete terms. Advances in high-resolution microscopy and image analysis continue to make cellular interaction mapping possible in an increasing variety of biological systems and tissues, broadening the further potential application of this approach. Understanding the higher-order properties of complex cellular assemblies provides the opportunity to explore the evolution and constraints of cell organization, establishing structure-function relationships that can guide future organ design.}, }
@article {pmid28988859, year = {2017}, author = {Vermeij, GJ}, title = {How the Land Became the Locus of Major Evolutionary Innovations.}, journal = {Current biology : CB}, volume = {27}, number = {20}, pages = {3178-3182.e1}, doi = {10.1016/j.cub.2017.08.076}, pmid = {28988859}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; *Embryophyta/anatomy &amp; histology/physiology ; *Environment ; *Invertebrates/anatomy &amp; histology/physiology ; *Vertebrates/anatomy &amp; histology/physiology ; }, abstract = {Life originated in the sea and evolved its early metabolic pathways in water [1, 2]. Nevertheless, activities of organisms on land have influenced and enriched marine ecosystems with oxygen and nutrients for billions of years [3-7]. In contrast to the history of species diversity in the sea and on land [8-10] and the flows of resources within and between these two realms [11], little is known about the times and places of origin of major metabolic and ecological innovations during the Phanerozoic. Many innovations among multicellular organisms originated in the sea during or before the Cambrian, including predation and most of its variations, biomineralization, colonial or clonal growth, bioerosion, deposit feeding, bioturbation by animals, communication at a distance by vision and olfaction, photosymbiosis, chemosymbiosis, suspension feeding, osmotrophy, internal fertilization, jet propulsion, undulatory locomotion, and appendages for movement. Activity is less constrained in air than in the denser, more viscous medium of water [9, 12-14]. I therefore predict that high-performance metabolic and ecological innovations should predominantly originate on land after the Ordovician once organisms had conquered the challenges of life away from water and later appeared in the sea, either in marine-colonizing clades or by arising separately in clades that never left the sea. In support of this hypothesis, I show that 11 of 13 major post-Ordovician innovations appeared first or only on land. This terrestrial locus of innovation cannot be explained by the Cretaceous to recent expansion of diversity on land. It reveals one of several irreversible shifts in the history of life.}, }
@article {pmid28985561, year = {2017}, author = {Bowman, JL and Kohchi, T and Yamato, KT and Jenkins, J and Shu, S and Ishizaki, K and Yamaoka, S and Nishihama, R and Nakamura, Y and Berger, F and Adam, C and Aki, SS and Althoff, F and Araki, T and Arteaga-Vazquez, MA and Balasubrmanian, S and Barry, K and Bauer, D and Boehm, CR and Briginshaw, L and Caballero-Perez, J and Catarino, B and Chen, F and Chiyoda, S and Chovatia, M and Davies, KM and Delmans, M and Demura, T and Dierschke, T and Dolan, L and Dorantes-Acosta, AE and Eklund, DM and Florent, SN and Flores-Sandoval, E and Fujiyama, A and Fukuzawa, H and Galik, B and Grimanelli, D and Grimwood, J and Grossniklaus, U and Hamada, T and Haseloff, J and Hetherington, AJ and Higo, A and Hirakawa, Y and Hundley, HN and Ikeda, Y and Inoue, K and Inoue, SI and Ishida, S and Jia, Q and Kakita, M and Kanazawa, T and Kawai, Y and Kawashima, T and Kennedy, M and Kinose, K and Kinoshita, T and Kohara, Y and Koide, E and Komatsu, K and Kopischke, S and Kubo, M and Kyozuka, J and Lagercrantz, U and Lin, SS and Lindquist, E and Lipzen, AM and Lu, CW and De Luna, E and Martienssen, RA and Minamino, N and Mizutani, M and Mizutani, M and Mochizuki, N and Monte, I and Mosher, R and Nagasaki, H and Nakagami, H and Naramoto, S and Nishitani, K and Ohtani, M and Okamoto, T and Okumura, M and Phillips, J and Pollak, B and Reinders, A and Rövekamp, M and Sano, R and Sawa, S and Schmid, MW and Shirakawa, M and Solano, R and Spunde, A and Suetsugu, N and Sugano, S and Sugiyama, A and Sun, R and Suzuki, Y and Takenaka, M and Takezawa, D and Tomogane, H and Tsuzuki, M and Ueda, T and Umeda, M and Ward, JM and Watanabe, Y and Yazaki, K and Yokoyama, R and Yoshitake, Y and Yotsui, I and Zachgo, S and Schmutz, J}, title = {Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.}, journal = {Cell}, volume = {171}, number = {2}, pages = {287-304.e15}, doi = {10.1016/j.cell.2017.09.030}, pmid = {28985561}, issn = {1097-4172}, mesh = {Adaptation, Biological ; *Biological Evolution ; Embryophyta/*genetics/physiology ; Gene Expression Regulation, Plant ; *Genome, Plant ; Marchantia/*genetics/physiology ; Molecular Sequence Annotation ; Signal Transduction ; Transcription, Genetic ; }, abstract = {The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.}, }
@article {pmid28973893, year = {2017}, author = {van Gestel, J and Tarnita, CE}, title = {On the origin of biological construction, with a focus on multicellularity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {42}, pages = {11018-11026}, doi = {10.1073/pnas.1704631114}, pmid = {28973893}, issn = {1091-6490}, mesh = {*Biological Evolution ; Life Cycle Stages ; *Morphogenesis ; Selection, Genetic ; }, abstract = {Biology is marked by a hierarchical organization: all life consists of cells; in some cases, these cells assemble into groups, such as endosymbionts or multicellular organisms; in turn, multicellular organisms sometimes assemble into yet other groups, such as primate societies or ant colonies. The construction of new organizational layers results from hierarchical evolutionary transitions, in which biological units (e.g., cells) form groups that evolve into new units of biological organization (e.g., multicellular organisms). Despite considerable advances, there is no bottom-up, dynamical account of how, starting from the solitary ancestor, the first groups originate and subsequently evolve the organizing principles that qualify them as new units. Guided by six central questions, we propose an integrative bottom-up approach for studying the dynamics underlying hierarchical evolutionary transitions, which builds on and synthesizes existing knowledge. This approach highlights the crucial role of the ecology and development of the solitary ancestor in the emergence and subsequent evolution of groups, and it stresses the paramount importance of the life cycle: only by evaluating groups in the context of their life cycle can we unravel the evolutionary trajectory of hierarchical transitions. These insights also provide a starting point for understanding the types of subsequent organizational complexity. The central research questions outlined here naturally link existing research programs on biological construction (e.g., on cooperation, multilevel selection, self-organization, and development) and thereby help integrate knowledge stemming from diverse fields of biology.}, }
@article {pmid28968519, year = {2017}, author = {Crocker, J and Ilsley, GR}, title = {Using synthetic biology to study gene regulatory evolution.}, journal = {Current opinion in genetics &amp; development}, volume = {47}, number = {}, pages = {91-101}, doi = {10.1016/j.gde.2017.09.001}, pmid = {28968519}, issn = {1879-0380}, mesh = {Binding Sites ; Drosophila Proteins/genetics ; *Enhancer Elements, Genetic ; *Evolution, Molecular ; Gene Expression Regulation/genetics ; Gene Regulatory Networks/*genetics ; Protein Binding ; *Synthetic Biology ; Transcription, Genetic ; }, abstract = {Transcriptional enhancers specify the precise time, level, and location of gene expression. Disentangling and characterizing the components of enhancer activity in multicellular eukaryotic development has proven challenging because enhancers contain activator and repressor binding sites for multiple factors that each exert nuanced, context-dependent control of enhancer activity. Recent advances in synthetic biology provide an almost unlimited ability to create and modify regulatory elements and networks, offering unprecedented power to study gene regulation. Here we review several studies demonstrating the utility of synthetic biology for studying enhancer function during development and evolution. These studies clearly show that synthetic biology can provide a way to reverse-engineer and reengineer transcriptional regulation in animal genomes with enormous potential for understanding evolution.}, }
@article {pmid28961459, year = {2018}, author = {Deb, J and Bland, HM and Østergaard, L}, title = {Developmental cartography: coordination via hormonal and genetic interactions during gynoecium formation.}, journal = {Current opinion in plant biology}, volume = {41}, number = {}, pages = {54-60}, doi = {10.1016/j.pbi.2017.09.004}, pmid = {28961459}, issn = {1879-0356}, support = {BBS/E/J/00000613//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Development in multicellular organisms requires the establishment of tissue identity through polarity cues. The Arabidopsis gynoecium presents an excellent model to study this coordination, as it comprises a complex tissue structure which is established through multiple polarity systems. The gynoecium is derived from the fusion of two carpels and forms in the centre of the flower. Many regulators of carpel development also have roles in leaf development, emphasizing the evolutionary origin of carpels as modified leaves. The gynoecium can therefore be considered as having evolved from a simple setup followed by adjustment in tissue polarity to facilitate efficient reproduction. Here, we discuss concepts to understand how hormonal and genetic systems interact to pattern the gynoecium.}, }
@article {pmid28959054, year = {2017}, author = {Attwood, MM and Krishnan, A and Almén, MS and Schiöth, HB}, title = {Highly diversified expansions shaped the evolution of membrane bound proteins in metazoans.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {12387}, doi = {10.1038/s41598-017-11543-z}, pmid = {28959054}, issn = {2045-2322}, abstract = {The dramatic increase in membrane proteome complexity is arguably one of the most pivotal evolutionary events that underpins the origin of multicellular animals. However, the origin of a significant number of membrane families involved in metazoan development has not been clarified. In this study, we have manually curated the membrane proteomes of 22 metazoan and 2 unicellular holozoan species. We identify 123,014 membrane proteins in these 24 eukaryotic species and classify 86% of the dataset. We determine 604 functional clusters that are present from the last holozoan common ancestor (LHCA) through many metazoan species. Intriguingly, we show that more than 70% of the metazoan membrane protein families have a premetazoan origin. The data show that enzymes are more highly represented in the LHCA and expand less than threefold throughout metazoan species; in contrast to receptors that are relatively few in the LHCA but expand nearly eight fold within metazoans. Expansions related to cell adhesion, communication, immune defence, and developmental processes are shown in conjunction with emerging biological systems, such as neuronal development, cytoskeleton organization, and the adaptive immune response. This study defines the possible LHCA membrane proteome and describes the fundamental functional clusters that underlie metazoan diversity and innovation.}, }
@article {pmid28943404, year = {2017}, author = {Rubin, IN and Doebeli, M}, title = {Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.}, journal = {Journal of theoretical biology}, volume = {435}, number = {}, pages = {248-264}, doi = {10.1016/j.jtbi.2017.09.020}, pmid = {28943404}, issn = {1095-8541}, mesh = {Biological Evolution ; Biological Variation, Population ; *Cultural Evolution ; Environment ; *Models, Theoretical ; Mutation ; *Phenotype ; Specialization/economics/*trends ; }, abstract = {Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, &quot;bet-hedging&quot; in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into the evolutionary dynamics, effectively guaranteeing eventual branching. Large mutations allow the second order disruptive selection to dominate the first order selection toward phenotypic heterogeneity.}, }
@article {pmid28938124, year = {2017}, author = {Hinshaw, SM and Makrantoni, V and Harrison, SC and Marston, AL}, title = {The Kinetochore Receptor for the Cohesin Loading Complex.}, journal = {Cell}, volume = {171}, number = {1}, pages = {72-84.e13}, doi = {10.1016/j.cell.2017.08.017}, pmid = {28938124}, issn = {1097-4172}, support = {107827//Wellcome Trust/United Kingdom ; }, mesh = {Cell Cycle Proteins/*metabolism ; Centromere/metabolism ; Chromosomal Proteins, Non-Histone/*metabolism ; Cytoskeletal Proteins/metabolism ; Kinetochores/*metabolism ; Multiprotein Complexes/metabolism ; Phosphorylation ; Phylogeny ; Saccharomyces cerevisiae/cytology/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; X-Ray Diffraction ; }, abstract = {The ring-shaped cohesin complex brings together distant DNA domains to maintain, express, and segregate the genome. Establishing specific chromosomal linkages depends on cohesin recruitment to defined loci. One such locus is the budding yeast centromere, which is a paradigm for targeted cohesin loading. The kinetochore, a multiprotein complex that connects centromeres to microtubules, drives the recruitment of high levels of cohesin to link sister chromatids together. We have exploited this system to determine the mechanism of specific cohesin recruitment. We show that phosphorylation of the Ctf19 kinetochore protein by a conserved kinase, DDK, provides a binding site for the Scc2/4 cohesin loading complex, thereby directing cohesin loading to centromeres. A similar mechanism targets cohesin to chromosomes in vertebrates. These findings represent a complete molecular description of targeted cohesin loading, a phenomenon with wide-ranging importance in chromosome segregation and, in multicellular organisms, transcription regulation.}, }
@article {pmid28936730, year = {2017}, author = {Conigliaro, A and Fontana, S and Raimondo, S and Alessandro, R}, title = {Exosomes: Nanocarriers of Biological Messages.}, journal = {Advances in experimental medicine and biology}, volume = {998}, number = {}, pages = {23-43}, doi = {10.1007/978-981-10-4397-0_2}, pmid = {28936730}, issn = {0065-2598}, mesh = {Animals ; Exosomes/genetics/*metabolism/ultrastructure ; Humans ; Intracellular Signaling Peptides and Proteins/*metabolism ; *Lipid Metabolism ; *Nanoparticles ; Nucleic Acids/*metabolism ; Organelle Size ; Protein Transport ; *Signal Transduction ; }, abstract = {Cell-cell communication is crucial to maintain homeostasis in multicellular organism. Cells communicate each other by direct contact or by releasing factors that, soluble or packaged in membrane vesicles, can reach different regions of the organism. To date numerous studies highlighted the existence of several types of extracellular vesicles that, differing for dimension, origin and contents, play a role in physiological and/or pathological processes. Among extracellular vesicles, exosomes are emerging as efficient players to modulate target cells phenotype and as new non-invasive diagnostic and prognostic tools in multiple diseases. They, in fact, strictly reflect the type and functional status of the producing cells and are able to deliver their contents even over a long distance. The results accumulated in the last two decades and collected in this chapter, indicated that exosomes, can carry RNAs, microRNAs, long non-coding RNAs, DNA, lipids, metabolites and proteins; a deeper understanding of their contents is therefore needed to get the most from this incredible cell product.}, }
@article {pmid28923586, year = {2017}, author = {Dennis, JW}, title = {Genetic code asymmetry supports diversity through experimentation with posttranslational modifications.}, journal = {Current opinion in chemical biology}, volume = {41}, number = {}, pages = {1-11}, doi = {10.1016/j.cbpa.2017.08.012}, pmid = {28923586}, issn = {1879-0402}, mesh = {Animals ; Evolution, Molecular ; *Genetic Code ; Humans ; Protein Processing, Post-Translational/*genetics ; Proteins/*genetics/*metabolism ; Selection, Genetic ; }, abstract = {Protein N-glycosylation has been identified in all three domains of life presumably conserved for its early role in glycoprotein folding. However, the N-glycans added to proteins in the secretory pathway of multicellular organisms are remodeling in the Golgi, increasing structural diversity exponentially and adding new layers of functionality in immunity, metabolism and other systems. The branching and elongation of N-glycan chains found on cell surface receptors generates a gradation of affinities for carbohydrate-binding proteins, the galectin, selectin and siglec families. These interactions adapt cellular responsiveness to environmental conditions, but their complexity presents a daunting challenge to drug design. To gain further insight, I review how N-glycans biosynthesis and biophysical properties provide a selective advantage in the form of tunable and ultrasensitive stimulus-response relationships. In addition, the N-glycosylation motif favors step-wise mutational experimentation with sites. Glycoproteins display accelerated evolution during vertebrate radiation, and the encoding asymmetry of NXS/T(X≠P) has left behind phylogenetic evidence suggesting that the genetic code may have been selected to optimize diversity in part through emerging posttranslational modifications.}, }
@article {pmid28916791, year = {2017}, author = {Yamazaki, T and Ichihara, K and Suzuki, R and Oshima, K and Miyamura, S and Kuwano, K and Toyoda, A and Suzuki, Y and Sugano, S and Hattori, M and Kawano, S}, title = {Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11679}, doi = {10.1038/s41598-017-11677-0}, pmid = {28916791}, issn = {2045-2322}, abstract = {The evolution of sex chromosomes and mating loci in organisms with UV systems of sex/mating type determination in haploid phases via genes on UV chromosomes is not well understood. We report the structure of the mating type (MT) locus and its evolutionary history in the green seaweed Ulva partita, which is a multicellular organism with an isomorphic haploid-diploid life cycle and mating type determination in the haploid phase. Comprehensive comparison of a total of 12.0 and 16.6 Gb of genomic next-generation sequencing data for mt- and mt+ strains identified highly rearranged MT loci of 1.0 and 1.5 Mb in size and containing 46 and 67 genes, respectively, including 23 gametologs. Molecular evolutionary analyses suggested that the MT loci diverged over a prolonged period in the individual mating types after their establishment in an ancestor. A gene encoding an RWP-RK domain-containing protein was found in the mt- MT locus but was not an ortholog of the chlorophycean mating type determination gene MID. Taken together, our results suggest that the genomic structure and its evolutionary history in the U. partita MT locus are similar to those on other UV chromosomes and that the MT locus genes are quite different from those of Chlorophyceae.}, }
@article {pmid28916376, year = {2017}, author = {Peng, L and Wang, L and Yang, YF and Zou, MM and He, WY and Wang, Y and Wang, Q and Vasseur, L and You, MS}, title = {Transcriptome profiling of the Plutella xylostella (Lepidoptera: Plutellidae) ovary reveals genes involved in oogenesis.}, journal = {Gene}, volume = {637}, number = {}, pages = {90-99}, doi = {10.1016/j.gene.2017.09.020}, pmid = {28916376}, issn = {1879-0038}, mesh = {Animals ; Female ; Gene Expression Profiling/*methods ; Gene Regulatory Networks ; Insect Proteins/*genetics/metabolism ; Insecticide Resistance/*genetics ; Moths/*genetics/growth &amp; development/metabolism ; *Oogenesis ; Ovary/growth &amp; development/*metabolism ; Phylogeny ; Reproduction ; *Transcriptome ; }, abstract = {BACKGROUND: As a specialized organ, the insect ovary performs valuable functions by ensuring fecundity and population survival. Oogenesis is the complex physiological process resulting in the production of mature eggs, which are involved in epigenetic programming, germ cell behavior, cell cycle regulation, etc. Identification of the genes involved in ovary development and oogenesis is critical to better understand the reproductive biology and screening for the potential molecular targets in Plutella xylostella, a worldwide destructive pest of economically major crops.<br><br>RESULTS: Based on transcriptome sequencing, a total of 7.88Gb clean nucleotides was obtained, with 19,934 genes and 1861 new transcripts being identified. Expression profiling indicated that 61.7% of the genes were expressed (FPKM≥1) in the P. xylostella ovary. GO annotation showed that the pathways of multicellular organism reproduction and multicellular organism reproduction process, as well as gamete generation and chorion were significantly enriched. Processes that were most likely relevant to reproduction included the spliceosome, ubiquitin mediated proteolysis, endocytosis, PI3K-Akt signaling pathway, insulin signaling pathway, cAMP signaling pathway, and focal adhesion were identified in the top 20 'highly represented' KEGG pathways. Functional genes involved in oogenesis were further analyzed and validated by qRT-PCR to show their potential predominant roles in P. xylostella reproduction.<br><br>CONCLUSIONS: Our newly developed P. xylostella ovary transcriptome provides an overview of the gene expression profiling in this specialized tissue and the functional gene network closely related to the ovary development and oogenesis. This is the first genome-wide transcriptome dataset of P. xylostella ovary that includes a subset of functionally activated genes. This global approach will be the basis for further studies on molecular mechanisms of P. xylostella reproduction aimed at screening potential molecular targets for integrated pest management.}, }
@article {pmid28904210, year = {2017}, author = {Willy, NM and Ferguson, JP and Huber, SD and Heidotting, SP and Aygün, E and Wurm, SA and Johnston-Halperin, E and Poirier, MG and Kural, C}, title = {Membrane mechanics govern spatiotemporal heterogeneity of endocytic clathrin coat dynamics.}, journal = {Molecular biology of the cell}, volume = {28}, number = {24}, pages = {3480-3488}, doi = {10.1091/mbc.E17-05-0282}, pmid = {28904210}, issn = {1939-4586}, support = {R01 AI121124/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biomechanical Phenomena ; Cell Line, Tumor ; Cell Membrane/metabolism/physiology ; Cells, Cultured ; Cercopithecus aethiops ; Clathrin/metabolism ; Clathrin-Coated Vesicles/metabolism/*physiology ; Coated Pits, Cell-Membrane/metabolism/physiology ; Cytoplasm/metabolism ; Drosophila ; Endocytosis/physiology ; Humans ; Spatio-Temporal Analysis ; }, abstract = {Dynamics of endocytic clathrin-coated structures can be remarkably divergent across different cell types, cells within the same culture, or even distinct surfaces of the same cell. The origin of this astounding heterogeneity remains to be elucidated. Here we show that cellular processes associated with changes in effective plasma membrane tension induce significant spatiotemporal alterations in endocytic clathrin coat dynamics. Spatiotemporal heterogeneity of clathrin coat dynamics is also observed during morphological changes taking place within developing multicellular organisms. These findings suggest that tension gradients can lead to patterning and differentiation of tissues through mechanoregulation of clathrin-mediated endocytosis.}, }
@article {pmid28899581, year = {2017}, author = {Kennedy, P and Baron, G and Qiu, B and Freitak, D and Helanterä, H and Hunt, ER and Manfredini, F and O'Shea-Wheller, T and Patalano, S and Pull, CD and Sasaki, T and Taylor, D and Wyatt, CDR and Sumner, S}, title = {Deconstructing Superorganisms and Societies to Address Big Questions in Biology.}, journal = {Trends in ecology &amp; evolution}, volume = {32}, number = {11}, pages = {861-872}, doi = {10.1016/j.tree.2017.08.004}, pmid = {28899581}, issn = {1872-8383}, mesh = {Animals ; *Behavior, Animal ; Biological Evolution ; Hymenoptera/*physiology ; Isoptera/*physiology ; *Social Behavior ; }, abstract = {Social insect societies are long-standing models for understanding social behaviour and evolution. Unlike other advanced biological societies (such as the multicellular body), the component parts of social insect societies can be easily deconstructed and manipulated. Recent methodological and theoretical innovations have exploited this trait to address an expanded range of biological questions. We illustrate the broadening range of biological insight coming from social insect biology with four examples. These new frontiers promote open-minded, interdisciplinary exploration of one of the richest and most complex of biological phenomena: sociality.}, }
@article {pmid28898926, year = {2018}, author = {Mosaffa, P and Rodríguez-Ferran, A and Muñoz, JJ}, title = {Hybrid cell-centred/vertex model for multicellular systems with equilibrium-preserving remodelling.}, journal = {International journal for numerical methods in biomedical engineering}, volume = {34}, number = {3}, pages = {}, doi = {10.1002/cnm.2928}, pmid = {28898926}, issn = {2040-7947}, abstract = {We present a hybrid cell-centred/vertex model for mechanically simulating planar cellular monolayers undergoing cell reorganisation. Cell centres are represented by a triangular nodal network, while the cell boundaries are formed by an associated vertex network. The two networks are coupled through a kinematic constraint which we allow to relax progressively. Special attention is paid to the change of cell-cell connectivity due to cell reorganisation or remodelling events. We handle these situations by using a variable resting length and applying an Equilibrium-Preserving Mapping on the new connectivity, which computes a new set of resting lengths that preserve nodal and vertex equilibrium. We illustrate the properties of the model by simulating monolayers subjected to imposed extension and during a wound healing process. The evolution of forces and the Equilibrium-Preserving Mapping are analysed during the remodelling events. As a by-product, the proposed technique enables to recover fully vertex or fully cell-centred models in a seamless manner by modifying a numerical parameter of the model.}, }
@article {pmid28898640, year = {2017}, author = {Ferrer-Bonet, M and Ruiz-Trillo, I}, title = {Capsaspora owczarzaki.}, journal = {Current biology : CB}, volume = {27}, number = {17}, pages = {R829-R830}, doi = {10.1016/j.cub.2017.05.074}, pmid = {28898640}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*classification/*cytology/genetics ; Genome ; Phylogeny ; }, abstract = {Capsaspora owczarzaki is a unicellular eukaryote that is becoming pivotal to understanding the origin of animal multicellularity.}, }
@article {pmid28893859, year = {2017}, author = {Rübsam, M and Broussard, JA and Wickström, SA and Nekrasova, O and Green, KJ and Niessen, CM}, title = {Adherens Junctions and Desmosomes Coordinate Mechanics and Signaling to Orchestrate Tissue Morphogenesis and Function: An Evolutionary Perspective.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/cshperspect.a029207}, pmid = {28893859}, issn = {1943-0264}, support = {P30 AR057216/AR/NIAMS NIH HHS/United States ; R01 AR043380/AR/NIAMS NIH HHS/United States ; T32 AR007593/AR/NIAMS NIH HHS/United States ; R01 CA122151/CA/NCI NIH HHS/United States ; R01 AR041836/AR/NIAMS NIH HHS/United States ; }, abstract = {Cadherin-based adherens junctions (AJs) and desmosomes are crucial to couple intercellular adhesion to the actin or intermediate filament cytoskeletons, respectively. As such, these intercellular junctions are essential to provide not only integrity to epithelia and other tissues but also the mechanical machinery necessary to execute complex morphogenetic and homeostatic intercellular rearrangements. Moreover, these spatially defined junctions serve as signaling hubs that integrate mechanical and chemical pathways to coordinate tissue architecture with behavior. This review takes an evolutionary perspective on how the emergence of these two essential intercellular junctions at key points during the evolution of multicellular animals afforded metazoans with new opportunities to integrate adhesion, cytoskeletal dynamics, and signaling. We discuss known literature on cross-talk between the two junctions and, using the skin epidermis as an example, provide a model for how these two junctions function in concert to orchestrate tissue organization and function.}, }
@article {pmid28889015, year = {2017}, author = {He, HH and Chi, YM and Yuan, K and Li, XY and Weng, SP and He, JG and Chen, YH}, title = {Functional characterization of a reactive oxygen species modulator 1 gene in Litopenaeus vannamei.}, journal = {Fish &amp; shellfish immunology}, volume = {70}, number = {}, pages = {270-279}, doi = {10.1016/j.fsi.2017.09.024}, pmid = {28889015}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/*genetics/*immunology ; Base Sequence ; Cell Line ; Drosophila melanogaster ; Gene Expression Regulation ; *Immunity, Innate ; Penaeidae/*genetics/*immunology ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Sequence Alignment ; Vibrio alginolyticus/physiology ; White spot syndrome virus 1/physiology ; }, abstract = {Reactive oxygen species (ROS) imparts a dual effect on multicellular organisms, wherein high levels are usually harmful, and low levels could facilitate in combating pathogenic microorganisms; therefore, the regulation of ROS production is critical. Previous studies have suggested that ROS contributes to resistance to the white spot syndrome virus (WSSV) or Vibrio alginolyticus in Litopenaeus vannamei. However, the regulation of ROS metabolism in L. vannamei remains elusive. In the present study, we proved that the overexpression of L. vannamei reactive oxygen species modulator 1 (LvROMO1) increases ROS production in Drosophila Schneider 2 (S2) cells. Real-time RT-PCR analysis indicated that LvROMO1 is induced by WSSV or V. alginolyticus infection and β-glucan or microcystin (MC-LR) injection. Further investigation showed that LvROMO1 responding to MC-LR, thereby inducing hemocytes to undergo apoptosis, and ultimately resulting in hepatopancreatic damage. And LvROMO1 downregulation induced an increase in the cumulative mortality of WSSV-infected shrimp by reducing ROS production and suppressing the expression of antimicrobial peptides genes. The findings of present study suggest that LvROMO1 plays an important role in ROS production in L. vannamei and is involved in innate immunity.}, }
@article {pmid28866006, year = {2017}, author = {Witting, L}, title = {The natural selection of metabolism and mass selects allometric transitions from prokaryotes to mammals.}, journal = {Theoretical population biology}, volume = {117}, number = {}, pages = {23-42}, doi = {10.1016/j.tpb.2017.08.005}, pmid = {28866006}, issn = {1096-0325}, mesh = {Animals ; Basal Metabolism ; Biological Evolution ; Body Size ; Ecology ; Mammals/*metabolism ; Models, Biological ; Prokaryotic Cells/*metabolism ; Selection, Genetic/*physiology ; }, abstract = {The exponents of inter-specific allometries for several life history (metabolism, lifespan, reproductive rate, survival) and ecological (population density, home range) traits may evolve from the spatial dimensionality (d) of the intra-specific interactive competition that selects net assimilated energy into mass, with 1∕4 exponents being the two-dimensional (2D) case of the more general 1∕2d (Witting, 1995). While the exponents for mass-specific metabolism cluster around the predicted -1/4 and -1/6 in terrestrial and pelagic vertebrates, the allometries of mobile organisms are more diverse than the prediction. An exponent around zero has been reported for protists and protozoa (Makarieva et al., 2005, 2008), and the exponent appears to be strongly positive in prokaryotes with a value of about 5/6 (DeLong et al., 2010). I show that the natural selection of metabolism and mass is sufficient to explain exponents for mass-specific metabolism that decline from 5/6 over zero to -1∕6 in 3D, and from 3/4 over zero to -1∕4 in 2D. These results suggest that mass-specific metabolism is selected as the pace of the resource handling that generates net energy for self-replication and the selection of mass, with the decline in the metabolic exponent following from a decline in the importance of mass-specific metabolism for the selection of mass. The body mass variation in prokaryotes is found to be selected from primary variation in mass-specific metabolism, while the variation in multicellular animals is selected from primary variation in the handling and/or densities of the underlying resources, with protists and protozoa being selected as an intermediate lifeform.}, }
@article {pmid28864113, year = {2017}, author = {Li, DD and Luo, Z and Chen, GH and Song, YF and Wei, CC and Pan, YX}, title = {Identification of apoptosis-related genes Bcl2 and Bax from yellow catfish Pelteobagrus fulvidraco and their transcriptional responses to waterborne and dietborne zinc exposure.}, journal = {Gene}, volume = {633}, number = {}, pages = {1-8}, doi = {10.1016/j.gene.2017.08.029}, pmid = {28864113}, issn = {1879-0038}, mesh = {Animals ; Apoptosis/*genetics/physiology ; Catfishes/*genetics/metabolism ; DNA, Complementary/genetics ; Down-Regulation ; Environmental Exposure ; Fish Proteins/classification/*genetics/physiology ; Lipid Metabolism/genetics ; Liver/metabolism ; Phylogeny ; RNA, Messenger/genetics/metabolism ; *Transcription, Genetic ; Up-Regulation ; Water/chemistry ; Zinc/analysis/*metabolism ; bcl-2-Associated X Protein/classification/*genetics/physiology ; bcl-Associated Death Protein/classification/*genetics/physiology ; }, abstract = {Apoptosis plays a key role in the physiology of multicellular organisms, and has been well studied in mammals, but not in teleosts. Zinc (Zn) has been shown to be an important regulator of apoptosis and apoptosis involves in the regulation of lipid metabolism. Moreover, our recent study indicated that waterborne and dietborne Zn exposure differently influenced lipid metabolism in Pelteobagrus fulvidraco, but further mechanism remained unknown. The hypothesis of the present study is that apoptosis mediated the Zn-induced changes of lipid metabolism of P. fulvidraco subjected to different exposure pathways. To this end, we cloned full-length cDNA sequences of Bcl2 and three Bax subtypes involved in apoptosis in P. fulvidraco, explored their mRNA expressions in responses to different Zn exposure pathways. Bcl2 and three Bax subtypes shared similar domain structure as typical pro- and anti-apoptotic Bcl2 family members. Their mRNAs were widely expressed among various tissues, but at variable levels. Waterborne Zn exposure down-regulated mRNA levels of Baxg and ratios of Baxa/Bcl2, and Baxg/Bcl2, but showed no significant effects on mRNA abundances of Bcl2, Baxa and Baxb, and the ratio of Baxb/Bcl2. In contrast, dietborne Zn exposure up-regulated mRNA levels of Bcl2, Baxa, Baxb and Baxg, but reduced the ratios of Baxa/Bcl2, Baxb/Bcl2, and Baxg/Bcl2. Considering their important roles of these genes in apoptosis induced by Zn, apoptosis may mediate the Zn-induced changes of hepatic lipid metabolism of Pelteobagrus fulvidraco under different Zn exposure pathways. For the first time, we characterized the full-length cDNA sequences of Bcl2 and three Bax subtypes, determined their expression profiles and transcriptional responses to different Zn exposure pathways, which would contribute to our understanding of the molecular basis of apoptosis, and also provide new insights into physiological responses to different Zn exposure pathways.}, }
@article {pmid28861094, year = {2017}, author = {Rauch, C and Jahns, P and Tielens, AGM and Gould, SB and Martin, WF}, title = {On Being the Right Size as an Animal with Plastids.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {1402}, doi = {10.3389/fpls.2017.01402}, pmid = {28861094}, issn = {1664-462X}, abstract = {Plastids typically reside in plant or algal cells-with one notable exception. There is one group of multicellular animals, sea slugs in the order Sacoglossa, members of which feed on siphonaceous algae. The slugs sequester the ingested plastids in the cytosol of cells in their digestive gland, giving the animals the color of leaves. In a few species of slugs, including members of the genus Elysia, the stolen plastids (kleptoplasts) can remain morphologically intact for weeks and months, surrounded by the animal cytosol, which is separated from the plastid stroma by only the inner and outer plastid membranes. The kleptoplasts of the Sacoglossa are the only case described so far in nature where plastids interface directly with the metazoan cytosol. That makes them interesting in their own right, but it has also led to the idea that it might someday be possible to engineer photosynthetic animals. Is that really possible? And if so, how big would the photosynthetic organs of such animals need to be? Here we provide two sets of calculations: one based on a best case scenario assuming that animals with kleptoplasts can be, on a per cm2 basis, as efficient at CO2 fixation as maize leaves, and one based on 14CO2 fixation rates measured in plastid-bearing sea slugs. We also tabulate an overview of the literature going back to 1970 reporting direct measurements or indirect estimates of the CO2 fixing capabilities of Sacoglossan slugs with plastids.}, }
@article {pmid28859625, year = {2017}, author = {Koch, R and Kupczok, A and Stucken, K and Ilhan, J and Hammerschmidt, K and Dagan, T}, title = {Plasticity first: molecular signatures of a complex morphological trait in filamentous cyanobacteria.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {209}, doi = {10.1186/s12862-017-1053-5}, pmid = {28859625}, issn = {1471-2148}, support = {281357//European Research Council/International ; }, mesh = {*Biological Evolution ; Cyanobacteria/*classification/cytology/*genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation ; Phenotype ; *Regulatory Sequences, Nucleic Acid ; Sucrose/metabolism ; Transcription Initiation Site ; }, abstract = {BACKGROUND: Filamentous cyanobacteria that differentiate multiple cell types are considered the peak of prokaryotic complexity and their evolution has been studied in the context of multicellularity origins. Species that form true-branching filaments exemplify the most complex cyanobacteria. However, the mechanisms underlying the true-branching morphology remain poorly understood despite of several investigations that focused on the identification of novel genes or pathways. An alternative route for the evolution of novel traits is based on existing phenotypic plasticity. According to that scenario - termed genetic assimilation - the fixation of a novel phenotype precedes the fixation of the genotype.<br><br>RESULTS: Here we show that the evolution of transcriptional regulatory elements constitutes a major mechanism for the evolution of new traits. We found that supplementation with sucrose reconstitutes the ancestral branchless phenotype of two true-branching Fischerella species and compared the transcription start sites (TSSs) between the two phenotypic states. Our analysis uncovers several orthologous TSSs whose transcription level is correlated with the true-branching phenotype. These TSSs are found in genes that encode components of the septosome and elongasome (e.g., fraC and mreB).<br><br>CONCLUSIONS: The concept of genetic assimilation supplies a tenable explanation for the evolution of novel traits but testing its feasibility is hindered by the inability to recreate and study the evolution of present-day traits. We present a novel approach to examine transcription data for the plasticity first route and provide evidence for its occurrence during the evolution of complex colony morphology in true-branching cyanobacteria. Our results reveal a route for evolution of the true-branching phenotype in cyanobacteria via modification of the transcription level of pre-existing genes. Our study supplies evidence for the 'plasticity-first' hypothesis and highlights the importance of transcriptional regulation in the evolution of novel traits.}, }
@article {pmid28859623, year = {2017}, author = {Patel, VD and Capra, JA}, title = {Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {672}, doi = {10.1186/s12864-017-4073-z}, pmid = {28859623}, issn = {1471-2164}, mesh = {Animals ; Disease/*genetics ; *Evolution, Molecular ; Humans ; MicroRNAs/*genetics ; Phylogeny ; Transcriptome ; }, abstract = {BACKGROUND: microRNAs (miRNAs) are essential to the regulation of gene expression in eukaryotes, and improper expression of miRNAs contributes to hundreds of diseases. Despite the essential functions of miRNAs, the evolutionary dynamics of how they are integrated into existing gene regulatory and functional networks is not well understood. Knowledge of the origin and evolutionary history a gene has proven informative about its functions and disease associations; we hypothesize that incorporating the evolutionary origins of miRNAs into analyses will help resolve differences in their functional dynamics and how they influence disease.<br><br>RESULTS: We computed the phylogenetic age of miRNAs across 146 species and quantified the relationship between human miRNA age and several functional attributes. Older miRNAs are significantly more likely to be associated with disease than younger miRNAs, and the number of associated diseases increases with age. As has been observed for genes, the miRNAs associated with different diseases have different age profiles. For example, human miRNAs implicated in cancer are enriched for origins near the dawn of animal multicellularity. Consistent with the increasing contribution of miRNAs to disease with age, older miRNAs target more genes than younger miRNAs, and older miRNAs are expressed in significantly more tissues. Furthermore, miRNAs of all ages exhibit a strong preference to target older genes; 93% of validated miRNA gene targets were in existence at the origin of the targeting miRNA. Finally, we find that human miRNAs in evolutionarily related families are more similar in their targets and expression profiles than unrelated miRNAs.<br><br>CONCLUSIONS: Considering the evolutionary origin and history of a miRNA provides useful context for the analysis of its function. Consistent with recent work in Drosophila, our results support a model in which miRNAs increase their expression and functional regulatory interactions over evolutionary time, and thus older miRNAs have increased potential to cause disease. We anticipate that these patterns hold across mammalian species; however, comprehensively evaluating them will require refining miRNA annotations across species and collecting functional data in non-human systems.}, }
@article {pmid28859501, year = {2017}, author = {Csaba, G}, title = {Is there a hormonal regulation of phagocytosis at unicellular and multicellular levels? A critical review.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {64}, number = {4}, pages = {357-372}, doi = {10.1556/030.64.2017.024}, pmid = {28859501}, issn = {1217-8950}, mesh = {Animals ; Hormones/*immunology ; Humans ; Macrophages/cytology/*immunology ; *Phagocytosis ; }, abstract = {Phagocytosis is an ancient cell function, which is similar at unicellular and multicellular levels. Unicells synthesize, store, and secrete multicellular (mammalian) hormones, which influence their phagocytosis. Amino acid hormones, such as histamine, serotonin, epinephrine, and melatonin stimulate phagocytosis, whereas peptide hormones, such as adrenocorticotropic hormone (ACTH), insulin, opioids, arginine vasopressin, and atrial natriuretic peptide decreased it, independently on their chemical structure or function in multicellulars. Macrophage phagocytosis of multicellulars is also stimulated by amino acid hormones, such as histamine, epinephrine, melatonin, and thyroid hormones, however, the effect of peptide hormones is not uniform: prolactin, insulin, glucagon, somatostatin, and leptin have positive effects, whereas ACTH, human chorionic gonadotropin, opioids, and ghrelin have negative ones. Steroid hormones, such as estrogen, hydrocortisone, and dexamethasone are stimulating macrophage phagocytosis, whereas progesterone, aldosterone, and testosterone are depressing it. Considering the data and observations there is not a specific phagocytosis hormone, or a hormonal regulation of phagocytosis neither unicellular, nor multicellular level, however, hormones having specific functions in multicellulars also influence phagocytosis at both levels universally (in unicellulars) or individually (in macrophages). Nevertheless, the hormonal influence cannot be neglected, as phagocytosis (as a function) is rather sensitive to minute dose of hormones and endocrine disruptors. The hormonal influence of phagocytosis by macrophages can be deduced to the events at unicellular level.}, }
@article {pmid28856734, year = {2017}, author = {Deines, P and Lachnit, T and Bosch, TCG}, title = {Competing forces maintain the Hydra metaorganism.}, journal = {Immunological reviews}, volume = {279}, number = {1}, pages = {123-136}, doi = {10.1111/imr.12564}, pmid = {28856734}, issn = {1600-065X}, mesh = {Animals ; *Biological Evolution ; Homeostasis ; Host-Pathogen Interactions ; Humans ; Hydra/*physiology ; *Immunity, Innate ; Symbiosis ; }, abstract = {Our conventional view of multicellular organisms often overlooks the fact that they are metaorganisms. They consist of a host, which is comprised of both a community of self-replicating cells that can compete as well as cooperate and a community of associated microorganisms. This newly discovered complexity raises a profound challenge: How to maintain such a multicellular association that includes independently replicating units and even different genotypes? Here, we identify competing forces acting at the host tissue level, the host-microbe interface, and within the microbial community as key factors to maintain the metaorganism Hydra. Maintenance of host tissue integrity, as well as proper regulation and management of the multiorganismic interactions are fundamental to organismal survival and health. Findings derived from the in vivo context of the Hydra model may provide one of the simplest possible systems to address questions on how a metaorganism is established and remains in balance over time.}, }
@article {pmid28852499, year = {2017}, author = {Buzanskas, ME and Grossi, DDA and Ventura, RV and Schenkel, FS and Chud, TCS and Stafuzza, NB and Rola, LD and Meirelles, SLC and Mokry, FB and Mudadu, MA and Higa, RH and da Silva, MVGB and de Alencar, MM and Regitano, LCA and Munari, DP}, title = {Candidate genes for male and female reproductive traits in Canchim beef cattle.}, journal = {Journal of animal science and biotechnology}, volume = {8}, number = {}, pages = {67}, doi = {10.1186/s40104-017-0199-8}, pmid = {28852499}, issn = {1674-9782}, abstract = {BACKGROUND: Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals.<br><br>RESULTS: Associated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction.<br><br>CONCLUSIONS: Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program.}, }
@article {pmid28846170, year = {2017}, author = {Votaw, HR and Ostrowski, EA}, title = {Stalk size and altruism investment within and among populations of the social amoeba.}, journal = {Journal of evolutionary biology}, volume = {30}, number = {11}, pages = {2017-2030}, doi = {10.1111/jeb.13172}, pmid = {28846170}, issn = {1420-9101}, mesh = {Altruism ; Dictyostelium/*cytology/genetics/*physiology ; Epistasis, Genetic ; Genotype ; Reproduction ; }, abstract = {Reproductive division of labour is common in many societies, including those of eusocial insects, cooperatively breeding vertebrates, and most forms of multicellularity. However, conflict over what is best for the individual vs. the group can prevent an optimal division of labour from being achieved. In the social amoeba Dictyostelium discoideum, cells aggregate to become multicellular and a fraction behaves altruistically, forming a dead stalk that supports the rest. Theory suggests that intra-organismal conflict over spore-stalk cell fate can drive rapid evolutionary change in allocation traits, leading to polymorphisms within populations or rapid divergence between them. Here, we assess several proxies for stalk size and spore-stalk allocation as metrics of altruism investment among strains and across geographic regions. We observe geographic divergence in stalk height that can be partly explained by differences in multicellular size, as well as variation among strains in clonal spore-stalk allocation, suggesting within-population variation in altruism investment. Analyses of chimeras comprised of strains from the same vs. different populations indicated genotype-by-genotype epistasis, where the morphology of the chimeras deviated significantly from the average morphology of the strains developed clonally. The significantly negative epistasis observed for allopatric pairings suggests that populations are diverging in their spore-stalk allocation behaviours, generating incompatibilities when they encounter one another. Our results demonstrate divergence in microbial social traits across geographically separated populations and demonstrate how quantification of genotype-by-genotype interactions can elucidate the trajectory of social trait evolution in nature.}, }
@article {pmid28839913, year = {2017}, author = {Shapiro, JA}, title = {Biological action in Read-Write genome evolution.}, journal = {Interface focus}, volume = {7}, number = {5}, pages = {20160115}, doi = {10.1098/rsfs.2016.0115}, pmid = {28839913}, issn = {2042-8898}, abstract = {Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with 'non-coding' DNA content rather than with protein-coding capacity in the genome. Coincidentally, 'non-coding' RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.}, }
@article {pmid28830343, year = {2017}, author = {Chen, IK and Velicer, GJ and Yu, YN}, title = {Divergence of functional effects among bacterial sRNA paralogs.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {199}, doi = {10.1186/s12862-017-1037-5}, pmid = {28830343}, issn = {1471-2148}, mesh = {Alleles ; Base Sequence ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Myxococcus xanthus/*genetics/growth &amp; development ; Phylogeny ; RNA, Bacterial/*genetics ; *Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: Non-coding small RNAs (sRNAs) regulate a variety of important biological processes across all life domains, including bacteria. However, little is known about the functional evolution of sRNAs in bacteria, which might occur via changes in sRNA structure and/or stability or changes in interactions between sRNAs and their associated regulatory networks, including target mRNAs. The sRNA Pxr functions as a developmental gatekeeper in the model cooperative bacterium Myxococcus xanthus. Specifically, Pxr prevents the initiation of fruiting body development when nutrients are abundant. Previous work has shown that Pxr appears to have a recent origin within a sub-clade of the myxobacteria, which allowed us to infer the most recent common ancestor of pxr and examine the divergence of Pxr since its origin.<br><br>RESULTS: To test for inter-specific divergence in functional effects, extant pxr homologs from several species and their inferred ancestor were introduced into an M. xanthus deletion mutant lacking pxr. Both the inferred ancestral pxr and all extant alleles from species containing only one copy of pxr were found to control development in M. xanthus in a qualitatively similar manner to the native M. xanthus allele. However, multiple paralogs present in Cystobacter species exhibited divergent effects, with two paralogs controlling M. xanthus development but two others failing to do so. These differences may have occurred through changes in gene expression caused by apparent structural differences in the sRNA variants encoded by these paralogs.<br><br>CONCLUSIONS: Taken together, our results suggest that Pxr plays a common fundamental role in developmental gene regulation across diverse species of myxobacteria but also that the functional effects of some Pxr variants may be evolving in some lineages.}, }
@article {pmid28827358, year = {2017}, author = {Larsen, NB and Liberti, SE and Vogel, I and Jørgensen, SW and Hickson, ID and Mankouri, HW}, title = {Stalled replication forks generate a distinct mutational signature in yeast.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {36}, pages = {9665-9670}, doi = {10.1073/pnas.1706640114}, pmid = {28827358}, issn = {1091-6490}, mesh = {DNA Replication/*genetics ; DNA, Fungal/genetics/metabolism ; DNA, Single-Stranded/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Exodeoxyribonucleases/genetics/metabolism ; Genes, Reporter ; Genetic Engineering ; Humans ; Models, Biological ; Mutagenesis ; Mutation ; Nuclear Proteins/genetics/metabolism ; RecQ Helicases/genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Recombinational DNA Repair ; Replication Origin ; Saccharomyces cerevisiae/*genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Proliferating cells acquire genome alterations during the act of DNA replication. This leads to mutation accumulation and somatic cell mosaicism in multicellular organisms, and is also implicated as an underlying cause of aging and tumorigenesis. The molecular mechanisms of DNA replication-associated genome rearrangements are poorly understood, largely due to methodological difficulties in analyzing specific replication forks in vivo. To provide an insight into this process, we analyzed the mutagenic consequences of replication fork stalling at a single, site-specific replication barrier (the Escherichia coli Tus/Ter complex) engineered into the yeast genome. We demonstrate that transient stalling at this barrier induces a distinct pattern of genome rearrangements in the newly replicated region behind the stalled fork, which primarily consist of localized losses and duplications of DNA sequences. These genetic alterations arise through the aberrant repair of a single-stranded DNA gap, in a process that is dependent on Exo1- and Shu1-dependent homologous recombination repair (HRR). Furthermore, aberrant processing of HRR intermediates, and elevated HRR-associated mutagenesis, is detectable in a yeast model of the human cancer predisposition disorder, Bloom's syndrome. Our data reveal a mechanism by which cellular responses to stalled replication forks can actively generate genomic alterations and genetic diversity in normal proliferating cells.}, }
@article {pmid28825126, year = {2018}, author = {Chi, S and Liu, T and Wang, X and Wang, R and Wang, S and Wang, G and Shan, G and Liu, C}, title = {Functional genomics analysis reveals the biosynthesis pathways of important cellular components (alginate and fucoidan) of Saccharina.}, journal = {Current genetics}, volume = {64}, number = {1}, pages = {259-273}, doi = {10.1007/s00294-017-0733-4}, pmid = {28825126}, issn = {1432-0983}, support = {41376143//National Natural Science Foundation of China/ ; 14-2-4-104-jch//Qingdao applied basic research project/ ; }, mesh = {Alginates/*metabolism ; *Biosynthetic Pathways/genetics ; Computational Biology/methods ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genome ; *Genomics/methods ; Glucuronic Acid/metabolism ; Hexuronic Acids/metabolism ; High-Throughput Nucleotide Sequencing ; Phaeophyta/classification/*genetics/*metabolism ; Phylogeny ; Polysaccharides/*metabolism ; Symbiosis/genetics ; Transcriptome ; }, abstract = {Although alginate and fucoidan are unique cellular components and have important biological significance in brown algae, and many possible involved genes are present in brown algal genomes, their functions and regulatory mechanisms have not been fully revealed. Both polysaccharides may play important roles in the evolution of multicellular brown algae, but specific and in-depth studies are still limited. In this study, a functional genomics analysis of alginate and fucoidan biosynthesis routes was conducted in Saccharina, and the key events in these pathways in brown algae were identified. First, genes from different sources, including eukaryotic hosts via endosymbiotic gene transfer and bacteria via horizontal gene transfer, were combined to build a complete pathway framework. Then, a critical event occurred to drive these pathways to have real function: one of the mannose-6-phosphate isomerase homologs that arose by gene duplication subsequently adopted the function of the mannose-1-phosphate guanylyltransferase (MGP) gene, which was absent in algal genomes. Further, downstream pathway genes proceeded with gene expansions and complex transcriptional mechanisms, which may be conducive to the synthesis of alginate and fucoidan with diverse structures and contents depending on the developmental stage, tissue structure, and environmental conditions. This study revealed the alginate and fucoidan synthesis pathways and all included genes from separate phylogenetic sources in brown algae. Enzyme assays confirmed the function of key genes and led to the determination of a substitute for the missing MPG. All gene families had constitutively expressed member(s) to maintain the basic synthesis; and the gene function differentiation, enzyme characterization and gene expression regulation differences separated brown algae from other algae lineages and were considered to be the major driving forces for sophisticated system evolution of brown algae.}, }
@article {pmid28820125, year = {2017}, author = {Stajich, JE}, title = {Fungal Genomes and Insights into the Evolution of the Kingdom.}, journal = {Microbiology spectrum}, volume = {5}, number = {4}, pages = {}, doi = {10.1128/microbiolspec.FUNK-0055-2016}, pmid = {28820125}, issn = {2165-0497}, support = {S10 OD016290/OD/NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Fungi/*genetics ; Genes, Fungal/*genetics ; Genome, Fungal/*genetics ; }, abstract = {The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.}, }
@article {pmid28820115, year = {2017}, author = {Nagy, LG and Tóth, R and Kiss, E and Slot, J and Gácser, A and Kovács, GM}, title = {Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases.}, journal = {Microbiology spectrum}, volume = {5}, number = {4}, pages = {}, doi = {10.1128/microbiolspec.FUNK-0036-2016}, pmid = {28820115}, issn = {2165-0497}, mesh = {*Biological Evolution ; Cell Lineage/genetics ; Evolution, Molecular ; Fruiting Bodies, Fungal/*growth &amp; development ; Fungi/*genetics/*growth &amp; development ; Hyphae/*growth &amp; development ; Mycorrhizae/physiology ; Phylogeny ; Plants/microbiology ; }, abstract = {The fungal lineage is one of the three large eukaryotic lineages that dominate terrestrial ecosystems. They share a common ancestor with animals in the eukaryotic supergroup Opisthokonta and have a deeper common ancestry with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among all living organisms. This article provides an overview of some of the most important fungal traits, how they evolve, and what major genes and gene families contribute to their development. The traits highlighted here represent just a sample of the characteristics that have evolved in fungi, including polarized multicellular growth, fruiting body development, dimorphism, secondary metabolism, wood decay, and mycorrhizae. However, a great number of other important traits also underlie the evolution of the taxonomically and phenotypically hyperdiverse fungal kingdom, which could fill up a volume on its own. After reviewing the evolution of these six well-studied traits in fungi, we discuss how the recurrent evolution of phenotypic similarity, that is, convergent evolution in the broad sense, has shaped their phylogenetic distribution in extant species.}, }
@article {pmid28819830, year = {2017}, author = {Liu, A and He, F and Gu, X}, title = {Identification and characterization of tyrosine kinases in anole lizard indicate the conserved tyrosine kinase repertoire in vertebrates.}, journal = {Molecular genetics and genomics : MGG}, volume = {292}, number = {6}, pages = {1405-1418}, doi = {10.1007/s00438-017-1356-7}, pmid = {28819830}, issn = {1617-4623}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Lizards/classification/genetics/*metabolism ; Phylogeny ; Protein-Tyrosine Kinases/chemistry/*genetics ; }, abstract = {The tyrosine kinases (TKs) play principal roles in regulation of multicellular aspects of the organism and are implicated in many cancer types and congenital disorders. The anole lizard has recently been introduced as a model organism for laboratory-based studies of organismal function and field studies of ecology and evolution. However, the TK family of anole lizard has not been systematically identified and characterized yet. In this study, we identified 82 TK-encoding genes in the anole lizard genome and classified them into 28 subfamilies through phylogenetic analysis, with no member from ROS and STYK1 subfamilies identified. Although TK domain sequences and domain organization in each subfamily were conserved, the total number of TKs in different species was much variable. In addition, extensive evolutionary analysis in metazoans indicated that TK repertoire in vertebrates tends to be remarkably stable. Phylogenetic analysis of Eph subfamily indicated that the divergence of EphA and EphB occurred prior to the whole genome duplication (WGD) but after the split of Urochordates and vertebrates. Moreover, the expression pattern analysis of lizard TK genes among 9 different tissues showed that 14 TK genes exhibited tissue-specific expression and 6 TK genes were widely expressed. Comparative analysis of TK expression suggested that the tissue specifically expressed genes showed different expression pattern but the widely expressed genes showed similar pattern between anole lizard and human. These results may provide insights into the evolutionary diversification of animal TK genes and would aid future studies on TK protein regulation of key growth and developmental processes.}, }
@article {pmid28812655, year = {2017}, author = {Griffith, OW and Wagner, GP}, title = {The placenta as a model for understanding the origin and evolution of vertebrate organs.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {4}, pages = {72}, doi = {10.1038/s41559-017-0072}, pmid = {28812655}, issn = {2397-334X}, abstract = {How organs originate and evolve is a question fundamental to understanding the evolution of complex multicellular life forms. Vertebrates have a relatively standard body plan with more or less the same conserved set of organs. The placenta is a comparatively more recently evolved organ, derived in many lineages independently. Using placentas as a model, we discuss the genetic basis for organ origins. We show that the evolution of placentas occurs by acquiring new functional attributes to existing tissues, changes in the patterning and development of tissues, and the evolution of novel cell types. We argue that a diversity of genomic changes facilitated these physiological transformations and that these changes are likely to have occurred during the evolution of organs more broadly. Finally, we argue that a key aspect to understanding the evolutionary origin of organs is that they are likely to result from novel interactions between distinct cell populations.}, }
@article {pmid28812251, year = {2017}, author = {Pavlovich, E and Volkova, N and Yakymchuk, E and Perepelitsyna, O and Sydorenko, M and Goltsev, A}, title = {In Vitro Study of Influence of Au Nanoparticles on HT29 and SPEV Cell Lines.}, journal = {Nanoscale research letters}, volume = {12}, number = {1}, pages = {494}, doi = {10.1186/s11671-017-2264-9}, pmid = {28812251}, issn = {1931-7573}, abstract = {Cell culture models are excellent tools for potential toxicity of nanoparticles and fundamental investigations in cancer research. Thus, information about AuNP potential toxicity and effects on human health is necessary for the use of nanomaterials in clinical settings. The aim of our research is to examine the effects of AuNPs on the epithelial origin cell lines: continuous and oncogenic. Embryonic porcine kidney epithelial inoculated (SPEV) cell line and colorectal carcinoma cell line (HT29) were used. In the test cultures, the cell proliferation, necrosis/apoptosis, and multicellular spheroids generation were evaluated. We demonstrated that AuNP concentrations of 6-12 μg/ml reduced the proliferation of SPEV and HT29 cells and increased the cell number at early and late stages of apoptosis and necrosis. It was shown that small concentrations of AuNPs (1-3 μg/ml) stimulate multicellular spheroid formation by HT29 and SPEV cells. However, higher AuNP concentrations (6-12 μg/ml) had both cytotoxic and anti-cohesive effects on cell in suspension. The large sensitiveness to the action of AuNPs was shown by the line of HT29 (6 μg/ml) as compared to the SPEV cells (12 μg/ml). This experimental study of the effect of AuNPs on SPEV and HT29 cell lines will justify their further application in AuNP-mediated anticancer treatment.}, }
@article {pmid28804953, year = {2017}, author = {Gyoja, F}, title = {Basic helix-loop-helix transcription factors in evolution: Roles in development of mesoderm and neural tissues.}, journal = {Genesis (New York, N.Y. : 2000)}, volume = {55}, number = {9}, pages = {}, doi = {10.1002/dvg.23051}, pmid = {28804953}, issn = {1526-968X}, mesh = {Animals ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/chemistry/*genetics/metabolism ; *Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Mesoderm/growth &amp; development/*metabolism ; Nervous System/growth &amp; development/*metabolism ; }, abstract = {Basic helix-loop-helix (bHLH) transcription factors have attracted the attention of developmental and evolutionary biologists for decades because of their conserved functions in mesodermal and neural tissue formation in both vertebrates and fruit flies. Their evolutionary history is of special interest because it will likely provide insights into developmental processes and refinement of metazoan-specific traits. This review briefly considers advances in developmental biological studies on bHLHs/HLHs. I also discuss recent genome-wide surveys and molecular phylogenetic analyses of these factors in a wide range of metazoans. I hypothesize that interactions between metazoan-specific Group A, D, and E bHLH/HLH factors enabled a sophisticated transition system from cell proliferation to differentiation in multicellular development. This control mechanism probably emerged initially to organize a multicellular animal body and was subsequently recruited to form evolutionarily novel tissues, which differentiated during a later ontogenetic phase.}, }
@article {pmid28802203, year = {2017}, author = {Campbell, S and Aswad, A and Katzourakis, A}, title = {Disentangling the origins of virophages and polintons.}, journal = {Current opinion in virology}, volume = {25}, number = {}, pages = {59-65}, doi = {10.1016/j.coviro.2017.07.011}, pmid = {28802203}, issn = {1879-6265}, mesh = {DNA Transposable Elements/*genetics ; DNA, Viral/genetics ; Eukaryota/*virology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Viral ; Giant Viruses/*genetics/physiology ; Phylogeny ; Virophages/*genetics ; Virus Diseases/genetics/transmission ; }, abstract = {Virophages and polintons are part of a complex system that also involves eukaryotes, giant viruses, as well as other viruses and transposable elements. Virophages are cosmopolitan, being found in environments ranging from the Amazon River to Antarctic hypersaline lakes, while polintons are found in many single celled and multicellular eukaryotes. Virophages and polintons have a shared ancestry, but their exact origins are unknown and obscured by antiquity and extensive horizontal gene transfer (HGT). Paleovirology can help disentangle the complicated gene flow between these two, as well as their giant viral and eukaryotic hosts. We outline the evidence and theoretical support for polintons being descended from viruses and not vice versa. In order to disentangle the natural history of polintons and virophages, we suggest that there is much to be gained by embracing rigorous metagenomics and evolutionary analyses. Methods from paleovirology will play a pivotal role in unravelling ancient relationships, HGT and patterns of cross-species transmission.}, }
@article {pmid28798739, year = {2017}, author = {Song, H and Liu, J and Song, Q and Zhang, Q and Tian, P and Nan, Z}, title = {Comprehensive Analysis of Codon Usage Bias in Seven Epichloë Species and Their Peramine-Coding Genes.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1419}, doi = {10.3389/fmicb.2017.01419}, pmid = {28798739}, issn = {1664-302X}, abstract = {Codon usage bias plays an important role in shaping genomes and genes in unicellular species and multicellular species. Here, we first analyzed codon usage bias in seven Epichloë species and their peramine-coding genes. Our results showed that both natural selection and mutation pressure played a role in forming codon usage bias in seven Epichloë species. All seven Epichloë species contained a peramine-coding gene cluster. Interestingly, codon usage bias of peramine-coding genes were not affected by natural selection or mutation pressure. There were 13 codons more frequently found in Epichloë genome sequences, peramine-coding gene clusters and orthologous peramine-coding genes, all of which had a bias to end with a C nucleotide. In the seven genomes analyzed, codon usage was biased in highly expressed coding sequences (CDSs) with shorter length and higher GC content. Genes in the peramine-coding gene cluster had higher GC content at the third nucleotide position of the codon, and highly expressed genes had higher GC content at the second position. In orthologous peramine-coding CDSs, high expression level was not significantly correlated with CDS length and GC content. Analysis of selection pressure identified that the genes orthologous to peramine genes were under purifying selection. There were no differences in codon usage bias and selection pressure between peramine product genes and non-functional peramine product genes. Our results provide insights into understanding codon evolution in Epichloë species.}, }
@article {pmid28798731, year = {2017}, author = {Ibáñez de Aldecoa, AL and Zafra, O and González-Pastor, JE}, title = {Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1390}, doi = {10.3389/fmicb.2017.01390}, pmid = {28798731}, issn = {1664-302X}, abstract = {The capacity to release genetic material into the extracellular medium has been reported in cultures of numerous species of bacteria, archaea, and fungi, and also in the context of multicellular microbial communities such as biofilms. Moreover, extracellular DNA (eDNA) of microbial origin is widespread in natural aquatic and terrestrial environments. Different specific mechanisms are involved in eDNA release, such as autolysis and active secretion, as well as through its association with membrane vesicles. It is noteworthy that in microorganisms, in which DNA release has been studied in detail, the production of eDNA is coordinated by the population when it reaches a certain cell density, and is induced in a subpopulation in response to the accumulation of quorum sensing signals. Interestingly, in several bacteria there is also a relationship between eDNA release and the development of natural competence (the ability to take up DNA from the environment), which is also controlled by quorum sensing. Then, what is the biological function of eDNA? A common biological role has not been proposed, since different functions have been reported depending on the microorganism. However, it seems to be important in biofilm formation, can be used as a nutrient source, and could be involved in DNA damage repair and gene transfer. This review covers several aspects of eDNA research: (i) its occurrence and distribution in natural environments, (ii) the mechanisms and regulation of its release in cultured microorganisms, and (iii) its biological roles. In addition, we propose that eDNA release could be considered a social behavior, based on its quorum sensing-dependent regulation and on the described functions of eDNA in the context of microbial communities.}, }
@article {pmid28786729, year = {2017}, author = {Gerlee, P and Basanta, D and Anderson, ARA}, title = {The Influence of Cellular Characteristics on the Evolution of Shape Homeostasis.}, journal = {Artificial life}, volume = {23}, number = {3}, pages = {424-448}, doi = {10.1162/ARTL_a_00240}, pmid = {28786729}, issn = {1064-5462}, abstract = {The importance of individual cells in a developing multicellular organism is well known, but precisely how the individual cellular characteristics of those cells collectively drive the emergence of robust, homeostatic structures is less well understood. For example, cell communication via a diffusible factor allows for information to travel across large distances within the population, and cell polarization makes it possible to form structures with a particular orientation, but how do these processes interact to produce a more robust and regulated structure? In this study we investigate the ability of cells with different cellular characteristics to grow and maintain homeostatic structures. We do this in the context of an individual-based model where cell behavior is driven by an intracellular network that determines the cell phenotype. More precisely, we investigated evolution with 96 different permutations of our model, where cell motility, cell death, long-range growth factor (LGF), short-range growth factor (SGF), and cell polarization were either present or absent. The results show that LGF has the largest positive influence on the fitness of the evolved solutions. SGF and polarization also contribute, but all other capabilities essentially increase the search space, effectively making it more difficult to achieve a solution. By perturbing the evolved solutions, we found that they are highly robust to both mutations and wounding. In addition, we observed that by evolving solutions in more unstable environments they produce structures that were more robust and adaptive. In conclusion, our results suggest that robust collective behavior is most likely to evolve when cells are endowed with long-range communication, cell polarisation, and selection pressure from an unstable environment.}, }
@article {pmid28774341, year = {2017}, author = {Riffle, S and Hegde, RS}, title = {Modeling tumor cell adaptations to hypoxia in multicellular tumor spheroids.}, journal = {Journal of experimental &amp; clinical cancer research : CR}, volume = {36}, number = {1}, pages = {102}, doi = {10.1186/s13046-017-0570-9}, pmid = {28774341}, issn = {1756-9966}, support = {R01 CA207068/CA/NCI NIH HHS/United States ; }, mesh = {Cell Line, Tumor ; Cell Proliferation/*drug effects ; Humans ; Spheroids, Cellular/*metabolism ; }, abstract = {Under hypoxic conditions, tumor cells undergo a series of adaptations that promote evolution of a more aggressive tumor phenotype including the activation of DNA damage repair proteins, altered metabolism, and decreased proliferation. Together these changes mitigate the negative impact of oxygen deprivation and allow preservation of genomic integrity and proliferative capacity, thus contributing to tumor growth and metastasis. As a result the presence of a hypoxic microenvironment is considered a negative clinical feature of many solid tumors. Hypoxic niches in tumors also represent a therapeutically privileged environment in which chemo- and radiation therapy is less effective. Although the negative impact of tumor hypoxia has been well established, the precise effect of oxygen deprivation on tumor cell behavior, and the molecular signals that allow a tumor cell to survive in vivo are poorly understood. Multicellular tumor spheroids (MCTS) have been used as an in vitro model for the avascular tumor niche, capable of more accurately recreating tumor genomic profiles and predicting therapeutic response. However, relatively few studies have used MCTS to study the molecular mechanisms driving tumor cell adaptations within the hypoxic tumor environment. Here we will review what is known about cell proliferation, DNA damage repair, and metabolic pathways as modeled in MCTS in comparison to observations made in solid tumors. A more precise definition of the cell populations present within 3D tumor models in vitro could better inform our understanding of the heterogeneity within tumors as well as provide a more representative platform for the testing of therapeutic strategies.}, }
@article {pmid28768887, year = {2017}, author = {Tong, K and Wang, Y and Su, Z}, title = {Phosphotyrosine signalling and the origin of animal multicellularity.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1860}, pages = {}, doi = {10.1098/rspb.2017.0681}, pmid = {28768887}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; *Cell Communication ; Eukaryota/enzymology/*genetics ; Phosphotyrosine/*metabolism ; Protein-Tyrosine Kinases/*metabolism ; *Signal Transduction ; }, abstract = {The evolution of multicellular animals (i.e. metazoans) from a unicellular ancestor is one of the most important yet least understood evolutionary transitions. Historically, given its indispensable functions in intercellular communication and exclusive presence in metazoans, phosphotyrosine (pTyr) signalling was considered a metazoan-specific evolutionary innovation that might have contributed to the origin of metazoan multicellularity. However, recent studies have led to a new understanding of pTyr signalling evolution and its role in the metazoan origin. Sequence analyses have unravelled a much earlier emergence of pTyr signalling in eukaryotic evolution. Even so, several distinct properties of holozoan pTyr signalling may have paved the way for a hypothesized functional transition of pTyr signalling at the multicellular origin, from environmental sensing to intercellular communication, and for it to evolve as a powerful intercellular signalling system for multicellularity. Biochemical analyses of premetazoan pTyr signalling components have further revealed the premetazoan origin of many key features of metazoan pTyr signalling, and the metazoan establishment of others, including the Csk-mediated negative regulation of the activity of Src, a conserved tyrosine kinase in the Holozoa. Finally, potential future directions are discussed, with a stress on the biological functions of premetazoan pTyr signalling via newly developed gene manipulation tools in non-animal holozoans.}, }
@article {pmid28762573, year = {2017}, author = {Zanchi, C and Johnston, PR and Rolff, J}, title = {Evolution of defence cocktails: Antimicrobial peptide combinations reduce mortality and persistent infection.}, journal = {Molecular ecology}, volume = {26}, number = {19}, pages = {5334-5343}, doi = {10.1111/mec.14267}, pmid = {28762573}, issn = {1365-294X}, mesh = {Animals ; Bacterial Load ; Gene Knockdown Techniques ; Host-Pathogen Interactions ; *Immunity, Innate ; Insect Proteins/genetics/*immunology ; RNA Interference ; Staphylococcal Infections/*immunology ; Staphylococcus aureus ; Tenebrio/*immunology ; }, abstract = {The simultaneous expression of costly immune effectors such as multiple antimicrobial peptides is a hallmark of innate immunity of multicellular organisms, yet the adaptive advantage remains unresolved. Here, we test current hypotheses on the evolution of such defence cocktails. We use RNAi gene knock-down to explore, the effects of three highly expressed antimicrobial peptides, displaying different degrees of activity in vitro against Staphylococcus aureus, during an infection in the beetle Tenebrio molitor. We find that a defensin confers no survival benefit but reduces bacterial loads. A coleoptericin contributes to host survival without affecting bacterial loads. An attacin has no individual effect. Simultaneous knock-down of the defensin with the other AMPs results in increased mortality and elevated bacterial loads. Contrary to common expectations, the effects on host survival and bacterial load can be independent. The expression of multiple AMPs increases host survival and contributes to the control of persisting infections and tolerance. This is an emerging property that explains the adaptive benefit of defence cocktails.}, }
@article {pmid28761011, year = {2017}, author = {Borges, RM}, title = {Co-niche construction between hosts and symbionts: ideas and evidence.}, journal = {Journal of genetics}, volume = {96}, number = {3}, pages = {483-489}, pmid = {28761011}, issn = {0973-7731}, mesh = {Animals ; Biological Evolution ; *Ecosystem ; Gene Transfer, Horizontal ; Genome/genetics ; Host Specificity/*genetics ; *Inheritance Patterns ; Phenotype ; Symbiosis/*genetics ; }, abstract = {Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host phenotype, such as resource acquisition, protection from predation by acquisition of toxicity, as well as behaviour. Once symbiosis is established, its fidelity between generations must be ensured. Hosts evolve various mechanisms to screen unwanted symbionts and to facilitate faithful transmission of mutualistic partners between generations. Microbes are the most important symbionts that have influenced plant and animal phenotypes; multicellular organisms engage in developmental symbioses with microbes at many stages in ontogeny. The co-construction of niches may result in composite organisms that are physically nested within each other. While it has been advocated that these composite organisms need new evolutionary theories and perspectives to describe their properties and evolutionary trajectories, it appears that standard evolutionary theories are adequate to explore selection pressures on their composite or individual traits. Recent advances in our understanding of composite organisms open up many important questions regarding the stability and transmission of these units.}, }
@article {pmid28755343, year = {2017}, author = {Abdelbar, OH}, title = {Histological Analysis of the Developmental Stages of Direct Somatic Embryogenesis Induced from In Vitro Leaf Explants of Date Palm.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1637}, number = {}, pages = {145-162}, doi = {10.1007/978-1-4939-7156-5_13}, pmid = {28755343}, issn = {1940-6029}, mesh = {Culture Media/chemistry ; Germination ; In Vitro Techniques ; Inflorescence/*cytology ; Phoeniceae/cytology/*growth &amp; development ; Plant Leaves/growth &amp; development ; Plant Somatic Embryogenesis Techniques/*methods ; Regeneration ; Seeds/growth &amp; development ; }, abstract = {Somatic embryogenesis is an ideal technique for the micropropagation of date palm using different explant tissue; however, histological studies describing the ontogenesis of plant regeneration are limited. This chapter provides a simple protocol for the histological analysis of the successive developmental stages of direct somatic embryogenesis induced from in vitro leaf explants. Direct somatic embryos are obtained from Murashige and Skoog (MS) medium containing 2 mg/L 6-benzylaminopurine. In order to observe the different developmental stages, histological analysis is carried out on samples at 15-day intervals for 60 days. Samples are fixed in formalin acetic alcohol and embedded in paraffin wax. Stain serial transverse and longitudinal sections, 8 μm thick, are stained with safranin-Fast Green. After 15 days on the induction medium, somatic embryos exhibit multicellular origin directly from the procambium cells, whereas the mesophyll and the epidermal cells are not involved in this process. After 2 months, several developmental stages (pre-globular, globular, early bipolar, bipolar, and cotyledonary-shaped) are observed. These embryos germinate after transferring to MS medium without plant growth regulators and rooting on 2 mg/L NAA-containing medium resulting in complete plantlets.}, }
@article {pmid28749982, year = {2017}, author = {Yoshida, Y and Koutsovoulos, G and Laetsch, DR and Stevens, L and Kumar, S and Horikawa, DD and Ishino, K and Komine, S and Kunieda, T and Tomita, M and Blaxter, M and Arakawa, K}, title = {Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus.}, journal = {PLoS biology}, volume = {15}, number = {7}, pages = {e2002266}, doi = {10.1371/journal.pbio.2002266}, pmid = {28749982}, issn = {1545-7885}, mesh = {Animals ; Base Sequence ; Chromosome Mapping/veterinary ; DNA/chemistry/metabolism ; Desiccation ; Extremophiles/*genetics/growth &amp; development/physiology ; Gene Expression Profiling/veterinary ; *Gene Expression Regulation ; Gene Transfer, Horizontal ; Genetic Linkage ; Genome Size ; Genome-Wide Association Study/veterinary ; Genomic Library ; High-Throughput Nucleotide Sequencing/veterinary ; Multigene Family ; Phylogeny ; Proteome/genetics/*metabolism ; Reproducibility of Results ; Species Specificity ; Tardigrada/*genetics/growth &amp; development/physiology ; }, abstract = {Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.}, }
@article {pmid28745003, year = {2018}, author = {Müller, V and de Boer, RJ and Bonhoeffer, S and Szathmáry, E}, title = {An evolutionary perspective on the systems of adaptive immunity.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {1}, pages = {505-528}, doi = {10.1111/brv.12355}, pmid = {28745003}, issn = {1469-185X}, abstract = {We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates.}, }
@article {pmid28741966, year = {2017}, author = {Bryja, V and Červenka, I and Čajánek, L}, title = {The connections of Wnt pathway components with cell cycle and centrosome: side effects or a hidden logic?.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {52}, number = {6}, pages = {614-637}, doi = {10.1080/10409238.2017.1350135}, pmid = {28741966}, issn = {1549-7798}, support = {166533//Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; Cell Communication ; *Cell Cycle ; Cell Polarity ; Centrosome/*metabolism ; Humans ; *Wnt Signaling Pathway ; }, abstract = {Wnt signaling cascade has developed together with multicellularity to orchestrate the development and homeostasis of complex structures. Wnt pathway components - such as β-catenin, Dishevelled (DVL), Lrp6, and Axin-- are often dedicated proteins that emerged in evolution together with the Wnt signaling cascade and are believed to function primarily in the Wnt cascade. It is interesting to see that in recent literature many of these proteins are connected with cellular functions that are more ancient and not limited to multicellular organisms - such as cell cycle regulation, centrosome biology, or cell division. In this review, we summarize the recent literature describing this crosstalk. Specifically, we attempt to find the answers to the following questions: Is the response to Wnt ligands regulated by the cell cycle? Is the centrosome and/or cilium required to activate the Wnt pathway? How do Wnt pathway components regulate the centrosomal cycle and cilia formation and function? We critically review the evidence that describes how these connections are regulated and how they help to integrate cell-to-cell communication with the cell and the centrosomal cycle in order to achieve a fine-tuned, physiological response.}, }
@article {pmid28729688, year = {2017}, author = {Stepanauskas, R and Fergusson, EA and Brown, J and Poulton, NJ and Tupper, B and Labonté, JM and Becraft, ED and Brown, JM and Pachiadaki, MG and Povilaitis, T and Thompson, BP and Mascena, CJ and Bellows, WK and Lubys, A}, title = {Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {84}, doi = {10.1038/s41467-017-00128-z}, pmid = {28729688}, issn = {2041-1723}, mesh = {Base Composition ; Cell Size ; Deinococcus/cytology/*genetics ; Escherichia coli/cytology/*genetics ; Flow Cytometry ; Genome, Bacterial/*genetics ; Genome, Viral/*genetics ; Nucleic Acid Amplification Techniques ; Prochlorococcus/cytology/*genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Single-Cell Analysis ; Virion/*genetics ; }, abstract = {Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils. By integrating WGA-X with calibrated index-cell sorting and high-throughput genomic sequencing, we are able to analyze genomic sequences and cell sizes of hundreds of individual, uncultured bacteria, archaea, protists, and viral particles, obtained directly from marine and soil samples, in a single experiment. This approach may find diverse applications in microbiology and in biomedical and forensic studies of humans and other multicellular organisms.Single-cell genomics can be used to study uncultured microorganisms. Here, Stepanauskas et al. present a method combining improved multiple displacement amplification and FACS, to obtain genomic sequences and cell size information from uncultivated microbial cells and viral particles in environmental samples.}, }
@article {pmid28726632, year = {2017}, author = {Grau-Bové, X and Torruella, G and Donachie, S and Suga, H and Leonard, G and Richards, TA and Ruiz-Trillo, I}, title = {Dynamics of genomic innovation in the unicellular ancestry of animals.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, doi = {10.7554/eLife.26036}, pmid = {28726632}, issn = {2050-084X}, support = {616960//European Research Council/International ; }, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; *Genome, Protozoan ; Genomics ; }, abstract = {Which genomic innovations underpinned the origin of multicellular animals is still an open debate. Here, we investigate this question by reconstructing the genome architecture and gene family diversity of ancestral premetazoans, aiming to date the emergence of animal-like traits. Our comparative analysis involves genomes from animals and their closest unicellular relatives (the Holozoa), including four new genomes: three Ichthyosporea and Corallochytrium limacisporum. Here, we show that the earliest animals were shaped by dynamic changes in genome architecture before the emergence of multicellularity: an early burst of gene diversity in the ancestor of Holozoa, enriched in transcription factors and cell adhesion machinery, was followed by multiple and differently-timed episodes of synteny disruption, intron gain and genome expansions. Thus, the foundations of animal genome architecture were laid before the origin of complex multicellularity - highlighting the necessity of a unicellular perspective to understand early animal evolution.}, }
@article {pmid28719054, year = {2018}, author = {Plattner, H}, title = {Evolutionary Cell Biology of Proteins from Protists to Humans and Plants.}, journal = {The Journal of eukaryotic microbiology}, volume = {65}, number = {2}, pages = {255-289}, doi = {10.1111/jeu.12449}, pmid = {28719054}, issn = {1550-7408}, abstract = {During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while &quot;closed for repair work&quot; was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging &quot;evolutionary cell biology.&quot; Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca2+ channels in cilia and replacement by other types during evolution. Altogether components serving Ca2+ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca2+ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H+ -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in Paramecium. One of the most flexible proteins is centrin when its intracellular localization and function throughout evolution is traced. There are many more examples documenting evolutionary flexibility of translation products depending on requirements and potential for implantation within the actual cellular context at different levels of evolution. From estimates of gene and protein numbers per organism, it appears that much of the basic inventory of protozoan precursors could be transmitted to highest eukaryotic levels, with some losses and also with important additional &quot;inventions.&quot;}, }
@article {pmid28716924, year = {2017}, author = {Brawley, SH and Blouin, NA and Ficko-Blean, E and Wheeler, GL and Lohr, M and Goodson, HV and Jenkins, JW and Blaby-Haas, CE and Helliwell, KE and Chan, CX and Marriage, TN and Bhattacharya, D and Klein, AS and Badis, Y and Brodie, J and Cao, Y and Collén, J and Dittami, SM and Gachon, CMM and Green, BR and Karpowicz, SJ and Kim, JW and Kudahl, UJ and Lin, S and Michel, G and Mittag, M and Olson, BJSC and Pangilinan, JL and Peng, Y and Qiu, H and Shu, S and Singer, JT and Smith, AG and Sprecher, BN and Wagner, V and Wang, W and Wang, ZY and Yan, J and Yarish, C and Zäuner-Riek, S and Zhuang, Y and Zou, Y and Lindquist, EA and Grimwood, J and Barry, KW and Rokhsar, DS and Schmutz, J and Stiller, JW and Grossman, AR and Prochnik, SE}, title = {Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {31}, pages = {E6361-E6370}, doi = {10.1073/pnas.1703088114}, pmid = {28716924}, issn = {1091-6490}, support = {P20 GM103418/GM/NIGMS NIH HHS/United States ; P20 GM103638/GM/NIGMS NIH HHS/United States ; BB/1013164/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Actins/genetics ; Calcium Signaling/genetics ; Cell Cycle/genetics ; Cell Wall/genetics/metabolism ; Chromatin/genetics ; Cytoskeleton/*genetics ; *Evolution, Molecular ; Genome, Plant/*genetics ; Kinesin/genetics ; Phylogeny ; Porphyra/*cytology/*genetics ; }, abstract = {Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra, lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.}, }
@article {pmid28714591, year = {2017}, author = {Kloesener, MH and Bose, J and Schulte, RD}, title = {Experimental evolution with a multicellular host causes diversification within and between microbial parasite populations-Differences in emerging phenotypes of two different parasite strains.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {9}, pages = {2194-2205}, doi = {10.1111/evo.13306}, pmid = {28714591}, issn = {1558-5646}, mesh = {Animals ; *Bacillus thuringiensis ; Biological Evolution ; Caenorhabditis elegans/parasitology ; Genotype ; *Host-Parasite Interactions ; Parasites ; Phenotype ; Selection, Genetic ; }, abstract = {Host-parasite coevolution is predicted to have complex evolutionary consequences, potentially leading to the emergence of genetic and phenotypic diversity for both antagonists. However, little is known about variation in phenotypic responses to coevolution between different parasite strains exposed to the same experimental conditions. We infected Caenorhabditis elegans with one of two strains of Bacillus thuringiensis and either allowed the host and the parasite to experimentally coevolve (coevolution treatment) or allowed only the parasite to adapt to the host (one-sided parasite adaptation). By isolating single parasite clones from evolved populations, we found phenotypic diversification of the ancestral strain into distinct clones, which varied in virulence toward ancestral hosts and competitive ability against other parasite genotypes. Parasite phenotypes differed remarkably not only between the two strains, but also between and within different replicate populations, indicating diversification of the clonal population caused by selection. This study highlights that the evolutionary selection pressure mediated by a multicellular host causes phenotypic diversification, but not necessarily with the same phenotypic outcome for different parasite strains.}, }
@article {pmid28713189, year = {2017}, author = {Keijzer, F and Arnellos, A}, title = {The animal sensorimotor organization: a challenge for the environmental complexity thesis.}, journal = {Biology &amp; philosophy}, volume = {32}, number = {3}, pages = {421-441}, doi = {10.1007/s10539-017-9565-3}, pmid = {28713189}, issn = {0169-3867}, abstract = {Godfrey-Smith's environmental complexity thesis (ECT) is most often applied to multicellular animals and the complexity of their macroscopic environments to explain how cognition evolved. We think that the ECT may be less suited to explain the origins of the animal bodily organization, including this organization's potentiality for dealing with complex macroscopic environments. We argue that acquiring the fundamental sensorimotor features of the animal body may be better explained as a consequence of dealing with internal bodily-rather than environmental complexity. To press and elucidate this option, we develop the notion of an animal sensorimotor organization (ASMO) that derives from an internal coordination account for the evolution of early nervous systems. The ASMO notion is a reply to the question how a collection of single cells can become integrated such that the resulting multicellular organization becomes sensitive to and can manipulate macroscopic features of both the animal body and its environment. In this account, epithelial contractile tissues play the central role in the organization behind complex animal bodies. In this paper, we relate the ASMO concept to recent work on epithelia, which provides empirical evidence that supports central assumptions behind the ASMO notion. Second, we discuss to what extent the notion applies to basic animal architectures, exemplified by sponges and jellyfish. We conclude that the features exhibited by the ASMO are plausibly explained by internal constraints acting on and within this multicellular organization, providing a challenge for the role the ECT plays in this context.}, }
@article {pmid28709942, year = {2017}, author = {Leslie, MP and Shelton, DE and Michod, RE}, title = {Generation time and fitness tradeoffs during the evolution of multicellularity.}, journal = {Journal of theoretical biology}, volume = {430}, number = {}, pages = {92-102}, doi = {10.1016/j.jtbi.2017.07.007}, pmid = {28709942}, issn = {1095-8541}, mesh = {*Adaptation, Physiological ; *Biological Evolution ; Cell Differentiation ; Cell Survival ; Fertility ; *Genetic Fitness ; Models, Biological ; Time Factors ; }, abstract = {The evolution of multicellular organisms from their unicellular ancestors is an example of an evolutionary transition in individuality (ETI), i.e. a change in the units of selection and adaptation. The theory of ETIs poses particular challenges because, by definition, key theoretical constructs such as fitness are shifting during an ETI. Past work emphasized the importance of life history tradeoffs during ETIs in which lower level units form groups and become individuals at a higher level. In particular, it has been hypothesized that the convexity of the lower-level tradeoff between viability and fecundity changes with group size and determines the optimality of lower-level specialization in the fitness components of the group. This is important because lower-level specialization is a key indicator of higher-level individuality. Here we show that increasing generation time can increase the convexity of the lower-level viability-fecundity tradeoff. This effect is a novel hypothesis for the positive association between cell-group size and cellular specialization in a major model system for ETIs, the volvocine algae. The pattern in this clade is thought to be an example of a more general size-complexity rule. Our hypothesis is that larger groups have longer generation times and longer generation times lead to more convex lower-level viability-fecundity tradeoffs, which could account for specialization being optimal only in larger cell groups (colonies). We discuss the robustness of this effect to various changes in the assumptions of our model. Our work is important for the study of ETIs in general because viability and fecundity are fundamental components of fitness in all systems and because generation time is expected to be changing during many ETIs.}, }
@article {pmid28704372, year = {2017}, author = {Trail, F and Wang, Z and Stefanko, K and Cubba, C and Townsend, JP}, title = {The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi.}, journal = {PLoS genetics}, volume = {13}, number = {7}, pages = {e1006867}, doi = {10.1371/journal.pgen.1006867}, pmid = {28704372}, issn = {1553-7404}, mesh = {Bayes Theorem ; *Biological Evolution ; Fruiting Bodies, Fungal/genetics ; Fungi/genetics ; Gene Expression Regulation, Fungal/genetics ; Gene Knockout Techniques ; Genome, Fungal/*genetics ; Neurospora crassa/genetics ; Phenotype ; Phylogeny ; Sex Differentiation/*genetics ; Sordariales/genetics/growth &amp; development ; Transcriptome/*genetics ; }, abstract = {Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.}, }
@article {pmid28700638, year = {2017}, author = {Ashrafi, S and Helaly, S and Schroers, HJ and Stadler, M and Richert-Poeggeler, KR and Dababat, AA and Maier, W}, title = {Ijuhya vitellina sp. nov., a novel source for chaetoglobosin A, is a destructive parasite of the cereal cyst nematode Heterodera filipjevi.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180032}, doi = {10.1371/journal.pone.0180032}, pmid = {28700638}, issn = {1932-6203}, mesh = {Animals ; Hyphae/growth &amp; development ; Hypocreales/classification/genetics/metabolism/*pathogenicity ; Indole Alkaloids/*metabolism ; Oocytes/microbiology ; Phylogeny ; Tylenchoidea/growth &amp; development/microbiology ; }, abstract = {Cyst nematodes are globally important pathogens in agriculture. Their sedentary lifestyle and long-term association with the roots of host plants render cyst nematodes especially good targets for attack by parasitic fungi. In this context fungi were specifically isolated from nematode eggs of the cereal cyst nematode Heterodera filipjevi. Here, Ijuhya vitellina (Ascomycota, Hypocreales, Bionectriaceae), encountered in wheat fields in Turkey, is newly described on the basis of phylogenetic analyses, morphological characters and life-style related inferences. The species destructively parasitises eggs inside cysts of H. filipjevi. The parasitism was reproduced in in vitro studies. Infected eggs were found to harbour microsclerotia produced by I. vitellina that resemble long-term survival structures also known from other ascomycetes. Microsclerotia were also formed by this species in pure cultures obtained from both, solitarily isolated infected eggs obtained from fields and artificially infected eggs. Hyphae penetrating the eggshell colonised the interior of eggs and became transformed into multicellular, chlamydospore-like structures that developed into microsclerotia. When isolated on artificial media, microsclerotia germinated to produce multiple emerging hyphae. The specific nature of morphological structures produced by I. vitellina inside nematode eggs is interpreted as a unique mode of interaction allowing long-term survival of the fungus inside nematode cysts that are known to survive periods of drought or other harsh environmental conditions. Generic classification of the new species is based on molecular phylogenetic inferences using five different gene regions. I. vitellina is the only species of the genus known to parasitise nematodes and produce microsclerotia. Metabolomic analyses revealed that within the Ijuhya species studied here, only I. vitellina produces chaetoglobosin A and its derivate 19-O-acetylchaetoglobosin A. Nematicidal and nematode-inhibiting activities of these compounds have been demonstrated suggesting that the production of these compounds may represent an adaptation to nematode parasitism.}, }
@article {pmid28683136, year = {2017}, author = {Ballinger, MJ and Perlman, SJ}, title = {Generality of toxins in defensive symbiosis: Ribosome-inactivating proteins and defense against parasitic wasps in Drosophila.}, journal = {PLoS pathogens}, volume = {13}, number = {7}, pages = {e1006431}, doi = {10.1371/journal.ppat.1006431}, pmid = {28683136}, issn = {1553-7374}, mesh = {Animals ; Bacterial Proteins/genetics/metabolism/*toxicity ; Bacterial Toxins/genetics/metabolism/*toxicity ; Biological Evolution ; Drosophila/genetics/*microbiology/*parasitology/physiology ; Larva/genetics/microbiology/parasitology/physiology ; Ribosome Inactivating Proteins/genetics/metabolism/*toxicity ; Spiroplasma/genetics/*metabolism ; *Symbiosis ; Wasps/*drug effects/physiology ; }, abstract = {While it has become increasingly clear that multicellular organisms often harbor microbial symbionts that protect their hosts against natural enemies, the mechanistic underpinnings underlying most defensive symbioses are largely unknown. Spiroplasma bacteria are widespread associates of terrestrial arthropods, and include strains that protect diverse Drosophila flies against parasitic wasps and nematodes. Recent work implicated a ribosome-inactivating protein (RIP) encoded by Spiroplasma, and related to Shiga-like toxins in enterohemorrhagic Escherichia coli, in defense against a virulent parasitic nematode in the woodland fly, Drosophila neotestacea. Here we test the generality of RIP-mediated protection by examining whether Spiroplasma RIPs also play a role in wasp protection, in D. melanogaster and D. neotestacea. We find strong evidence for a major role of RIPs, with ribosomal RNA (rRNA) from the larval endoparasitic wasps, Leptopilina heterotoma and Leptopilina boulardi, exhibiting the hallmarks of RIP activity. In Spiroplasma-containing hosts, parasitic wasp ribosomes show abundant site-specific depurination in the α-sarcin/ricin loop of the 28S rRNA, with depurination occurring soon after wasp eggs hatch inside fly larvae. Interestingly, we found that the pupal ectoparasitic wasp, Pachycrepoideus vindemmiae, escapes protection by Spiroplasma, and its ribosomes do not show high levels of depurination. We also show that fly ribosomes show little evidence of targeting by RIPs. Finally, we find that the genome of D. neotestacea's defensive Spiroplasma encodes a diverse repertoire of RIP genes, which are differ in abundance. This work suggests that specificity of defensive symbionts against different natural enemies may be driven by the evolution of toxin repertoires, and that toxin diversity may play a role in shaping host-symbiont-enemy interactions.}, }
@article {pmid28682226, year = {2017}, author = {El Kafsi, H and Gorochov, G and Larsen, M}, title = {.}, journal = {Biologie aujourd'hui}, volume = {211}, number = {1}, pages = {39-49}, doi = {10.1051/jbio/2017010}, pmid = {28682226}, issn = {2105-0686}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics/*immunology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Immune System/metabolism/*physiology ; Immunity, Cellular/physiology ; Immunity, Humoral/physiology ; Immunoglobulin A, Secretory/physiology ; Inheritance Patterns ; Symbiosis/*genetics/*immunology ; }, abstract = {Genetic evolution of multicellular organisms occurred as a response to environmental challenges, in particular competition for nutrients, climatic change, physical and chemical stressors and pathogens. However organism fitness depends on both the efficiency of its defences and its capacities for benefiting from its symbiotic organisms. Indeed microbes not only engender pathogenies, but enable efficient uptake of host non-self biodegradable nutriments. Furthermore, microbes play an important role in the development of host immunity. We shall review here the associations between some specific genes of the host, microbiota and the immune system. Recent genome-wide association studies disclose that symbiosis between host and microbiota results from a stringent genetic co-evolution. On the other hand, a microbe subset isolated from murine and human microbiotes has been identified on the basis of its interaction with both the host genetics and immunity. Remarkably, microbes which have two such connections are taxonomically related. The best performing bacterial genuses in these two perspectives are Bifidobacterium, Lactobacillus and Akkermansia. We conclude that future therapies targeting microbiota within the framework of chronic inflammatory diseases must consider together host immune and genetic characters associated with microbiota homeostasis.}, }
@article {pmid28681487, year = {2017}, author = {Wloch-Salamon, DM and Fisher, RM and Regenberg, B}, title = {Division of labour in the yeast: Saccharomyces cerevisiae.}, journal = {Yeast (Chichester, England)}, volume = {34}, number = {10}, pages = {399-406}, doi = {10.1002/yea.3241}, pmid = {28681487}, issn = {1097-0061}, mesh = {Adaptation, Physiological ; Apoptosis ; Biofilms/growth &amp; development ; Biological Evolution ; Phenotype ; Resting Phase, Cell Cycle ; Saccharomyces cerevisiae/genetics/*physiology ; }, abstract = {Division of labour between different specialized cell types is a central part of how we describe complexity in multicellular organisms. However, it is increasingly being recognized that division of labour also plays an important role in the lives of predominantly unicellular organisms. Saccharomyces cerevisiae displays several phenotypes that could be considered a division of labour, including quiescence, apoptosis and biofilm formation, but they have not been explicitly treated as such. We discuss each of these examples, using a definition of division of labour that involves phenotypic variation between cells within a population, cooperation between cells performing different tasks and maximization of the inclusive fitness of all cells involved. We then propose future research directions and possible experimental tests using S. cerevisiae as a model organism for understanding the genetic mechanisms and selective pressures that can lead to the evolution of the very first stages of a division of labour. Copyright © 2017 John Wiley &amp; Sons, Ltd.}, }
@article {pmid28679746, year = {2017}, author = {Lyons, NA and Kolter, R}, title = {Bacillus subtilis Protects Public Goods by Extending Kin Discrimination to Closely Related Species.}, journal = {mBio}, volume = {8}, number = {4}, pages = {}, doi = {10.1128/mBio.00723-17}, pmid = {28679746}, issn = {2150-7511}, support = {R01 GM058213/GM/NIGMS NIH HHS/United States ; }, mesh = {*Antibiosis ; Bacillus/physiology ; Bacillus subtilis/*genetics/*physiology ; Bacterial Proteins/metabolism ; Biofilms ; Biological Evolution ; Biota ; Gene Expression Regulation, Bacterial ; Microbial Interactions ; Phenotype ; Phylogeny ; }, abstract = {Kin discrimination systems are found in numerous communal contexts like multicellularity and are theorized to prevent exploitation of cooperative behaviors. The kin discrimination system in Bacillus subtilis differs from most other such systems because it excludes nonkin cells rather than including kin cells. Because nonkin are the target of the system, B. subtilis can potentially distinguish degrees of nonkin relatedness, not just kin versus nonkin. We examined this by testing a large strain collection of diverse Bacillus species against B. subtilis in different multicellular contexts. The effects of kin discrimination extend to nearby species, as the other subtilis clade species were treated with the same antagonism as nonkin. Species in the less-related pumilus clade started to display varied phenotypes but were mostly still discriminated against, while cereus clade members and beyond were no longer subject to kin discrimination. Seeking a reason why other species are perceived as antagonistic nonkin, we tested the ability of B. subtilis to steal communally produced surfactant from these species. We found that the species treated as nonkin were the only ones that made a surfactant that B. subtilis could utilize and that nonkin antagonism prevented such stealing when the two strains were mixed. The nonkin exclusion kin discrimination method thus allows effective protection of the cooperative behaviors prevalent in multicellularity while still permitting interactions with more distant species that are not a threat.IMPORTANCE Multicellular systems like bacterial biofilms and swarms rely on cooperative behaviors that could be undermined by exploitative invaders. Discriminating kin from nonkin is one way to help guard against such exploitation but has thus far been examined only intraspecifically, so the phylogenetic range of this important trait is unknown. We tested whether Bacillus subtilis treats other species as nonkin by testing a single strain against a diverse collection of Bacillus isolates. We found that the species in the same clade were treated as nonkin, which then lessened in more distant relatives. Further experiments showed that these nonkin species produced a cooperative good that could be stolen by B. subtilis and that treating each other as nonkin largely prevented this exploitation. These results impact our understanding of interspecies interactions, as bacterial populations can interact only after they have diverged enough to no longer be a threat to their cooperative existences.}, }
@article {pmid28673540, year = {2017}, author = {Song, Y and Botvinnik, OB and Lovci, MT and Kakaradov, B and Liu, P and Xu, JL and Yeo, GW}, title = {Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation.}, journal = {Molecular cell}, volume = {67}, number = {1}, pages = {148-161.e5}, doi = {10.1016/j.molcel.2017.06.003}, pmid = {28673540}, issn = {1097-4164}, support = {R01 AI095277/AI/NIAID NIH HHS/United States ; R01 AI123202/AI/NIAID NIH HHS/United States ; P30 NS047101/NS/NINDS NIH HHS/United States ; R01 HG004659/HG/NHGRI NIH HHS/United States ; U19 MH107367/MH/NIMH NIH HHS/United States ; R01 HD085902/HD/NICHD NIH HHS/United States ; R01 NS075449/NS/NINDS NIH HHS/United States ; }, mesh = {Algorithms ; *Alternative Splicing ; Bayes Theorem ; Cell Line ; Computer Simulation ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Humans ; Kinetics ; Male ; Models, Genetic ; Nerve Tissue Proteins/*biosynthesis/genetics ; Neural Stem Cells/*metabolism ; *Neurogenesis ; Neurons/*metabolism ; Phenotype ; Pluripotent Stem Cells/*metabolism ; RNA, Messenger/genetics/*metabolism ; *Single-Cell Analysis ; }, abstract = {Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational framework consisting of outrigger, a de novo splice graph transversal algorithm to detect AS; anchor, a Bayesian approach to assign modalities; and bonvoyage, a visualization tool using non-negative matrix factorization to display modality changes. Applying Expedition to single pluripotent stem cells undergoing neuronal differentiation, we discover that up to 20% of AS exons exhibit bimodality. Bimodal exons are flanked by more conserved intronic sequences harboring distinct cis-regulatory motifs, constitute much of cell-type-specific splicing, are highly dynamic during cellular transitions, preserve reading frame, and reveal intricacy of cell states invisible to conventional gene expression analysis. Systematic AS characterization in single cells redefines our understanding of AS complexity in cell biology.}, }
@article {pmid28669817, year = {2017}, author = {Timoshevskiy, VA and Lampman, RT and Hess, JE and Porter, LL and Smith, JJ}, title = {Deep ancestry of programmed genome rearrangement in lampreys.}, journal = {Developmental biology}, volume = {429}, number = {1}, pages = {31-34}, doi = {10.1016/j.ydbio.2017.06.032}, pmid = {28669817}, issn = {1095-564X}, support = {R01 GM104123/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA/metabolism ; Gene Rearrangement/*genetics ; *Genome ; Germ Cells/metabolism ; Lampreys/*genetics ; *Phylogeny ; }, abstract = {In most multicellular organisms, the structure and content of the genome is rigorously maintained over the course of development. However some species have evolved genome biologies that permit, or require, developmentally regulated changes in the physical structure and content of the genome (programmed genome rearrangement: PGR). Relatively few vertebrates are known to undergo PGR, although all agnathans surveyed to date (several hagfish and one lamprey: Petromyzon marinus) show evidence of large scale PGR. To further resolve the ancestry of PGR within vertebrates, we developed probes that allow simultaneous tracking of nearly all sequences eliminated by PGR in P. marinus and a second lamprey species (Entosphenus tridentatus). These comparative analyses reveal conserved subcellular structures (lagging chromatin and micronuclei) associated with PGR and provide the first comparative embryological evidence in support of the idea that PGR represents an ancient and evolutionarily stable strategy for regulating inherent developmental/genetic conflicts between germline and soma.}, }
@article {pmid28663071, year = {2017}, author = {Rosa-Fernandes, L and Maselli, LMF and Maeda, NY and Palmisano, G and Bydlowski, SP}, title = {Outside-in, inside-out: Proteomic analysis of endothelial stress mediated by 7-ketocholesterol.}, journal = {Chemistry and physics of lipids}, volume = {207}, number = {Pt B}, pages = {231-238}, doi = {10.1016/j.chemphyslip.2017.06.008}, pmid = {28663071}, issn = {1873-2941}, mesh = {Cell Survival/drug effects ; Cells, Cultured ; Computational Biology ; Dose-Response Relationship, Drug ; Human Umbilical Vein Endothelial Cells/*drug effects ; Humans ; Ketocholesterols/*pharmacology ; Mass Spectrometry ; Oxidative Stress/*drug effects ; Platelet Aggregation/drug effects ; *Proteomics ; Structure-Activity Relationship ; }, abstract = {Oxysterols are cholesterol oxidation products formed through enzymatic or autoxidation mechanisms. 7-ketocholeterol (7KC) is one of most abundant oxysterols found in atherosclerotic lesions. Its role in atherosclerosis pathogenesis has been broadly studied in a variety of models. The arterial microenvironment is a multicellular dynamic compartment that, among other systemic factors, is continuously stimulated by 7KC. Endothelial cells have a key role on that environment, being in intimate contact with both the blood stream and the vessel wall, the site of disease origin. 7KC has been shown to promote endothelial cell death and/or dysfunction, depending on its concentration. However, its contribution to the cell microenvironment through cell stimulation has not received much attention. Here we applied mass spectrometry-based proteomics followed by bioinformatics workflow to analyze the effect of a non-toxic 7KC concentration on endothelial cell protein expression and secretion in vitro. Trypsin digests were prepared from the secretome of the endothelial cells and from the total cell pellet after 24h exposure to 7KC. All samples were analyzed by high resolution and accurate mass nano-LC MS/MS. After database search and statistical analysis, differentially expressed proteins were selected for further studies. Our workflow identified 1805 secreted proteins and 2203 intracellular proteins, and of these, 48 and 53, respectively, were regulated. Regulated proteins upon 7KC exposure are involved in unfolded protein response, vascular homeostasis, and reduced control of angiogenesis. Moreover, blood coagulation was another main pathway regulated through Tissue Factor Pathway Inhibitor (TFPI), an antithrombotic agent associated with coronary disease that we found to be more than 2 times downregulated. Taken together, these data show differential endothelial protein regulation and secretion upon 7KC exposure for short time periods under non-toxic conditions. Herewith, these data support the role of 7KC in atherosclerosis pathophysiology and thus reinforce the deleterious effect of endothelial cells stress in the arterial microenvironment.}, }
@article {pmid28648822, year = {2017}, author = {Hehenberger, E and Tikhonenkov, DV and Kolisko, M and Del Campo, J and Esaulov, AS and Mylnikov, AP and Keeling, PJ}, title = {Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals.}, journal = {Current biology : CB}, volume = {27}, number = {13}, pages = {2043-2050.e6}, doi = {10.1016/j.cub.2017.06.006}, pmid = {28648822}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*classification/genetics/*physiology ; Evolution, Molecular ; Fetal Proteins/genetics/metabolism ; *Predatory Behavior ; RNA, Ribosomal, 18S/genetics ; *Signal Transduction ; T-Box Domain Proteins/genetics/metabolism ; }, abstract = {Our understanding of the origin of animals has been transformed by characterizing their most closely related, unicellular sisters: the choanoflagellates, filastereans, and ichthyosporeans. Together with animals, these lineages make up the Holozoa [1, 2]. Many traits previously considered &quot;animal specific&quot; were subsequently found in other holozoans [3, 4], showing that they evolved before animals, although exactly when is currently uncertain because several key relationships remain unresolved [2, 5]. Here we report the morphology and transcriptome sequencing from three novel unicellular holozoans: Pigoraptor vietnamica and Pigoraptor chileana, which are related to filastereans, and Syssomonas multiformis, which forms a new lineage with Corallochytrium in phylogenomic analyses. All three species are predatory flagellates that feed on large eukaryotic prey, and all three also appear to exhibit complex life histories with several distinct stages, including multicellular clusters. Examination of genes associated with multicellularity in animals showed that the new filastereans contain a cell-adhesion gene repertoire similar to those of other species in this group. Syssomonas multiformis possessed a smaller complement overall but does encode genes absent from the earlier-branching ichthyosporeans. Analysis of the T-box transcription factor domain showed expansion of T-box transcription factors based on combination with a non-T-box domain (a receiver domain), which has not been described outside of vertebrates. This domain and other domains we identified in all unicellular holozoans are part of the two-component signaling system that has been lost in animals, suggesting the continued use of this system in the closest relatives of animals and emphasizing the importance of studying loss of function as well as gain in major evolutionary transitions.}, }
@article {pmid28637850, year = {2017}, author = {Heim, NA and Payne, JL and Finnegan, S and Knope, ML and Kowalewski, M and Lyons, SK and McShea, DW and Novack-Gottshall, PM and Smith, FA and Wang, SC}, title = {Hierarchical complexity and the size limits of life.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1857}, pages = {}, doi = {10.1098/rspb.2017.1039}, pmid = {28637850}, issn = {1471-2954}, mesh = {*Biological Evolution ; Earth (Planet) ; *Eukaryota ; *Prokaryotic Cells ; }, abstract = {Over the past 3.8 billion years, the maximum size of life has increased by approximately 18 orders of magnitude. Much of this increase is associated with two major evolutionary innovations: the evolution of eukaryotes from prokaryotic cells approximately 1.9 billion years ago (Ga), and multicellular life diversifying from unicellular ancestors approximately 0.6 Ga. However, the quantitative relationship between organismal size and structural complexity remains poorly documented. We assessed this relationship using a comprehensive dataset that includes organismal size and level of biological complexity for 11 172 extant genera. We find that the distributions of sizes within complexity levels are unimodal, whereas the aggregate distribution is multimodal. Moreover, both the mean size and the range of size occupied increases with each additional level of complexity. Increases in size range are non-symmetric: the maximum organismal size increases more than the minimum. The majority of the observed increase in organismal size over the history of life on the Earth is accounted for by two discrete jumps in complexity rather than evolutionary trends within levels of complexity. Our results provide quantitative support for an evolutionary expansion away from a minimal size constraint and suggest a fundamental rescaling of the constraints on minimal and maximal size as biological complexity increases.}, }
@article {pmid28637420, year = {2017}, author = {Baig, AM and Rana, Z and Tariq, SS and Ahmad, HR}, title = {Bioinformatic Insights on Target Receptors of Amiodarone in Human and Acanthamoeba castellanii.}, journal = {Infectious disorders drug targets}, volume = {17}, number = {3}, pages = {160-177}, doi = {10.2174/1871526517666170622075154}, pmid = {28637420}, issn = {2212-3989}, mesh = {Acanthamoeba castellanii/chemistry/*drug effects/metabolism ; Amiodarone/*metabolism/*pharmacology ; Calcium Channels/*chemistry/genetics ; *Computational Biology ; Cytochrome P-450 CYP3A/*chemistry/genetics ; Humans ; Intramolecular Transferases/chemistry/genetics ; Ligands ; Models, Molecular ; Protein Binding ; Protozoan Proteins/*chemistry/metabolism ; Sequence Homology, Amino Acid ; Trypanosoma cruzi/chemistry/drug effects/genetics ; }, abstract = {BACKGROUND: Amiodarone is prescribed for certain cardiac arrhythmias in current medical practice. The drug targets and inhibits voltage dependent sodium (Na+ v), calcium (Ca+2 v), potassium (K+ v) channels, enzymes like cytochrome P450 and oxidosqualene cyclase. Past studies have shown that amiodarone exerts antiparasitic effects against Trypanosoma cruzi and Acanthamoeba castellanii.<br><br>OBJECTIVES: The presence of aforementioned targets and the type of cell death induced by amiodarone in pathogenic eukaryotes like Acanthamoeba castellanii remains to be established. We inferred the presence of homologous targets of amiodarone in A. castellanii compared with humans.<br><br>METHODS: This study used bioinformatics exploration for amino acid sequence homology, ligand binding attribute predictions, 3D structural model development, and experimental assays that highlight similarity between certain target proteins in Acanthamoeba as compared to humans.<br><br>RESULTS: The sequence identity scores for amino acids and 3D models show that A. castellanii expresses similar types of targets of amiodarone like Na+ v - K+1 v channels, cytochrome P450 3A4, and lanosterol synthase (oxidosqualene cyclase). We show that even though human like L-type and two pore Ca+2 channels are present in A. castellanii, there was no evidence of the expression of T-type voltage dependent Ca+2 channels. Growth assays showed amoebicidal and amoebistatic effects at doses of 40-80μg/ml.<br><br>CONCLUSION: The existing bioinformatics tools, ligand binding attribute prediction, and model building offer a specific method to establish homology of proteins, discover drug targets, and facilitate the investigation of the evolution of several types of cardinal ion channels from unicellular eukaryotes to multicellular species as humans.}, }
@article {pmid28633034, year = {2017}, author = {Nagy, LG}, title = {Evolution: Complex Multicellular Life with 5,500 Genes.}, journal = {Current biology : CB}, volume = {27}, number = {12}, pages = {R609-R612}, doi = {10.1016/j.cub.2017.04.032}, pmid = {28633034}, issn = {1879-0445}, abstract = {The origin of complex multicellularity was a major transition in evolution and is generally associated with higher genomic complexity. However, some complex multicellular fungi defy this principle, having small genomes that resemble those of unicellular yeasts rather than those of other complex multicellular organisms.}, }
@article {pmid28631149, year = {2017}, author = {Krsmanovic, P}, title = {Vigor of survival determinism: subtle evolutionary gradualism interspersed with robust phylogenetic leaping.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {136}, number = {3-4}, pages = {141-151}, doi = {10.1007/s12064-017-0251-4}, pmid = {28631149}, issn = {1611-7530}, mesh = {Animals ; *Biological Evolution ; Caenorhabditis elegans ; Cell Lineage ; Drosophila melanogaster ; Female ; Genetic Drift ; Genetic Variation ; Genetics, Population ; Genomics ; Male ; Models, Genetic ; Mutagenesis ; Mutation ; *Phylogeny ; Saccharomyces cerevisiae ; *Selection, Genetic ; Stochastic Processes ; }, abstract = {Discussions of the survival determinism concept have previously focused on its primary role in the evolution of early unicellular organisms in the light of findings which have been reported on a number of diseases. The rationale for such parallel was in the view according to which multicellular organisms could be regarded as sophisticated colonies of semi-autonomous, single-celled entities, whereby various diseases were described as conditions arising upon the activation of the respective survival mechanisms in a milieu unsuitable for such robust stress response. The cellular mechanisms that were discussed in these contexts have been known to play various roles in other biological processes. The proposed notion could thereby be further extended to discussion on mechanisms for the implementation of the respective survival pathways in the development of metazoa, considering that they would have been propagated in their evolution for so long. This manuscript first presents a concise overview of the model previously discussed, followed by the discussion on the role of respective mechanism(s) in origins and development of metazoa. Finally, a reflection on the concept in relation to the prominent evolutionary models is put forward to illustrate a broader context of what is being discussed.}, }
@article {pmid28630027, year = {2017}, author = {Sapir, L and Tzlil, S}, title = {Talking over the extracellular matrix: How do cells communicate mechanically?.}, journal = {Seminars in cell &amp; developmental biology}, volume = {71}, number = {}, pages = {99-105}, doi = {10.1016/j.semcdb.2017.06.010}, pmid = {28630027}, issn = {1096-3634}, mesh = {Animals ; Biomechanical Phenomena ; Cell Communication ; Cell Movement ; *Extracellular Matrix ; Humans ; Myocardium/cytology ; }, abstract = {Communication between cells enables them to coordinate their activity and is crucial for the differentiation, development, and function of tissues and multicellular organisms. Cell-cell communication is discussed almost exclusively as having a chemical or electrical origin. Only recently, a new mode of cell communication was elucidated: mechanical communication through the extracellular matrix (ECM). Cells can communicate mechanically by responding either to mechanical deformations generated by their neighbors or to a change in the mechanical properties of the ECM induced by a neighboring cell. This newly resolved mode of communication possesses unique features that complement the cellular ability to receive and share information, and to consequently act in a cooperative way with surrounding cells. Herein, we review several examples of mechanical communication, discuss their unique properties, and comment on the major challenges facing the field.}, }
@article {pmid28629791, year = {2017}, author = {Xie, N and Ruprich-Robert, G and Chapeland-Leclerc, F and Coppin, E and Lalucque, H and Brun, S and Debuchy, R and Silar, P}, title = {Inositol-phosphate signaling as mediator for growth and sexual reproduction in Podospora anserina.}, journal = {Developmental biology}, volume = {429}, number = {1}, pages = {285-305}, doi = {10.1016/j.ydbio.2017.06.017}, pmid = {28629791}, issn = {1095-564X}, mesh = {Amino Acid Sequence ; Cell Nucleus/metabolism ; Fertility ; Fruiting Bodies, Fungal/metabolism ; Fungal Proteins/chemistry/metabolism ; Genes, Fungal ; Green Fluorescent Proteins/metabolism ; Inositol/metabolism ; Inositol Phosphates/*metabolism ; MAP Kinase Signaling System ; Mosaicism ; Mutation/genetics ; Phenotype ; Pigments, Biological/metabolism ; Podospora/enzymology/genetics/*growth &amp; development/*metabolism ; Protein Transport ; Reproduction ; *Signal Transduction ; Sordariales/metabolism ; Spores, Fungal/metabolism ; Temperature ; Zygote/metabolism ; }, abstract = {The molecular pathways involved in the development of multicellular fruiting bodies in fungi are still not well known. Especially, the interplay between the mycelium, the female tissues and the zygotic tissues of the fruiting bodies is poorly documented. Here, we describe PM154, a new strain of the model ascomycetes Podospora anserina able to mate with itself and that enabled the easy recovery of new mutants affected in fruiting body development. By complete genome sequencing of spod1, one of the new mutants, we identified an inositol phosphate polykinase gene as essential, especially for fruiting body development. A factor present in the wild type and diffusible in mutant hyphae was able to induce the development of the maternal tissues of the fruiting body in spod1, but failed to promote complete development of the zygotic ones. Addition of myo-inositol in the growth medium was able to increase the number of developing fruiting bodies in the wild type, but not in spod1. Overall, the data indicated that inositol and inositol polyphosphates were involved in promoting fruiting body maturation, but also in regulating the number of fruiting bodies that developed after fertilization. The same effect of inositol was seen in two other fungi, Sordaria macrospora and Chaetomium globosum. Key role of the inositol polyphosphate pathway during fruiting body maturation appears thus conserved during the evolution of Sordariales fungi.}, }
@article {pmid28627239, year = {2017}, author = {Csaba, G}, title = {Complex multicellular functions at a unicellular eukaryote level: Learning, memory, and immunity.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {64}, number = {2}, pages = {105-120}, doi = {10.1556/030.64.2017.013}, pmid = {28627239}, issn = {1217-8950}, mesh = {Animals ; Eukaryota/genetics/*immunology/*physiology ; Humans ; Learning ; Memory ; }, abstract = {According to experimental data, eukaryote unicellulars are able to learn, have immunity and memory. Learning is carried out in a very primitive form, and the memory is not neural but an epigenetic one. However, this epigenetic memory, which is well justified by the presence and manifestation of hormonal imprinting, is strong and permanent in the life of cell and also in its progenies. This memory is epigenetically executed by the alteration and fixation of methylation pattern of genes without changes in base sequences. The immunity of unicellulars is based on self/non-self discrimination, which leads to the destruction of non-self invaders and utilization of them as nourishment (by phagocytosis). The tools of learning, memory, and immunity of unicellulars are uniformly found in plasma membrane receptors, which formed under the effect of dynamic receptor pattern generation, suggested by Koch et al., and this is the basis of hormonal imprinting, by which the encounter between a chemical substance and the cell is specifically memorized. The receptors and imprinting are also used in the later steps of evolution up to mammals (including man) in each mentioned functions. This means that learning, memory, and immunity can be deduced to a unicellular eukaryote level.}, }
@article {pmid28610890, year = {2017}, author = {Brodie, J and Chan, CX and De Clerck, O and Cock, JM and Coelho, SM and Gachon, C and Grossman, AR and Mock, T and Raven, JA and Smith, AG and Yoon, HS and Bhattacharya, D}, title = {The Algal Revolution.}, journal = {Trends in plant science}, volume = {22}, number = {8}, pages = {726-738}, doi = {10.1016/j.tplants.2017.05.005}, pmid = {28610890}, issn = {1878-4372}, mesh = {Biodiversity ; Biological Evolution ; Biotechnology ; Ecology ; Gene Transfer, Horizontal ; *Photosynthesis ; Stramenopiles/*genetics/physiology ; Symbiosis ; }, abstract = {Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput 'omic' and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.}, }
@article {pmid28605523, year = {2017}, author = {Vergara, Z and Sequeira-Mendes, J and Morata, J and Peiró, R and Hénaff, E and Costas, C and Casacuberta, JM and Gutierrez, C}, title = {Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin.}, journal = {Nucleic acids research}, volume = {45}, number = {14}, pages = {8358-8368}, doi = {10.1093/nar/gkx524}, pmid = {28605523}, issn = {1362-4962}, mesh = {Arabidopsis/cytology/*genetics/metabolism ; Cell Line ; Chromatin/genetics/metabolism ; Chromosome Mapping ; *DNA Replication ; DNA, Plant/genetics/metabolism ; GC Rich Sequence/genetics ; Genome, Plant/genetics ; Heterochromatin/*genetics/metabolism ; Histones/metabolism ; Lysine/metabolism ; Methylation ; Microscopy, Confocal ; Replication Origin/*genetics ; Retroelements/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic ; }, abstract = {Genomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. The DNA and chromatin features determining ORI specification are not presently known. We have generated a high-resolution genome-wide map of 3230 ORIs in cultured Arabidopsis thaliana cells. Here, we focused on defining the features associated with ORIs in heterochromatin. In pericentromeric gene-poor domains ORIs associate almost exclusively with the retrotransposon class of transposable elements (TEs), in particular of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with retrotransposons is determined by their transposition mechanism based on transcription, and a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin and of the entire genome.}, }
@article {pmid28603898, year = {2017}, author = {Dhouailly, D and Godefroit, P and Martin, T and Nonchev, S and Caraguel, F and Oftedal, O}, title = {Getting to the root of scales, feather and hair: As deep as odontodes?.}, journal = {Experimental dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/exd.13391}, pmid = {28603898}, issn = {1600-0625}, abstract = {While every jawed vertebrate, or its recent ancestor, possesses teeth, skin appendages are characteristic of the living clades: skin denticles (odontodes) in chondrichthyans, dermal scales in teleosts, ducted multicellular glands in amphibians, epidermal scales in squamates, feathers in birds and hair-gland complexes in mammals, all of them showing a dense periodic patterning. While the odontode origin of teleost scales is generally accepted, the origin of both feather and hair is still debated. They appear long before mammals and birds, at least in the Jurassic in mammaliaforms and in ornithodires (pterosaurs and dinosaurs), and are contemporary to scales of early squamates. Epidermal scales might have appeared several times in evolution, and basal amniotes could not have developed a scaled dry integument, as the function of hair follicle requires its association with glands. In areas such as amnion, cornea or plantar pads, the formation of feather and hair is prevented early in embryogenesis, but can be easily reverted by playing with the Wnt/BMP/Shh pathways, which both imply the plasticity and the default competence of ectoderm. Conserved ectodermal/mesenchymal signalling pathways lead to placode formation, while later the crosstalk differs, as well as the final performing tissue(s): both epidermis and dermis for teeth and odontodes, mostly dermis for teleosts scales and only epidermis for squamate scale, feather and hair. We therefore suggest that tooth, dermal scale, epidermal scale, feather and hair evolved in parallel from a shared placode/dermal cell unit, which was present in a common ancestor, an early vertebrate gnathostome with odontodes, ca. 420 million years ago.}, }
@article {pmid28592899, year = {2017}, author = {Nan, F and Feng, J and Lv, J and Liu, Q and Fang, K and Gong, C and Xie, S}, title = {Origin and evolutionary history of freshwater Rhodophyta: further insights based on phylogenomic evidence.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2934}, doi = {10.1038/s41598-017-03235-5}, pmid = {28592899}, issn = {2045-2322}, abstract = {Freshwater representatives of Rhodophyta were sampled and the complete chloroplast and mitochondrial genomes were determined. Characteristics of the chloroplast and mitochondrial genomes were analyzed and phylogenetic relationship of marine and freshwater Rhodophyta were reconstructed based on the organelle genomes. The freshwater member Compsopogon caeruleus was determined for the largest chloroplast genome among multicellular Rhodophyta up to now. Expansion and subsequent reduction of both the genome size and GC content were observed in the Rhodophyta except for the freshwater Compsopogon caeruleus. It was inferred that the freshwater members of Rhodophyta occurred through diverse origins based on evidence of genome size, GC-content, phylogenomic analysis and divergence time estimation. The freshwater species Compsopogon caeruleus and Hildenbrandia rivularis originated and evolved independently at the inland water, whereas the Bangia atropurpurea, Batrachospermum arcuatum and Thorea hispida are derived from the marine relatives. The typical freshwater representatives Thoreales and Batrachospermales are probably derived from the marine relative Palmaria palmata at approximately 415-484 MYA. The origin and evolutionary history of freshwater Rhodophyta needs to be testified with more organelle genome sequences and wider global sampling.}, }
@article {pmid28588313, year = {2017}, author = {Salmeán, AA and Duffieux, D and Harholt, J and Qin, F and Michel, G and Czjzek, M and Willats, WGT and Hervé, C}, title = {Insoluble (1 → 3), (1 → 4)-β-D-glucan is a component of cell walls in brown algae (Phaeophyceae) and is masked by alginates in tissues.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2880}, doi = {10.1038/s41598-017-03081-5}, pmid = {28588313}, issn = {2045-2322}, abstract = {Brown algae are photosynthetic multicellular marine organisms. They belong to the phylum of Stramenopiles, which are not closely related to land plants and green algae. Brown algae share common evolutionary features with other photosynthetic and multicellular organisms, including a carbohydrate-rich cell-wall. Brown algal cell walls are composed predominantly of the polyanionic polysaccharides alginates and fucose-containing sulfated polysaccharides. These polymers are prevalent over neutral and crystalline components, which are believed to be mostly, if not exclusively, cellulose. In an attempt to better understand brown algal cell walls, we performed an extensive glycan array analysis of a wide range of brown algal species. Here we provide the first demonstration that mixed-linkage (1 → 3), (1 → 4)-β-D-glucan (MLG) is common in brown algal cell walls. Ultra-Performance Liquid Chromatography analyses indicate that MLG in brown algae solely consists of trisaccharide units of contiguous (1 → 4)-β-linked glucose residues joined by (1 → 3)-β-linkages. This regular conformation may allow long stretches of the molecule to align and to form well-structured microfibrils. At the tissue level, immunofluorescence studies indicate that MLG epitopes in brown algae are unmasked by a pre-treatment with alginate lyases to remove alginates. These findings are further discussed in terms of the origin and evolution of MLG in the Stramenopile lineage.}, }
@article {pmid28584082, year = {2017}, author = {Vergara, HM and Bertucci, PY and Hantz, P and Tosches, MA and Achim, K and Vopalensky, P and Arendt, D}, title = {Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of Platynereis dumerilii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {23}, pages = {5878-5885}, doi = {10.1073/pnas.1610602114}, pmid = {28584082}, issn = {1091-6490}, mesh = {Algorithms ; Animals ; *Biological Evolution ; Body Patterning/genetics ; Cell Differentiation ; Gene Expression Profiling/methods ; Gene Expression Regulation, Developmental ; Models, Biological ; Neurons/cytology ; Polychaeta/cytology/*genetics ; }, abstract = {The comparative study of cell types is a powerful approach toward deciphering animal evolution. To avoid selection biases, however, comparisons ideally involve all cell types present in a multicellular organism. Here, we use image registration and a newly developed &quot;Profiling by Signal Probability Mapping&quot; algorithm to generate a cellular resolution 3D expression atlas for an entire animal. We investigate three-segmented young worms of the marine annelid Platynereis dumerilii, with a rich diversity of differentiated cells present in relatively low number. Starting from whole-mount expression images for close to 100 neural specification and differentiation genes, our atlas identifies and molecularly characterizes 605 bilateral pairs of neurons at specific locations in the ventral nerve cord. Among these pairs, we identify sets of neurons expressing similar combinations of transcription factors, located at spatially coherent anterior-posterior, dorsal-ventral, and medial-lateral coordinates that we interpret as cell types. Comparison with motor and interneuron types in the vertebrate neural tube indicates conserved combinations, for example, of cell types cospecified by Gata1/2/3 and Tal transcription factors. These include V2b interneurons and the central spinal fluid-contacting Kolmer-Agduhr cells in the vertebrates, and several neuron types in the intermediate ventral ganglionic mass in the annelid. We propose that Kolmer-Agduhr cell-like mechanosensory neurons formed part of the mucociliary sole in protostome-deuterostome ancestors and diversified independently into several neuron types in annelid and vertebrate descendants.}, }
@article {pmid28580966, year = {2017}, author = {Driscoll, WW and Travisano, M}, title = {Synergistic cooperation promotes multicellular performance and unicellular free-rider persistence.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {15707}, doi = {10.1038/ncomms15707}, pmid = {28580966}, issn = {2041-1723}, abstract = {The evolution of multicellular life requires cooperation among cells, which can be undermined by intra-group selection for selfishness. Theory predicts that selection to avoid non-cooperators limits social interactions among non-relatives, yet previous evolution experiments suggest that intra-group conflict is an outcome, rather than a driver, of incipient multicellular life cycles. Here we report the evolution of multicellularity via two distinct mechanisms of group formation in the unicellular budding yeast Kluyveromyces lactis. Cells remain permanently attached following mitosis, giving rise to clonal clusters (staying together); clusters then reversibly assemble into social groups (coming together). Coming together amplifies the benefits of multicellularity and allows social clusters to collectively outperform solitary clusters. However, cooperation among non-relatives also permits fast-growing unicellular lineages to 'free-ride' during selection for increased size. Cooperation and competition for the benefits of multicellularity promote the stable coexistence of unicellular and multicellular genotypes, underscoring the importance of social and ecological context during the transition to multicellularity.}, }
@article {pmid28571799, year = {2017}, author = {Salerian, AJ}, title = {Human body may produce bacteria.}, journal = {Medical hypotheses}, volume = {103}, number = {}, pages = {131-132}, doi = {10.1016/j.mehy.2017.05.005}, pmid = {28571799}, issn = {1532-2777}, mesh = {Animals ; *Bacteria ; *Bacterial Physiological Phenomena ; Fermentation ; *Human Body ; Humans ; Models, Theoretical ; Muscles/physiology ; Origin of Life ; }, abstract = {&quot;Human body may produce bacteria&quot; proposes that human body may produce bacteria and represent an independent source of infections contrary to the current paradigm of infectious disorders proposed by Louis Pasteur in 1880. The following observations are consistent with this hypothesis: A. Bidirectional transformations of both living and nonliving things have been commonly observed in nature. B. Complex multicellular organisms harbor the necessary properties to produce bacteria (water, nitrogen and oxygen). C. Physical laws suggest any previously observed phenomenon or action will occur again (life began on earth; a non living thing). D. Animal muscle cells may generate energy (fermentation). E. Sterilized food products (i.e. boiled eggs), may produce bacteria and fungus under special conditions and without any exposure to foreign living cells. &quot;Human body may produce bacteria&quot; may challenge the current medical paradigm that views human infectious disorders as the exclusive causative byproducts of invading foreign cells. It may also introduce new avenues to treat infectious disorders.}, }
@article {pmid28560344, year = {2017}, author = {Knoll, AH and Nowak, MA}, title = {The timetable of evolution.}, journal = {Science advances}, volume = {3}, number = {5}, pages = {e1603076}, doi = {10.1126/sciadv.1603076}, pmid = {28560344}, issn = {2375-2548}, mesh = {*Biological Evolution ; *Ecosystem ; *Models, Biological ; }, abstract = {The integration of fossils, phylogeny, and geochronology has resulted in an increasingly well-resolved timetable of evolution. Life appears to have taken root before the earliest known minimally metamorphosed sedimentary rocks were deposited, but for a billion years or more, evolution played out beneath an essentially anoxic atmosphere. Oxygen concentrations in the atmosphere and surface oceans first rose in the Great Oxygenation Event (GOE) 2.4 billion years ago, and a second increase beginning in the later Neoproterozoic Era [Neoproterozoic Oxygenation Event (NOE)] established the redox profile of modern oceans. The GOE facilitated the emergence of eukaryotes, whereas the NOE is associated with large and complex multicellular organisms. Thus, the GOE and NOE are fundamental pacemakers for evolution. On the time scale of Earth's entire 4 billion-year history, the evolutionary dynamics of the planet's biosphere appears to be fast, and the pace of evolution is largely determined by physical changes of the planet. However, in Phanerozoic ecosystems, interactions between new functions enabled by the accumulation of characters in a complex regulatory environment and changing biological components of effective environments appear to have an important influence on the timing of evolutionary innovations. On the much shorter time scale of transient environmental perturbations, such as those associated with mass extinctions, rates of genetic accommodation may have been limiting for life.}, }
@article {pmid28550046, year = {2017}, author = {Vijg, J and Dong, X and Milholland, B and Zhang, L}, title = {Genome instability: a conserved mechanism of ageing?.}, journal = {Essays in biochemistry}, volume = {61}, number = {3}, pages = {305-315}, doi = {10.1042/EBC20160082}, pmid = {28550046}, issn = {1744-1358}, support = {P01 AG017242/AG/NIA NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; P30 AG038072/AG/NIA NIH HHS/United States ; R01 CA180126/CA/NCI NIH HHS/United States ; }, mesh = {Aging/genetics/*physiology ; Animals ; DNA Repair/genetics/physiology ; Genomic Instability/genetics/*physiology ; Humans ; Mutation/genetics ; }, abstract = {DNA is the carrier of genetic information and the primary template from which all cellular information is ultimately derived. Changes in the DNA information content through mutation generate diversity for evolution through natural selection but are also a source of deleterious effects. It has since long been hypothesized that mutation accumulation in somatic cells of multicellular organisms could causally contribute to age-related cellular degeneration and death. Assays to detect different types of mutations, from base substitutions to large chromosomal aberrations, have been developed and show unequivocally that mutations accumulate in different tissues and cell types of ageing humans and animals. More recently, next-generation sequencing-based methods have been developed to accurately determine the complete landscape of base substitution mutations in single cells. The first results show that the somatic mutation rate is much higher than the germline mutation rate and that base substitution loads in somatic cells are high enough to potentially affect cellular function.}, }
@article {pmid28529980, year = {2017}, author = {Moran, Y and Agron, M and Praher, D and Technau, U}, title = {The evolutionary origin of plant and animal microRNAs.}, journal = {Nature ecology &amp; evolution}, volume = {1}, number = {3}, pages = {27}, doi = {10.1038/s41559-016-0027}, pmid = {28529980}, issn = {2397-334X}, support = {637456//European Research Council/International ; }, abstract = {microRNAs (miRNAs) are a unique class of short endogenous RNAs that became known in the last few decades as major players in gene regulation at the post-transcriptional level. Their regulatory roles make miRNAs crucial for normal development and physiology in several distinct groups of eukaryotes including plants and animals. The common notion in the field is that miRNAs have evolved independently in those distinct lineages, but recent evidence from non-bilaterian metazoans, plants, as well as various algae raise the possibility that already the last common ancestor of these lineages might have employed a miRNA pathway for post-transcriptional regulation. In this review we present the commonalities and differences of the miRNA pathways in various eukaryotes and discuss the contrasting scenarios of their possible evolutionary origin and their proposed link to organismal complexity and multicellularity.}, }
@article {pmid28525299, year = {2017}, author = {Berbee, ML and James, TY and Strullu-Derrien, C}, title = {Early Diverging Fungi: Diversity and Impact at the Dawn of Terrestrial Life.}, journal = {Annual review of microbiology}, volume = {71}, number = {}, pages = {41-60}, doi = {10.1146/annurev-micro-030117-020324}, pmid = {28525299}, issn = {1545-3251}, mesh = {*Evolution, Molecular ; Fungi/*classification/*genetics ; *Genetic Variation ; }, abstract = {As decomposers or plant pathogens, fungi deploy invasive growth and powerful carbohydrate active enzymes to reduce multicellular plant tissues to humus and simple sugars. Fungi are perhaps also the most important mutualistic symbionts in modern ecosystems, transporting poorly soluble mineral nutrients to plants and thus enhancing the growth of vegetation. However, at their origin over a billion years ago, fungi, like plants and animals, were unicellular marine microbes. Like the other multicellular kingdoms, Fungi evolved increased size, complexity, and metabolic functioning. Interactions of fungi with plants changed terrestrial ecology and geology and modified the Earth's atmosphere. In this review, we discuss the diversification and ecological roles of the fungi over their first 600 million years, from their origin through their colonization of land, drawing on phylogenomic evidence for their relationships and metabolic capabilities and on molecular dating, fossils, and modeling of Earth's paleoclimate.}, }
@article {pmid28509401, year = {2017}, author = {Dittami, SM and Heesch, S and Olsen, JL and Collén, J}, title = {Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae.}, journal = {Journal of phycology}, volume = {53}, number = {4}, pages = {731-745}, doi = {10.1111/jpy.12547}, pmid = {28509401}, issn = {1529-8817}, mesh = {Adaptation, Biological ; *Biological Evolution ; *Ecosystem ; Fresh Water ; *Phaeophyta ; *Plants ; Seawater ; }, abstract = {Marine-freshwater and freshwater-marine transitions have been key events in the evolution of life, and most major groups of organisms have independently undergone such events at least once in their history. Here, we first compile an inventory of bidirectional freshwater and marine transitions in multicellular photosynthetic eukaryotes. While green and red algae have mastered multiple transitions in both directions, brown algae have colonized freshwater on a maximum of six known occasions, and angiosperms have made the transition to marine environments only two or three times. Next, we review the early evolutionary events leading to the colonization of current habitats. It is commonly assumed that the conquest of land proceeded in a sequence from marine to freshwater habitats. However, recent evidence suggests that early photosynthetic eukaryotes may have arisen in subaerial or freshwater environments and only later colonized marine environments as hypersaline oceans were diluted to the contemporary level. Although this hypothesis remains speculative, it is important to keep these alternative scenarios in mind when interpreting the current habitat distribution of plants and algae. Finally, we discuss the roles of structural and functional adaptations of the cell wall, reactive oxygen species scavengers, osmoregulation, and reproduction. These are central for acclimatization to freshwater or to marine environments. We observe that successful transitions appear to have occurred more frequently in morphologically simple forms and conclude that, in addition to physiological studies of euryhaline species, comparative studies of closely related species fully adapted to one or the other environment are necessary to better understand the adaptive processes.}, }
@article {pmid28508537, year = {2018}, author = {Boomsma, JJ and Gawne, R}, title = {Superorganismality and caste differentiation as points of no return: how the major evolutionary transitions were lost in translation.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {93}, number = {1}, pages = {28-54}, doi = {10.1111/brv.12330}, pmid = {28508537}, issn = {1469-185X}, abstract = {More than a century ago, William Morton Wheeler proposed that social insect colonies can be regarded as superorganisms when they have morphologically differentiated reproductive and nursing castes that are analogous to the metazoan germ-line and soma. Following the rise of sociobiology in the 1970s, Wheeler's insights were largely neglected, and we were left with multiple new superorganism concepts that are mutually inconsistent and uninformative on how superorganismality originated. These difficulties can be traced to the broadened sociobiological concept of eusociality, which denies that physical queen-worker caste differentiation is a universal hallmark of superorganismal colonies. Unlike early evolutionary naturalists and geneticists such as Weismann, Huxley, Fisher and Haldane, who set out to explain the acquisition of an unmated worker caste, the goal of sociobiology was to understand the evolution of eusociality, a broad-brush convenience category that covers most forms of cooperative breeding. By lumping a diverse spectrum of social systems into a single category, and drawing attention away from the evolution of distinct quantifiable traits, the sociobiological tradition has impeded straightforward connections between inclusive fitness theory and the major evolutionary transitions paradigm for understanding irreversible shifts to higher organizational complexity. We evaluate the history by which these inconsistencies accumulated, develop a common-cause approach for understanding the origins of all major transitions in eukaryote hierarchical complexity, and use Hamilton's rule to argue that they are directly comparable. We show that only Wheeler's original definition of superorganismality can be unambiguously linked to irreversible evolutionary transitions from context-dependent reproductive altruism to unconditional differentiation of permanently unmated castes in the ants, corbiculate bees, vespine wasps and higher termites. We argue that strictly monogamous parents were a necessary, albeit not sufficient condition for all transitions to superorganismality, analogous to single-zygote bottlenecking being a necessary but not sufficient condition for the convergent origins of complex soma across multicellular eukaryotes. We infer that conflict reduction was not a necessary condition for the origin of any of these major transitions, and conclude that controversies over the status of inclusive fitness theory primarily emanate from the arbitrarily defined sociobiological concepts of superorganismality and eusociality, not from the theory itself.}, }
@article {pmid28506208, year = {2017}, author = {Labocha, MK and Yuan, W and Aleman-Meza, B and Zhong, W}, title = {A strategy to apply quantitative epistasis analysis on developmental traits.}, journal = {BMC genetics}, volume = {18}, number = {1}, pages = {42}, doi = {10.1186/s12863-017-0508-4}, pmid = {28506208}, issn = {1471-2156}, support = {K99 HG004724/HG/NHGRI NIH HHS/United States ; R00 HG004724/HG/NHGRI NIH HHS/United States ; R01 DA018341/DA/NIDA NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*genetics/*growth &amp; development ; Caenorhabditis elegans Proteins/genetics ; *Epistasis, Genetic ; High-Throughput Nucleotide Sequencing/methods ; Models, Genetic ; *Quantitative Trait Loci ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits.<br><br>METHODS: In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement.<br><br>RESULTS: Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions.<br><br>CONCLUSIONS: We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.}, }
@article {pmid28505429, year = {2017}, author = {Siu, KH and Chen, W}, title = {Control of the Yeast Mating Pathway by Reconstitution of Functional α-Factor Using Split Intein-Catalyzed Reactions.}, journal = {ACS synthetic biology}, volume = {6}, number = {8}, pages = {1453-1460}, doi = {10.1021/acssynbio.7b00078}, pmid = {28505429}, issn = {2161-5063}, mesh = {Catalysis ; Gene Expression Regulation, Fungal/*genetics ; Genes, Mating Type, Fungal/*genetics ; Inteins/*genetics ; Metabolic Engineering/*methods ; Metabolic Networks and Pathways/*genetics ; Models, Genetic ; Pheromones/*genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Signal Transduction/genetics ; }, abstract = {Synthetic control strategies using signaling peptides to regulate and coordinate cellular behaviors in multicellular organisms and synthetic consortia remain largely underdeveloped because of the complexities necessitated by heterologous peptide expression. Using recombinant proteins that exploit split intein-mediated reactions, we presented here a new strategy for reconstituting functional signaling peptides capable of eliciting desired cellular responses in S. cerevisiae. These designs can potentially be tailored to any signaling peptides to be reconstituted, as the split inteins are promiscuous and both the peptides and the reactions are amenable to changes by directed evolution and other protein engineering tools, thereby offering a general strategy to implement synthetic control strategies in a large variety of applications.}, }
@article {pmid28498101, year = {2017}, author = {Hinman, V and Cary, G}, title = {The evolution of gene regulation.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, doi = {10.7554/eLife.27291}, pmid = {28498101}, issn = {2050-084X}, abstract = {The gene regulation mechanisms necessary for the development of complex multicellular animals have been found in sponges.}, }
@article {pmid28497122, year = {2017}, author = {Franco-Obregón, A and Gilbert, JA}, title = {The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals.}, journal = {mSystems}, volume = {2}, number = {3}, pages = {}, doi = {10.1128/mSystems.00018-17}, pmid = {28497122}, issn = {2379-5077}, abstract = {Lynn Margulis in the 1960s elegantly proposed a shared phylogenetic history between bacteria and mitochondria; this relationship has since become a cornerstone of modern cellular biology. Yet, an interesting facet of the interaction between the microbiome and mitochondria has been mostly ignored, that of the systems biology relationship that underpins host health and longevity. The mitochondria are descendants of primordial aerobic pleomorphic bacteria (likely genus Rickettsia) that entered (literally and functionally) into a mutualistic partnership with ancient anaerobic microbes (likely Archaea). A stable symbiosis was established, given the metabolic versatility of the early mitochondria, which were capable of providing energy with or without oxygen, whereas nutrient gathering was the assumed responsibility of the host. While microbial relationships with single-cell protists must have occurred in the past, as they occur today, the evolution of multicellular organisms generated a new framework for symbiosis with the microbial world, taking the ancient partnership to an entirely new level. Cell-cell communication between microbes and single-cell protists was augmented through multicellularity to allow distant communication between the host cells and the microbiome, resulting in the development of complex metabolic relationships and an immune system to manage these interactions. Thus, the host is now the body and its resident mitochondria, and the microbiome is an essential supplier of metabolites that act at the level of mitochondria in skeletal muscle to stabilize host metabolism. We humans are caretakers of a profoundly vast and diverse microbiota, the majority of which resides in the gut. Indeed, the microbial genetic diversity of our microbiota outstrips our own by several orders of magnitude, and the cellular abundance is roughly equivalent to our somatic selves. Modern clinical science has elegantly highlighted the importance of the microbiome for metabolic health and well-being. This perspective underscores one fundamental facet of this symbiosis, the ancestral mitochondrion-microbiome axis.}, }
@article {pmid28484005, year = {2017}, author = {Trigos, AS and Pearson, RB and Papenfuss, AT and Goode, DL}, title = {Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {24}, pages = {6406-6411}, doi = {10.1073/pnas.1617743114}, pmid = {28484005}, issn = {1091-6490}, mesh = {Animals ; Carcinogenesis/genetics ; Cell Transformation, Neoplastic/genetics ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Genome, Human ; Humans ; Models, Genetic ; Neoplasms/etiology/*genetics ; Oncogenes ; Phenotype ; Stress, Physiological/genetics ; Systems Biology ; }, abstract = {Tumors of distinct tissues of origin and genetic makeup display common hallmark cellular phenotypes, including sustained proliferation, suppression of cell death, and altered metabolism. These phenotypic commonalities have been proposed to stem from disruption of conserved regulatory mechanisms evolved during the transition to multicellularity to control fundamental cellular processes such as growth and replication. Dating the evolutionary emergence of human genes through phylostratigraphy uncovered close association between gene age and expression level in RNA sequencing data from The Cancer Genome Atlas for seven solid cancers. Genes conserved with unicellular organisms were strongly up-regulated, whereas genes of metazoan origin were primarily inactivated. These patterns were most consistent for processes known to be important in cancer, implicating both selection and active regulation during malignant transformation. The coordinated expression of strongly interacting multicellularity and unicellularity processes was lost in tumors. This separation of unicellular and multicellular functions appeared to be mediated by 12 highly connected genes, marking them as important general drivers of tumorigenesis. Our findings suggest common principles closely tied to the evolutionary history of genes underlie convergent changes at the cellular process level across a range of solid cancers. We propose altered activity of genes at the interfaces between multicellular and unicellular regions of human gene regulatory networks activate primitive transcriptional programs, driving common hallmark features of cancer. Manipulation of cross-talk between biological processes of different evolutionary origins may thus present powerful and broadly applicable treatment strategies for cancer.}, }
@article {pmid28481398, year = {2017}, author = {Lei, Y and Anders, HJ}, title = {Evolutionary trade-offs in kidney injury and repair.}, journal = {Histology and histopathology}, volume = {32}, number = {11}, pages = {1099-1113}, doi = {10.14670/HH-11-900}, pmid = {28481398}, issn = {1699-5848}, mesh = {Animals ; *Biological Evolution ; Humans ; Kidney/*injuries ; *Regeneration ; }, abstract = {Evolutionary medicine has proven helpful to understand the origin of human disease, e.g. in identifying causal roles of recent environmental changes impacting on human physiology (environment-phenotype mismatch). In contrast, diseases affecting only a limited number of members of a species often originate from evolutionary trade-offs for usually physiologic adaptations assuring reproductive success in the context of extrinsic threats. For example, the G1 and G2 variants of the APOL1 gene supporting control of Trypanosoma infection come with the trade-off that they promote the progression of kidney disease. In this review we extend the concept of evolutionary nephrology by discussing how the physiologic adaptations (danger responses) to tissue injury create evolutionary trade-offs that drive histopathological changes underlying acute and chronic kidney diseases. The evolution of multicellular organisms positively selected a number of danger response programs for their overwhelming benefits in assuring survival such as clotting, inflammation, epithelial healing and mesenchymal healing, i.e. fibrosis and sclerosis. Upon kidney injury these danger programs often present as pathomechanisms driving persistent nephron loss and renal failure. We explore how classic kidney disease entities involve insufficient or overshooting activation of these danger response programs for which the underlying genetic basis remains largely to be defined. Dissecting the causative and hierarchical relationships between danger programs should help to identify molecular targets to control kidney injury and to improve disease outcomes.}, }
@article {pmid28479986, year = {2017}, author = {van Duijn, M}, title = {Phylogenetic origins of biological cognition: convergent patterns in the early evolution of learning.}, journal = {Interface focus}, volume = {7}, number = {3}, pages = {20160158}, doi = {10.1098/rsfs.2016.0158}, pmid = {28479986}, issn = {2042-8898}, abstract = {Various forms of elementary learning have recently been discovered in organisms lacking a nervous system, such as protists, fungi and plants. This finding has fundamental implications for how we view the role of convergent evolution in biological cognition. In this article, I first review the evidence for basic forms of learning in aneural organisms, focusing particularly on habituation and classical conditioning and considering the plausibility for convergent evolution of these capacities. Next, I examine the possible role of convergent evolution regarding these basic learning abilities during the early evolution of nervous systems. The evolution of nervous systems set the stage for at least two major events relevant to convergent evolution that are central to biological cognition: (i) nervous systems evolved, perhaps more than once, because of strong selection pressures for sustaining sensorimotor strategies in increasingly larger multicellular organisms and (ii) associative learning was a subsequent adaptation that evolved multiple times within the neuralia. Although convergent evolution of basic forms of learning among distantly related organisms such as protists, plants and neuralia is highly plausible, more research is needed to verify whether these forms of learning within the neuralia arose through convergent or parallel evolution.}, }
@article {pmid28479598, year = {2017}, author = {Sebé-Pedrós, A and Degnan, BM and Ruiz-Trillo, I}, title = {The origin of Metazoa: a unicellular perspective.}, journal = {Nature reviews. Genetics}, volume = {18}, number = {8}, pages = {498-512}, doi = {10.1038/nrg.2017.21}, pmid = {28479598}, issn = {1471-0064}, mesh = {Animals ; *Biological Evolution ; Eukaryota/classification/cytology/*genetics ; Humans ; Phylogeny ; }, abstract = {The first animals evolved from an unknown single-celled ancestor in the Precambrian period. Recently, the identification and characterization of the genomic and cellular traits of the protists most closely related to animals have shed light on the origin of animals. Comparisons of animals with these unicellular relatives allow us to reconstruct the first evolutionary steps towards animal multicellularity. Here, we review the results of these investigations and discuss their implications for understanding the earliest stages of animal evolution, including the origin of metazoan genes and genome function.}, }
@article {pmid28459980, year = {2017}, author = {Fares, MA and Sabater-Muñoz, B and Toft, C}, title = {Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations.}, journal = {Genome biology and evolution}, volume = {9}, number = {5}, pages = {1229-1240}, doi = {10.1093/gbe/evx085}, pmid = {28459980}, issn = {1759-6653}, mesh = {Adaptation, Biological ; *Gene Duplication ; *Mutation ; Mutation Rate ; Promoter Regions, Genetic ; Saccharomyces cerevisiae/*genetics/*physiology ; Stress, Physiological ; *Transcription, Genetic ; }, abstract = {Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting duplicated genes in Saccharomyces led to the origin of major metabolic innovations, which have been the source of the unique biotechnological capabilities in the Baker's yeast Saccharomyces cerevisiae. What factors have determined the fate of duplicated genes remains unknown. Here, we report the first demonstration that the local genome mutation and transcription rates determine the fate of duplicates. We show, for the first time, a preferential location of duplicated genes in the mutational and transcriptional hotspots of S. cerevisiae genome. The mechanism of duplication matters, with whole-genome duplicates exhibiting different preservation trends compared to small-scale duplicates. Genome mutational and transcriptional hotspots are rich in duplicates with large repetitive promoter elements. Saccharomyces cerevisiae shows more tolerance to deleterious mutations in duplicates with repetitive promoter elements, which in turn exhibit higher transcriptional plasticity against environmental perturbations. Our data demonstrate that the genome traps duplicates through the accelerated regulatory and functional divergence of their gene copies providing a source of novel adaptations in yeast.}, }
@article {pmid28457024, year = {2017}, author = {Golstein, P}, title = {Conserved nucleolar stress at the onset of cell death.}, journal = {The FEBS journal}, volume = {284}, number = {22}, pages = {3791-3800}, doi = {10.1111/febs.14095}, pmid = {28457024}, issn = {1742-4658}, mesh = {Animals ; *Cell Death ; Cell Nucleolus/metabolism/*pathology ; Humans ; Nuclear Proteins/*metabolism ; *Stress, Physiological ; }, abstract = {Cell death pervasiveness among multicellular eukaryotes suggested that some core steps of cell death may be conserved. This could be addressed by comparing the course of cell death in organisms belonging to distinct eukaryotic kingdoms. A search for early cell death events in a protist revealed nucleolar disorganization similar to the nucleolar stress often reported in dying animal cells. This indicated a conserved role for the nucleolus at the onset of eukaryotic cell death and leads one to consider the course of cell death as a succession of unequally conserved modules.}, }
@article {pmid28453786, year = {2017}, author = {Porath, HT and Schaffer, AA and Kaniewska, P and Alon, S and Eisenberg, E and Rosenthal, J and Levanon, EY and Levy, O}, title = {A-to-I RNA Editing in the Earliest-Diverging Eumetazoan Phyla.}, journal = {Molecular biology and evolution}, volume = {34}, number = {8}, pages = {1890-1901}, doi = {10.1093/molbev/msx125}, pmid = {28453786}, issn = {1537-1719}, support = {311257//European Research Council/International ; }, mesh = {Adenosine Deaminase/*genetics/metabolism ; Animals ; Anthozoa/*genetics/metabolism ; Base Sequence ; Evolution, Molecular ; Genome ; Genomics ; Humans ; Mammals/genetics ; Phylogeny ; RNA ; RNA Editing/*genetics ; RNA, Messenger/genetics ; RNA-Binding Proteins/genetics ; }, abstract = {The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.}, }
@article {pmid28441401, year = {2017}, author = {Cisneros, L and Bussey, KJ and Orr, AJ and Miočević, M and Lineweaver, CH and Davies, P}, title = {Ancient genes establish stress-induced mutation as a hallmark of cancer.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0176258}, doi = {10.1371/journal.pone.0176258}, pmid = {28441401}, issn = {1932-6203}, mesh = {Animals ; Cell Cycle/genetics ; DNA Repair/genetics ; Databases, Genetic ; Humans ; *Mutation ; Neoplasms/*genetics ; *Oncogenes ; Phenotype ; Phylogeny ; }, abstract = {Cancer is sometimes depicted as a reversion to single cell behavior in cells adapted to live in a multicellular assembly. If this is the case, one would expect that mutation in cancer disrupts functional mechanisms that suppress cell-level traits detrimental to multicellularity. Such mechanisms should have evolved with or after the emergence of multicellularity. This leads to two related, but distinct hypotheses: 1) Somatic mutations in cancer will occur in genes that are younger than the emergence of multicellularity (1000 million years [MY]); and 2) genes that are frequently mutated in cancer and whose mutations are functionally important for the emergence of the cancer phenotype evolved within the past 1000 million years, and thus would exhibit an age distribution that is skewed to younger genes. In order to investigate these hypotheses we estimated the evolutionary ages of all human genes and then studied the probability of mutation and their biological function in relation to their age and genomic location for both normal germline and cancer contexts. We observed that under a model of uniform random mutation across the genome, controlled for gene size, genes less than 500 MY were more frequently mutated in both cases. Paradoxically, causal genes, defined in the COSMIC Cancer Gene Census, were depleted in this age group. When we used functional enrichment analysis to explain this unexpected result we discovered that COSMIC genes with recessive disease phenotypes were enriched for DNA repair and cell cycle control. The non-mutated genes in these pathways are orthologous to those underlying stress-induced mutation in bacteria, which results in the clustering of single nucleotide variations. COSMIC genes were less common in regions where the probability of observing mutational clusters is high, although they are approximately 2-fold more likely to harbor mutational clusters compared to other human genes. Our results suggest this ancient mutational response to stress that evolved among prokaryotes was co-opted to maintain diversity in the germline and immune system, while the original phenotype is restored in cancer. Reversion to a stress-induced mutational response is a hallmark of cancer that allows for effectively searching &quot;protected&quot; genome space where genes causally implicated in cancer are located and underlies the high adaptive potential and concomitant therapeutic resistance that is characteristic of cancer.}, }
@article {pmid28427949, year = {2017}, author = {Freese, JM and Lane, CE}, title = {Parasitism finds many solutions to the same problems in red algae (Florideophyceae, Rhodophyta).}, journal = {Molecular and biochemical parasitology}, volume = {214}, number = {}, pages = {105-111}, doi = {10.1016/j.molbiopara.2017.04.006}, pmid = {28427949}, issn = {1872-9428}, mesh = {*Biological Evolution ; *Host-Parasite Interactions ; Microscopy ; Phylogeny ; Rhodophyta/classification/cytology/*genetics/*physiology ; }, abstract = {Parasitic red algae evolve from a common ancestor with their hosts, parasitizing cousins using familiar cellular mechanisms. They have independently evolved over one hundred times within the exclusively multicellular red algal class Florideophyceae. Reduced morphology, a lack of pigmentation, and direct cell-cell connections with their hosts are markers of red algal parasitism. With so many potential evolutionary pathways, red algal parasite diversity offers a unique test case to understand the earliest stages of this lifestyle transition. Molecular and morphological investigations led to the categorization of these parasites based on their relationship to their host. &quot;Adelphoparasites&quot; are phylogenetically close to their hosts, often infecting a sister species, whereas &quot;alloparasites&quot; are more distantly related to their hosts. The differentiation of these parasites, based on their phylogenetic relationship to their host, has resulted in a simplified classification of these parasites that may not reflect the many evolutionary pathways they take to arrive at a similar endpoint. Accordingly, many parasites fall into a gray area between adelphoparasite and alloparasite definitions, challenging the established features we use to classify them. Molecular phylogenetic research has been essential in identifying gaps in knowledge, but microscopy needs to be reincorporated in order to address red algal parasite developmental variation to establish a new paradigm. The joint utilization of molecular and microscopic methods will be critical in identifying the genomic and physiological traits of both nascent and well-established parasites.}, }
@article {pmid28427910, year = {2017}, author = {Bury-Moné, S and Sclavi, B}, title = {Stochasticity of gene expression as a motor of epigenetics in bacteria: from individual to collective behaviors.}, journal = {Research in microbiology}, volume = {168}, number = {6}, pages = {503-514}, doi = {10.1016/j.resmic.2017.03.009}, pmid = {28427910}, issn = {1769-7123}, mesh = {Bacteria/*genetics ; Environment ; *Epigenesis, Genetic ; *Gene Expression ; *Gene Regulatory Networks ; Models, Genetic ; Phenotype ; Stochastic Processes ; }, abstract = {Measuring gene expression at the single cell and single molecule level has recently made possible the quantitative measurement of stochasticity of gene expression. This enables identification of the probable sources and roles of noise. Gene expression noise can result in bacterial population heterogeneity, offering specific advantages for fitness and survival in various environments. This trait is therefore selected during the evolution of the species, and is consequently regulated by a specific genetic network architecture. Examples exist in stress-response mechanisms, as well as in infection and pathogenicity strategies, pointing to advantages for multicellularity of bacterial populations.}, }
@article {pmid28427501, year = {2017}, author = {Fonseca, NA and Cruz, AF and Moura, V and Simões, S and Moreira, JN}, title = {The cancer stem cell phenotype as a determinant factor of the heterotypic nature of breast tumors.}, journal = {Critical reviews in oncology/hematology}, volume = {113}, number = {}, pages = {111-121}, doi = {10.1016/j.critrevonc.2017.03.016}, pmid = {28427501}, issn = {1879-0461}, mesh = {Breast Neoplasms/metabolism/pathology/*physiopathology ; Epithelial-Mesenchymal Transition ; Female ; Humans ; Neoplastic Stem Cells/*metabolism/physiology ; Neovascularization, Pathologic ; *Phosphoproteins ; *RNA-Binding Proteins ; *Signal Transduction ; *Tumor Microenvironment ; }, abstract = {Gathering evidence supports the existence of a population of cells with stem-like characteristics, named cancer stem cells (CSC), which is involved not only in tumor recurrence but also in tumorigenicity, metastization and drug resistance. Several markers have been used to identify putative CSC sub-populations in different cancers. Notwithstanding, it has been acknowledged that breast CSC may originate from non-stem cancer cells (non-SCC), interconverting through an epithelial-to-mesenchymal transition-mediated process, and presenting several deregulated canonical and developmental signaling pathways. These support the heterogeneity that, directly or indirectly, influences fundamental biological features supporting breast tumor development. Accordingly, CSC have increasingly become highly relevant cellular targets. In this review, we will address the stemness concept in cancer, setting the perspective on CSC and their origin, by exploring their relation and regulation within the tumor microenvironment, in the context of emerging therapeutic targets. Within this framework, we will discuss nucleolin, a protein that has been associated with angiogenesis and, more recently, with the stemness phenotype, becoming a common denominator between CSC and non-SCC for multicellular targeting.}, }
@article {pmid28425150, year = {2017}, author = {Grochau-Wright, ZI and Hanschen, ER and Ferris, PJ and Hamaji, T and Nozaki, H and Olson, BJSC and Michod, RE}, title = {Genetic basis for soma is present in undifferentiated volvocine green algae.}, journal = {Journal of evolutionary biology}, volume = {30}, number = {6}, pages = {1205-1218}, doi = {10.1111/jeb.13100}, pmid = {28425150}, issn = {1420-9101}, support = {NNX13AH41G//NASA/ ; T32 GM084905/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; *Biological Evolution ; Chlorophyta ; *Phylogeny ; Stress, Physiological ; *Volvox ; }, abstract = {Somatic cellular differentiation plays a critical role in the transition from unicellular to multicellular life, but the evolution of its genetic basis remains poorly understood. By definition, somatic cells do not reproduce to pass on genes and so constitute an extreme form of altruistic behaviour. The volvocine green algae provide an excellent model system to study the evolution of multicellularity and somatic differentiation. In Volvox carteri, somatic cell differentiation is controlled by the regA gene, which is part of a tandem duplication of genes known as the reg cluster. Although previous work found the reg cluster in divergent Volvox species, its origin and distribution in the broader group of volvocine algae has not been known. Here, we show that the reg cluster is present in many species without somatic cells and determine that the genetic basis for soma arose before the phenotype at the origin of the family Volvocaceae approximately 200 million years ago. We hypothesize that the ancestral function was involved in regulating reproduction in response to stress and that this function was later co-opted to produce soma. Determining that the reg cluster was co-opted to control somatic cell development provides insight into how cellular differentiation, and with it greater levels of complexity and individuality, evolves.}, }
@article {pmid28424311, year = {2017}, author = {Deora, T and Gundiah, N and Sane, SP}, title = {Mechanics of the thorax in flies.}, journal = {The Journal of experimental biology}, volume = {220}, number = {Pt 8}, pages = {1382-1395}, doi = {10.1242/jeb.128363}, pmid = {28424311}, issn = {1477-9145}, mesh = {Animals ; Biomechanical Phenomena ; Body Size ; Diptera/anatomy &amp; histology/*physiology ; *Flight, Animal ; Wings, Animal/anatomy &amp; histology/*physiology ; }, abstract = {Insects represent more than 60% of all multicellular life forms, and are easily among the most diverse and abundant organisms on earth. They evolved functional wings and the ability to fly, which enabled them to occupy diverse niches. Insects of the hyper-diverse orders show extreme miniaturization of their body size. The reduced body size, however, imposes steep constraints on flight ability, as their wings must flap faster to generate sufficient forces to stay aloft. Here, we discuss the various physiological and biomechanical adaptations of the thorax in flies which enabled them to overcome the myriad constraints of small body size, while ensuring very precise control of their wing motion. One such adaptation is the evolution of specialized myogenic or asynchronous muscles that power the high-frequency wing motion, in combination with neurogenic or synchronous steering muscles that control higher-order wing kinematic patterns. Additionally, passive cuticular linkages within the thorax coordinate fast and yet precise bilateral wing movement, in combination with an actively controlled clutch and gear system that enables flexible flight patterns. Thus, the study of thoracic biomechanics, along with the underlying sensory-motor processing, is central in understanding how the insect body form is adapted for flight.}, }
@article {pmid28418331, year = {2017}, author = {Fidler, AL and Darris, CE and Chetyrkin, SV and Pedchenko, VK and Boudko, SP and Brown, KL and Gray Jerome, W and Hudson, JK and Rokas, A and Hudson, BG}, title = {Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, doi = {10.7554/eLife.24176}, pmid = {28418331}, issn = {2050-084X}, support = {P60 DK020593/DK/NIDDK NIH HHS/United States ; R24 DK103067/DK/NIDDK NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK018381/DK/NIDDK NIH HHS/United States ; U2C DK059637/DK/NIDDK NIH HHS/United States ; P30 EY008126/EY/NEI NIH HHS/United States ; P30 DK020593/DK/NIDDK NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; U24 DK059637/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Basement Membrane/*chemistry ; Collagen Type IV/*analysis/*genetics ; Ctenophora/cytology/genetics/metabolism/*physiology ; Evolution, Molecular ; Extracellular Matrix/*chemistry ; }, abstract = {The role of the cellular microenvironment in enabling metazoan tissue genesis remains obscure. Ctenophora has recently emerged as one of the earliest-branching extant animal phyla, providing a unique opportunity to explore the evolutionary role of the cellular microenvironment in tissue genesis. Here, we characterized the extracellular matrix (ECM), with a focus on collagen IV and its variant, spongin short-chain collagens, of non-bilaterian animal phyla. We identified basement membrane (BM) and collagen IV in Ctenophora, and show that the structural and genomic features of collagen IV are homologous to those of non-bilaterian animal phyla and Bilateria. Yet, ctenophore features are more diverse and distinct, expressing up to twenty genes compared to six in vertebrates. Moreover, collagen IV is absent in unicellular sister-groups. Collectively, we conclude that collagen IV and its variant, spongin, are primordial components of the extracellular microenvironment, and as a component of BM, collagen IV enabled the assembly of a fundamental architectural unit for multicellular tissue genesis.}, }
@article {pmid28409312, year = {2017}, author = {Garcin, CL and Habib, SJ}, title = {A Comparative Perspective on Wnt/β-Catenin Signalling in Cell Fate Determination.}, journal = {Results and problems in cell differentiation}, volume = {61}, number = {}, pages = {323-350}, doi = {10.1007/978-3-319-53150-2_15}, pmid = {28409312}, issn = {0080-1844}, mesh = {Animals ; Body Patterning/physiology ; Cell Differentiation/*physiology ; Embryonic Development/*physiology ; Humans ; Wnt Signaling Pathway/*physiology ; }, abstract = {The Wnt/β-catenin pathway is an ancient and highly conserved signalling pathway that plays fundamental roles in the regulation of embryonic development and adult homeostasis. This pathway has been implicated in numerous cellular processes, including cell proliferation, differentiation, migration, morphological changes and apoptosis. In this chapter, we aim to illustrate with specific examples the involvement of Wnt/β-catenin signalling in cell fate determination. We discuss the roles of the Wnt/β-catenin pathway in specifying cell fate throughout evolution, how its function in patterning during development is often reactivated during regeneration and how perturbation of this pathway has negative consequences for the control of cell fate.The origin of all life was a single cell that had the capacity to respond to cues from the environment. With evolution, multicellular organisms emerged, and as a result, subsets of cells arose to form tissues able to respond to specific instructive signals and perform specialised functions. This complexity and specialisation required two types of messages to direct cell fate: intra- and intercellular. A fundamental question in developmental biology is to understand the underlying mechanisms of cell fate choice. Amongst the numerous external cues involved in the generation of cellular diversity, a prominent pathway is the Wnt signalling pathway in all its forms.}, }
@article {pmid28406446, year = {2017}, author = {Breviario, D}, title = {Is There any Alternative to Canonical DNA Barcoding of Multicellular Eukaryotic Species? A Case for the Tubulin Gene Family.}, journal = {International journal of molecular sciences}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/ijms18040827}, pmid = {28406446}, issn = {1422-0067}, mesh = {DNA/chemistry/metabolism ; *DNA Barcoding, Taxonomic ; Eukaryota/*genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Tubulin/*genetics ; }, abstract = {Modern taxonomy is largely relying on DNA barcoding, a nucleotide sequence-based approach that provides automated species identification using short orthologous DNA regions, mainly of organellar origin when applied to multicellular Eukaryotic species. Target DNA loci have been selected that contain a minimal amount of nucleotide sequence variation within species while diverging among species. This strategy is quite effective for the identification of vertebrates and other animal lineages but poses a problem in plants where different combinations of two or three loci are constantly used. Even so, species discrimination in such plant categories as ornamentals and herbals remain problematic as well as the confident identification of subspecies, ecotypes, and closely related or recently evolved species. All these limitations may be successfully solved by the application of a different strategy, based on the use of a multi-locus, ubiquitous, nuclear marker, that is tubulin. In fact, the tubulin-based polymorphism method can release specific genomic profiles to any plant species independently from its taxonomic group. This offers the rare possibility of an effective yet generic genomic fingerprint. In a more general context, the issue is raised about the possibility that approaches alternative to systematic DNA sequencing may still provide useful and simple solutions.}, }
@article {pmid28405374, year = {2017}, author = {Pratlong, M and Haguenauer, A and Chenesseau, S and Brener, K and Mitta, G and Toulza, E and Bonabaud, M and Rialle, S and Aurelle, D and Pontarotti, P}, title = {Evidence for a genetic sex determination in Cnidaria, the Mediterranean red coral (Corallium rubrum).}, journal = {Royal Society open science}, volume = {4}, number = {3}, pages = {160880}, doi = {10.1098/rsos.160880}, pmid = {28405374}, issn = {2054-5703}, abstract = {Sexual reproduction is widespread among eukaryotes, and the sex-determining processes vary greatly among species. While genetic sex determination (GSD) has been intensively described in bilaterian species, no example has yet been recorded among non-bilaterians. However, the quasi-ubiquitous repartition of GSD among multicellular species suggests that similar evolutionary forces can promote this system, and that these forces could occur also in non-bilaterians. Studying sex determination across the range of Metazoan diversity is indeed important to understand better the evolution of this mechanism and its lability. We tested the existence of sex-linked genes in the gonochoric red coral (Corallium rubrum, Cnidaria) using restriction site-associated DNA sequencing. We analysed 27 461 single nucleotide polymorphisms (SNPs) in 354 individuals from 12 populations including 53 that were morphologically sexed. We found a strong association between the allele frequencies of 472 SNPs and the sex of individuals, suggesting an XX/XY sex-determination system. This result was confirmed by the identification of 435 male-specific loci. An independent test confirmed that the amplification of these loci enabled us to identify males with absolute certainty. This is the first demonstration of a GSD system among non-bilaterian species and a new example of its convergence in multicellular eukaryotes.}, }
@article {pmid28398223, year = {2017}, author = {Cao, TJ and Huang, XQ and Qu, YY and Zhuang, Z and Deng, YY and Lu, S}, title = {Cloning and Functional Characterization of a Lycopene β-Cyclase from Macrophytic Red Alga Bangia fuscopurpurea.}, journal = {Marine drugs}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/md15040116}, pmid = {28398223}, issn = {1660-3397}, mesh = {Amino Acid Sequence ; Base Sequence ; Carotenoids/*genetics/*metabolism ; Cloning, Molecular/methods ; Escherichia coli/genetics ; Intramolecular Lyases/*genetics/*metabolism ; Photosynthesis/physiology ; Phylogeny ; Rhodophyta/*genetics/*metabolism ; Zeaxanthins/genetics/metabolism ; beta Carotene/genetics/metabolism ; }, abstract = {Lycopene cyclases cyclize the open ends of acyclic lycopene (ψ,ψ-carotene) into β- or ε-ionone rings in the crucial bifurcation step of carotenoid biosynthesis. Among all carotenoid constituents, β-carotene (β,β-carotene) is found in all photosynthetic organisms, except for purple bacteria and heliobacteria, suggesting a ubiquitous distribution of lycopene β-cyclase activity in these organisms. In this work, we isolated a gene (BfLCYB) encoding a lycopene β-cyclase from Bangia fuscopurpurea, a red alga that is considered to be one of the primitive multicellular eukaryotic photosynthetic organisms and accumulates carotenoid constituents with both β- and ε-rings, including β-carotene, zeaxanthin, α-carotene (β,ε-carotene) and lutein. Functional complementation in Escherichia coli demonstrated that BfLCYB is able to catalyze cyclization of lycopene into monocyclic γ-carotene (β,ψ-carotene) and bicyclic β-carotene, and cyclization of the open end of monocyclic δ-carotene (ε,ψ-carotene) to produce α-carotene. No ε-cyclization activity was identified for BfLCYB. Sequence comparison showed that BfLCYB shares conserved domains with other functionally characterized lycopene cyclases from different organisms and belongs to a group of ancient lycopene cyclases. Although B. fuscopurpurea also synthesizes α-carotene and lutein, its enzyme-catalyzing ε-cyclization is still unknown.}, }
@article {pmid28395144, year = {2017}, author = {Gaiti, F and Jindrich, K and Fernandez-Valverde, SL and Roper, KE and Degnan, BM and Tanurdžić, M}, title = {Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, doi = {10.7554/eLife.22194}, pmid = {28395144}, issn = {2050-084X}, mesh = {Animals ; *Biological Evolution ; *Gene Expression Regulation ; *Histone Code ; Porifera/*genetics ; }, abstract = {Combinatorial patterns of histone modifications regulate developmental and cell type-specific gene expression and underpin animal complexity, but it is unclear when this regulatory system evolved. By analysing histone modifications in a morphologically-simple, early branching animal, the sponge Amphimedonqueenslandica, we show that the regulatory landscape used by complex bilaterians was already in place at the dawn of animal multicellularity. This includes distal enhancers, repressive chromatin and transcriptional units marked by H3K4me3 that vary with levels of developmental regulation. Strikingly, Amphimedon enhancers are enriched in metazoan-specific microsyntenic units, suggesting that their genomic location is extremely ancient and likely to place constraints on the evolution of surrounding genes. These results suggest that the regulatory foundation for spatiotemporal gene expression evolved prior to the divergence of sponges and eumetazoans, and was necessary for the evolution of animal multicellularity.}, }
@article {pmid28392224, year = {2017}, author = {Schiffmann, Y}, title = {The non-equilibrium basis of Turing Instability and localised biological work.}, journal = {Progress in biophysics and molecular biology}, volume = {127}, number = {}, pages = {12-32}, doi = {10.1016/j.pbiomolbio.2017.04.002}, pmid = {28392224}, issn = {1873-1732}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; *Biological Evolution ; Humans ; Hydrolysis ; *Models, Biological ; }, abstract = {Turing's theory for biological pattern formation is based on the instability of the homogeneous state, which occurs if certain key criteria are met. The problem of how chemical energy is converted to localised biological work requires one to understand not only the basis of localised power generation, but also the age-old puzzle of how organisms decrease their entropy; these problems can only be solved by the identification of the Turing Instability. At the heart of this is how natural selection, not chemistry, has fashioned the large non-equilibrium overall affinity (ΔG is a large negative quantity) for the oxidation of the fuel molecules. Natural selection has also resulted in the homeostasis at non-equilibrium values of the hydrolysis of molecules like ATP, GTP, which are the energy links between the overall oxidation of the fuel and biological work. The conditions for such homeostasis are central requirements for the Turing Instability and are the essence of being alive. The Turing-Child (TC) patterns are the spontaneous primary spatial cause not only of localised biological work in multicellular systems (especially those in patterning and development) but also of intracellular patterns including the mitotic spindle and the contractile ring. The Turing picture comprises the nonuniform distribution of the concentrations of the Turing morphogens, cAMP and ATP, and the Child picture is the resulting nonuniform distribution of the metabolic rate and of power. The TC pattern is shaped as the dominant eigenfunction in the combination of eigenfunctions which provides the spatial pattern of the Turing morphogens. The TC patterns and the bifurcation parameter manifest quantisation and symmetry as in music and in applications of quantum mechanics. The notion of correlation diagrams is also introduced.}, }
@article {pmid28386213, year = {2017}, author = {Levy, E}, title = {Exosomes in the Diseased Brain: First Insights from In vivo Studies.}, journal = {Frontiers in neuroscience}, volume = {11}, number = {}, pages = {142}, doi = {10.3389/fnins.2017.00142}, pmid = {28386213}, issn = {1662-4548}, support = {P01 AG017617/AG/NIA NIH HHS/United States ; }, abstract = {Extracellular vesicles (EVs) are nanoscale size vesicles secreted by cells and are important mediators of intercellular communication and genetic exchange. Exosomes, EVs generated in endosomal multivesicular bodies, have been the focus of numerous publications as they have emerged as clinically valuable markers of disease states. Exosomes have been mostly studied from conditioned culture media and body fluids, with the difficulty of isolating exosomes from tissues having delayed their study in vivo. The implementation of a method designed to isolate exosomes from tissues, however, has yielded the first insights into characteristics of exosomes in the brain. It has been observed that brain exosomes from murine models of neurodegenerative diseases and human postmortem brains tend to mirror the protein content of the cells of origin, and interestingly, they are enriched with toxic proteins. Whether this enrichment with neurotoxic proteins is beneficial by relieving neurons of accumulated toxic material or detrimental to the brain by propagating pathogenicity throughout the brain remains to be answered. Here is summarized the first group of studies describing exosomes isolated from brain, results that demonstrate that exosomes in vivo reflect complex multicellular pathogenic processes in neurodegenerative disorders and the brain's response to injury and damage.}, }
@article {pmid28384293, year = {2017}, author = {Olariu, V and Nilsson, J and Jönsson, H and Peterson, C}, title = {Different reprogramming propensities in plants and mammals: Are small variations in the core network wirings responsible?.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0175251}, doi = {10.1371/journal.pone.0175251}, pmid = {28384293}, issn = {1932-6203}, mesh = {Animals ; Mammals/*physiology ; Mice ; *Plant Physiological Phenomena ; }, abstract = {Although the plant and animal kingdoms were separated more than 1,6 billion years ago, multicellular development is for both guided by similar transcriptional, epigenetic and posttranscriptional machinery. One may ask to what extent there are similarities and differences in the gene regulation circuits and their dynamics when it comes to important processes like stem cell regulation. The key players in mouse embryonic stem cells governing pluripotency versus differentiation are Oct4, Sox2 and Nanog. Correspondingly, the WUSCHEL and CLAVATA3 genes represent a core in the Shoot Apical Meristem regulation for plants. In addition, both systems have designated genes that turn on differentiation. There is very little molecular homology between mammals and plants for these core regulators. Here, we focus on functional homologies by performing a comparison between the circuitry connecting these players in plants and animals and find striking similarities, suggesting that comparable regulatory logics have been evolved for stem cell regulation in both kingdoms. From in silico simulations we find similar differentiation dynamics. Further when in the differentiated state, the cells are capable of regaining the stem cell state. We find that the propensity for this is higher for plants as compared to mammalians. Our investigation suggests that, despite similarity in core regulatory networks, the dynamics of these can contribute to plant cells being more plastic than mammalian cells, i.e. capable to reorganize from single differentiated cells to whole plants-reprogramming. The presence of an incoherent feed-forward loop in the mammalian core circuitry could be the origin of the different reprogramming behaviour.}, }
@article {pmid28383827, year = {2017}, author = {Palazzo, L and Mikoč, A and Ahel, I}, title = {ADP-ribosylation: new facets of an ancient modification.}, journal = {The FEBS journal}, volume = {284}, number = {18}, pages = {2932-2946}, doi = {10.1111/febs.14078}, pmid = {28383827}, issn = {1742-4658}, support = {101794//Wellcome Trust/United Kingdom ; C35050/A22284//Cancer Research UK/United Kingdom ; }, mesh = {ADP Ribose Transferases/*genetics/metabolism ; Aging/genetics/*metabolism ; Animals ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biological Evolution ; DNA Damage ; *DNA Repair ; DNA Replication ; Gene Expression ; Humans ; Isoenzymes/genetics/metabolism ; Phosphoric Diester Hydrolases/genetics/metabolism ; Poly Adenosine Diphosphate Ribose/*metabolism ; *Protein Processing, Post-Translational ; Pyrophosphatases/genetics/metabolism ; Signal Transduction ; Viruses/genetics/metabolism ; }, abstract = {Rapid response to environmental changes is achieved by uni- and multicellular organisms through a series of molecular events, often involving modification of macromolecules, including proteins, nucleic acids and lipids. Amongst these, ADP-ribosylation is of emerging interest because of its ability to modify different macromolecules in the cells, and its association with many key biological processes, such as DNA-damage repair, DNA replication, transcription, cell division, signal transduction, stress and infection responses, microbial pathogenicity and aging. In this review, we provide an update on novel pathways and mechanisms regulated by ADP-ribosylation in organisms coming from all kingdoms of life.}, }
@article {pmid28368386, year = {2017}, author = {Barber, J}, title = {A mechanism for water splitting and oxygen production in photosynthesis.}, journal = {Nature plants}, volume = {3}, number = {}, pages = {17041}, doi = {10.1038/nplants.2017.41}, pmid = {28368386}, issn = {2055-0278}, mesh = {Biological Evolution ; Models, Biological ; Oxidation-Reduction ; Oxygen/*metabolism ; *Photosynthesis ; Photosystem II Protein Complex/*chemistry ; Plants/*metabolism ; Water/*metabolism ; }, abstract = {Sunlight is absorbed and converted to chemical energy by photosynthetic organisms. At the heart of this process is the most fundamental reaction on Earth, the light-driven splitting of water into its elemental constituents. In this way molecular oxygen is released, maintaining an aerobic atmosphere and creating the ozone layer. The hydrogen that is released is used to convert carbon dioxide into the organic molecules that constitute life and were the origin of fossil fuels. Oxidation of these organic molecules, either by respiration or combustion, leads to the recombination of the stored hydrogen with oxygen, releasing energy and reforming water. This water splitting is achieved by the enzyme photosystem II (PSII). Its appearance at least 3 billion years ago, and linkage through an electron transfer chain to photosystem I, directly led to the emergence of eukaryotic and multicellular organisms. Before this, biological organisms had been dependent on hydrogen/electron donors, such as H2S, NH3, organic acids and Fe2+, that were in limited supply compared with the oceans of liquid water. However, it is likely that water was also used as a hydrogen source before the emergence of PSII, as found today in anaerobic prokaryotic organisms that use carbon monoxide as an energy source to split water. The enzyme that catalyses this reaction is carbon monoxide dehydrogenase (CODH). Similarities between PSII and the iron- and nickel-containing form of this enzyme (Fe-Ni CODH) suggest a possible mechanism for the photosynthetic O-O bond formation.}, }
@article {pmid28360330, year = {2017}, author = {Soo, RM and Hemp, J and Parks, DH and Fischer, WW and Hugenholtz, P}, title = {On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria.}, journal = {Science (New York, N.Y.)}, volume = {355}, number = {6332}, pages = {1436-1440}, doi = {10.1126/science.aal3794}, pmid = {28360330}, issn = {1095-9203}, mesh = {Aerobiosis ; Bacterial Proteins/classification/genetics/*metabolism ; Biological Evolution ; Cyanobacteria/classification/*enzymology/genetics ; Electron Transport Complex III/classification/genetics/*metabolism ; Electron Transport Complex IV/genetics/*metabolism ; Genome, Bacterial ; Oxygen/*metabolism ; Photosynthesis/genetics/*physiology ; Phylogeny ; }, abstract = {The origin of oxygenic photosynthesis in Cyanobacteria led to the rise of oxygen on Earth ~2.3 billion years ago, profoundly altering the course of evolution by facilitating the development of aerobic respiration and complex multicellular life. Here we report the genomes of 41 uncultured organisms related to the photosynthetic Cyanobacteria (class Oxyphotobacteria), including members of the class Melainabacteria and a new class of Cyanobacteria (class Sericytochromatia) that is basal to the Melainabacteria and Oxyphotobacteria All members of the Melainabacteria and Sericytochromatia lack photosynthetic machinery, indicating that phototrophy was not an ancestral feature of the Cyanobacteria and that Oxyphotobacteria acquired the genes for photosynthesis relatively late in cyanobacterial evolution. We show that all three classes independently acquired aerobic respiratory complexes, supporting the hypothesis that aerobic respiration evolved after oxygenic photosynthesis.}, }
@article {pmid28359330, year = {2017}, author = {Szafranski, P}, title = {Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {269}, doi = {10.1186/s12864-017-3626-5}, pmid = {28359330}, issn = {1471-2164}, mesh = {Animals ; Electron Transport Complex IV/chemistry/*genetics ; *Evolution, Molecular ; Gene Expression Regulation ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Hydrophobic and Hydrophilic Interactions ; Mitochondrial Dynamics/*genetics ; *Mutagenesis, Insertional ; Phylogeny ; Polyadenylation ; }, abstract = {BACKGROUND: Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted speculation that, as in protists and plants, some bilaterian mitogenomes may continue to lose their canonical genes, or may even acquire new genes. To shed more light on this phenomenon, a PCR-based screen was conducted to assess fast-evolving mtDNAs of apocritan Hymenoptera (Arthropoda, Insecta) for genomic rearrangements that might be associated with the modification of mitochondrial gene content.<br><br>RESULTS: Sequencing of segmental inversions, identified in the screen, revealed that the cytochrome oxidase subunit II gene (cox2) of Campsomeris (Dielis) (Scoliidae) was split into two genes coding for COXIIA and COXIIB. The COXII-derived complementary polypeptides apparently form a heterodimer, have reduced hydrophobicity compared with the majority of mitogenome-encoded COX subunits, and one of them, COXIIB, features increased content of Cys residues. Analogous cox2 fragmentation is known only in two clades of protists (chlorophycean algae and alveolates), where it has been associated with piecewise relocation of this gene into the nucleus. In Campsomeris mtDNA, cox2a and cox2b loci are separated by a 3-kb large cluster of several antiparallel overlapping ORFs, one of which, qnu, seems to encode a nuclease that may have played a role in cox2 fission.<br><br>CONCLUSIONS: Although discontinuous mitochondrial protein genes encoding fragmented, complementary polypeptides are known in protists and some plants, split cox2 of Campsomeris is the first case of such a gene arrangement found in animals. The reported data also indicate that bilaterian animal mitogenomes may be carrying lineage-specific genes more often than previously thought, and suggest a homing endonuclease-based mechanism for insertional mitochondrial gene fission.}, }
@article {pmid28357395, year = {2017}, author = {Mignot, T and Nöllmann, M}, title = {New insights into the function of a versatile class of membrane molecular motors from studies of Myxococcus xanthus surface (gliding) motility.}, journal = {Microbial cell (Graz, Austria)}, volume = {4}, number = {3}, pages = {98-100}, doi = {10.15698/mic2017.03.563}, pmid = {28357395}, issn = {2311-2638}, abstract = {Cell motility is a central function of living cells, as it empowers colonization of new environmental niches, cooperation, and development of multicellular organisms. This process is achieved by complex yet precise energy-consuming machineries in both eukaryotes and bacteria. Bacteria move on surfaces using extracellular appendages such as flagella and pili but also by a less-understood process called gliding motility. During this process, rod-shaped bacteria move smoothly along their long axis without any visible morphological changes besides occasional bending. For this reason, the molecular mechanism of gliding motility and its origin have long remained a complete mystery. An important breakthrough in the understanding of gliding motility came from single cell and genetic studies in the delta-proteobacterium Myxococcus xanthus. These early studies revealed, for the first time, the existence of bacterial Focal Adhesion complexes (FA). FAs are formed at the bacterial pole and rapidly move towards the opposite cell pole. Their attachment to the underlying surface is linked to cell propulsion, in a process similar to the rearward translocation of actomyosin complexes in Apicomplexans. The protein machinery that forms at FAs was shown to contain up to seventeen proteins predicted to localize in all layers of the bacterial cell envelope, the cytosolic face, the inner membrane (IM), the periplasmic space and the outer membrane (OM). Among these proteins, a proton-gated channel at the inner membrane was identified as the molecular motor. Thus, thrust generation requires the transduction of traction forces generated at the inner membrane through the cell envelope beyond the rigid barrier of the bacterial peptidoglycan.}, }
@article {pmid28355288, year = {2017}, author = {Werfel, J and Ingber, DE and Bar-Yam, Y}, title = {Theory and associated phenomenology for intrinsic mortality arising from natural selection.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173677}, doi = {10.1371/journal.pone.0173677}, pmid = {28355288}, issn = {1932-6203}, mesh = {Aging/*physiology ; Animals ; Biological Evolution ; Herbivory/physiology ; Host-Pathogen Interactions ; Longevity/*physiology ; *Models, Biological ; *Models, Statistical ; Plants ; Poaceae/physiology ; Predatory Behavior/physiology ; Reproduction/physiology ; Selection, Genetic/*physiology ; }, abstract = {Standard evolutionary theories of aging and mortality, implicitly based on assumptions of spatial averaging, hold that natural selection cannot favor shorter lifespan without direct compensating benefit to individual reproductive success. However, a number of empirical observations appear as exceptions to or are difficult to reconcile with this view, suggesting explicit lifespan control or programmed death mechanisms inconsistent with the classic understanding. Moreover, evolutionary models that take into account the spatial distributions of populations have been shown to exhibit a variety of self-limiting behaviors, maintained through environmental feedback. Here we extend recent work on spatial modeling of lifespan evolution, showing that both theory and phenomenology are consistent with programmed death. Spatial models show that self-limited lifespan robustly results in long-term benefit to a lineage; longer-lived variants may have a reproductive advantage for many generations, but shorter lifespan ultimately confers long-term reproductive advantage through environmental feedback acting on much longer time scales. Numerous model variations produce the same qualitative result, demonstrating insensitivity to detailed assumptions; the key conditions under which self-limited lifespan is favored are spatial extent and locally exhaustible resources. Factors including lower resource availability, higher consumption, and lower dispersal range are associated with evolution of shorter lifespan. A variety of empirical observations can parsimoniously be explained in terms of long-term selective advantage for intrinsic mortality. Classically anomalous empirical data on natural lifespans and intrinsic mortality, including observations of longer lifespan associated with increased predation, and evidence of programmed death in both unicellular and multicellular organisms, are consistent with specific model predictions. The generic nature of the spatial model conditions under which intrinsic mortality is favored suggests a firm theoretical basis for the idea that evolution can quite generally select for shorter lifespan directly.}, }
@article {pmid28342854, year = {2017}, author = {Holzer, G and Roux, N and Laudet, V}, title = {Evolution of ligands, receptors and metabolizing enzymes of thyroid signaling.}, journal = {Molecular and cellular endocrinology}, volume = {459}, number = {}, pages = {5-13}, doi = {10.1016/j.mce.2017.03.021}, pmid = {28342854}, issn = {1872-8057}, mesh = {Animals ; Biological Evolution ; Cnidaria/anatomy &amp; histology/physiology ; Gene Expression Regulation, Developmental ; Humans ; Insecta/anatomy &amp; histology/physiology ; Iodide Peroxidase/genetics/*metabolism ; Ligands ; Phylogeny ; Receptors, Thyroid Hormone/genetics/*metabolism ; Signal Transduction/*physiology ; Species Specificity ; Thyroid Gland/*physiology ; Thyroxine/genetics/*metabolism ; Triiodothyronine/analogs &amp; derivatives/genetics/*metabolism ; }, abstract = {Thyroid hormones (THs) play important roles in vertebrates such as the control of the metabolism, development and seasonality. Given the pleiotropic effects of thyroid disorders (developmental delay, mood disorder, tachycardia, etc), THs signaling is highly investigated, specially using mammalian models. In addition, the critical role of TH in controlling frog metamorphosis has led to the use of Xenopus as another prominent model to study THs action. Nevertheless, animals regarded as non-model species can also improve our understanding of THs signaling. For instance, studies in amphioxus highlighted the role of Triac as a bona fide thyroid hormone receptor (TR) ligand. In this review, we discuss our current understanding of the THs signaling in the different taxa forming the metazoans (multicellular animals) group. We mainly focus on three actors of the THs signaling: the ligand, the receptor and the deiodinases, enzymes playing a critical role in THs metabolism. By doing so, we also pinpoint many key questions that remain unanswered. How can THs accelerate metamorphosis in tunicates and echinoderms while their TRs have not been yet demonstrated as functional THs receptors in these species? Do THs have a biological effect in insects and cnidarians even though they do not have any TR? What is the basic function of THs in invertebrate protostomia? These questions can appear disconnected from pharmacological issues and human applications, but the investigation of THs signaling at the metazoans scale can greatly improve our understanding of this major endocrinological pathway.}, }
@article {pmid28324731, year = {2017}, author = {Jayadev, R and Sherwood, DR}, title = {Basement membranes.}, journal = {Current biology : CB}, volume = {27}, number = {6}, pages = {R207-R211}, doi = {10.1016/j.cub.2017.02.006}, pmid = {28324731}, issn = {1879-0445}, mesh = {Animals ; Basement Membrane/*physiology ; Caenorhabditis elegans/growth &amp; development/*physiology ; Disease Susceptibility/*physiopathology ; Drosophila/growth &amp; development/*physiology ; Growth/physiology ; Homeostasis/physiology ; Humans ; Mice ; }, abstract = {Basement membranes (BMs) are thin, dense sheets of specialized, self-assembled extracellular matrix that surround most animal tissues (Figure 1, top). The emergence of BMs coincided with the origin of multicellularity in animals, suggesting that they were essential for the formation of tissues. Their sheet-like structure derives from two independent polymeric networks - one of laminin and one of type IV collagen (Figure 1, bottom). These independent collagen and laminin networks are thought to be linked by several additional extracellular matrix proteins, including nidogen and perlecan (Figure 1, bottom). BMs are usually associated with cells and are anchored to cell surfaces through interactions with adhesion receptors and sulfated glycolipids (Figure 1, bottom). Various combinations of other proteins, glycoproteins, and proteoglycans - including fibulin, hemicentin, SPARC, agrin, and type XVIII collagen - are present in BMs, creating biochemically and biophysically distinct structures that serve a wide variety of functions. BMs have traditionally been viewed as static protein assemblies that provide structural support to tissues. However, recent studies have begun to uncover dynamic, active roles for BMs in many developmental processes. Here, we discuss established and emerging roles of BMs in development, tissue construction, and tissue homeostasis. We also explore how cells traverse BM barriers, the roles of BMs in human diseases, and future directions for the field.}, }
@article {pmid28317949, year = {2017}, author = {Rudd, TR and Preston, MD and Yates, EA}, title = {The nature of the conserved basic amino acid sequences found among 437 heparin binding proteins determined by network analysis.}, journal = {Molecular bioSystems}, volume = {13}, number = {5}, pages = {852-865}, doi = {10.1039/c6mb00857g}, pmid = {28317949}, issn = {1742-2051}, mesh = {Amino Acid Sequence ; Binding Sites ; Computational Biology/methods ; Conserved Sequence ; Heparin/*metabolism ; Heparitin Sulfate/*metabolism ; Humans ; Models, Molecular ; Protein Binding ; Protein Interaction Maps ; Proteins/*chemistry/*metabolism ; }, abstract = {In multicellular organisms, a large number of proteins interact with the polyanionic polysaccharides heparan sulphate (HS) and heparin. These interactions are usually assumed to be dominated by charge-charge interactions between the anionic carboxylate and/or sulfate groups of the polysaccharide and cationic amino acids of the protein. A major question is whether there exist conserved amino acid sequences for HS/heparin binding among these diverse proteins. Potentially conserved HS/heparin binding sequences were sought amongst 437 HS/heparin binding proteins. Amino acid sequences were extracted and compared using a Levenshtein distance metric. The resultant similarity matrices were visualised as graphs, enabling extraction of strongly conserved sequences from highly variable primary sequences while excluding short, core regions. This approach did not reveal extensive, conserved HS/heparin binding sequences, rather a number of shorter, more widely spaced sequences that may work in unison to form heparin-binding sites on protein surfaces, arguing for convergent evolution. Thus, it is the three-dimensional arrangement of these conserved motifs on the protein surface, rather than the primary sequence per se, which are the evolutionary elements.}, }
@article {pmid28294448, year = {2017}, author = {Inglis, RF and Ryu, E and Asikhia, O and Strassmann, JE and Queller, DC}, title = {Does high relatedness promote cheater-free multicellularity in synthetic lifecycles?.}, journal = {Journal of evolutionary biology}, volume = {30}, number = {5}, pages = {985-993}, doi = {10.1111/jeb.13067}, pmid = {28294448}, issn = {1420-9101}, mesh = {*Biological Evolution ; Dictyostelium/*growth &amp; development ; *Life Cycle Stages ; }, abstract = {The evolution of multicellularity is one of the key transitions in evolution and requires extreme levels of cooperation between cells. However, even when cells are genetically identical, noncooperative cheating mutants can arise that cause a breakdown in cooperation. How then, do multicellular organisms maintain cooperation between cells? A number of mechanisms that increase relatedness amongst cooperative cells have been implicated in the maintenance of cooperative multicellularity including single-cell bottlenecks and kin recognition. In this study, we explore how relatively simple biological processes such as growth and dispersal can act to increase relatedness and promote multicellular cooperation. Using experimental populations of pseudo-organisms, we found that manipulating growth and dispersal of clones of a social amoeba to create high levels of relatedness was sufficient to prevent the spread of cheating mutants. By contrast, cheaters were able to spread under low-relatedness conditions. Most surprisingly, we saw the largest increase in cheating mutants under an experimental treatment that should create intermediate levels of relatedness. This is because one of the factors raising relatedness, structured growth, also causes high vulnerability to growth rate cheaters.}, }
@article {pmid28291791, year = {2017}, author = {Bengtson, S and Sallstedt, T and Belivanova, V and Whitehouse, M}, title = {Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae.}, journal = {PLoS biology}, volume = {15}, number = {3}, pages = {e2000735}, doi = {10.1371/journal.pbio.2000735}, pmid = {28291791}, issn = {1545-7885}, mesh = {*Fossils ; Geologic Sediments ; *Geological Phenomena ; India ; Phylogeny ; Radiometry ; Rhodophyta/*cytology/ultrastructure ; Subcellular Fractions/metabolism ; Time Factors ; }, abstract = {The ~1.6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites. We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes (red algae). The filamentous form Rafatazmia chitrakootensis n. gen, n. sp. has uniserial rows of large cells and grows through diffusely distributed septation. Each cell has a centrally suspended, conspicuous rhomboidal disk interpreted as a pyrenoid. The septa between the cells have central structures that may represent pit connections and pit plugs. Another filamentous form, Denaricion mendax n. gen., n. sp., has coin-like cells reminiscent of those in large sulfur-oxidizing bacteria but much more recalcitrant than the liquid-vacuole-filled cells of the latter. There are also resemblances with oscillatoriacean cyanobacteria, although cell volumes in the latter are much smaller. The wider affinities of Denaricion are uncertain. Ramathallus lobatus n. gen., n. sp. is a lobate sessile alga with pseudoparenchymatous thallus, &quot;cell fountains,&quot; and apical growth, suggesting florideophycean affinity. If these inferences are correct, Rafatazmia and Ramathallus represent crown-group multicellular rhodophytes, antedating the oldest previously accepted red alga in the fossil record by about 400 million years.}, }
@article {pmid28284906, year = {2017}, author = {Lochab, AK and Extavour, CG}, title = {Bone Morphogenetic Protein (BMP) signaling in animal reproductive system development and function.}, journal = {Developmental biology}, volume = {427}, number = {2}, pages = {258-269}, doi = {10.1016/j.ydbio.2017.03.002}, pmid = {28284906}, issn = {1095-564X}, mesh = {Animals ; *Biological Evolution ; Bone Morphogenetic Proteins/*metabolism ; Cell Lineage ; Genitalia/embryology/*metabolism ; *Germ Cells/metabolism ; Humans ; Reproduction ; Signal Transduction ; }, abstract = {In multicellular organisms, the specification, maintenance, and transmission of the germ cell lineage to subsequent generations are critical processes that ensure species survival. A number of studies suggest that the Bone Morphogenetic Protein (BMP) pathway plays multiple roles in this cell lineage. We wished to use a comparative framework to examine the role of BMP signaling in regulating these processes, to determine if patterns would emerge that might shed light on the evolution of molecular mechanisms that may play germ cell-specific or other reproductive roles across species. To this end, here we review evidence to date from the literature supporting a role for BMP signaling in reproductive processes across Metazoa. We focus on germ line-specific processes, and separately consider somatic reproductive processes. We find that from primordial germ cell (PGC) induction to maintenance of PGC identity and gametogenesis, BMP signaling regulates these processes throughout embryonic development and adult life in multiple deuterostome and protostome clades. In well-studied model organisms, functional genetic evidence suggests that BMP signaling is required in the germ line across all life stages, with the exception of PGC specification in species that do not use inductive signaling to induce germ cell formation. The current evidence is consistent with the hypothesis that BMP signaling is ancestral in bilaterian inductive PGC specification. While BMP4 appears to be the most broadly employed ligand for the reproductive processes considered herein, we also noted evidence for sex-specific usage of different BMP ligands. In gametogenesis, BMP6 and BMP15 seem to have roles restricted to oogenesis, while BMP8 is restricted to spermatogenesis. We hypothesize that a BMP-based mechanism may have been recruited early in metazoan evolution to specify the germ line, and was subsequently co-opted for use in other germ line-specific and somatic reproductive processes. We suggest that if future studies assessing the function of the BMP pathway across extant species were to include a reproductive focus, that we would be likely to find continued evidence in favor of an ancient association between BMP signaling and the reproductive cell lineage in animals.}, }
@article {pmid28258564, year = {2017}, author = {Ishibashi, K and Morishita, Y and Tanaka, Y}, title = {The Evolutionary Aspects of Aquaporin Family.}, journal = {Advances in experimental medicine and biology}, volume = {969}, number = {}, pages = {35-50}, doi = {10.1007/978-94-024-1057-0_2}, pmid = {28258564}, issn = {0065-2598}, mesh = {Amino Acid Sequence ; Animals ; Aquaporins/chemistry/classification/*genetics/metabolism ; Biological Evolution ; Biological Transport ; Conserved Sequence ; Fungi/classification/*genetics/metabolism ; Gene Duplication ; Gene Expression ; Gene Transfer, Horizontal ; Invertebrates/classification/*genetics/metabolism ; Phylogeny ; Plants/classification/*genetics/metabolism ; Prokaryotic Cells/classification/*metabolism ; Protein Domains ; Vertebrates/classification/*genetics/metabolism ; }, abstract = {Aquaporins (AQPs) are a family of transmembrane proteins present in almost all species including virus. They are grossly divided into three subfamilies based on the sequence around a highly conserved pore-forming NPA motif: (1) classical water -selective AQP (CAQP), (2) glycerol -permeable aquaglyceroporin (AQGP) and (3) AQP super-gene channel, superaquaporin (SAQP). AQP is composed of two tandem repeats of conserved three transmembrane domains and a NPA motif. AQP ancestors probably started in prokaryotes by the duplication of half AQP genes to be diversified into CAQPs or AQGPs by evolving a subfamily-specific carboxyl-terminal NPA motif. Both AQP subfamilies may have been carried over to unicellular eukaryotic ancestors, protists and further to multicellular organisms. Although fungus lineage has kept both AQP subfamilies, the plant lineage has lost AQGP after algal ancestors with extensive diversifications of CAQPs into PIP, TIP, SIP, XIP, HIP and LIP with a possible horizontal transfer of NIP from bacteria. Interestingly, the animal lineage has obtained new SAQP subfamily with highly deviated NPA motifs, especially at the amino-terminal halves in both prostomial and deuterostomial animals. The prostomial lineage has lost AQGP after hymenoptera, while the deuterostomial lineage has kept all three subfamilies up to the vertebrate with diversified CAQPs (AQP0, 1, 2, 4, 5, 6, 8) and AQGPs (AQP3, 7, 9, 10) with limited SAQPs (AQP11, 12) in mammals. Whole-genome duplications, local gene duplications and horizontal gene transfers may have produced the AQP diversity with adaptive selections and functional alternations in response to environment changes. With the above evolutionary perspective in mind, the function of each AQP could be speculated by comparison among species to get new insights into physiological roles of AQPs . This evolutionary guidance in AQP research will lead to deeper understandings of water and solute homeostasis.}, }
@article {pmid28253955, year = {2017}, author = {López-Otín, C and Mariño, G}, title = {Tagged ATG8-Coding Constructs for the In Vitro and In Vivo Assessment of ATG4 Activity.}, journal = {Methods in enzymology}, volume = {587}, number = {}, pages = {189-205}, doi = {10.1016/bs.mie.2016.11.001}, pmid = {28253955}, issn = {1557-7988}, mesh = {Animals ; Autophagy ; Autophagy-Related Protein 8 Family/*genetics/metabolism ; Autophagy-Related Proteins/genetics/metabolism ; Cells, Cultured ; Cysteine Endopeptidases/analysis/genetics/*metabolism ; Genetic Vectors ; Humans ; Mammals/genetics ; Mice ; Molecular Biology/*methods ; Recombinant Proteins/genetics/metabolism ; Transfection ; }, abstract = {Autophagy is a catabolic pathway, which mediates the degradation of cytoplasmic components and sustains many essential cellular functions. More than 30 genes have been involved in different aspects of this essential process in simple eukaryotes as yeast. Among these genes, those coding for members of the Atg4-Atg8 proteolytic system have acquired a high degree of complexity throughout evolution. Contrasting with the situation in unicellular eukaryotes, in which the system is composed by just a single protease (Atg4) and a single substrate (Atg8), evolution has led to the presence of several members for both Atg4 and Atg8 families in multicellular organisms. In human cells, there are four Atg4 proteases and six Atg8 substrates, which have probably evolved to cope with specific requirements for autophagic pathway in more complex scenarios. Despite these considerations, the reasons for the evolutionarily acquired complexity of this proteolytic system are still not completely understood. In this work, we describe two different applications of a relatively simple but useful technique to analyze protease-substrate specificity of this system in mammalian cells. By using the described technique, it is possible to determine the cellular efficiency in the initial cleavage for each of the Atg8 family members in diverse experimental settings both in cultured cells and live laboratory mice.}, }
@article {pmid28250339, year = {2017}, author = {Cahill, MA}, title = {The evolutionary appearance of signaling motifs in PGRMC1.}, journal = {Bioscience trends}, volume = {11}, number = {2}, pages = {179-192}, doi = {10.5582/bst.2017.01009}, pmid = {28250339}, issn = {1881-7823}, mesh = {Animals ; Humans ; Membrane Proteins/genetics/*metabolism ; Receptors, Progesterone/genetics/*metabolism ; Signal Transduction/genetics/physiology ; }, abstract = {A complex PGRMC1-centred regulatory system controls multiple cell functions. Although PGRMC1 is phosphorylated at several positions, we do not understand the mechanisms regulating its function. PGRMC1 is the archetypal member of the membrane associated progesterone receptor (MAPR) family. Phylogentic comparison of MAPR proteins suggests that the ancestral metazoan &quot;PGRMC-like&quot; MAPR gene resembled PGRMC1/PGRMC2, containing the equivalents of PGRMC1 Y139 and Y180 SH2 target motifs. It later acquired a CK2 site with phosphoacceptor at S181. Separate PGRMC1 and PGRMC2 genes with this &quot;PGRMC-like&quot; structure diverged after the separation of vertebrates from protochordates. Terrestrial tetrapods possess a novel proline-rich PGRMC1 SH3 target motif centred on P64 which in mammals is augmented by a phosphoacceptor at PGRMC1 S54, and in primates by an additional S57 CK2 site. All of these phosphoacceptors are phosphorylated in vivo. This study suggests that an increasingly sophisticated system of PGRMC1-modulated multicellular functional regulation has characterised animal evolution since Precambrian times.}, }
@article {pmid28247585, year = {2017}, author = {Frenk, S and Pizza, G and Walker, RV and Houseley, J}, title = {Aging yeast gain a competitive advantage on non-optimal carbon sources.}, journal = {Aging cell}, volume = {16}, number = {3}, pages = {602-604}, doi = {10.1111/acel.12582}, pmid = {28247585}, issn = {1474-9726}, support = {BBS/E/B/0000H247//Biotechnology and Biological Sciences Research Council/United Kingdom ; 088335//Wellcome Trust/United Kingdom ; //Medical Research Council/United Kingdom ; }, mesh = {Acetic Acid/metabolism/pharmacology ; Adaptation, Physiological/*genetics ; Carbon/*metabolism ; Cell Division ; Fermentation ; Galactose/metabolism/pharmacology ; Glucose/metabolism/pharmacology ; Metabolic Networks and Pathways/*genetics ; Raffinose/metabolism/pharmacology ; Saccharomyces cerevisiae/*drug effects/genetics/growth &amp; development/*metabolism ; }, abstract = {Animals, plants and fungi undergo an aging process with remarkable physiological and molecular similarities, suggesting that aging has long been a fact of life for eukaryotes and one to which our unicellular ancestors were subject. Key biochemical pathways that impact longevity evolved prior to multicellularity, and the interactions between these pathways and the aging process therefore emerged in ancient single-celled eukaryotes. Nevertheless, we do not fully understand how aging impacts the fitness of unicellular organisms, and whether such cells gain a benefit from modulating rather than simply suppressing the aging process. We hypothesized that age-related loss of fitness in single-celled eukaryotes may be counterbalanced, partly or wholly, by a transition from a specialist to a generalist life-history strategy that enhances adaptability to other environments. We tested this hypothesis in budding yeast using competition assays and found that while young cells are more successful in glucose, highly aged cells outcompete young cells on other carbon sources such as galactose. This occurs because aged yeast divide faster than young cells in galactose, reversing the normal association between age and fitness. The impact of aging on single-celled organisms is therefore complex and may be regulated in ways that anticipate changing nutrient availability. We propose that pathways connecting nutrient availability with aging arose in unicellular eukaryotes to capitalize on age-linked diversity in growth strategy and that individual cells in higher eukaryotes may similarly diversify during aging to the detriment of the organism as a whole.}, }
@article {pmid28242741, year = {2017}, author = {Cavalier-Smith, T}, title = {Correction to 'Origin of animal multicellularity: precursors, causes, consequences-the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion'.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1718}, pages = {}, doi = {10.1098/rstb.2017.0001}, pmid = {28242741}, issn = {1471-2970}, }
@article {pmid28241893, year = {2017}, author = {Zemková, M and Zahradník, D and Mokrejš, M and Flegr, J}, title = {Parasitism as the main factor shaping peptide vocabularies in current organisms.}, journal = {Parasitology}, volume = {144}, number = {7}, pages = {975-983}, doi = {10.1017/S0031182017000191}, pmid = {28241893}, issn = {1469-8161}, mesh = {Animals ; *Biological Evolution ; Helminth Proteins/*analysis ; *Host-Parasite Interactions ; Peptides/*analysis ; *Proteome ; Protozoan Proteins/*analysis ; }, abstract = {Self/non-self-discrimination by vertebrate immune systems is based on the recognition of the presence of peptides in proteins of a parasite that are not contained in the proteins of a host. Therefore, a reduction of the number of 'words' in its own peptide vocabulary could be an efficient evolutionary strategy of parasites for escaping recognition. Here, we compared peptide vocabularies of 30 endoparasitic and 17 free-living unicellular organisms and also eight multicellular parasitic and 16 multicellular free-living organisms. We found that both unicellular and multicellular parasites used a significantly lower number of different pentapeptides than free-living controls. Impoverished pentapeptide vocabularies in parasites were observed across all five clades that contain both the parasitic and free-living species. The effect of parasitism on a number of peptides used in an organism's proteins is larger than effects of all other studied factors, including the size of a proteome, the number of encoded proteins, etc. This decrease of pentapeptide diversity was partly compensated for by an increased number of hexapeptides. Our results support the hypothesis of parasitism-associated reduction of peptide vocabulary and suggest that T-cell receptors mostly recognize the five amino acids-long part of peptides that are presented in the groove of major histocompatibility complex molecules.}, }
@article {pmid28222679, year = {2017}, author = {Skippington, E and Barkman, TJ and Rice, DW and Palmer, JD}, title = {Comparative mitogenomics indicates respiratory competence in parasitic Viscum despite loss of complex I and extreme sequence divergence, and reveals horizontal gene transfer and remarkable variation in genome size.}, journal = {BMC plant biology}, volume = {17}, number = {1}, pages = {49}, doi = {10.1186/s12870-017-0992-8}, pmid = {28222679}, issn = {1471-2229}, mesh = {DNA, Plant ; Electron Transport Chain Complex Proteins/genetics ; Electron Transport Complex I/*genetics/metabolism ; *Evolution, Molecular ; Gene Deletion ; *Gene Transfer, Horizontal ; Genes, Plant ; *Genetic Variation ; Genome, Mitochondrial ; *Genome, Plant ; Molecular Sequence Annotation ; Plant Proteins/genetics ; RNA, Plant ; RNA, Ribosomal ; Sequence Analysis, DNA ; Species Specificity ; Viscum/*genetics/metabolism ; Viscum album/genetics/metabolism ; }, abstract = {BACKGROUND: Aerobically respiring eukaryotes usually contain four respiratory-chain complexes (complexes I-IV) and an ATP synthase (complex V). In several lineages of aerobic microbial eukaryotes, complex I has been lost, with an alternative, nuclear-encoded NADH dehydrogenase shown in certain cases to bypass complex I and oxidize NADH without proton translocation. The first loss of complex I in any multicellular eukaryote was recently reported in two studies; one sequenced the complete mitogenome of the hemiparasitic aerial mistletoe, Viscum scurruloideum, and the other sequenced the V. album mitogenome. The V. scurruloideum study reported no significant additional loss of mitochondrial genes or genetic function, but the V. album study postulated that mitochondrial genes encoding all ribosomal RNAs and proteins of all respiratory complexes are either absent or pseudogenes, thus raising questions as to whether the mitogenome and oxidative respiration are functional in this plant.<br><br>RESULTS: To determine whether these opposing conclusions about the two Viscum mitogenomes reflect a greater degree of reductive/degenerative evolution in V. album or instead result from interpretative and analytical differences, we reannotated and reanalyzed the V. album mitogenome and compared it with the V. scurruloideum mitogenome. We find that the two genomes share a complete complement of mitochondrial rRNA genes and a typical complement of genes encoding respiratory complexes II-V. Most Viscum mitochondrial protein genes exhibit very high levels of divergence yet are evolving under purifying, albeit relaxed selection. We discover two cases of horizontal gene transfer in V. album and show that the two Viscum mitogenomes differ by 8.6-fold in size (66 kb in V. scurruloideum; 565 kb in V. album).<br><br>CONCLUSIONS: Viscum mitogenomes are extraordinary compared to other plant mitogenomes in terms of their wide size range, high rates of synonymous substitutions, degree of relaxed selection, and unprecedented loss of respiratory complex I. However, contrary to the initial conclusions regarding V. album, both Viscum mitogenomes possess conventional sets of rRNA and, excepting complex I, respiratory genes. Both plants should therefore be able to carry out aerobic respiration. Moreover, with respect to size, the V. scurruloideum mitogenome has experienced a greater level of reductive evolution.}, }
@article {pmid28217903, year = {2017}, author = {Arias Del Angel, JA and Escalante, AE and Martínez-Castilla, LP and Benítez, M}, title = {An Evo-Devo Perspective on Multicellular Development of Myxobacteria.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {328}, number = {1-2}, pages = {165-178}, doi = {10.1002/jez.b.22727}, pmid = {28217903}, issn = {1552-5015}, mesh = {*Biological Evolution ; *Developmental Biology ; Gene Expression Regulation, Bacterial/*physiology ; Myxococcales/*cytology/*genetics ; }, abstract = {The transition to multicellularity, recognized as one the major transitions in evolution, has occurred independently several times. While multicellular development has been extensively studied in zygotic organisms including plant and animal groups, just a few aggregative multicellular organisms have been employed as model organisms for the study of multicellularity. Studying different evolutionary origins and modes of multicellularity enables comparative analyses that can help identifying lineage-specific aspects of multicellular evolution and generic factors and mechanisms involved in the transition to multicellularity. Among aggregative multicellular organisms, myxobacteria are a valuable system to explore the particularities that aggregation confers to the evolution of multicellularity and mechanisms shared with clonal organisms. Moreover, myxobacteria species develop fruiting bodies displaying a range of morphological diversity. In this review, we aim to synthesize diverse lines of evidence regarding myxobacteria development and discuss them in the context of Evo-Devo concepts and approaches. First, we briefly describe the developmental processes in myxobacteria, present an updated comparative analysis of the genes involved in their developmental processes and discuss these and other lines of evidence in terms of co-option and developmental system drift, two concepts key to Evo-Devo studies. Next, as has been suggested from Evo-Devo approaches, we discuss how broad comparative studies and integration of diverse genetic, physicochemical, and environmental factors into experimental and theoretical models can further our understanding of myxobacterial development, phenotypic variation, and evolution.}, }
@article {pmid28214944, year = {2017}, author = {Basile, A and Fambrini, M and Pugliesi, C}, title = {The vascular plants: open system of growth.}, journal = {Development genes and evolution}, volume = {227}, number = {2}, pages = {129-157}, doi = {10.1007/s00427-016-0572-1}, pmid = {28214944}, issn = {1432-041X}, mesh = {*Evolution, Molecular ; Magnoliopsida/*genetics/growth &amp; development/metabolism ; Meristem/*genetics/growth &amp; development/metabolism ; Plant Growth Regulators/metabolism ; Plant Proteins/genetics/metabolism ; }, abstract = {What is fascinating in plants (true also in sessile animals such as corals and hydroids) is definitely their open and indeterminate growth, as a result of meristematic activity. Plants as well as animals are characterized by a multicellular organization, with which they share a common set of genes inherited from a common eukaryotic ancestor; nevertheless, circa 1.5 billion years of evolutionary history made the two kingdoms very different in their own developmental biology. Flowering plants, also known as angiosperms, arose during the Cretaceous Period (145-65 million years ago), and up to date, they count around 235,000 species, representing the largest and most diverse group within the plant kingdom. One of the foundations of their success relies on the plant-pollinator relationship, essentially unique to angiosperms that pushed large speciation in both plants and insects and on the presence of the carpel, the structure devoted to seed enclosure. A seed represents the main organ preserving the genetic information of a plant; during embryogenesis, the primary axis of development is established by two groups of pluripotent cells: the shoot apical meristem (SAM), responsible for gene rating all aboveground organs, and the root apical meristem (RAM), responsible for producing all underground organs. During postembryonic shoot development, axillary meristem (AM) initiation and outgrowth are responsible for producing all secondary axes of growth including inflorescence branches or flowers. The production of AMs is tightly linked to the production of leaves and their separation from SAM. As leaf primordia are formed on the flanks of the SAM, a region between the apex and the developing organ is established and referred to as boundary zone. Interaction between hormones and the gene network in the boundary zone is fundamental for AM initiation. AMs only develop at the adaxial base of the leaf; thus, AM initiation is also strictly associated with leaf polarity. AMs function as new SAMs: form axillary buds with a few leaves and then the buds can either stay dormant or develop into shoot branches to define a plant architecture, which in turn affects assimilate production and reproductive efficiency. Therefore, the radiation of angiosperms was accompanied by a huge diversification in growth forms that determine an enormous morphological plasticity helping plants to environmental changes. In this review, we focused on the developmental processes of AM initiation and outgrowth. In particular, we summarized the primary growth of SAM, the key role of positional signals for AM initiation, and the dissection of molecular players involved in AM initiation and outgrowth. Finally, the interaction between phytohormone signals and gene regulatory network controlling AM development was discussed.}, }
@article {pmid28207760, year = {2017}, author = {Neeb, ZT and Hogan, DJ and Katzman, S and Zahler, AM}, title = {Preferential expression of scores of functionally and evolutionarily diverse DNA and RNA-binding proteins during Oxytricha trifallax macronuclear development.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0170870}, doi = {10.1371/journal.pone.0170870}, pmid = {28207760}, issn = {1932-6203}, support = {T32 GM008646/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Protozoan/*genetics ; *Evolution, Molecular ; *Gene Expression Profiling ; Gene Expression Regulation ; High-Throughput Nucleotide Sequencing ; Macronucleus/genetics/*metabolism ; Oxytricha/genetics/growth &amp; development/*metabolism ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; RNA-Binding Proteins/genetics/*metabolism ; }, abstract = {During its sexual reproduction, the stichotrichous ciliate Oxytricha trifallax orchestrates a remarkable transformation of one of the newly formed germline micronuclear genomes. Hundreds of thousands of gene pieces are stitched together, excised from chromosomes, and replicated dozens of times to yield a functional somatic macronuclear genome composed of ~16,000 distinct DNA molecules that typically encode a single gene. Little is known about the proteins that carry out this process. We profiled mRNA expression as a function of macronuclear development and identified hundreds of mRNAs preferentially expressed at specific times during the program. We find that a disproportionate number of these mRNAs encode proteins that are involved in DNA and RNA functions. Many mRNAs preferentially expressed during macronuclear development have paralogs that are either expressed constitutively or are expressed at different times during macronuclear development, including many components of the RNA polymerase II machinery and homologous recombination complexes. Hundreds of macronuclear development-specific genes encode proteins that are well-conserved among multicellular eukaryotes, including many with links to germline functions or development. Our work implicates dozens of DNA and RNA-binding proteins with diverse evolutionary trajectories in macronuclear development in O. trifallax. It suggests functional connections between the process of macronuclear development in unicellular ciliates and germline specialization and differentiation in multicellular organisms, and argues that gene duplication is a key source of evolutionary innovation in this process.}, }
@article {pmid28204813, year = {2017}, author = {Agnati, LF and Marcoli, M and Leo, G and Maura, G and Guidolin, D}, title = {Homeostasis and the concept of 'interstitial fluids hierarchy': Relevance of cerebrospinal fluid sodium concentrations and brain temperature control (Review).}, journal = {International journal of molecular medicine}, volume = {39}, number = {3}, pages = {487-497}, doi = {10.3892/ijmm.2017.2874}, pmid = {28204813}, issn = {1791-244X}, mesh = {Animals ; Biological Evolution ; Body Temperature Regulation ; Brain/*physiology ; Cerebrospinal Fluid/metabolism ; Extracellular Fluid/*metabolism ; Feedback, Physiological ; *Homeostasis ; Humans ; Kidney/physiology ; Sodium/metabolism ; }, abstract = {In this review, the aspects and further developments of the concept of homeostasis are discussed also in the perspective of their possible impact in the clinical practice, particularly as far as psychic homeostasis is concerned. A brief historical survey and comments on the concept of homeostasis and allostasis are presented to introduce our proposal that is based on the classical assumption of the interstitial fluid (ISF) as the internal medium for multicellular organisms. However, the new concept of a hierarchic role of ISF of the various organs is introduced. Additionally, it is suggested that particularly for some chemico‑physical parameters, oscillatory rhythms within their proper set‑ranges should be considered a fundamental component of homeostasis. Against this background, we propose that the brain ISF has the highest hierarchic role in human beings, providing the optimal environment, not simply for brain cell survival, but also for brain complex functions and the oscillatory rhythms of some parameters, such as cerebrospinal fluid sodium and brain ISF pressure waves, which may play a crucial role in brain physio‑pathological states. Thus, according to this proposal, the brain ISF represents the real internal medium since the maintenance of its dynamic intra-set-range homeostasis is the main factor for a free and independent life of higher vertebrates. Furthermore, the evolutionary links between brain and kidney and their synergistic role in H2O/Na balance and brain temperature control are discussed. Finally, it is surmised that these two interrelated parameters have deep effects on the Central Nervous System (CNS) higher integrative actions such those linked to psychic homeostasis.}, }
@article {pmid28204529, year = {2016}, author = {Herrero, A and Stavans, J and Flores, E}, title = {The multicellular nature of filamentous heterocyst-forming cyanobacteria.}, journal = {FEMS microbiology reviews}, volume = {40}, number = {6}, pages = {831-854}, doi = {10.1093/femsre/fuw029}, pmid = {28204529}, issn = {1574-6976}, mesh = {Anabaena ; Cell Physiological Phenomena/*physiology ; *Cyanobacteria/cytology/physiology ; }, abstract = {Cyanobacteria carry out oxygenic photosynthesis, play a key role in the cycling of carbon and nitrogen in the biosphere, and have had a large impact on the evolution of life and the Earth itself. Many cyanobacterial strains exhibit a multicellular lifestyle, growing as filaments that can be hundreds of cells long and endowed with intercellular communication. Furthermore, under depletion of combined nitrogen, filament growth requires the activity of two interdependent cell types: vegetative cells that fix CO2 and heterocysts that fix N2. Intercellular molecular transfer is essential for signaling involved in the regulation of heterocyst differentiation and for reciprocal nutrition of heterocysts and vegetative cells. Here we review various aspects of multicellularity in cyanobacterial filaments and their differentiation, including filament architecture with emphasis on the structures used for intercellular communication; we survey theoretical models that have been put forward to understand heterocyst patterning and discuss the factors that need to be considered for these models to reflect the biological entity; and finally, since cell division in filamentous cyanobacteria has the peculiarity of producing linked instead of independent cells, we review distinct aspects of cell division in these organisms.}, }
@article {pmid28194138, year = {2017}, author = {Rodríguez-Torres, MD and Islas-Robles, Á and Gómez-Lunar, Z and Delaye, L and Hernández-González, I and Souza, V and Travisano, M and Olmedo-Álvarez, G}, title = {Phenotypic Microdiversity and Phylogenetic Signal Analysis of Traits Related to Social Interaction in Bacillus spp. from Sediment Communities.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {29}, doi = {10.3389/fmicb.2017.00029}, pmid = {28194138}, issn = {1664-302X}, abstract = {Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites. A subsample of 141 Bacillus spp. isolates from sediment, with seven well-represented species was chosen to evaluate the heterogeneity and the phylogenetic signal of phenotypic traits that are known to diverge within small clades, such as substrate utilization, and traits that are conserved deep in the lineage, such as prototrophy, swarming and biofilm formation. We were especially interested in evaluating social traits, such as swarming and biofilm formation, for which cooperation is needed to accomplish a multicellular behavior and for which there is little information from natural communities. The phylogenetic distribution of traits, evaluated by the Purvis and Fritz's D statistics approached a Brownian model of evolution. Analysis of the phylogenetic relatedness of the clusters of members sharing the trait using consenTRAIT algorithm, revealed more clustering and deeper phylogenetic signal for prototrophy, biofilm and swimming compared to the data obtained for substrate utilization. The explanation to the observed Brownian evolution of social traits could be either loss due to complete dispensability or to compensated trait loss due to the availability of public goods. Since many of the evaluated traits can be considered to be collective action traits, such as swarming, motility and biofilm formation, the observed microdiversity within taxonomic groups might be explained by distributed functions in structured communities.}, }
@article {pmid28189637, year = {2017}, author = {Sieber, KB and Bromley, RE and Dunning Hotopp, JC}, title = {Lateral gene transfer between prokaryotes and eukaryotes.}, journal = {Experimental cell research}, volume = {358}, number = {2}, pages = {421-426}, doi = {10.1016/j.yexcr.2017.02.009}, pmid = {28189637}, issn = {1090-2422}, support = {DP2 OD007372/OD/NIH HHS/United States ; R01 CA206188/CA/NCI NIH HHS/United States ; T32 DK067872/DK/NIDDK NIH HHS/United States ; 1-R01-CA206188/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/physiology ; Humans ; Mitochondria/metabolism ; Prokaryotic Cells/*cytology ; }, abstract = {Lateral gene transfer (LGT) is an all-encompassing term for the movement of DNA between diverse organisms. LGT is synonymous with horizontal gene transfer, and the terms are used interchangeably throughout the scientific literature. While LGT has been recognized within the bacteria domain of life for decades, inter-domain LGTs are being increasingly described. LGTs between bacteria and complex multicellular organisms are of interest because they challenge the long-held dogma that such transfers could only occur in closely-related, single-celled organisms. Scientists will continue to challenge our understanding of LGT as we sequence more, diverse organisms, as we sequence more endosymbiont-colonized arthropods, and as we continue to appreciate LGT events, both young and old.}, }
@article {pmid28188480, year = {2017}, author = {Sekimoto, H}, title = {Sexual reproduction and sex determination in green algae.}, journal = {Journal of plant research}, volume = {130}, number = {3}, pages = {423-431}, doi = {10.1007/s10265-017-0908-6}, pmid = {28188480}, issn = {1618-0860}, mesh = {Biological Evolution ; Cell Adhesion/physiology ; Cell Fusion ; Chlamydomonas reinhardtii/genetics/growth &amp; development ; Chlorophyta/*genetics/growth &amp; development/*physiology ; Closterium/genetics/growth &amp; development ; Fresh Water ; Life Cycle Stages/genetics/physiology ; Membrane Fusion/physiology ; Reproduction/*genetics/*physiology ; Sex Determination Processes/*genetics/*physiology ; Volvox/genetics/growth &amp; development ; }, abstract = {The sexual reproductive processes of some representative freshwater green algae are reviewed. Chlamydomonas reinhardtii is a unicellular volvocine alga having two mating types: mating type plus (mt+) and mating type minus (mt-), which are controlled by a single, complex mating-type locus. Sexual adhesion between the gametes is mediated by sex-specific agglutinin molecules on their flagellar membranes. Cell fusion is initiated by an adhesive interaction between the mt+ and mt- mating structures, followed by localized membrane fusion. The loci of sex-limited genes and the conformation of sex-determining regions have been rearranged during the evolution of volvocine algae; however, the essential function of the sex-determining genes of the isogamous unicellular Chlamydomonas reinhardtii is conserved in the multicellular oogamous Volvox carteri. The sexual reproduction of the unicellular charophycean alga, Closterium peracerosum-strigosum-littorale complex, is also focused on here. The sexual reproductive processes of heterothallic strains are controlled by two multifunctional sex pheromones, PR-IP and PR-IP Inducer, which independently promote multiple steps in conjugation at the appropriate times through different induction mechanisms. The molecules involved in sexual reproduction and sex determination have also been characterized.}, }
@article {pmid28188197, year = {2017}, author = {Drumm, BT and Baker, SA}, title = {Teaching a changing paradigm in physiology: a historical perspective on gut interstitial cells.}, journal = {Advances in physiology education}, volume = {41}, number = {1}, pages = {100-109}, doi = {10.1152/advan.00154.2016}, pmid = {28188197}, issn = {1522-1229}, mesh = {Animals ; Gastrointestinal Motility/*physiology ; Gastrointestinal Tract/*cytology/*physiology ; Humans ; Muscle, Smooth/cytology/physiology ; Physiology/*education ; Teaching/*trends ; }, abstract = {The study and teaching of gastrointestinal (GI) physiology necessitates an understanding of the cellular basis of contractile and electrical coupling behaviors in the muscle layers that comprise the gut wall. Our knowledge of the cellular origin of GI motility has drastically changed over the last 100 yr. While the pacing and coordination of GI contraction was once thought to be solely attributable to smooth muscle cells, it is now widely accepted that the motility patterns observed in the GI tract exist as a result of a multicellular system, consisting of not only smooth muscle cells but also enteric neurons and distinct populations of specialized interstitial cells that all work in concert to ensure proper GI functions. In this historical perspective, we focus on the emerging role of interstitial cells in GI motility and examine the key discoveries and experiments that led to a major shift in a paradigm of GI physiology regarding the role of interstitial cells in modulating GI contractile patterns. A review of these now classic experiments and papers will enable students and educators to fully appreciate the complex, multicellular nature of GI muscles as well as impart lessons on how shifting paradigms in physiology are fueled by new technologies that lead to new emerging discoveries.}, }
@article {pmid28179656, year = {2017}, author = {Hotamisligil, GS}, title = {Inflammation, metaflammation and immunometabolic disorders.}, journal = {Nature}, volume = {542}, number = {7640}, pages = {177-185}, doi = {10.1038/nature21363}, pmid = {28179656}, issn = {1476-4687}, support = {R01 DK052539/DK/NIDDK NIH HHS/United States ; R01 HL125753/HL/NHLBI NIH HHS/United States ; R01 AI116901/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptive Immunity/genetics ; Animals ; Clinical Trials as Topic ; Cytokines/metabolism ; Evolution, Molecular ; Genome-Wide Association Study ; Hormones/metabolism ; Humans ; Inflammation/complications/genetics/*immunology/*metabolism ; Invertebrates/immunology/metabolism ; Metabolic Diseases/complications/genetics/*immunology/*metabolism ; Obesity/complications/genetics/immunology/metabolism ; Organelles/metabolism ; Signal Transduction ; }, abstract = {Proper regulation and management of energy, substrate diversity and quantity, as well as macromolecular synthesis and breakdown processes, are fundamental to cellular and organismal survival and are paramount to health. Cellular and multicellular organization are defended by the immune response, a robust and critical system through which self is distinguished from non-self, pathogenic signals are recognized and eliminated, and tissue homeostasis is safeguarded. Many layers of evolutionarily conserved interactions occur between immune response and metabolism. Proper maintenance of this delicate balance is crucial for health and has important implications for many pathological states such as obesity, diabetes, and other chronic non-communicable diseases.}, }
@article {pmid28176784, year = {2017}, author = {Nguyen, TA and Cissé, OH and Yun Wong, J and Zheng, P and Hewitt, D and Nowrousian, M and Stajich, JE and Jedd, G}, title = {Innovation and constraint leading to complex multicellularity in the Ascomycota.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {14444}, doi = {10.1038/ncomms14444}, pmid = {28176784}, issn = {2041-1723}, support = {P01 GM068087/GM/NIGMS NIH HHS/United States ; }, abstract = {The advent of complex multicellularity (CM) was a pivotal event in the evolution of animals, plants and fungi. In the fungal Ascomycota, CM is based on hyphal filaments and arose in the Pezizomycotina. The genus Neolecta defines an enigma: phylogenetically placed in a related group containing mostly yeasts, Neolecta nevertheless possesses Pezizomycotina-like CM. Here we sequence the Neolecta irregularis genome and identify CM-associated functions by searching for genes conserved in Neolecta and the Pezizomycotina, which are absent or divergent in budding or fission yeasts. This group of 1,050 genes is enriched for functions related to diverse endomembrane systems and their organization. Remarkably, most show evidence for divergence in both yeasts. Using functional genomics, we identify new genes involved in fungal complexification. Together, these data show that rudimentary multicellularity is deeply rooted in the Ascomycota. Extensive parallel gene divergence during simplification and constraint leading to CM suggest a deterministic process where shared modes of cellular organization select for similarly configured organelle- and transport-related machineries.}, }
@article {pmid28174248, year = {2017}, author = {Jones, VA and Dolan, L}, title = {MpWIP regulates air pore complex development in the liverwort Marchantia polymorpha.}, journal = {Development (Cambridge, England)}, volume = {144}, number = {8}, pages = {1472-1476}, doi = {10.1242/dev.144287}, pmid = {28174248}, issn = {1477-9129}, mesh = {Marchantia/anatomy &amp; histology/*embryology/*metabolism/ultrastructure ; Mutation/genetics ; Plant Epidermis/cytology/*embryology/ultrastructure ; Plant Proteins/genetics/*metabolism ; Promoter Regions, Genetic/genetics ; Repressor Proteins/metabolism ; Transcription, Genetic ; }, abstract = {The colonisation of the land by plants was accompanied by the evolution of complex tissues and multicellular structures comprising different cell types as morphological adaptations to the terrestrial environment. Here, we show that the single WIP protein in the early-diverging land plant Marchantia polymorpha L. is required for the development of the multicellular gas exchange structure: the air pore complex. This 16-cell barrel-shaped structure surrounds an opening between epidermal cells that facilitates the exchange of gases between the chamber containing the photosynthetic cells inside the plant and the air outside. MpWIP is expressed in cells of the developing air pore complex and the morphogenesis of the complex is defective in plants with reduced MpWIP function. The role of WIP proteins in the control of different multicellular structures in M. polymorpha and the flowering plant Arabidopsis thaliana suggests that these proteins controlled the development of multicellular structures in the common ancestor of land plants. We hypothesise that WIP genes were subsequently co-opted in the control of morphogenesis of novel multicellular structures that evolved during the diversification of land plants.}, }
@article {pmid28173090, year = {2017}, author = {Gallagher, MD and Macqueen, DJ}, title = {Evolution and Expression of Tissue Globins in Ray-Finned Fishes.}, journal = {Genome biology and evolution}, volume = {9}, number = {1}, pages = {32-47}, doi = {10.1093/gbe/evw266}, pmid = {28173090}, issn = {1759-6653}, support = {BB/J01446X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; *Evolution, Molecular ; Fish Proteins/*genetics ; Fishes/*classification/*genetics ; Globins/*genetics ; Phylogeny ; }, abstract = {The globin gene family encodes oxygen-binding hemeproteins conserved across the major branches of multicellular life. The origins and evolutionary histories of complete globin repertoires have been established for many vertebrates, but there remain major knowledge gaps for ray-finned fish. Therefore, we used phylogenetic, comparative genomic and gene expression analyses to discover and characterize canonical “non-blood” globin family members (i.e., myoglobin, cytoglobin, neuroglobin, globin-X, and globin-Y) across multiple ray-finned fish lineages, revealing novel gene duplicates (paralogs) conserved from whole genome duplication (WGD) and small-scale duplication events. Our key findings were that: (1) globin-X paralogs in teleosts have been retained from the teleost-specific WGD, (2) functional paralogs of cytoglobin, neuroglobin, and globin-X, but not myoglobin, have been conserved from the salmonid-specific WGD, (3) triplicate lineage-specific myoglobin paralogs are conserved in arowanas (Osteoglossiformes), which arose by tandem duplication and diverged under positive selection, (4) globin-Y is retained in multiple early branching fish lineages that diverged before teleosts, and (5) marked variation in tissue-specific expression of globin gene repertoires exists across ray-finned fish evolution, including several previously uncharacterized sites of expression. In this respect, our data provide an interesting link between myoglobin expression and the evolution of air breathing in teleosts. Together, our findings demonstrate great-unrecognized diversity in the repertoire and expression of nonblood globins that has arisen during ray-finned fish evolution.}, }
@article {pmid28168289, year = {2017}, author = {Paulet, D and David, A and Rivals, E}, title = {Ribo-seq enlightens codon usage bias.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {24}, number = {3}, pages = {303-210}, doi = {10.1093/dnares/dsw062}, pmid = {28168289}, issn = {1756-1663}, mesh = {Animals ; Codon/analysis/*genetics ; Eukaryota/genetics ; Evolution, Molecular ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; *Protein Biosynthesis ; RNA, Messenger ; Ribosomes ; Sequence Analysis, RNA ; *Transcriptome ; }, abstract = {Codon usage is biased between lowly and highly expressed genes in a genome-specific manner. This universal bias has been well assessed in some unicellular species, but remains problematic to assess in more complex species. We propose a new method to compute codon usage bias based on genome wide translational data. A new technique based on sequencing of ribosome protected mRNA fragments (Ribo-seq) allowed us to rank genes and compute codon usage bias with high precision for a great variety of species, including mammals. Genes ranking using Ribo-Seq data confirms the influence of the tRNA pool on codon usage bias and shows a decreasing bias in multicellular species. Ribo-Seq analysis also makes possible to detect preferred codons without information on genes function.}, }
@article {pmid28161621, year = {2017}, author = {Tollis, M and Schiffman, JD and Boddy, AM}, title = {Evolution of cancer suppression as revealed by mammalian comparative genomics.}, journal = {Current opinion in genetics &amp; development}, volume = {42}, number = {}, pages = {40-47}, doi = {10.1016/j.gde.2016.12.004}, pmid = {28161621}, issn = {1879-0380}, mesh = {Animals ; Carcinogenesis/*genetics ; Conserved Sequence/genetics ; DNA Damage/genetics ; DNA Repair/genetics ; *Evolution, Molecular ; *Genomics ; Humans ; Mammals ; Neoplasms/*genetics/pathology ; }, abstract = {Cancer suppression is an important feature in the evolution of large and long-lived animals. While some tumor suppression pathways are conserved among all multicellular organisms, others mechanisms of cancer resistance are uniquely lineage specific. Comparative genomics has become a powerful tool to discover these unique and shared molecular adaptations in respect to cancer suppression. These findings may one day be translated to human patients through evolutionary medicine. Here, we will review theory and methods of comparative cancer genomics and highlight major findings of cancer suppression across mammals. Our current knowledge of cancer genomics suggests that more efficient DNA repair and higher sensitivity to DNA damage may be the key to tumor suppression in large or long-lived mammals.}, }
@article {pmid28148211, year = {2017}, author = {Buonanno, F and Anesi, A and Giuseppe, GD and Guella, G and Ortenzi, C}, title = {Chemical Defense by Erythrolactones in the Euryhaline Ciliated Protist, Pseudokeronopsis erythrina.}, journal = {Zoological science}, volume = {34}, number = {1}, pages = {42-51}, doi = {10.2108/zs160123}, pmid = {28148211}, issn = {0289-0003}, mesh = {Animals ; Ciliophora/genetics/*metabolism ; Invertebrates ; Lactones/*chemistry/metabolism/*toxicity ; Molecular Structure ; Phylogeny ; Predatory Behavior ; }, abstract = {Pseudokeronopsis erythrina produces three new secondary metabolites, erythrolactones A2, B2 and C2, and their respective sulfate esters (A1, B1, C1), the structures of which have been recently elucidated on the basis of NMR spectroscopic data coupled to high resolution mass measurements (HR-MALDI-TOF). An analysis of the discharge of the protozoan pigment granules revealed that the non-sulfonated erythrolactones are exclusively stored in these cortical organelles, which are commonly used by a number of ciliates as chemical weapons in offense/defense interactions with prey and predators. We evaluated the toxic activity of pigment granule discharge on a panel of free-living ciliates and micro-invertebrates, and the activity of each single purified erythrolactone on three ciliate species. We also observed predator-prey interactions of P. erythrina with unicellular and multicellular predators. Experimental results confirm that only P. erythrina cells with discharged pigment granules were preferentially or exclusively hunted and eaten by at least some of its predators, whereas almost all intact (fully pigmented) cells remained alive. Our results indicate that erythrolactones are very effective as a chemical defense in P. erythrina.}, }
@article {pmid28131316, year = {2017}, author = {Tompitak, M and Vaillant, C and Schiessel, H}, title = {Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions.}, journal = {Biophysical journal}, volume = {112}, number = {3}, pages = {505-511}, doi = {10.1016/j.bpj.2016.12.041}, pmid = {28131316}, issn = {1542-0086}, mesh = {Animals ; Base Sequence ; DNA/genetics/metabolism ; *Evolution, Molecular ; Genome, Human/*genetics ; Humans ; Nucleosomes/genetics/*metabolism ; *Promoter Regions, Genetic ; Saccharomyces cerevisiae/genetics ; }, abstract = {Sequences that influence nucleosome positioning in promoter regions, and their relation to gene regulation, have been the topic of much research over the last decade. In yeast, significant nucleosome-depleted regions are found, which facilitate transcription. With the arrival of nucleosome positioning maps for the human genome, it was discovered that in our genome, unlike in that of yeast, promoters encode for high nucleosome occupancy. In this work, we look at the genomes of a range of different organisms, to provide a catalog of nucleosome positioning signals in promoters across the tree of life. We utilize a computational model of the nucleosome, based on crystallographic analyses of the structure and elasticity of the nucleosome, to predict the nucleosome positioning signals in promoter regions. To be able to apply our model to large genomic datasets, we introduce an approximative scheme that makes use of the limited range of correlations in nucleosomal sequence preferences to create a computationally efficient approximation of the full biophysical model. Our predictions show that a clear distinction between unicellular and multicellular life is visible in the intrinsically encoded nucleosome affinity. Furthermore, the strength of the nucleosome positioning signals correlates with the complexity of the organism. We conclude that encoding for high nucleosome occupancy, as in the human genome, is in fact a universal feature of multicellular life.}, }
@article {pmid28126046, year = {2017}, author = {Gaisin, VA and Kalashnikov, AM and Grouzdev, DS and Sukhacheva, MV and Kuznetsov, BB and Gorlenko, VM}, title = {Chloroflexus islandicus sp. nov., a thermophilic filamentous anoxygenic phototrophic bacterium from a geyser.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {67}, number = {5}, pages = {1381-1386}, doi = {10.1099/ijsem.0.001820}, pmid = {28126046}, issn = {1466-5034}, mesh = {Bacterial Proteins/chemistry ; Bacterial Typing Techniques ; Bacteriochlorophylls/chemistry ; Base Composition ; Carotenoids/chemistry ; Chloroflexus/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Iceland ; Nucleic Acid Hybridization ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Water Microbiology ; }, abstract = {A novel, thermophilic filamentous anoxygenic phototrophic bacterium, strain isl-2T, was isolated from the Strokkur Geyser, Iceland. Strain isl-2T formed unbranched multicellular filaments with gliding motility. The cells formed no spores and stained Gram-negative. The existence of pili was described in a species of the genus Chloroflexus for the first time, to our knowledge. Optimal growth occurred at a pH range of 7.5-7.7 and at a temperature of 55 °C. Strain isl-2T grew photoheterotrophically under anaerobic conditions in the light and chemoheterotrophically under aerobic conditions in the dark. The major cellular fatty acids were C18 : 1ω9, C16 : 0, C18 : 0 and C18 : 0-OH. The major quinone was menaquinone-10. The photosynthetic pigments were bacteriochlorophylls c and a as well as β- and γ-carotenes. The results of phylogenetic analysis of the 16S rRNA gene sequences placed strain isl-2T into the genus Chloroflexus of the phylum Chloroflexi with Chloroflexus aggregans DSM 9485T as the closest relative (97.0 % identity). The whole-genome sequence of isl-2T was determined. Average nucleotide identity values obtained for isl-2T in comparison to available genomic sequences of other strains of members of the genus Chloroflexus were 81.4 % or less and digital DNA-DNA hybridisation values 22.8 % or less. The results of additional phylogenetic analysis of the PufLM and BchG amino acid sequences supported the separate position of the isl-2T phylotype from the phylotypes of other members of the genus Chloroflexus. On the basis of physiological and phylogenetic data as well as genomic data, it was suggested that isl-2T represents a novel species within the genus Chloroflexus, with the proposed name Chloroflexus islandicus sp. nov. The type strain of the species is isl-2T (=VKM B-2978T,=DSM 29225T,=JCM 30533T).}, }
@article {pmid28116828, year = {2017}, author = {Arenas-Mena, C}, title = {The origins of developmental gene regulation.}, journal = {Evolution &amp; development}, volume = {19}, number = {2}, pages = {96-107}, doi = {10.1111/ede.12217}, pmid = {28116828}, issn = {1525-142X}, mesh = {Animals ; *Biological Evolution ; Enhancer Elements, Genetic ; Eukaryota/cytology/genetics ; *Gene Expression Regulation, Developmental ; Prokaryotic Cells/metabolism ; Promoter Regions, Genetic ; }, abstract = {The leap from simple unicellularity to complex multicellularity remains one of life's major enigmas. The origins of metazoan developmental gene regulatory mechanisms are sought by analyzing gene regulation in extant eumetazoans, sponges, and unicellular organisms. The main hypothesis of this manuscript is that, developmental enhancers evolved from unicellular inducible promoters that diversified the expression of regulatory genes during metazoan evolution. Promoters and enhancers are functionally similar; both can regulate the transcription of distal promoters and both direct local transcription. Additionally, enhancers have experimentally characterized structural features that reveal their origin from inducible promoters. The distal co-operative regulation among promoters identified in unicellular opisthokonts possibly represents the precursor of distal regulation of promoters by enhancers. During metazoan evolution, constitutive-type promoters of regulatory genes would have acquired novel receptivity to distal regulatory inputs from promoters of inducible genes that eventually specialized as enhancers. The novel regulatory interactions would have caused constitutively expressed genes controlling differential gene expression in unicellular organisms to become themselves differentially expressed. The consequence of the novel regulatory interactions was that regulatory pathways of unicellular organisms became interlaced and ultimately evolved into the intricate developmental gene regulatory networks (GRNs) of extant metazoans.}, }
@article {pmid28115992, year = {2017}, author = {Navratilova, P and Danks, GB and Long, A and Butcher, S and Manak, JR and Thompson, EM}, title = {Sex-specific chromatin landscapes in an ultra-compact chordate genome.}, journal = {Epigenetics &amp; chromatin}, volume = {10}, number = {}, pages = {3}, doi = {10.1186/s13072-016-0110-4}, pmid = {28115992}, issn = {1756-8935}, mesh = {Animals ; Chromatin/genetics/*metabolism ; Chromatin Immunoprecipitation ; DNA Methylation ; DNA Transposable Elements/genetics ; Female ; *Genome ; Histones/chemistry/genetics/metabolism ; Male ; Ovary/metabolism ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; RNA Polymerase II/genetics/metabolism ; Testis/metabolism ; Urochordata/*genetics ; }, abstract = {BACKGROUND: In multicellular organisms, epigenome dynamics are associated with transitions in the cell cycle, development, germline specification, gametogenesis and inheritance. Evolutionarily, regulatory space has increased in complex metazoans to accommodate these functions. In tunicates, the sister lineage to vertebrates, we examine epigenome adaptations to strong secondary genome compaction, sex chromosome evolution and cell cycle modes.<br><br>RESULTS: Across the 70 MB Oikopleura dioica genome, we profiled 19 histone modifications, and RNA polymerase II, CTCF and p300 occupancies, to define chromatin states within two homogeneous tissues with distinct cell cycle modes: ovarian endocycling nurse nuclei and mitotically proliferating germ nuclei in testes. Nurse nuclei had active chromatin states similar to other metazoan epigenomes, with large domains of operon-associated transcription, a general lack of heterochromatin, and a possible role of Polycomb PRC2 in dosage compensation. Testis chromatin states reflected transcriptional activity linked to spermatogenesis and epigenetic marks that have been associated with establishment of transgenerational inheritance in other organisms. We also uncovered an unusual chromatin state specific to the Y-chromosome, which combined active and heterochromatic histone modifications on specific transposable elements classes, perhaps involved in regulating their activity.<br><br>CONCLUSIONS: Compacted regulatory space in this tunicate genome is accompanied by reduced heterochromatin and chromatin state domain widths. Enhancers, promoters and protein-coding genes have conserved epigenomic features, with adaptations to the organization of a proportion of genes in operon units. We further identified features specific to sex chromosomes, cell cycle modes, germline identity and dosage compensation, and unusual combinations of histone PTMs with opposing consensus functions.}, }
@article {pmid28112403, year = {2018}, author = {Torday, JS and Miller, WB}, title = {A systems approach to physiologic evolution: From micelles to consciousness.}, journal = {Journal of cellular physiology}, volume = {233}, number = {1}, pages = {162-167}, doi = {10.1002/jcp.25820}, pmid = {28112403}, issn = {1097-4652}, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; Body Temperature Regulation ; Homeostasis ; Humans ; Lung/physiology ; Physiology/*methods ; Pulmonary Ventilation ; *Systems Biology ; *Systems Integration ; Time Factors ; }, abstract = {A systems approach to evolutionary biology offers the promise of an improved understanding of the fundamental principles of life through the effective integration of many biologic disciplines. It is presented that any critical integrative approach to evolutionary development involves a paradigmatic shift in perspective, more than just the engagement of a large number of disciplines. Critical to this differing viewpoint is the recognition that all biological processes originate from the unicellular state and remain permanently anchored to that phase throughout evolutionary development despite their macroscopic appearances. Multicellular eukaryotic development can, therefore, be viewed as a series of connected responses to epiphenomena that proceeds from that base in continuous iterative maintenance of collective cellular homeostatic equipoise juxtaposed against an ever-changing and challenging environment. By following this trajectory of multicellular eukaryotic evolution from within unicellular First Principles of Physiology forward, the mechanistic nature of complex physiology can be identified through a step-wise analysis of a continuous arc of vertebrate evolution based upon serial exaptations.}, }
@article {pmid28106309, year = {2017}, author = {Wang, D and Qu, Z and Yang, L and Zhang, Q and Liu, ZH and Do, T and Adelson, DL and Wang, ZY and Searle, I and Zhu, JK}, title = {Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants.}, journal = {The Plant journal : for cell and molecular biology}, volume = {90}, number = {1}, pages = {133-146}, doi = {10.1111/tpj.13481}, pmid = {28106309}, issn = {1365-313X}, support = {R01 GM059138/GM/NIGMS NIH HHS/United States ; R01 GM070795/GM/NIGMS NIH HHS/United States ; }, mesh = {Abscisic Acid/pharmacology ; Arabidopsis/drug effects/genetics ; Cold Temperature ; DNA Transposable Elements/*genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects/genetics ; Oryza/drug effects/genetics ; RNA, Long Noncoding/*genetics ; RNA, Plant/*genetics ; Sodium Chloride/pharmacology ; Zea mays/drug effects/genetics ; }, abstract = {Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these noncoding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown. By using strand-specific RNA-sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified 47 611 and 398 TE-associated lincRNAs (TE-lincRNAs), respectively. TE-lincRNAs were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lincRNAs. We validated the expression of these TE-lincRNAs by strand-specific RT-PCR and also demonstrated tissue-specific transcription and stress-induced TE-lincRNAs either after salt, abscisic acid (ABA) or cold treatments. For Arabidopsis TE-lincRNA11195, mutants had reduced sensitivity to ABA as demonstrated by longer roots and higher shoot biomass when compared to wild-type. Finally, by altering the chromatin state in the Arabidopsis chromatin remodelling mutant ddm1, unique lincRNAs including TE-lincRNAs were generated from the preceding untranscribed regions and interestingly inherited in a wild-type background in subsequent generations. Our findings not only demonstrate that TE-associated lincRNAs play important roles in plant abiotic stress responses but lincRNAs and TE-lincRNAs might act as an adaptive reservoir in eukaryotes.}, }
@article {pmid28102347, year = {2017}, author = {Fernández, L and González, S and Campelo, AB and Martínez, B and Rodríguez, A and García, P}, title = {Low-level predation by lytic phage phiIPLA-RODI promotes biofilm formation and triggers the stringent response in Staphylococcus aureus.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40965}, doi = {10.1038/srep40965}, pmid = {28102347}, issn = {2045-2322}, mesh = {*Bacteriolysis ; Biofilms/*growth &amp; development ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; Host-Parasite Interactions ; Sequence Analysis, RNA ; Staphylococcus Phages/*growth &amp; development ; Staphylococcus aureus/*physiology/*virology ; *Stress, Physiological ; }, abstract = {An important lesson from the war on pathogenic bacteria has been the need to understand the physiological responses and evolution of natural microbial communities. Bacterial populations in the environment are generally forming biofilms subject to some level of phage predation. These multicellular communities are notoriously resistant to antimicrobials and, consequently, very difficult to eradicate. This has sparked the search for new therapeutic alternatives, including phage therapy. This study demonstrates that S. aureus biofilms formed in the presence of a non-lethal dose of phage phiIPLA-RODI exhibit a unique physiological state that could potentially benefit both the host and the predator. Thus, biofilms formed under phage pressure are thicker and have a greater DNA content. Also, the virus-infected biofilm displayed major transcriptional differences compared to an untreated control. Significantly, RNA-seq data revealed activation of the stringent response, which could slow down the advance of the bacteriophage within the biofilm. The end result would be an equilibrium that would help bacterial cells to withstand environmental challenges, while maintaining a reservoir of sensitive bacterial cells available to the phage upon reactivation of the dormant carrier population.}, }
@article {pmid28096354, year = {2017}, author = {Xing, S and Mehlhorn, DG and Wallmeroth, N and Asseck, LY and Kar, R and Voss, A and Denninger, P and Schmidt, VA and Schwarzländer, M and Stierhof, YD and Grossmann, G and Grefen, C}, title = {Loss of GET pathway orthologs in Arabidopsis thaliana causes root hair growth defects and affects SNARE abundance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {8}, pages = {E1544-E1553}, doi = {10.1073/pnas.1619525114}, pmid = {28096354}, issn = {1091-6490}, mesh = {Adenosine Triphosphatases/metabolism ; Animals ; Arabidopsis/*physiology ; Arabidopsis Proteins/*metabolism ; Cell Membrane/*metabolism ; Cytosol/metabolism ; Endoplasmic Reticulum/metabolism ; Guanine Nucleotide Exchange Factors/metabolism ; Homeostasis/physiology ; Mammals/physiology ; Membrane Fusion/physiology ; Molecular Chaperones/metabolism ; Phylogeny ; Plant Roots/*growth &amp; development/metabolism ; Plants, Genetically Modified ; SNARE Proteins/genetics/*metabolism ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction/*physiology ; Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins ; }, abstract = {Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins are key players in cellular trafficking and coordinate vital cellular processes, such as cytokinesis, pathogen defense, and ion transport regulation. With few exceptions, SNAREs are tail-anchored (TA) proteins, bearing a C-terminal hydrophobic domain that is essential for their membrane integration. Recently, the Guided Entry of Tail-anchored proteins (GET) pathway was described in mammalian and yeast cells that serve as a blueprint of TA protein insertion [Schuldiner M, et al. (2008) Cell 134(4):634-645; Stefanovic S, Hegde RS (2007) Cell 128(6):1147-1159]. This pathway consists of six proteins, with the cytosolic ATPase GET3 chaperoning the newly synthesized TA protein posttranslationally from the ribosome to the endoplasmic reticulum (ER) membrane. Structural and biochemical insights confirmed the potential of pathway components to facilitate membrane insertion, but the physiological significance in multicellular organisms remains to be resolved. Our phylogenetic analysis of 37 GET3 orthologs from 18 different species revealed the presence of two different GET3 clades. We identified and analyzed GET pathway components in Arabidopsis thaliana and found reduced root hair elongation in Atget lines, possibly as a result of reduced SNARE biogenesis. Overexpression of AtGET3a in a receptor knockout (KO) results in severe growth defects, suggesting presence of alternative insertion pathways while highlighting an intricate involvement for the GET pathway in cellular homeostasis of plants.}, }
@article {pmid28094816, year = {2017}, author = {Cramer, JM and Pohlmann, D and Gomez, F and Mark, L and Kornegay, B and Hall, C and Siraliev-Perez, E and Walavalkar, NM and Sperlazza, MJ and Bilinovich, S and Prokop, JW and Hill, AL and Williams, DC}, title = {Methylation specific targeting of a chromatin remodeling complex from sponges to humans.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40674}, doi = {10.1038/srep40674}, pmid = {28094816}, issn = {2045-2322}, support = {K01 ES025435/ES/NIEHS NIH HHS/United States ; T32 GM008570/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; R01 GM098264/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Chromatin Assembly and Disassembly ; DNA/chemistry/metabolism ; *DNA Methylation ; DNA-Binding Proteins/chemistry/genetics/metabolism ; Gene Knockdown Techniques ; Humans ; Models, Molecular ; Nucleic Acid Conformation ; Phenotype ; Porifera/*genetics/metabolism ; Protein Conformation ; }, abstract = {DNA cytosine methylation and methyl-cytosine binding domain (MBD) containing proteins are found throughout all vertebrate species studied to date. However, both the presence of DNA methylation and pattern of methylation varies among invertebrate species. Invertebrates generally have only a single MBD protein, MBD2/3, that does not always contain appropriate residues for selectively binding methylated DNA. Therefore, we sought to determine whether sponges, one of the most ancient extant metazoan lineages, possess an MBD2/3 capable of recognizing methylated DNA and recruiting the associated nucleosome remodeling and deacetylase (NuRD) complex. We find that Ephydatia muelleri has genes for each of the NuRD core components including an EmMBD2/3 that selectively binds methylated DNA. NMR analyses reveal a remarkably conserved binding mode, showing almost identical chemical shift changes between binding to methylated and unmethylated CpG dinucleotides. In addition, we find that EmMBD2/3 and EmGATAD2A/B proteins form a coiled-coil interaction known to be critical for the formation of NuRD. Finally, we show that knockdown of EmMBD2/3 expression disrupts normal cellular architecture and development of E. muelleri. These data support a model in which the MBD2/3 methylation-dependent functional role emerged with the earliest multicellular organisms and has been maintained to varying degrees across animal evolution.}, }
@article {pmid28090383, year = {2016}, author = {Arensburger, P and Piégu, B and Bigot, Y}, title = {The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?.}, journal = {Mobile genetic elements}, volume = {6}, number = {6}, pages = {e1256852}, doi = {10.1080/2159256X.2016.1256852}, pmid = {28090383}, issn = {2159-2543}, abstract = {Transposable element (TE) science has been significantly influenced by the pioneering ideas of David Finnegan near the end of the last century, as well as by the classification systems that were subsequently developed. Today, whole genome TE annotation is mostly done using tools that were developed to aid gene annotation rather than to specifically study TEs. We argue that further progress in the TE field is impeded both by current TE classification schemes and by a failure to recognize that TE biology is fundamentally different from that of multicellular organisms. Novel genome wide TE annotation methods are helping to redefine our understanding of TE sequence origins and evolution. We briefly discuss some of these new methods as well as ideas for possible alternative classification schemes. Our hope is to encourage the formation of a society to organize a larger debate on these questions and to promote the adoption of standards for annotation and an improved TE classification.}, }
@article {pmid28088333, year = {2017}, author = {Baffy, G}, title = {Mitochondrial uncoupling in cancer cells: Liabilities and opportunities.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1858}, number = {8}, pages = {655-664}, doi = {10.1016/j.bbabio.2017.01.005}, pmid = {28088333}, issn = {0005-2728}, mesh = {Animals ; Antineoplastic Agents/pharmacokinetics ; Cell Hypoxia ; Cell Line, Tumor ; Cellular Reprogramming ; Drug Resistance, Neoplasm/physiology ; Drug Synergism ; Energy Metabolism ; Humans ; Mitochondria/drug effects/*metabolism ; Mitochondrial Uncoupling Proteins/*physiology ; Models, Biological ; Neoplasm Proteins/physiology ; Neoplasms/drug therapy/*metabolism ; Oxidative Phosphorylation/drug effects ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Symbiosis ; Uncoupling Agents/pharmacology/therapeutic use ; }, abstract = {Acquisition of the endosymbiotic ancestor of mitochondria was a critical event in eukaryote evolution. Mitochondria offered an unparalleled source of metabolic energy through oxidative phosphorylation and allowed the development of multicellular life. However, as molecular oxygen had become the terminal electron acceptor in most eukaryotic cells, the electron transport chain proved to be the largest intracellular source of superoxide, contributing to macromolecular injury, aging, and cancer. Hence, the 'contract of endosymbiosis' represents a compromise between the possibilities and perils of multicellular life. Uncoupling proteins (UCPs), a group of the solute carrier family of transporters, may remove some of the physiologic constraints that link mitochondrial respiration and ATP synthesis by mediating inducible proton leak and limiting oxidative cell injury. This important property makes UCPs an ancient partner in the metabolic adaptation of cancer cells. Efforts are underway to explore the therapeutic opportunities stemming from the intriguing relationship of UCPs and cancer. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux.}, }
@article {pmid28078674, year = {2017}, author = {Bustamante, DE and Won, BY and Miller, KA and Cho, TO}, title = {Wilsonosiphonia gen. nov. (Rhodomelaceae, Rhodophyta) based on molecular and morpho-anatomical characters.}, journal = {Journal of phycology}, volume = {53}, number = {2}, pages = {368-380}, doi = {10.1111/jpy.12512}, pmid = {28078674}, issn = {1529-8817}, mesh = {DNA, Ribosomal ; Phylogeny ; Rhodophyta/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Morphological, anatomical, and molecular sequence data were used to assess the establishment and phylogenetic position of the genus Wilsonosiphonia gen. nov. Phylogenies based on rbcL and concatenated rbcL and cox1 loci support recognition of Wilsonosiphonia gen. nov., sister to Herposiphonia. Diagnostic features for Wilsonosiphonia are rhizoids located at distal ends of pericentral cells and taproot-shaped multicellular tips of rhizoids. Wilsonosiphonia includes three species with diagnostic rbcL and cox1 sequences, Wilsonosiphonia fujiae sp. nov. (the generitype), W. howei comb. nov., and W. indica sp. nov. These three species resemble each other in external morphology, but W. fujiae is distinguished by having two tetrasporangia per segment rather than one, W. indica by having abundant and persistent trichoblasts, and W. howei by having few and deciduous trichoblasts.}, }
@article {pmid28066387, year = {2016}, author = {Zhang, Z and Claessen, D and Rozen, DE}, title = {Understanding Microbial Divisions of Labor.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2070}, doi = {10.3389/fmicb.2016.02070}, pmid = {28066387}, issn = {1664-302X}, abstract = {Divisions of labor are ubiquitous in nature and can be found at nearly every level of biological organization, from the individuals of a shared society to the cells of a single multicellular organism. Many different types of microbes have also evolved a division of labor among its colony members. Here we review several examples of microbial divisions of labor, including cases from both multicellular and unicellular microbes. We first discuss evolutionary arguments, derived from kin selection, that allow divisions of labor to be maintained in the face of non-cooperative cheater cells. Next we examine the widespread natural variation within species in their expression of divisions of labor and compare this to the idea of optimal caste ratios in social insects. We highlight gaps in our understanding of microbial caste ratios and argue for a shift in emphasis from understanding the maintenance of divisions of labor, generally, to instead focusing on its specific ecological benefits for microbial genotypes and colonies. Thus, in addition to the canonical divisions of labor between, e.g., reproductive and vegetative tasks, we may also anticipate divisions of labor to evolve to reduce the costly production of secondary metabolites or secreted enzymes, ideas we consider in the context of streptomycetes. The study of microbial divisions of labor offers opportunities for new experimental and molecular insights across both well-studied and novel model systems.}, }
@article {pmid28063828, year = {2017}, author = {Terauchi, M and Yamagishi, T and Hanyuda, T and Kawai, H}, title = {Genome-wide computational analysis of the secretome of brown algae (Phaeophyceae).}, journal = {Marine genomics}, volume = {32}, number = {}, pages = {49-59}, doi = {10.1016/j.margen.2016.12.002}, pmid = {28063828}, issn = {1876-7478}, mesh = {Amino Acid Sequence ; *Genome ; Genome-Wide Association Study ; Phaeophyta/*genetics ; Sequence Alignment ; }, abstract = {Brown algae have evolved complex multicellularity in the heterokont lineage. They are phylogenetically distant to land plants, fungi and animals. Especially, the members of Laminariales (so-called kelps) have developed highly differentiated tissues. Extracellular matrix (ECM) plays pivotal roles in a number of essential processes in multicellular organisms, such as cell adhesion, cell and tissue differentiations, cell-to-cell communication, and responses to environmental stimuli. In these processes, a set of extracellular secreted proteins called the secretome operates remodeling of the physicochemical nature of ECM and signal transduction by interacting with cell surface proteins and signaling molecules. Characterization of the secretome is a critical step to clarify the contributions of ECM to the multicellularity of brown algae. However, the identity of the brown algal secretome has been poorly understood. In order to reveal the repertory of the brown algal secretome and its involvement in the evolution of Laminariales, we conducted a genome-wide analysis of the brown algal secretome utilizing the published complete genome data of Ectocarpus siliculosus and Saccharina japonica as well as newly obtained RNA-seq data of seven laminarialean species (Agarum clathratum, Alaria crassifolia, Aureophycus aleuticus, Costaria costata, Pseudochorda nagaii, Saccharina angustata and Undaria pinnatifida) largely covering the laminarialean families. We established the in silico pipeline to systematically and accurately detect the secretome by combining multiple prediction algorithms for the N-terminal signal peptide and transmembrane domain within the protein sequence. From 16,189 proteins of E. siliculosus and 18,733 proteins of S. japonica, 552 and 964 proteins respectively were predicted to be classified as the secretome. Conserved domain analysis showed that the domain repertory were very similar to each other, and that of the brown algal secretome was partially common with that of the secretome of other multicellular organisms (land plants, fungi and animals). In the laminarialean species, it was estimated that the gene abundance and the domain architecture of putative ECM remodeling-related proteins were altered compared with those of E. siliculosus, and that the alteration started from the basal group of Laminariales. These results suggested that brown algae have developed their own secretome, and its functions became more elaborated in the more derived members in Laminariales.}, }
@article {pmid28058671, year = {2017}, author = {Sommese, L and Zullo, A and Schiano, C and Mancini, FP and Napoli, C}, title = {Possible Muscle Repair in the Human Cardiovascular System.}, journal = {Stem cell reviews}, volume = {13}, number = {2}, pages = {170-191}, doi = {10.1007/s12015-016-9711-3}, pmid = {28058671}, issn = {1558-6804}, mesh = {Animals ; Cardiovascular Diseases/genetics/physiopathology/therapy ; Cardiovascular System/injuries/*metabolism/*physiopathology ; Cell Differentiation/genetics ; Cell Proliferation/genetics ; *Cellular Reprogramming ; Humans ; Myocardium/*metabolism/pathology ; Regeneration/genetics ; Regenerative Medicine/methods ; }, abstract = {The regenerative potential of tissues and organs could promote survival, extended lifespan and healthy life in multicellular organisms. Niches of adult stemness are widely distributed and lead to the anatomical and functional regeneration of the damaged organ. Conversely, muscular regeneration in mammals, and humans in particular, is very limited and not a single piece of muscle can fully regrow after a severe injury. Therefore, muscle repair after myocardial infarction is still a chimera. Recently, it has been recognized that epigenetics could play a role in tissue regrowth since it guarantees the maintenance of cellular identity in differentiated cells and, therefore, the stability of organs and tissues. The removal of these locks can shift a specific cell identity back to the stem-like one. Given the gradual loss of tissue renewal potential in the course of evolution, in the last few years many different attempts to retrieve such potential by means of cell therapy approaches have been performed in experimental models. Here we review pathways and mechanisms involved in the in vivo repair of cardiovascular muscle tissues in humans. Moreover, we address the ongoing research on mammalian cardiac muscle repair based on adult stem cell transplantation and pro-regenerative factor delivery. This latter issue, involving genetic manipulations of adult cells, paves the way for developing possible therapeutic strategies in the field of cardiovascular muscle repair.}, }
@article {pmid28057261, year = {2017}, author = {Sebé-Pedrós, A and Ruiz-Trillo, I}, title = {Evolution and Classification of the T-Box Transcription Factor Family.}, journal = {Current topics in developmental biology}, volume = {122}, number = {}, pages = {1-26}, doi = {10.1016/bs.ctdb.2016.06.004}, pmid = {28057261}, issn = {1557-8933}, mesh = {Animals ; Base Sequence ; Conserved Sequence ; *Evolution, Molecular ; Fetal Proteins/chemistry/genetics ; Humans ; Morphogenesis ; Phylogeny ; T-Box Domain Proteins/chemistry/*classification/*genetics ; }, abstract = {T-box proteins are key developmental transcription factors in Metazoa. Until recently they were thought to be animal specific and many T-box classes were considered bilaterian specific. Recent genome data from both early-branching animals and their closest unicellular relatives have radically changed this scenario. Thus, we now know that T-box genes originated in premetazoans, being present in the genomes of some extant early-branching fungi and unicellular holozoans. Here, we update the evolutionary classification of T-box families and review the evolution of T-box function in early-branching animals (sponges, ctenophores, placozoans, and cnidarians) and nonmodel bilaterians. We show that concomitant with the origin of Metazoa, the T-box family radiated into the major known T-box classes. On the other hand, while functional studies are still missing for many T-box classes, the emerging picture is that T-box genes have key roles in multiple aspects of development and in adult terminal cell-type differentiation in different animal lineages. A paradigmatic example is that of Brachyury, the founding member of the T-box family, for which several studies indicate a widely conserved role in regulating cell motility in different animal lineages and probably even before the advent of animal multicellularity. Overall, we here review the evolutionary history of T-box genes from holozoans to animals and discuss both their functional diversity and conservation.}, }
@article {pmid28049657, year = {2017}, author = {Macaisne, N and Liu, F and Scornet, D and Peters, AF and Lipinska, A and Perrineau, MM and Henry, A and Strittmatter, M and Coelho, SM and Cock, JM}, title = {The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes.}, journal = {Development (Cambridge, England)}, volume = {144}, number = {3}, pages = {409-418}, doi = {10.1242/dev.141523}, pmid = {28049657}, issn = {1477-9129}, support = {638240//European Research Council/International ; }, mesh = {Algal Proteins/antagonists &amp; inhibitors/chemistry/*genetics ; Amino Acid Sequence ; Cloning, Molecular ; Cysteine/chemistry ; Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Models, Genetic ; Multigene Family ; Mutation ; Phaeophyta/*genetics/growth &amp; development/virology ; Phylogeny ; RNA Interference ; Sequence Homology, Amino Acid ; Viral Proteins/chemistry/genetics ; }, abstract = {The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared with the majority of brown algae. The first cell division is symmetrical and the apical-basal axis is established late in development. In the immediate upright (imm) mutant, the initial cell undergoes an asymmetric division to immediately establish the apical-basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function that contains a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus EsV-1. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles, suggesting that the expansion of this family might have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.}, }
@article {pmid28048969, year = {2017}, author = {Veloso, FA}, title = {On the developmental self-regulatory dynamics and evolution of individuated multicellular organisms.}, journal = {Journal of theoretical biology}, volume = {417}, number = {}, pages = {84-99}, doi = {10.1016/j.jtbi.2016.12.025}, pmid = {28048969}, issn = {1095-8541}, mesh = {Animals ; *Biological Evolution ; Cell Differentiation/*genetics ; Cell Line ; Computational Biology ; Drosophila melanogaster ; *Epigenesis, Genetic ; *Gene Expression Regulation ; Histones/metabolism ; Humans ; Mice ; Protein Processing, Post-Translational ; RNA, Messenger/analysis ; Transcription Initiation Site ; }, abstract = {Changes in gene expression are thought to regulate the cell differentiation process intrinsically through complex epigenetic mechanisms. In fundamental terms, however, this assumed regulation refers only to the intricate propagation of changes in gene expression or else leads to non-explanatory regresses. The developmental self-regulatory dynamics and evolution of individuated multicellular organisms also lack a unified and falsifiable description. To fill this gap, I computationally analyzed publicly available high-throughput data of histone H3 post-translational modifications and mRNA abundance for different Homo sapiens, Mus musculus, and Drosophila melanogaster cell-type/developmental-period samples. My analysis of genomic regions adjacent to transcription start sites generated a profile from pairwise partial correlations between histone modifications controlling for the respective mRNA levels for each cell-type/developmental-period dataset. I found that these profiles, while explicitly uncorrelated with the respective transcriptional &quot;identities&quot; by construction, associate strongly with cell differentiation states. This association is not expected if cell differentiation is, in effect, regulated by epigenetic mechanisms. Based on these results, I propose a general, falsifiable theory of individuated multicellularity, which relies on the synergistic coupling across the extracellular space of two explicitly uncorrelated &quot;self-organizing&quot; systems constraining histone modification states at the same sites. This theory describes how the simplest multicellular individual-understood as an intrinsic, higher-order constraint-emerges from proliferating undifferentiated cells, and could explain the intrinsic regulation of gene transcriptional changes for cell differentiation and the evolution of individuated multicellular organisms.}, }
@article {pmid29687830, year = {2017}, author = {Cazzolla Gatti, R}, title = {Adaptation, Evolution And Reproduction Of Gaia By The Means Of Our Species.}, journal = {Theoretical biology forum}, volume = {110}, number = {1-2}, pages = {25-45}, doi = {10.19272/201711402003}, pmid = {29687830}, issn = {0035-6050}, abstract = {Nowadays, the idea that life affects the development of the planetary environment, and can, in turn, affect the future evolution of itself (in a coevolutionary way) is well-accepted. However, since the proposal of the Gaia hypothesis, there has been widespread criticism. Most of it is related to teleology, the absence of natural selection at a universal scale, and the lack of planetary reproduction. Some of the problems concerning the 'internal' logic of the idea have been resolved. Nevertheless, it is not sure whether Earth can be considered a unit of selection and (therefore) Gaia can adapt according to Darwinian evolution. After Lovelock and Margulis, Gaia has been considered a symbiotic planet composed of biotic (the biosphere) and abiotic (the geosphere-atmosphere) interacting with and coevolving elements. Here I propose why and suggest how a Gaian system should be considered alive in any evolutionary sense. I take into consideration the three principal criticisms and I analyse them following a logic-inductive reasoning. I use thought experiments and analogical arguments to analyse the rationale and the mechanisms by which Gaia evolves and may reproduce. This reasoning could allow rejecting the aforementioned criticisms as outdated and insufficient to discredit the main idea. I argue that without invoking teleology - so without any foresight or planning - a Gaian planet can be considered a coevolutionary system analogous to a multicellular body: a super-unit of selection. I describe different situations according to which Gaia is able to reproduce and transfer her planetary genome to other uninhabited or inhabited planets. Then I suggest that Gaia can face exclusion- competition-coexistence states depending on the fitness of her biota compared to those of the other reproducing biospheres. This demonstrates that Gaia can reproduce and evolve in competition-cooperation with other planets. Some deep implications arise from this evidence, also in light of the recent discovery of a new solar system with Earth-like planets by NASA.}, }
@article {pmid28036012, year = {2016}, author = {Pauzaite, T and Thacker, U and Tollitt, J and Copeland, NA}, title = {Emerging Roles for Ciz1 in Cell Cycle Regulation and as a Driver of Tumorigenesis.}, journal = {Biomolecules}, volume = {7}, number = {1}, pages = {}, doi = {10.3390/biom7010001}, pmid = {28036012}, issn = {2218-273X}, mesh = {Animals ; Antineoplastic Agents/therapeutic use ; Carcinogenesis/*drug effects ; Cell Cycle ; *Cell Cycle Checkpoints ; Cell Transformation, Neoplastic ; Chromatin/metabolism ; Cyclin-Dependent Kinase 2/metabolism ; Cyclin-Dependent Kinase Inhibitor p21/metabolism ; *DNA Replication ; Humans ; Mice ; Nuclear Proteins/*metabolism ; }, abstract = {Precise duplication of the genome is a prerequisite for the health and longevity of multicellular organisms. The temporal regulation of origin specification, replication licensing, and firing at replication origins is mediated by the cyclin-dependent kinases. Here the role of Cip1 interacting Zinc finger protein 1 (Ciz1) in regulation of cell cycle progression is discussed. Ciz1 contributes to regulation of the G1/S transition in mammalian cells. Ciz1 contacts the pre-replication complex (pre-RC) through cell division cycle 6 (Cdc6) interactions and aids localization of cyclin A- cyclin-dependent kinase 2 (CDK2) activity to chromatin and the nuclear matrix during initiation of DNA replication. We discuss evidence that Ciz1 serves as a kinase sensor that regulates both initiation of DNA replication and prevention of re-replication. Finally, the emerging role for Ciz1 in cancer biology is discussed. Ciz1 is overexpressed in common tumors and tumor growth is dependent on Ciz1 expression, suggesting that Ciz1 is a driver of tumor growth. We present evidence that Ciz1 may contribute to deregulation of the cell cycle due to its ability to alter the CDK activity thresholds that are permissive for initiation of DNA replication. We propose that Ciz1 may contribute to oncogenesis by induction of DNA replication stress and that Ciz1 may be a multifaceted target in cancer therapy.}, }
@article {pmid28018750, year = {2016}, author = {Qiu, H and Yoon, HS and Bhattacharya, D}, title = {Red Algal Phylogenomics Provides a Robust Framework for Inferring Evolution of Key Metabolic Pathways.}, journal = {PLoS currents}, volume = {8}, number = {}, pages = {}, doi = {10.1371/currents.tol.7b037376e6d84a1be34af756a4d90846}, pmid = {28018750}, issn = {2157-3999}, abstract = {Red algae comprise an anciently diverged, species-rich phylum with morphologies that span unicells to large seaweeds. Here, leveraging a rich red algal genome and transcriptome dataset, we used 298 single-copy orthologous nuclear genes from 15 red algal species to erect a robust multi-gene phylogeny of Rhodophyta. This tree places red seaweeds (Bangiophyceae and Florideophyceae) at the base of the mesophilic red algae with the remaining non-seaweed mesophilic lineages forming a well-supported sister group. The early divergence of seaweeds contrasts with the evolution of multicellular land plants and brown algae that are nested among multiple, unicellular or filamentous sister lineages. Using this novel perspective on red algal evolution, we studied the evolution of the pathways for isoprenoid biosynthesis. This analysis revealed losses of the mevalonate pathway on at least three separate occasions in lineages that contain Cyanidioschyzon, Porphyridium, and Chondrus. Our results establish a framework for in-depth studies of the origin and evolution of genes and metabolic pathways in Rhodophyta.}, }
@article {pmid28013230, year = {2017}, author = {Ohtani, M and Akiyoshi, N and Takenaka, Y and Sano, R and Demura, T}, title = {Evolution of plant conducting cells: perspectives from key regulators of vascular cell differentiation.}, journal = {Journal of experimental botany}, volume = {68}, number = {1}, pages = {17-26}, doi = {10.1093/jxb/erw473}, pmid = {28013230}, issn = {1460-2431}, mesh = {Biological Evolution ; Cell Differentiation/*physiology ; Embryophyta/cytology/growth &amp; development/physiology ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/physiology ; Phloem/*cytology/growth &amp; development/physiology ; Xylem/*cytology/growth &amp; development/physiology ; }, abstract = {One crucial problem that plants faced during their evolution, particularly during the transition to growth on land, was how to transport water, nutrients, metabolites, and small signaling molecules within a large, multicellular body. As a solution to this problem, land plants developed specific tissues for conducting molecules, called water-conducting cells (WCCs) and food-conducting cells (FCCs). The well-developed WCCs and FCCs in extant plants are the tracheary elements and sieve elements, respectively, which are found in vascular plants. Recent molecular genetic studies revealed that transcriptional networks regulate the differentiation of tracheary and sieve elements, and that the networks governing WCC differentiation are largely conserved among land plant species. In this review, we discuss the molecular evolution of plant conducting cells. By focusing on the evolution of the key transcription factors that regulate vascular cell differentiation, the NAC transcription factor VASCULAR-RELATED NAC-DOMAIN for WCCs and the MYB-coiled-coil (CC)-type transcription factor ALTERED PHLOEM DEVELOPMENT for sieve elements, we describe how land plants evolved molecular systems to produce the specialized cells that function as WCCs and FCCs.}, }
@article {pmid28007886, year = {2017}, author = {Cleard, F and Wolle, D and Taverner, AM and Aoki, T and Deshpande, G and Andolfatto, P and Karch, F and Schedl, P}, title = {Different Evolutionary Strategies To Conserve Chromatin Boundary Function in the Bithorax Complex.}, journal = {Genetics}, volume = {205}, number = {2}, pages = {589-603}, doi = {10.1534/genetics.116.195586}, pmid = {28007886}, issn = {1943-2631}, support = {R01 GM043432/GM/NIGMS NIH HHS/United States ; R01 GM083228/GM/NIGMS NIH HHS/United States ; R56 GM043432/GM/NIGMS NIH HHS/United States ; T32 HG003284/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Chromatin/*genetics ; Conserved Sequence ; Drosophila/*genetics ; Drosophila Proteins/genetics/metabolism ; *Evolution, Molecular ; *Insulator Elements ; Transcription Factors/genetics/metabolism ; }, abstract = {Chromatin boundary elements subdivide chromosomes in multicellular organisms into physically independent domains. In addition to this architectural function, these elements also play a critical role in gene regulation. Here we investigated the evolution of a Drosophila Bithorax complex boundary element called Fab-7, which is required for the proper parasegment specific expression of the homeotic Abd-B gene. Using a &quot;gene&quot; replacement strategy, we show that Fab-7 boundaries from two closely related species, D. erecta and D. yakuba, and a more distant species, D. pseudoobscura, are able to substitute for the melanogaster boundary. Consistent with this functional conservation, the two known Fab-7 boundary factors, Elba and LBC, have recognition sequences in the boundaries from all species. However, the strategies used for maintaining binding and function in the face of sequence divergence is different. The first is conventional, and depends upon conservation of the 8 bp Elba recognition sequence. The second is unconventional, and takes advantage of the unusually large and flexible sequence recognition properties of the LBC boundary factor, and the deployment of multiple LBC recognition elements in each boundary. In the former case, binding is lost when the recognition sequence is altered. In the latter case, sequence divergence is accompanied by changes in the number, relative affinity, and location of the LBC recognition elements.}, }
@article {pmid27998811, year = {2016}, author = {Ramírez-Sánchez, O and Pérez-Rodríguez, P and Delaye, L and Tiessen, A}, title = {Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {14}, number = {6}, pages = {357-370}, doi = {10.1016/j.gpb.2016.06.003}, pmid = {27998811}, issn = {2210-3244}, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Eukaryota/classification/genetics/metabolism ; Evolution, Molecular ; Exons ; Genes, Plant ; Humans ; Linear Models ; Phylogeny ; Plant Proteins/*chemistry/genetics/metabolism ; Plants/classification/genetics/*metabolism ; Proteins/*chemistry/genetics/metabolism ; Symbiosis ; }, abstract = {Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt)]. Streptophyta have on average only ∼5.7 exons of medium size (∼230nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400nt). Among subcellular compartments, membrane proteins are the largest (∼520aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes.}, }
@article {pmid27996008, year = {2016}, author = {Zehr, JP and Shilova, IN and Farnelid, HM and Muñoz-Marín, MD and Turk-Kubo, KA}, title = {Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A.}, journal = {Nature microbiology}, volume = {2}, number = {}, pages = {16214}, doi = {10.1038/nmicrobiol.2016.214}, pmid = {27996008}, issn = {2058-5276}, abstract = {Nitrogen fixation - the reduction of dinitrogen (N2) gas to biologically available nitrogen (N) - is an important source of N for terrestrial and aquatic ecosystems. In terrestrial environments, N2-fixing symbioses involve multicellular plants, but in the marine environment these symbioses occur with unicellular planktonic algae. An unusual symbiosis between an uncultivated unicellular cyanobacterium (UCYN-A) and a haptophyte picoplankton alga was recently discovered in oligotrophic oceans. UCYN-A has a highly reduced genome, and exchanges fixed N for fixed carbon with its host. This symbiosis bears some resemblance to symbioses found in freshwater ecosystems. UCYN-A shares many core genes with the 'spheroid bodies' of Epithemia turgida and the endosymbionts of the amoeba Paulinella chromatophora. UCYN-A is widely distributed, and has diversified into a number of sublineages that could be ecotypes. Many questions remain regarding the physical and genetic mechanisms of the association, but UCYN-A is an intriguing model for contemplating the evolution of N2-fixing organelles.}, }
@article {pmid27994131, year = {2017}, author = {Jill Harrison, C}, title = {Development and genetics in the evolution of land plant body plans.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1713}, pages = {}, doi = {10.1098/rstb.2015.0490}, pmid = {27994131}, issn = {1471-2970}, support = {BB/L00224811//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Embryophyta/*genetics/*growth &amp; development ; *Genes, Plant ; Germ Cells, Plant/growth &amp; development ; }, abstract = {The colonization of land by plants shaped the terrestrial biosphere, the geosphere and global climates. The nature of morphological and molecular innovation driving land plant evolution has been an enigma for over 200 years. Recent phylogenetic and palaeobotanical advances jointly demonstrate that land plants evolved from freshwater algae and pinpoint key morphological innovations in plant evolution. In the haploid gametophyte phase of the plant life cycle, these include the innovation of mulitcellular forms with apical growth and multiple growth axes. In the diploid phase of the life cycle, multicellular axial sporophytes were an early innovation priming subsequent diversification of indeterminate branched forms with leaves and roots. Reverse and forward genetic approaches in newly emerging model systems are starting to identify the genetic basis of such innovations. The data place plant evo-devo research at the cusp of discovering the developmental and genetic changes driving the radiation of land plant body plans.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.}, }
@article {pmid27994119, year = {2017}, author = {Cavalier-Smith, T}, title = {Origin of animal multicellularity: precursors, causes, consequences-the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1713}, pages = {}, doi = {10.1098/rstb.2015.0476}, pmid = {27994119}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Choanoflagellata/growth &amp; development/physiology ; Evolution, Molecular ; Invertebrates/growth &amp; development/*physiology ; *Neurogenesis ; Porifera/growth &amp; development/physiology ; }, abstract = {Evolving multicellularity is easy, especially in phototrophs and osmotrophs whose multicells feed like unicells. Evolving animals was much harder and unique; probably only one pathway via benthic 'zoophytes' with pelagic ciliated larvae allowed trophic continuity from phagocytic protozoa to gut-endowed animals. Choanoflagellate protozoa produced sponges. Converting sponge flask cells mediating larval settling to synaptically controlled nematocysts arguably made Cnidaria. I replace Haeckel's gastraea theory by a sponge/coelenterate/bilaterian pathway: Placozoa, hydrozoan diploblasty and ctenophores were secondary; stem anthozoan developmental mutations arguably independently generated coelomate bilateria and ctenophores. I emphasize animal origin's conceptual aspects (selective, developmental) related to feeding modes, cell structure, phylogeny of related protozoa, sequence evidence, ecology and palaeontology. Epithelia and connective tissue could evolve only by compensating for dramatically lower feeding efficiency that differentiation into non-choanocytes entails. Consequentially, larger bodies enabled filtering more water for bacterial food and harbouring photosynthetic bacteria, together adding more food than cell differentiation sacrificed. A hypothetical presponge of sessile triploblastic sheets (connective tissue sandwiched between two choanocyte epithelia) evolved oogamy through selection for larger dispersive ciliated larvae to accelerate benthic trophic competence and overgrowing protozoan competitors. Extinct Vendozoa might be elaborations of this organismal grade with choanocyte-bearing epithelia, before poriferan water channels and cnidarian gut/nematocysts/synapses evolved.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.}, }
@article {pmid27994117, year = {2017}, author = {Bush, SJ and Chen, L and Tovar-Corona, JM and Urrutia, AO}, title = {Alternative splicing and the evolution of phenotypic novelty.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {372}, number = {1713}, pages = {}, doi = {10.1098/rstb.2015.0474}, pmid = {27994117}, issn = {1471-2970}, mesh = {*Alternative Splicing ; Animals ; *Biological Evolution ; Evolution, Molecular ; Gene Duplication ; *Phenotype ; Transcriptome ; }, abstract = {Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.}, }
@article {pmid27984033, year = {2017}, author = {Malagoli, D and Ottaviani, E}, title = {Cross-talk among immune and neuroendocrine systems in molluscs and other invertebrate models.}, journal = {Hormones and behavior}, volume = {88}, number = {}, pages = {41-44}, doi = {10.1016/j.yhbeh.2016.10.015}, pmid = {27984033}, issn = {1095-6867}, mesh = {Animals ; *Biological Evolution ; Cell Transdifferentiation/physiology ; Homeostasis/physiology ; Immune System/immunology/*metabolism ; Invertebrates/immunology/*metabolism ; Mollusca/immunology/*metabolism ; Neurosecretory Systems/immunology/*metabolism ; }, abstract = {The comparison between immune and neuroendocrine systems in vertebrates and invertebrates suggest an ancient origin and a high degree of conservation for the mechanisms underlying the integration between immune and stress responses. This suggests that in both vertebrates and invertebrates the stress response involves the integrated network of soluble mediators (e.g., neurotransmitters, hormones and cytokines) and cell functions (e.g., chemotaxis and phagocytosis), that interact with a common objective, i.e., the maintenance of body homeostasis. During evolution, several changes observed in the stress response of more complex taxa could be the result of new roles of ancestral molecules, such as ancient immune mediators may have been recruited as neurotransmitters and hormones, or vice versa. We review older and recent evidence suggesting that immune and neuro-endocrine functions during the stress response were deeply intertwined already at the dawn of multicellular organisms. These observations found relevant reflections in the demonstration that immune cells can transdifferentiate in olfactory neurons in crayfish and the recently re-proposed neural transdifferentiation in humans.}, }
@article {pmid27980068, year = {2017}, author = {Ihara, S and Nakayama, S and Murakami, Y and Suzuki, E and Asakawa, M and Kinoshita, T and Sawa, H}, title = {PIGN prevents protein aggregation in the endoplasmic reticulum independently of its function in the GPI synthesis.}, journal = {Journal of cell science}, volume = {130}, number = {3}, pages = {602-613}, doi = {10.1242/jcs.196717}, pmid = {27980068}, issn = {1477-9137}, mesh = {Animals ; Caenorhabditis elegans/cytology/*metabolism/ultrastructure ; Caenorhabditis elegans Proteins/*metabolism ; Conserved Sequence ; Endoplasmic Reticulum/*metabolism/ultrastructure ; Evolution, Molecular ; Glycosylphosphatidylinositols/*metabolism ; HEK293 Cells ; Humans ; Intracellular Membranes/metabolism ; Intracellular Space/metabolism ; Mutation/genetics ; Phosphotransferases/chemistry/*metabolism ; *Protein Aggregates ; Sequence Homology, Amino Acid ; }, abstract = {Quality control of proteins in the endoplasmic reticulum (ER) is essential for ensuring the integrity of secretory proteins before their release into the extracellular space. Secretory proteins that fail to pass quality control form aggregates. Here we show the PIGN-1/PIGN is required for quality control in Caenorhabditis elegans and in mammalian cells. In C. elegans pign-1 mutants, several proteins fail to be secreted and instead form abnormal aggregation. PIGN-knockout HEK293 cells also showed similar protein aggregation. Although PIGN-1/PIGN is responsible for glycosylphosphatidylinositol (GPI)-anchor biosynthesis in the ER, certain mutations in C. elegans pign-1 caused protein aggregation in the ER without affecting GPI-anchor biosynthesis. These results show that PIGN-1/PIGN has a conserved and non-canonical function to prevent deleterious protein aggregation in the ER independently of the GPI-anchor biosynthesis. PIGN is a causative gene for some human diseases including multiple congenital seizure-related syndrome (MCAHS1). Two pign-1 mutations created by CRISPR/Cas9 that correspond to MCAHS1 also cause protein aggregation in the ER, implying that the dysfunction of the PIGN non-canonical function might affect symptoms of MCAHS1 and potentially those of other diseases.}, }
@article {pmid27979655, year = {2017}, author = {Lalucque, H and Malagnac, F and Green, K and Gautier, V and Grognet, P and Chan Ho Tong, L and Scott, B and Silar, P}, title = {IDC2 and IDC3, two genes involved in cell non-autonomous signaling of fruiting body development in the model fungus Podospora anserina.}, journal = {Developmental biology}, volume = {421}, number = {2}, pages = {126-138}, doi = {10.1016/j.ydbio.2016.12.016}, pmid = {27979655}, issn = {1095-564X}, mesh = {Amino Acid Sequence ; Blotting, Western ; Cellulose/pharmacology ; Conserved Sequence ; Cysteine/metabolism ; Evolution, Molecular ; Fruiting Bodies, Fungal/*genetics/*growth &amp; development ; Fungal Proteins/chemistry/*genetics/metabolism ; Gene Deletion ; *Genes, Fungal ; Genetic Complementation Test ; Green Fluorescent Proteins/metabolism ; Mosaicism ; Mycelium/metabolism ; Phenotype ; Phosphorylation/drug effects ; Podospora/*genetics/*growth &amp; development ; Signal Transduction/*genetics ; Subcellular Fractions/metabolism ; Vacuoles/metabolism ; }, abstract = {Filamentous ascomycetes produce complex multicellular structures during sexual reproduction. Little is known about the genetic pathways enabling the construction of such structures. Here, with a combination of classical and reverse genetic methods, as well as genetic mosaic and graft analyses, we identify and provide evidence for key roles for two genes during the formation of perithecia, the sexual fruiting bodies, of the filamentous fungus Podospora anserina. Data indicate that the proteins coded by these two genes function cell-non-autonomously and that their activity depends upon conserved cysteines, making them good candidate for being involved in the transmission of a reactive oxygen species (ROS) signal generated by the PaNox1 NADPH oxidase inside the maturing fruiting body towards the PaMpk1 MAP kinase, which is located inside the underlying mycelium, in which nutrients are stored. These data provide important new insights to our understanding of how fungi build multicellular structures.}, }
@article {pmid27967109, year = {2016}, author = {Kirkegaard, JB and Goldstein, RE}, title = {Filter-feeding, near-field flows, and the morphologies of colonial choanoflagellates.}, journal = {Physical review. E}, volume = {94}, number = {5-1}, pages = {052401}, doi = {10.1103/PhysRevE.94.052401}, pmid = {27967109}, issn = {2470-0053}, support = {//Wellcome Trust/United Kingdom ; 097855//Wellcome Trust/United Kingdom ; }, mesh = {Choanoflagellata/*cytology/*physiology ; Feeding Behavior/*physiology ; *Water Movements ; }, abstract = {Efficient uptake of prey and nutrients from the environment is an important component in the fitness of all microorganisms, and its dependence on size may reveal clues to the origins of evolutionary transitions to multicellularity. Because potential benefits in uptake rates must be viewed in the context of other costs and benefits of size, such as varying predation rates and the increased metabolic costs associated with larger and more complex body plans, the uptake rate itself is not necessarily that which is optimized by evolution. Uptake rates can be strongly dependent on local organism geometry and its swimming speed, providing selective pressure for particular arrangements. Here we examine these issues for choanoflagellates, filter-feeding microorganisms that are the closest relatives of the animals. We explore the different morphological variations of the choanoflagellate Salpingoeca rosetta, which can exist as a swimming cell, as a sessile thecate cell, and as colonies of cells in various shapes. In the absence of other requirements and in a homogeneously nutritious environment, we find that the optimal strategy to maximize filter-feeding by the collar of microvilli is to swim fast, which favors swimming unicells. In large external flows, the sessile thecate cell becomes advantageous. Effects of prey diffusion are discussed and also found to be to the advantage of the swimming unicell.}, }
@article {pmid27965457, year = {2017}, author = {Däster, S and Amatruda, N and Calabrese, D and Ivanek, R and Turrini, E and Droeser, RA and Zajac, P and Fimognari, C and Spagnoli, GC and Iezzi, G and Mele, V and Muraro, MG}, title = {Induction of hypoxia and necrosis in multicellular tumor spheroids is associated with resistance to chemotherapy treatment.}, journal = {Oncotarget}, volume = {8}, number = {1}, pages = {1725-1736}, doi = {10.18632/oncotarget.13857}, pmid = {27965457}, issn = {1949-2553}, mesh = {Animals ; Antimetabolites, Antineoplastic/*pharmacology ; Cell Hypoxia/*physiology ; Colorectal Neoplasms/drug therapy/*pathology ; Drug Resistance, Neoplasm/*physiology ; Fluorouracil/*pharmacology ; Gene Expression Profiling ; HCT116 Cells ; HT29 Cells ; Humans ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Necrosis/*pathology ; Oxygen/metabolism ; Spheroids, Cellular/*physiology ; Tumor Cells, Cultured ; Xenograft Model Antitumor Assays ; }, abstract = {Culture of cancerous cells in standard monolayer conditions poorly mirrors growth in three-dimensional architectures typically observed in a wide majority of cancers of different histological origin. Multicellular tumor spheroid (MCTS) culture models were developed to mimic these features. However, in vivo tumor growth is also characterized by the presence of ischemic and necrotic areas generated by oxygenation gradients and differential access to nutrients. Hypoxia and necrosis play key roles in tumor progression and resistance to treatment. To provide in vitro models recapitulating these events in highly controlled and standardized conditions, we have generated colorectal cancer (CRC) cell spheroids of different sizes and analyzed their gene expression profiles and sensitivity to treatment with 5FU, currently used in therapeutic protocols. Here we identify three MCTS stages, corresponding to defined spheroid sizes, characterized by normoxia, hypoxia, and hypoxia plus necrosis, respectively. Importantly, we show that MCTS including both hypoxic and necrotic areas most closely mimic gene expression profiles of in vivo-developing tumors and display the highest resistance to 5FU. Taken together, our data indicate that MCTS may mimic in vitro generation of ischemic and necrotic areas in highly standardized and controlled conditions, thereby qualifying as relevant models for drug screening purposes.}, }
@article {pmid27936291, year = {2017}, author = {Hughes, KA and Leips, J}, title = {Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses.}, journal = {Annals of the New York Academy of Sciences}, volume = {1389}, number = {1}, pages = {76-91}, doi = {10.1111/nyas.13256}, pmid = {27936291}, issn = {1749-6632}, support = {F32 GM016990/GM/NIGMS NIH HHS/United States ; R01 DK084219/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Drosophila melanogaster ; *Genetic Pleiotropy ; *Genetic Variation ; *Genetics, Population ; Genome ; Genome-Wide Association Study ; *Genomics ; Humans ; Plants ; Quantitative Trait Loci ; Selection, Genetic ; }, abstract = {Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.}, }
@article {pmid27934708, year = {2016}, author = {Jones, JD and Vance, RE and Dangl, JL}, title = {Intracellular innate immune surveillance devices in plants and animals.}, journal = {Science (New York, N.Y.)}, volume = {354}, number = {6316}, pages = {}, doi = {10.1126/science.aaf6395}, pmid = {27934708}, issn = {1095-9203}, mesh = {Animals ; Evolution, Molecular ; Host-Pathogen Interactions ; *Immunity, Innate ; *Immunologic Surveillance ; NLR Proteins/chemistry/genetics/*immunology ; Plant Diseases/immunology/microbiology ; Plants/*immunology/*microbiology ; Protein Domains ; }, abstract = {Multicellular eukaryotes coevolve with microbial pathogens, which exert strong selective pressure on the immune systems of their hosts. Plants and animals use intracellular proteins of the nucleotide-binding domain, leucine-rich repeat (NLR) superfamily to detect many types of microbial pathogens. The NLR domain architecture likely evolved independently and convergently in each kingdom, and the molecular mechanisms of pathogen detection by plant and animal NLRs have long been considered to be distinct. However, microbial recognition mechanisms overlap, and it is now possible to discern important key trans-kingdom principles of NLR-dependent immune function. Here, we attempt to articulate these principles. We propose that the NLR architecture has evolved for pathogen-sensing in diverse organisms because of its utility as a tightly folded &quot;hair trigger&quot; device into which a virtually limitless number of microbial detection platforms can be integrated. Recent findings suggest means to rationally design novel recognition capabilities to counter disease.}, }
@article {pmid27917322, year = {2016}, author = {Grishaeva, TM and Kulichenko, D and Bogdanov, YF}, title = {Bioinformatical analysis of eukaryotic shugoshins reveals meiosis-specific features of vertebrate shugoshins.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2736}, doi = {10.7717/peerj.2736}, pmid = {27917322}, issn = {2167-8359}, abstract = {BACKGROUND: Shugoshins (SGOs) are proteins that protect cohesins located at the centromeres of sister chromatids from their early cleavage during mitosis and meiosis in plants, fungi, and animals. Their function is to prevent premature sister-chromatid disjunction and segregation. The study focused on the structural differences among SGOs acting during mitosis and meiosis that cause differences in chromosome behavior in these two types of cell division in different organisms.<br><br>METHODS: A bioinformatical analysis of protein domains, conserved amino acid motifs, and physicochemical properties of 32 proteins from 25 species of plants, fungi, and animals was performed.<br><br>RESULTS: We identified a C-terminal amino acid motif that is highly evolutionarily conserved among the SGOs protecting centromere cohesion of sister chromatids in meiotic anaphase I, but not among mitotic SGOs. This meiotic motif is arginine-rich in vertebrates. SGOs differ in different eukaryotic kingdoms by the sets and locations of amino acid motifs and the number of α-helical regions in the protein molecule.<br><br>DISCUSSION: These structural differences between meiotic and mitotic SGOs probably could be responsible for the prolonged SGOs resistance to degradation during meiotic metaphase I and anaphase I. We suggest that the &quot;arginine comb&quot; in C-end meiotic motifs is capable of interaction by hydrogen bonds with guanine bases in the minor groove of DNA helix, thus protecting SGOs from hydrolysis. Our findings support independent evolution of meiosis in different lineages of multicellular organisms.}, }
@article {pmid27916428, year = {2017}, author = {Kroos, L}, title = {Highly Signal-Responsive Gene Regulatory Network Governing Myxococcus Development.}, journal = {Trends in genetics : TIG}, volume = {33}, number = {1}, pages = {3-15}, doi = {10.1016/j.tig.2016.10.006}, pmid = {27916428}, issn = {0168-9525}, support = {R01 GM043585/GM/NIGMS NIH HHS/United States ; }, mesh = {Gene Expression Regulation, Bacterial/genetics ; Gene Regulatory Networks/*genetics ; Mutation ; Myxococcus xanthus/*genetics/growth &amp; development ; Signal Transduction/*genetics ; Spores, Bacterial/*genetics ; Transcriptional Activation/genetics ; }, abstract = {The bacterium Myxococcus xanthus undergoes multicellular development when starved. Thousands of cells build mounds in which some differentiate into spores. This remarkable feat and the genetic tractability of Myxococcus provide a unique opportunity to understand the evolution of gene regulatory networks (GRNs). Recent work has revealed a GRN involving interconnected cascades of signal-responsive transcriptional activators. Initially, starvation-induced intracellular signals direct changes in gene expression. Subsequently, self-generated extracellular signals provide morphological cues that regulate certain transcriptional activators. However, signals for many of the activators remain to be discovered. A key insight is that activators often work combinatorially, allowing signal integration. The Myxococcus GRN differs strikingly from those governing sporulation of Bacillus and Streptomyces, suggesting that Myxococcus evolved a highly signal-responsive GRN to enable complex multicellular development.}, }
@article {pmid27913751, year = {2017}, author = {Wu, Y and Gao, B and Zhu, S}, title = {New fungal defensin-like peptides provide evidence for fold change of proteins in evolution.}, journal = {Bioscience reports}, volume = {37}, number = {1}, pages = {}, doi = {10.1042/BSR20160438}, pmid = {27913751}, issn = {1573-4935}, mesh = {Amino Acid Sequence ; Ascomycota/*chemistry/genetics ; Cysteine/chemistry/genetics ; Defensins/*chemistry/genetics ; Evolution, Molecular ; Fungal Proteins/*chemistry/genetics ; Genes, Fungal ; Models, Molecular ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Folding ; Sequence Alignment ; }, abstract = {Defensins containing a consensus cystine framework, Cys[1]…Cys[2]X3Cys[3]…Cys[4]… Cys[5]X1Cys[6] (X, any amino acid except Cys; …, variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming the cysteine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation. By using a computational genomics approach, we identified a large superfamily of fungal defensin-like peptides (fDLPs) in the phytopathogenic fungal genus - Zymoseptoria, which includes 132 structurally typical and 63 atypical members. These atypical fDLPs exhibit an altered cystine framework and accompanying fold change associated with their secondary structure elements and disulfide bridge patterns, as identified by protein structure modelling. Despite this, they definitely are homologous with the typical fDLPs in view of their precise gene structure conservation and identical precursor organization. Sequence and structural analyses combined with functional data suggest that most of Zymoseptoria fDLPs might have lost their antimicrobial activity. The present study provides a clear example of fold change in the evolution of proteins and is valuable in establishing remote homology among peptide superfamily members with different folds.}, }
@article {pmid27903631, year = {2017}, author = {Dettman, JR and Rodrigue, N and Schoustra, SE and Kassen, R}, title = {Genomics of Compensatory Adaptation in Experimental Populations of Aspergillus nidulans.}, journal = {G3 (Bethesda, Md.)}, volume = {7}, number = {2}, pages = {427-436}, doi = {10.1534/g3.116.036152}, pmid = {27903631}, issn = {2160-1836}, support = {//CIHR/Canada ; }, mesh = {Adaptation, Physiological/*genetics ; Aspergillus nidulans/drug effects/*genetics/growth &amp; development ; Dioxoles/pharmacology ; Drug Resistance, Fungal ; *Evolution, Molecular ; *Genetic Fitness ; Genome, Fungal ; Genomics ; Osmotic Pressure/physiology ; Pyrroles/pharmacology ; }, abstract = {Knowledge of the number and nature of genetic changes responsible for adaptation is essential for understanding and predicting evolutionary trajectories. Here, we study the genomic basis of compensatory adaptation to the fitness cost of fungicide resistance in experimentally evolved strains of the filamentous fungus Aspergillus nidulans The original selection experiment tracked the fitness recovery of lines founded by an ancestral strain that was resistant to fludioxonil, but paid a fitness cost in the absence of the fungicide. We obtained whole-genome sequence data for the ancestral A. nidulans strain and eight experimentally evolved strains. We find that fludioxonil resistance in the ancestor was likely conferred by a mutation in histidine kinase nikA, part of the two-component signal transduction system of the high-osmolarity glycerol (HOG) stress response pathway. To compensate for the pleiotropic negative effects of the resistance mutation, the subsequent fitness gains observed in the evolved lines were likely caused by secondary modification of HOG pathway activity. Candidate genes for the compensatory fitness increases were significantly overrepresented by stress response functions, and some were specifically associated with the HOG pathway itself. Parallel evolution at the gene level was rare among evolved lines. There was a positive relationship between the predicted number of adaptive steps, estimated from fitness data, and the number of genomic mutations, determined by whole-genome sequencing. However, the number of genomic mutations was, on average, 8.45 times greater than the number of adaptive steps inferred from fitness data. This research expands our understanding of the genetic basis of adaptation in multicellular eukaryotes and lays out a framework for future work on the genomics of compensatory adaptation in A. nidulans.}, }
@article {pmid27889635, year = {2017}, author = {Brunkard, JO and Zambryski, PC}, title = {Plasmodesmata enable multicellularity: new insights into their evolution, biogenesis, and functions in development and immunity.}, journal = {Current opinion in plant biology}, volume = {35}, number = {}, pages = {76-83}, doi = {10.1016/j.pbi.2016.11.007}, pmid = {27889635}, issn = {1879-0356}, mesh = {*Biological Evolution ; *Organelle Biogenesis ; Plant Development ; Plant Immunity ; *Plant Physiological Phenomena ; Plasmodesmata/*physiology ; }, abstract = {Plant cells are connected by plasmodesmata (PD), cytosolic bridges that allow molecules to freely move across the cell wall. Recently resolved relationships among land plants and their algal relatives reveal that land plants evolved PD independently from algae. Proteomic and genetic screens illuminate new dimensions of the structural and regulatory pathways that control PD biogenesis. Biochemical studies demonstrate that immunological signals induce systemic defenses by moving from diseased cells through PD; subsequently, PD transport is restricted to quarantine diseased cells. Here, we review our expanding knowledge of the roles of PD in plant development, physiology, and immunity.}, }
@article {pmid27888167, year = {2017}, author = {Liao, BK and Oates, AC}, title = {Delta-Notch signalling in segmentation.}, journal = {Arthropod structure &amp; development}, volume = {46}, number = {3}, pages = {429-447}, doi = {10.1016/j.asd.2016.11.007}, pmid = {27888167}, issn = {1873-5495}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Body Patterning/genetics/*physiology ; Gene Expression Regulation, Developmental ; Phylogeny ; Receptors, Notch/genetics/*metabolism ; *Signal Transduction ; }, abstract = {Modular body organization is found widely across multicellular organisms, and some of them form repetitive modular structures via the process of segmentation. It's vastly interesting to understand how these regularly repeated structures are robustly generated from the underlying noise in biomolecular interactions. Recent studies from arthropods reveal similarities in segmentation mechanisms with vertebrates, and raise the possibility that the three phylogenetic clades, annelids, arthropods and chordates, might share homology in this process from a bilaterian ancestor. Here, we discuss vertebrate segmentation with particular emphasis on the role of the Notch intercellular signalling pathway. We introduce vertebrate segmentation and Notch signalling, pointing out historical milestones, then describe existing models for the Notch pathway in the synchronization of noisy neighbouring oscillators, and a new role in the modulation of gene expression wave patterns. We ask what functions Notch signalling may have in arthropod segmentation and explore the relationship between Notch-mediated lateral inhibition and synchronization. Finally, we propose open questions and technical challenges to guide future investigations into Notch signalling in segmentation.}, }
@article {pmid27886385, year = {2017}, author = {Frangedakis, E and Saint-Marcoux, D and Moody, LA and Rabbinowitsch, E and Langdale, JA}, title = {Nonreciprocal complementation of KNOX gene function in land plants.}, journal = {The New phytologist}, volume = {216}, number = {2}, pages = {591-604}, doi = {10.1111/nph.14318}, pmid = {27886385}, issn = {1469-8137}, mesh = {Bayes Theorem ; Embryophyta/*genetics ; Evolution, Molecular ; Gene Duplication ; *Genes, Plant ; *Genetic Complementation Test ; Likelihood Functions ; Loss of Function Mutation/genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Species Specificity ; Transgenes ; }, abstract = {Class I KNOTTED-LIKE HOMEOBOX (KNOX) proteins regulate development of the multicellular diploid sporophyte in both mosses and flowering plants; however, the morphological context in which they function differs. In order to determine how Class I KNOX function was modified as land plants evolved, phylogenetic analyses and cross-species complementation assays were performed. Our data reveal that a duplication within the charophyte sister group to land plants led to distinct Class I and Class II KNOX gene families. Subsequently, Class I sequences diverged substantially in the nonvascular bryophyte groups (liverworts, mosses and hornworts), with moss sequences being most similar to those in vascular plants. Despite this similarity, moss mutants were not complemented by vascular plant KNOX genes. Conversely, the Arabidopsis brevipedicellus (bp-9) mutant was complemented by the PpMKN2 gene from the moss Physcomitrella patens. Lycophyte KNOX genes also complemented bp-9 whereas fern genes only partially complemented the mutant. This lycophyte/fern distinction is mirrored in the phylogeny of KNOX-interacting BELL proteins, in that a gene duplication occurred after divergence of the two groups. Together, our results imply that the moss MKN2 protein can function in a broader developmental context than vascular plant KNOX proteins, the narrower scope having evolved progressively as lycophytes, ferns and flowering plants diverged.}, }
@article {pmid27882869, year = {2016}, author = {Kirkegaard, JB and Bouillant, A and Marron, AO and Leptos, KC and Goldstein, RE}, title = {Aerotaxis in the closest relatives of animals.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, doi = {10.7554/eLife.18109}, pmid = {27882869}, issn = {2050-084X}, support = {097855//Wellcome Trust/United Kingdom ; }, mesh = {*Chemotaxis ; Choanoflagellata/*drug effects/*physiology ; Lab-On-A-Chip Devices ; Oxygen/*metabolism ; }, abstract = {As the closest unicellular relatives of animals, choanoflagellates serve as useful model organisms for understanding the evolution of animal multicellularity. An important factor in animal evolution was the increasing ocean oxygen levels in the Precambrian, which are thought to have influenced the emergence of complex multicellular life. As a first step in addressing these conditions, we study here the response of the colony-forming choanoflagellate Salpingoeca rosetta to oxygen gradients. Using a microfluidic device that allows spatio-temporal variations in oxygen concentrations, we report the discovery that S. rosetta displays positive aerotaxis. Analysis of the spatial population distributions provides evidence for logarithmic sensing of oxygen, which enhances sensing in low oxygen neighborhoods. Analysis of search strategy models on the experimental colony trajectories finds that choanoflagellate aerotaxis is consistent with stochastic navigation, the statistics of which are captured using an effective continuous version based on classical run-and-tumble chemotaxis.}, }
@article {pmid27880891, year = {2017}, author = {Guzman, A and Sánchez Alemany, V and Nguyen, Y and Zhang, CR and Kaufman, LJ}, title = {A novel 3D in vitro metastasis model elucidates differential invasive strategies during and after breaching basement membrane.}, journal = {Biomaterials}, volume = {115}, number = {}, pages = {19-29}, doi = {10.1016/j.biomaterials.2016.11.014}, pmid = {27880891}, issn = {1878-5905}, mesh = {Batch Cell Culture Techniques/*methods ; Cell Line, Tumor ; Cell Membrane/metabolism/*pathology ; Extracellular Matrix/metabolism/pathology ; Humans ; Neoplasm Invasiveness ; Neoplasm Metastasis ; Neoplasms, Experimental/metabolism/*pathology/*secondary ; *Printing, Three-Dimensional ; *Tissue Scaffolds ; }, abstract = {Invasive breast cancer and other tumors of epithelial origin must breach a layer of basement membrane (BM) that surrounds the primary tumor before invading into the adjacent extracellular matrix. To analyze invasive strategies of breast cancer cells during BM breaching and subsequent invasion into a collagen I-rich extracellular matrix (ECM), we developed a physiologically relevant 3D in vitro model that recreates the architecture of a solid tumor with an intact, degradable, cell-assembled BM layer embedded in a collagen I environment. Using this model we demonstrate that while the BM layer fully prevents dissemination of non-malignant cells, cancer cells are capable of breaching it and invading into the surrounding collagen, indicating that the developed system recreates a hallmark of invasive disease. We demonstrate that cancer cells exhibiting individual invasion in collagen matrices preferentially adopt a specific mode of collective invasion when transmigrating a cell-assembled BM that is not observed in any other tested fibrillar, non-fibrillar, or composite ECM. Matrix-degrading enzymes are found to be crucial during BM breaching but not during subsequent invasion in the collagen matrix. It is further shown that multicellular transmigration of the BM is less susceptible to pharmacological MMP inhibition than multicellular invasion in composite collagen/basement membrane extract matrices. The newly developed in vitro model of metastasis allows 3D cancer cell invasion to be studied not only as a function of a particular tumor's genetics but also as a function of its heterogeneous environment and the different stages of invasion. As such, this model is a valuable new tool with which to dissect basic mechanisms of invasion and metastasis and develop new therapeutic approaches in a physiologically relevant, yet inexpensive and highly tunable, in vitro setting.}, }
@article {pmid27880868, year = {2017}, author = {Gaiti, F and Calcino, AD and Tanurdžić, M and Degnan, BM}, title = {Origin and evolution of the metazoan non-coding regulatory genome.}, journal = {Developmental biology}, volume = {427}, number = {2}, pages = {193-202}, doi = {10.1016/j.ydbio.2016.11.013}, pmid = {27880868}, issn = {1095-564X}, mesh = {Animals ; *Biological Evolution ; *Gene Expression Regulation ; *Genome ; Humans ; Regulatory Sequences, Nucleic Acid ; }, abstract = {Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa. High-throughput next-generation sequencing, largely in bilaterian model species, has led to the discovery of tens of thousands of non-coding RNA genes (ncRNAs), including short, long and circular forms, and uncovered the central roles they play in development. Based on the analysis of non-bilaterian metazoan, unicellular holozoan and fungal genomes, the evolution of some ncRNAs, such as Piwi-interacting RNAs, correlates with the emergence of metazoan multicellularity, while others, including microRNAs, long non-coding RNAs and circular RNAs, appear to be more ancient. Analysis of non-coding regulatory DNA and histone post-translational modifications have revealed that some cis-regulatory mechanisms, such as those associated with proximal promoters, are present in non-animal holozoans, while others appear to be metazoan innovations, most notably distal enhancers. In contrast, the cohesin-CTCF system for regulating higher-order chromatin structure and enhancer-promoter long-range interactions appears to be restricted to bilaterians. Taken together, most bilaterian non-coding regulatory mechanisms appear to have originated before the divergence of crown metazoans. However, differential expansion of non-coding RNA and cis-regulatory DNA repertoires in bilaterians may account for their increased regulatory and morphological complexity relative to non-bilaterians.}, }
@article {pmid27876853, year = {2016}, author = {Rodriguez-Pascual, F and Slatter, DA}, title = {Collagen cross-linking: insights on the evolution of metazoan extracellular matrix.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37374}, doi = {10.1038/srep37374}, pmid = {27876853}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Animals ; Collagen/classification/genetics/*metabolism ; Evolution, Molecular ; Extracellular Matrix/*metabolism ; Fibrillar Collagens/chemistry/genetics/*metabolism ; Humans ; Invertebrates/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Structure, Secondary ; Protein-Lysine 6-Oxidase/*metabolism ; Sequence Homology, Amino Acid ; Vertebrates/genetics/metabolism ; }, abstract = {Collagens constitute a large family of extracellular matrix (ECM) proteins that play a fundamental role in supporting the structure of various tissues in multicellular animals. The mechanical strength of fibrillar collagens is highly dependent on the formation of covalent cross-links between individual fibrils, a process initiated by the enzymatic action of members of the lysyl oxidase (LOX) family. Fibrillar collagens are present in a wide variety of animals, therefore often being associated with metazoan evolution, where the emergence of an ancestral collagen chain has been proposed to lead to the formation of different clades. While LOX-generated collagen cross-linking metabolites have been detected in different metazoan families, there is limited information about when and how collagen acquired this particular modification. By analyzing telopeptide and helical sequences, we identified highly conserved, potential cross-linking sites throughout the metazoan tree of life. Based on this analysis, we propose that they have importantly contributed to the formation and further expansion of fibrillar collagens.}, }
@article {pmid27871856, year = {2017}, author = {Pianca, N and Zaglia, T and Mongillo, M}, title = {Will cardiac optogenetics find the way through the obscure angles of heart physiology?.}, journal = {Biochemical and biophysical research communications}, volume = {482}, number = {4}, pages = {515-523}, doi = {10.1016/j.bbrc.2016.11.104}, pmid = {27871856}, issn = {1090-2104}, mesh = {Animals ; Arrhythmias, Cardiac/genetics/pathology/physiopathology/therapy ; Channelrhodopsins ; Equipment Design ; Heart/*physiology/physiopathology ; Humans ; Myocardium/metabolism/pathology ; Optogenetics/instrumentation/*methods ; }, abstract = {Optogenetics is a technique exploded in the last 10 years, which revolutionized several areas of biological research. The brightest side of this technology is the use of light to modulate non-invasively, with high spatial resolution and millisecond time scale, excitable cells genetically modified to express light-sensitive microbial ion channels (opsins). Neuroscience has first benefited from such fascinating strategy, in intact organisms. By shining light to specific neuronal subpopulations, optogenetics allowed unearth the mechanisms involved in cell-to-cell communication within the context of intact organs, such as the brain, formed by complex neuronal circuits. More recently, scientists looked at optogenetics as a tool to answer some of the questions, remained in the dark, of cardiovascular physiology. In this review, we focus on the application of optogenetics in the study of the heart, a complex multicellular organ, homing different populations of excitable cells, spatially and functionally interconnected. Moving from the first proof-of-principle works, published in 2010, to the present time, we discuss the in vitro and in vivo applications of optogenetics for the study of electrophysiology of the different cardiac cell types, and for the dissection of cellular mechanisms underlying arrhythmias. We also present how molecular biology and technology foster the evolution of cardiac optogenetics, with the aim to further our understanding of fundamental questions in cardiac physiology and pathology. Finally, we confer about the therapeutic potential of such biotechnological strategy for the treatment of heart rhythm disturbances (e.g. cardiac pacing, cardioversion).}, }
@article {pmid27870211, year = {2016}, author = {Cunningham, JA and Vargas, K and Marone, F and Bengtson, S and Donoghue, PC}, title = {A multicellular organism with embedded cell clusters from the Ediacaran Weng'an biota (Doushantuo Formation, South China).}, journal = {Evolution &amp; development}, volume = {18}, number = {5-6}, pages = {308-316}, doi = {10.1111/ede.12210}, pmid = {27870211}, issn = {1525-142X}, abstract = {Three-dimensional analyses of the early Ediacaran microfossils from the Weng'an biota (Doushantuo Formation) have focused predominantly on multicellular forms that have been interpreted as embryos, and yet they have defied phylogenetic interpretation principally because of absence of evidence from other stages in their life cycle. It is therefore unfortunate that the affinities of the various other Doushantuo microfossils have been neglected. A new conical fossil that is preserved at a cellular level is described here. The fossil contains distinct cell clusters that are characterized and analysed in three dimensions. These clusters are often exposed at the specimen surface, and the fossil preserves many hemispherical craters that are interpreted as positions where clusters have left the organism. The cell clusters may be either reproductive propagules or infesting organisms. Similar clusters are found in a variety of Doushantuo organisms including putative animal embryos and algae.}, }
@article {pmid27863931, year = {2016}, author = {Filyk, HA and Osborne, LC}, title = {The Multibiome: The Intestinal Ecosystem's Influence on Immune Homeostasis, Health, and Disease.}, journal = {EBioMedicine}, volume = {13}, number = {}, pages = {46-54}, doi = {10.1016/j.ebiom.2016.10.007}, pmid = {27863931}, issn = {2352-3964}, mesh = {Animals ; Disease Susceptibility ; Ecosystem ; *Gastrointestinal Microbiome ; *Homeostasis ; Host-Parasite Interactions/genetics/immunology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Immunity, Mucosal ; Immunomodulation ; Intestinal Mucosa/immunology/metabolism/microbiology ; Intestines/*physiology ; }, abstract = {Mammalian evolution has occurred in the presence of mutualistic, commensal, and pathogenic micro- and macro-organisms for millennia. The presence of these organisms during mammalian evolution has allowed for intimate crosstalk between these colonizing species and the host immune system. In this review, we introduce the concept of the 'multibiome' to holistically refer to the biodiverse collection of bacteria, viruses, fungi and multicellular helminthic worms colonizing the mammalian intestine. Furthermore, we discuss new insights into multibiome-host interactions in the context of host-protective immunity and immune-mediated diseases, including inflammatory bowel disease and multiple sclerosis. Finally, we provide reasons to account for the multibiome in experimental design, analysis and in therapeutic applications.}, }
@article {pmid27855631, year = {2016}, author = {Singh, R and Schilde, C and Schaap, P}, title = {A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {251}, doi = {10.1186/s12862-016-0825-7}, pmid = {27855631}, issn = {1471-2148}, support = {BB/K000799/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 100293/Z/12/Z//Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; Computational Biology ; Consensus Sequence ; Dictyostelium/*classification/*genetics ; *Genome, Protozoan ; *Phylogeny ; Protozoan Proteins/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa.<br><br>RESULTS: We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification.<br><br>CONCLUSIONS: The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum branching at the base of that whole clade. Given the data, the approximately unbiased test rejects all alternative topologies favoured by SSU rDNA and individual proteins with high statistical support. The test also rejects monophyletic origins for the genera Acytostelium, Polysphondylium and Dictyostelium. The current position of Acytostelium ellipticum in the consensus phylogeny indicates that somatic cells were lost twice in Dictyostelia.}, }
@article {pmid27853598, year = {2016}, author = {Nee, S}, title = {The evolutionary ecology of molecular replicators.}, journal = {Royal Society open science}, volume = {3}, number = {8}, pages = {160235}, doi = {10.1098/rsos.160235}, pmid = {27853598}, issn = {2054-5703}, abstract = {By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.}, }
@article {pmid27845495, year = {2016}, author = {Romero, D}, title = {Unicellular but not asocial. Life in community of a bacterium.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {19}, number = {2}, pages = {81-90}, doi = {10.2436/20.1501.01.266}, pmid = {27845495}, issn = {1139-6709}, mesh = {Bacillus/physiology ; Bacteria/*cytology ; Biological Evolution ; *Microbial Consortia ; }, abstract = {All living organisms have acquired the outstanding ability to overcome the limitations imposed by changeable environments through the gain of genetic traits over years of evolution and the tendency of individuals to associate in communities. The complementation of a singular weakness, the deployment of reinforcement for the good of the community, the better use of resources, or effective defense against external aggression are advantages gained by this communal behavior. Communication has been the cohesive element prompting the global responses that promote efficiency in two features of any community: specialization in differentiated labor and the spatio-temporal organization of the environment. These principles illustrate that what we call human ecology also applies to the cellular world and is exemplified in eukaryotic organisms, where sophisticated cell-to-cell communication networks coordinate cell differentiation and the specialization of multiple tissues consisting of numerous cells embedded in a multifunctional extracellular matrix. This sophisticated molecular machinery appears, however, to be invented by the &quot;simple&quot; but still fascinating bacteria. What I will try to expand in the following sections are notions of how &quot;single prokaryotic cells&quot; organize a multicellular community. [Int Microbiol 19(2):81-90 (2016)].}, }
@article {pmid27829356, year = {2016}, author = {Yamashita, S and Arakaki, Y and Kawai-Toyooka, H and Noga, A and Hirono, M and Nozaki, H}, title = {Alternative evolution of a spheroidal colony in volvocine algae: developmental analysis of embryogenesis in Astrephomene (Volvocales, Chlorophyta).}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {243}, doi = {10.1186/s12862-016-0794-x}, pmid = {27829356}, issn = {1471-2148}, mesh = {Basal Bodies/metabolism ; *Biological Evolution ; Cell Division ; Cell Lineage ; Cell Nucleus/metabolism ; Chlorophyta/*embryology/*genetics ; Fluorescent Antibody Technique, Indirect ; Phylogeny ; Protoplasts/metabolism ; Time-Lapse Imaging ; }, abstract = {BACKGROUND: Volvocine algae, which range from the unicellular Chlamydomonas to the multicellular Volvox with a germ-soma division of labor, are a model for the evolution of multicellularity. Within this group, the spheroidal colony might have evolved in two independent lineages: Volvocaceae and the goniacean Astrephomene. Astrephomene produces spheroidal colonies with posterior somatic cells. The feature that distinguishes Astrephomene from the volvocacean algae is lack of inversion during embryogenesis; the volvocacean embryo undergoes inversion after successive divisions to orient flagella toward the outside. The mechanisms of inversion at the molecular and cellular levels in volvocacean algae have been assessed in detail, particularly in Volvox carteri. However, embryogenesis in Astrephomene has not been subjected to such investigations.<br><br>RESULTS: This study relied on light microscopy time-lapse imaging using an actively growing culture of a newly established strain to conduct a developmental analysis of Astrephomene as well as to perform a comparison with the similar spheroidal volvocacean Eudorina. During the successive divisions involved in Astrephomene embryogenesis, gradual rotation of daughter protoplasts resulted in movement of their apical portions toward the embryonic posterior, forming a convex-to-spheroidal cell sheet with the apical ends of protoplasts on the outside. Differentiation of the posterior somatic cells from the embryo periphery was traced based on cell lineages during embryogenesis. In contrast, in Eudorina, the rotation of daughter protoplasts did not occur during successive cell divisions; however, inversion occurred after such divisions, and a spheroidal embryo was formed. Indirect immunofluorescence microscopy of basal bodies and nuclei verified this difference between Astrephomene and Eudorina in the movement of embryonic protoplasts.<br><br>CONCLUSIONS: These results suggest different tactics for spheroidal colony formation between the two lineages: rotation of daughter protoplasts during successive cell divisions in Astrephomene, and inversion after cell divisions in Eudorina. This study will facilitate further research into the molecular and genetic mechanisms of the parallel evolution of the spheroidal colony in volvocine algae.}, }
@article {pmid27818507, year = {2016}, author = {Arendt, D and Musser, JM and Baker, CVH and Bergman, A and Cepko, C and Erwin, DH and Pavlicev, M and Schlosser, G and Widder, S and Laubichler, MD and Wagner, GP}, title = {The origin and evolution of cell types.}, journal = {Nature reviews. Genetics}, volume = {17}, number = {12}, pages = {744-757}, doi = {10.1038/nrg.2016.127}, pmid = {27818507}, issn = {1471-0064}, mesh = {Animals ; *Biological Evolution ; *Cell Differentiation ; *Cell Lineage ; Cells/classification/*cytology ; *Gene Regulatory Networks ; Humans ; Phylogeny ; }, abstract = {Cell types are the basic building blocks of multicellular organisms and are extensively diversified in animals. Despite recent advances in characterizing cell types, classification schemes remain ambiguous. We propose an evolutionary definition of a cell type that allows cell types to be delineated and compared within and between species. Key to cell type identity are evolutionary changes in the 'core regulatory complex' (CoRC) of transcription factors, that make emergent sister cell types distinct, enable their independent evolution and regulate cell type-specific traits termed apomeres. We discuss the distinction between developmental and evolutionary lineages, and present a roadmap for future research.}, }
@article {pmid27818249, year = {2017}, author = {Currais, A}, title = {The origin of life at the origin of ageing?.}, journal = {Ageing research reviews}, volume = {35}, number = {}, pages = {297-300}, doi = {10.1016/j.arr.2016.10.007}, pmid = {27818249}, issn = {1872-9649}, mesh = {Aging/*physiology ; Animals ; Cell Survival/physiology ; Humans ; *Origin of Life ; }, abstract = {At first glance, the ageing of unicellular organisms would appear to be different from the ageing of complex, multicellular organisms. In an attempt to describe the nature of ageing in diverse organisms, the intimate links between the origins of life and ageing are examined. Departing from Leslie Orgel's initial ideas on why organisms age, it is then discussed how the potentially detrimental events characteristic of ageing are continuous, cell-autonomous and universal to all organisms. The manifestation of these alterations relies on the balance between their production and cellular renewal. Renewal is achieved not only by repair and maintenance mechanisms but, importantly, by the process of cell division such that every time cells divide ageing-associated effects are diluted.}, }
@article {pmid27816674, year = {2017}, author = {Shelton, DE and Leslie, MP and Michod, RE}, title = {Models of cell division initiation in Chlamydomonas: A challenge to the consensus view.}, journal = {Journal of theoretical biology}, volume = {412}, number = {}, pages = {186-197}, doi = {10.1016/j.jtbi.2016.10.018}, pmid = {27816674}, issn = {1095-8541}, mesh = {Cell Division/*physiology ; Chlamydomonas reinhardtii/*physiology ; *Models, Biological ; }, abstract = {We develop and compare two models for division initiation in cells of the unicellular green alga Chlamydomonas reinhardtii, a topic that has remained controversial in spite of years of empirical work. Achieving a better understanding of C. reinhardtii cell cycle regulation is important because this species is used in studies of fundamental eukaryotic cell features and in studies of the evolution of multicellularity. C. reinhardtii proliferates asexually by multiple fission, interspersing rapid rounds of symmetric division with prolonged periods of growth. Our Model 1 reflects major elements of the current consensus view on C. reinhardtii division initiation, with cells first growing to a specific size, then waiting for a particular time prior to division initiation. In Model 2, our proposed alternative, growing cells divide when they have reached a growth-rate-dependent target size. The two models imply a number of different empirical patterns. We highlight these differences alongside published data, which currently fall short of unequivocally distinguishing these differences in predicted cell behavior. Nevertheless, several lines of evidence are suggestive of more Model 2-like behavior than Model 1-like behavior. Our specification of these models adds rigor to issues that have too often been worked out in relation to loose, verbal models and is directly relevant to future development of informative experiments.}, }
@article {pmid27815194, year = {2017}, author = {Fletcher, E and Feizi, A and Bisschops, MMM and Hallström, BM and Khoomrung, S and Siewers, V and Nielsen, J}, title = {Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.}, journal = {Metabolic engineering}, volume = {39}, number = {}, pages = {19-28}, doi = {10.1016/j.ymben.2016.10.010}, pmid = {27815194}, issn = {1096-7184}, mesh = {Acids/*chemistry ; Adaptation, Physiological/*genetics ; Directed Molecular Evolution/*methods ; Gene Expression Regulation, Fungal/genetics ; Genetic Enhancement/methods ; *Hydrogen-Ion Concentration ; Saccharomyces cerevisiae/*chemistry/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Stress, Physiological/*genetics ; }, abstract = {Tolerance of yeast to acid stress is important for many industrial processes including organic acid production. Therefore, elucidating the molecular basis of long term adaptation to acidic environments will be beneficial for engineering production strains to thrive under such harsh conditions. Previous studies using gene expression analysis have suggested that both organic and inorganic acids display similar responses during short term exposure to acidic conditions. However, biological mechanisms that will lead to long term adaptation of yeast to acidic conditions remains unknown and whether these mechanisms will be similar for tolerance to both organic and inorganic acids is yet to be explored. We therefore evolved Saccharomyces cerevisiae to acquire tolerance to HCl (inorganic acid) and to 0.3M L-lactic acid (organic acid) at pH 2.8 and then isolated several low pH tolerant strains. Whole genome sequencing and RNA-seq analysis of the evolved strains revealed different sets of genome alterations suggesting a divergence in adaptation to these two acids. An altered sterol composition and impaired iron uptake contributed to HCl tolerance whereas the formation of a multicellular morphology and rapid lactate degradation was crucial for tolerance to high concentrations of lactic acid. Our findings highlight the contribution of both the selection pressure and nature of the acid as a driver for directing the evolutionary path towards tolerance to low pH. The choice of carbon source was also an important factor in the evolutionary process since cells evolved on two different carbon sources (raffinose and glucose) generated a different set of mutations in response to the presence of lactic acid. Therefore, different strategies are required for a rational design of low pH tolerant strains depending on the acid of interest.}, }
@article {pmid27814692, year = {2016}, author = {Schilde, C and Lawal, HM and Noegel, AA and Eichinger, L and Schaap, P and Glöckner, G}, title = {A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {871}, doi = {10.1186/s12864-016-3223-z}, pmid = {27814692}, issn = {1471-2164}, mesh = {Amoeba/classification/*genetics ; Conserved Sequence ; *Evolution, Molecular ; *Gene Expression ; Gene Expression Profiling ; Gene Knockout Techniques ; Gene Ontology ; Genome ; Mutation ; Phylogeny ; }, abstract = {BACKGROUND: The developmental cycle of Dictyostelid amoebae represents an early form of multicellularity with cell type differentiation. Mutant studies in the model Dictyostelium discoideum revealed that its developmental program integrates the actions of genes involved in signal transduction, adhesion, motility, autophagy and cell wall and matrix biosynthesis. However, due to functional redundancy and fail safe options not required in the laboratory, this single organism approach cannot capture all essential genes. To understand how multicellular organisms evolved, it is essential to recognize both the conserved core features of their developmental programs and the gene modifications that instigated phenotypic innovation. For complex organisms, such as animals, this is not within easy reach, but it is feasible for less complex forms, such as the Dictyostelid social amoebas.<br><br>RESULTS: We compared global profiles of gene expression during the development of four social amoebae species that represent 600 mya of Dictyostelia evolution, and identified orthologous conserved genes with similar developmental up-regulation of expression using three different methods. For validation, we disrupted five genes of this core set and examined the phenotypic consequences.<br><br>CONCLUSION: At least 71 of the developmentally regulated genes that were identified with all methods were likely to be already present in the last ancestor of all Dictyostelia. The lack of phenotypic changes in null mutants indicates that even highly conserved genes either participate in functionally redundant pathways or are necessary for developmental progression under adverse, non-standard laboratory conditions. Both mechanisms provide robustness to the developmental program, but impose a limit on the information that can be obtained from deleting single genes.}, }
@article {pmid27809776, year = {2016}, author = {Liu, Z and Ji, Z and Wang, G and Chao, T and Hou, L and Wang, J}, title = {Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {863}, doi = {10.1186/s12864-016-3212-2}, pmid = {27809776}, issn = {1471-2164}, mesh = {Animals ; Breeding ; Evolution, Molecular ; Gene Ontology ; Genetics, Population ; *Genome ; *Genome-Wide Association Study ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Mutation ; Phenotype ; Polymorphism, Single Nucleotide ; *Quantitative Trait, Heritable ; Reproduction/genetics ; *Selection, Genetic ; Sheep, Domestic/*genetics ; }, abstract = {BACKGROUND: Throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. Mongolian sheep is the common ancestor of the Chinese short fat-tailed sheep. Migration to different ecoregions leads to changes in selection pressures and results in microevolution. Mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. Genome-wide intraspecific variation is required to dissect the genetic basis of these traits.<br><br>RESULTS: This research resequenced 3 short fat-tailed sheep breeds with a 43.2-fold coverage of the sheep genome. We report more than 17 million single nucleotide polymorphisms and 2.9 million indels and identify 143 genomic regions with reduced pooled heterozygosity or increased genetic distance to each other breed that represent likely targets for selection during the migration. These regions harbor genes related to developmental processes, cellular processes, multicellular organismal processes, biological regulation, metabolic processes, reproduction, localization, growth and various components of the stress responses. Furthermore, we examined the haplotype diversity of 3 genomic regions involved in reproduction and found significant differences in TSHR and PRL gene regions among 8 sheep breeds.<br><br>CONCLUSIONS: Our results provide useful genomic information for identifying genes or causal mutations associated with important economic traits in sheep and for understanding the genetic basis of adaptation to different ecological environments.}, }
@article {pmid27807261, year = {2016}, author = {Regenberg, B and Hanghøj, KE and Andersen, KS and Boomsma, JJ}, title = {Clonal yeast biofilms can reap competitive advantages through cell differentiation without being obligatorily multicellular.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1842}, pages = {}, doi = {10.1098/rspb.2016.1303}, pmid = {27807261}, issn = {1471-2954}, mesh = {*Biofilms ; *Cell Differentiation ; Membrane Glycoproteins/*physiology ; Saccharomyces cerevisiae/*cytology/growth &amp; development ; Saccharomyces cerevisiae Proteins/*physiology ; }, abstract = {How differentiation between cell types evolved is a fundamental question in biology, but few studies have explored single-gene phenotypes that mediate first steps towards division of labour with selective advantage for groups of cells. Here, we show that differential expression of the FLO11 gene produces stable fractions of Flo11+ and Flo11- cells in clonal Saccharomyces cerevisiae biofilm colonies on medium with intermediate viscosity. Differentiated Flo11+/- colonies, consisting of adhesive and non-adhesive cells, obtain a fourfold growth advantage over undifferentiated colonies by overgrowing glucose resources before depleting them, rather than depleting them while they grow as undifferentiated Flo11- colonies do. Flo11+/- colonies maintain their structure and differentiated state by switching non-adhesive cells to adhesive cells with predictable probability. Mixtures of Flo11+ and Flo11- cells from mutant strains that are unable to use this epigenetic switch mechanism produced neither integrated colonies nor growth advantages, so the condition-dependent selective advantages of differentiated FLO11 expression can only be reaped by clone-mate cells. Our results show that selection for cell differentiation in clonal eukaryotes can evolve before the establishment of obligate undifferentiated multicellularity, and without necessarily leading to more advanced organizational complexity.}, }
@article {pmid27806710, year = {2016}, author = {Dueck, A and Evers, M and Henz, SR and Unger, K and Eichner, N and Merkl, R and Berezikov, E and Engelmann, JC and Weigel, D and Wenzl, S and Meister, G}, title = {Gene silencing pathways found in the green alga Volvox carteri reveal insights into evolution and origins of small RNA systems in plants.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {853}, doi = {10.1186/s12864-016-3202-4}, pmid = {27806710}, issn = {1471-2164}, mesh = {Argonaute Proteins/metabolism ; Base Sequence ; Binding Sites ; Computational Biology/methods ; DNA Transposable Elements ; *Evolution, Molecular ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Gene Silencing ; MicroRNAs/genetics ; Molecular Sequence Annotation ; Nucleotide Motifs ; Protein Binding ; RNA, Small Untranslated/*genetics ; Reproducibility of Results ; Transcriptome ; Volvox/*genetics ; }, abstract = {BACKGROUND: Volvox carteri (V. carteri) is a multicellular green alga used as model system for the evolution of multicellularity. So far, the contribution of small RNA pathways to these phenomena is not understood. Thus, we have sequenced V. carteri Argonaute 3 (VcAGO3)-associated small RNAs from different developmental stages.<br><br>RESULTS: Using this functional approach, we define the Volvox microRNA (miRNA) repertoire and show that miRNAs are not conserved in the closely related unicellular alga Chlamydomonas reinhardtii. Furthermore, we find that miRNAs are differentially expressed during different life stages of V. carteri. In addition to miRNAs, transposon-associated small RNAs or phased siRNA loci, which are common in higher land plants, are highly abundant in Volvox as well. Transposons not only give rise to miRNAs and other small RNAs, they are also targets of small RNAs.<br><br>CONCLUSION: Our analyses reveal a surprisingly complex small RNA network in Volvox as elaborate as in higher land plants. At least the identified VcAGO3-associated miRNAs are not conserved in C. reinhardtii suggesting fast evolution of small RNA systems. Thus, distinct small RNAs may contribute to multicellularity and also division of labor in reproductive and somatic cells.}, }
@article {pmid27796199, year = {2016}, author = {Trecartin, A and Danopoulos, S and Spurrier, R and Knaneh-Monem, H and Hiatt, M and Driscoll, B and Hochstim, C and Al-Alam, D and Grikscheit, TC}, title = {Establishing Proximal and Distal Regional Identities in Murine and Human Tissue-Engineered Lung and Trachea.}, journal = {Tissue engineering. Part C, Methods}, volume = {22}, number = {11}, pages = {1049-1057}, doi = {10.1089/ten.TEC.2016.0261}, pmid = {27796199}, issn = {1937-3392}, mesh = {Animals ; *Cell Lineage ; *Cell Proliferation ; Cells, Cultured ; Humans ; Lung/*cytology/physiology ; Lung Transplantation ; Mice ; Mice, Inbred C57BL ; Mice, Inbred NOD ; Mice, SCID ; Tissue Engineering/*methods ; Trachea/cytology/*metabolism ; *Wound Healing ; }, abstract = {The cellular and molecular mechanisms that underpin regeneration of the human lung are unknown, and the study of lung repair has been impeded by the necessity for reductionist models that may exclude key components. We hypothesized that multicellular epithelial and mesenchymal cell clusters or lung organoid units (LuOU) could be transplanted to recapitulate proximal and distal cellular structures of the native lung and airways. Transplantation of LuOU resulted in the growth of tissue-engineered lung (TELu) that contained the necessary cell types consistent with native adult lung tissue and demonstrated proliferative cells at 2 and 4 weeks. This technique recapitulated important elements of both mouse and human lungs featuring key components of both the proximal and distal lung regions. When LuOU were generated from whole lung, TELu contained key epithelial and mesenchymal cell types, and the origin of the cells was traced from both ActinGFP and SPCGFP donors to indicate that the cells in TELu were derived from the transplanted LuOU. Alveolar epithelial type 2 cells (AEC2s), club cells, ciliated cells marked by beta-tubulin IV, alveolar epithelial type I cells, Sox-2-positive proximal airway progenitors, p63-positive basal cells, and CGRP-positive pulmonary neuroendocrine cells were identified in the TELu. The mesenchymal components of peribronchial smooth muscle and nerve were identified with a CD31-positive donor endothelial cell contribution to TELu vasculature. TELu successfully grew from postnatal tissues from whole murine and human lung, distal murine lung, as well as murine and human trachea. These data support a model of postnatal lung regeneration containing the diverse cell types present in the entirety of the respiratory tract.}, }
@article {pmid27790999, year = {2016}, author = {Chen, X and Köllner, TG and Jia, Q and Norris, A and Santhanam, B and Rabe, P and Dickschat, JS and Shaulsky, G and Gershenzon, J and Chen, F}, title = {Terpene synthase genes in eukaryotes beyond plants and fungi: Occurrence in social amoebae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {43}, pages = {12132-12137}, doi = {10.1073/pnas.1610379113}, pmid = {27790999}, issn = {1091-6490}, support = {P01 HD039691/HD/NICHD NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Alkyl and Aryl Transferases/classification/*genetics/metabolism ; Biological Evolution ; Cloning, Molecular ; Dictyostelium/classification/enzymology/*genetics ; Escherichia coli/genetics/metabolism ; Gene Expression ; Gene Expression Regulation, Developmental ; *Genome, Protozoan ; Isoenzymes/classification/genetics/metabolism ; Multigene Family ; *Phylogeny ; Protozoan Proteins/classification/*genetics/metabolism ; Recombinant Proteins/genetics/metabolism ; Terpenes/*metabolism ; Volatilization ; }, abstract = {Terpenes are structurally diverse natural products involved in many ecological interactions. The pivotal enzymes for terpene biosynthesis, terpene synthases (TPSs), had been described only in plants and fungi in the eukaryotic domain. In this report, we systematically analyzed the genome sequences of a broad range of nonplant/nonfungus eukaryotes and identified putative TPS genes in six species of amoebae, five of which are multicellular social amoebae from the order of Dictyosteliida. A phylogenetic analysis revealed that amoebal TPSs are evolutionarily more closely related to fungal TPSs than to bacterial TPSs. The social amoeba Dictyostelium discoideum was selected for functional study of the identified TPSs. D. discoideum grows as a unicellular organism when food is abundant and switches from vegetative growth to multicellular development upon starvation. We found that expression of most D. discoideum TPS genes was induced during development. Upon heterologous expression, all nine TPSs from D. discoideum showed sesquiterpene synthase activities. Some also exhibited monoterpene and/or diterpene synthase activities. Direct measurement of volatile terpenes in cultures of D. discoideum revealed essentially no emission at an early stage of development. In contrast, a bouquet of terpenes, dominated by sesquiterpenes including β-barbatene and (E,E)-α-farnesene, was detected at the middle and late stages of development, suggesting a development-specific function of volatile terpenes in D. discoideum. The patchy distribution of TPS genes in the eukaryotic domain and the evidence for TPS function in D. discoideum indicate that the TPS genes mediate lineage-specific adaptations.}, }
@article {pmid27782327, year = {2016}, author = {Elvington, M and Liszewski, MK and Atkinson, JP}, title = {Evolution of the complement system: from defense of the single cell to guardian of the intravascular space.}, journal = {Immunological reviews}, volume = {274}, number = {1}, pages = {9-15}, doi = {10.1111/imr.12474}, pmid = {27782327}, issn = {1600-065X}, support = {T32 AR007279/AR/NIAMS NIH HHS/United States ; R01 GM099111/GM/NIGMS NIH HHS/United States ; P30 AR048335/AR/NIAMS NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; R01 AI041592/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Blood Vessels/*physiology ; Cell Membrane/metabolism ; Complement Activation ; Complement C3/*immunology ; Extracellular Space ; Humans ; Immunity ; Inflammation/*immunology ; Intracellular Space ; Liver/*physiology ; Models, Immunological ; }, abstract = {The complement system is an evolutionarily ancient component of immunity that revolves around the central component C3. With the recent description of intracellular C3 stores in many types of human cells, our view of the complement system has expanded. In this article, we hypothesize that a primitive version of C3 comprised the first element of the original complement system and initially functioned intracellularly and on the membrane of single-celled organisms. With increasing specialization and multicellularity, C3 evolved a secretory capacity that allowed it to play a protective role in the interstitial space. Upon development of a pumped circulatory system, C3 was synthesized in large amounts and secreted by the liver to protect the intravascular space. Recent discoveries of intracellular C3 activation, a C3-based recycling pathway and C3 being a driver and programmer of cell metabolism suggest that the complement system utilizes C3 to guard not only extracellular but also the intracellular environment. We predict that the major functions of C3 in all four locations (i.e. intracellular, membrane, interstitium and circulation) are similar: opsonization, membrane perturbation, triggering inflammation, and metabolic reprogramming.}, }
@article {pmid27782144, year = {2016}, author = {Balla, KM and Luallen, RJ and Bakowski, MA and Troemel, ER}, title = {Cell-to-cell spread of microsporidia causes Caenorhabditis elegans organs to form syncytia.}, journal = {Nature microbiology}, volume = {1}, number = {11}, pages = {16144}, doi = {10.1038/nmicrobiol.2016.144}, pmid = {27782144}, issn = {2058-5276}, support = {R01 GM114139/GM/NIGMS NIH HHS/United States ; T32 GM007240/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/cytology/*microbiology/physiology ; Cytoplasm/microbiology ; Giant Cells/*microbiology ; *Host-Pathogen Interactions ; Intestines/microbiology ; Microsporidia/classification/growth &amp; development/*physiology ; Muscles/microbiology ; Phylogeny ; }, abstract = {The growth of pathogens is dictated by their interactions with the host environment1. Obligate intracellular pathogens undergo several cellular decisions as they progress through their life cycles inside host cells2. We have studied this process for microsporidian species in the genus Nematocida as they grew and developed inside their co-evolved animal host, Caenorhabditis elegans3-5. We found that microsporidia can restructure multicellular host tissues into a single contiguous multinucleate cell. In particular, we found that all three Nematocida species we studied were able to spread across the cells of C. elegans tissues before forming spores, with two species causing syncytial formation in the intestine and one species causing syncytial formation in the muscle. We also found that the decision to switch from replication to differentiation in Nematocida parisii was altered by the density of infection, suggesting that environmental cues influence the dynamics of the pathogen life cycle. These findings show how microsporidia can maximize the use of host space for growth and that environmental cues in the host can regulate a developmental switch in the pathogen.}, }
@article {pmid27746046, year = {2016}, author = {Sebé-Pedrós, A and Peña, MI and Capella-Gutiérrez, S and Antó, M and Gabaldón, T and Ruiz-Trillo, I and Sabidó, E}, title = {High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation.}, journal = {Developmental cell}, volume = {39}, number = {2}, pages = {186-197}, doi = {10.1016/j.devcel.2016.09.019}, pmid = {27746046}, issn = {1878-1551}, support = {ERC-2012-CO-616960//European Research Council/International ; }, mesh = {Animals ; *Cell Differentiation ; Eukaryota/cytology/metabolism ; Evolution, Molecular ; Phosphorylation ; Phylogeny ; Protein Kinases/metabolism ; Proteome/metabolism ; Proteomics/*methods ; RNA, Messenger/genetics/metabolism ; *Signal Transduction ; Time Factors ; Transcription Factors/metabolism ; }, abstract = {Cell-specific regulation of protein levels and activity is essential for the distribution of functions among multiple cell types in animals. The finding that many genes involved in these regulatory processes have a premetazoan origin raises the intriguing possibility that the mechanisms required for spatially regulated cell differentiation evolved prior to the appearance of animals. Here, we use high-throughput proteomics in Capsaspora owczarzaki, a close unicellular relative of animals, to characterize the dynamic proteome and phosphoproteome profiles of three temporally distinct cell types in this premetazoan species. We show that life-cycle transitions are linked to extensive proteome and phosphoproteome remodeling and that they affect key genes involved in animal multicellularity, such as transcription factors and tyrosine kinases. The observation of shared features between Capsaspora and metazoans indicates that elaborate and conserved phosphosignaling and proteome regulation supported temporal cell-type differentiation in the unicellular ancestor of animals.}, }
@article {pmid27775817, year = {2017}, author = {Goldring, C and Antoine, DJ and Bonner, F and Crozier, J and Denning, C and Fontana, RJ and Hanley, NA and Hay, DC and Ingelman-Sundberg, M and Juhila, S and Kitteringham, N and Silva-Lima, B and Norris, A and Pridgeon, C and Ross, JA and Young, RS and Tagle, D and Tornesi, B and van de Water, B and Weaver, RJ and Zhang, F and Park, BK}, title = {Stem cell-derived models to improve mechanistic understanding and prediction of human drug-induced liver injury.}, journal = {Hepatology (Baltimore, Md.)}, volume = {65}, number = {2}, pages = {710-721}, doi = {10.1002/hep.28886}, pmid = {27775817}, issn = {1527-3350}, support = {BB/G021821/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; PG/09/027/27141//British Heart Foundation/United Kingdom ; MR/L006758/1//Medical Research Council/United Kingdom ; NC/K000225/1//National Centre for the Replacement, Refinement and Reduction of Animals in Research/International ; SP/15/9/31605//British Heart Foundation/United Kingdom ; G0801098//Medical Research Council/United Kingdom ; MR/K026666/1//Medical Research Council/United Kingdom ; G0700654//Medical Research Council/United Kingdom ; PG/14/59/31000//British Heart Foundation/United Kingdom ; G113/30//Medical Research Council/United Kingdom ; BBS/B/06164//Biotechnology and Biological Sciences Research Council/United Kingdom ; U01 DK065184/DK/NIDDK NIH HHS/United States ; BB/E006159/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L022974/1//Medical Research Council/United Kingdom ; }, mesh = {Cells, Cultured/drug effects ; Chemical and Drug Induced Liver Injury/*diagnosis ; Drug-Related Side Effects and Adverse Reactions/*diagnosis ; Hepatocytes/*drug effects/metabolism ; Humans ; In Vitro Techniques ; Pluripotent Stem Cells/*drug effects/metabolism ; Predictive Value of Tests ; Sensitivity and Specificity ; *Toxicity Tests ; }, abstract = {Current preclinical drug testing does not predict some forms of adverse drug reactions in humans. Efforts at improving predictability of drug-induced tissue injury in humans include using stem cell technology to generate human cells for screening for adverse effects of drugs in humans. The advent of induced pluripotent stem cells means that it may ultimately be possible to develop personalized toxicology to determine interindividual susceptibility to adverse drug reactions. However, the complexity of idiosyncratic drug-induced liver injury means that no current single-cell model, whether of primary liver tissue origin, from liver cell lines, or derived from stem cells, adequately emulates what is believed to occur during human drug-induced liver injury. Nevertheless, a single-cell model of a human hepatocyte which emulates key features of a hepatocyte is likely to be valuable in assessing potential chemical risk; furthermore, understanding how to generate a relevant hepatocyte will also be critical to efforts to build complex multicellular models of the liver. Currently, hepatocyte-like cells differentiated from stem cells still fall short of recapitulating the full mature hepatocellular phenotype. Therefore, we convened a number of experts from the areas of preclinical and clinical hepatotoxicity and safety assessment, from industry, academia, and regulatory bodies, to specifically explore the application of stem cells in hepatotoxicity safety assessment and to make recommendations for the way forward. In this short review, we particularly discuss the importance of benchmarking stem cell-derived hepatocyte-like cells to their terminally differentiated human counterparts using defined phenotyping, to make sure the cells are relevant and comparable between labs, and outline why this process is essential before the cells are introduced into chemical safety assessment. (Hepatology 2017;65:710-721).}, }
@article {pmid27751905, year = {2017}, author = {Woyda-Ploszczyca, AM and Jarmuszkiewicz, W}, title = {The conserved regulation of mitochondrial uncoupling proteins: From unicellular eukaryotes to mammals.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1858}, number = {1}, pages = {21-33}, doi = {10.1016/j.bbabio.2016.10.003}, pmid = {27751905}, issn = {0005-2728}, mesh = {Aldehydes/*metabolism ; Animals ; Eukaryota/*metabolism ; Fatty Acids, Nonesterified/*metabolism ; Mammals/*metabolism ; Mitochondrial Uncoupling Proteins/*metabolism ; Purine Nucleotides/*metabolism ; Ubiquinone/*metabolism ; }, abstract = {Uncoupling proteins (UCPs) belong to the mitochondrial anion carrier protein family and mediate regulated proton leak across the inner mitochondrial membrane. Free fatty acids, aldehydes such as hydroxynonenal, and retinoids activate UCPs. However, there are some controversies about the effective action of retinoids and aldehydes alone; thus, only free fatty acids are commonly accepted positive effectors of UCPs. Purine nucleotides such as GTP inhibit UCP-mediated mitochondrial proton leak. In turn, membranous coenzyme Q may play a role as a redox state-dependent metabolic sensor that modulates the complete activation/inhibition of UCPs. Such regulation has been observed for UCPs in microorganisms, plant and animal UCP1 homologues, and UCP1 in mammalian brown adipose tissue. The origin of UCPs is still under debate, but UCP homologues have been identified in all systematic groups of eukaryotes. Despite the differing levels of amino acid/DNA sequence similarities, functional studies in unicellular and multicellular organisms, from amoebae to mammals, suggest that the mechanistic regulation of UCP activity is evolutionarily well conserved. This review focuses on the regulatory feedback loops of UCPs involving free fatty acids, aldehydes, retinoids, purine nucleotides, and coenzyme Q (particularly its reduction level), which may derive from the early stages of evolution as UCP first emerged.}, }
@article {pmid27663234, year = {2017}, author = {Kadam, AA and Jubin, T and Mir, HA and Begum, R}, title = {Potential role of Apoptosis Inducing Factor in evolutionarily significant eukaryote, Dictyostelium discoideum survival.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1861}, number = {1 Pt A}, pages = {2942-2955}, doi = {10.1016/j.bbagen.2016.09.021}, pmid = {27663234}, issn = {0304-4165}, mesh = {Adenosine Triphosphate/metabolism ; Annexin A5/metabolism ; Apoptosis Inducing Factor/*metabolism ; *Biological Evolution ; Calcium/metabolism ; Cell Cycle/drug effects ; Cell Death/drug effects ; Cell Shape/drug effects ; Cytosol/drug effects/metabolism ; Dictyostelium/*cytology/growth &amp; development/*metabolism/ultrastructure ; Down-Regulation/drug effects ; Flow Cytometry ; Fluorescein-5-isothiocyanate/metabolism ; Fluorometry ; Glucose/pharmacology ; Membrane Potential, Mitochondrial/drug effects ; Mitochondria/drug effects/metabolism ; Models, Biological ; NAD/metabolism ; Oxidative Stress/drug effects ; Propidium/metabolism ; Protein Transport/drug effects ; RNA, Antisense/metabolism ; Reactive Oxygen Species/metabolism ; Staining and Labeling ; }, abstract = {Apoptosis Inducing Factor (AIF), a phylogenetically conserved mitochondrial inter-membrane space flavoprotein has an important role in caspase independent cell death. Nevertheless, AIF is also essential for cell survival. It is required for mitochondrial organization and energy metabolism. Upon apoptotic stimulation, AIF induces DNA fragmentation after its mitochondrio-nuclear translocation. Although it executes critical cellular functions in a coordinated manner, the exact mechanism still remains obscure. The present study aims to understand AIF's role in cell survival, growth and development by its down-regulation in an interesting unicellular eukaryote, D. discoideum which exhibits multicellularity upon starvation. Constitutive AIF down-regulated (dR) cells exhibited slower growth and delayed developmental morphogenesis. Also, constitutive AIF dR cells manifested high intracellular ROS, oxidative DNA damage and calcium levels with lower ATP content. Interestingly, constitutive AIF dR cells showed amelioration in cell growth upon antioxidant treatment, strengthening its role as ROS regulator. Under oxidative stress, AIF dR cells showed early mitochondrial membrane depolarization followed by AIF translocation from mitochondria to nucleus and exhibited necrotic cell death as compared to paraptoptic cell death of control cells. Thus, the results of this study provide an exemplar where AIF is involved in growth and development by regulating ROS levels and maintaining mitochondrial function in D. discoideum, an evolutionarily significant model organism exhibiting caspase independent apoptosis.}, }
@article {pmid27718356, year = {2016}, author = {Carmell, MA and Dokshin, GA and Skaletsky, H and Hu, YC and van Wolfswinkel, JC and Igarashi, KJ and Bellott, DW and Nefedov, M and Reddien, PW and Enders, GC and Uversky, VN and Mello, CC and Page, DC}, title = {A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, doi = {10.7554/eLife.19993}, pmid = {27718356}, issn = {2050-084X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Antigens, Nuclear/*genetics/metabolism ; Caenorhabditis elegans/genetics/growth &amp; development ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Expression Regulation/genetics ; Genome/genetics ; Genomics ; Germ Cells/growth &amp; development/*metabolism ; Meiosis/genetics ; Phylogeny ; Reproduction/*genetics ; }, abstract = {The advent of sexual reproduction and the evolution of a dedicated germline in multicellular organisms are critical landmarks in eukaryotic evolution. We report an ancient family of GCNA (germ cell nuclear antigen) proteins that arose in the earliest eukaryotes, and feature a rapidly evolving intrinsically disordered region (IDR). Phylogenetic analysis reveals that GCNA proteins emerged before the major eukaryotic lineages diverged; GCNA predates the origin of a dedicated germline by a billion years. Gcna gene expression is enriched in reproductive cells across eukarya - either just prior to or during meiosis in single-celled eukaryotes, and in stem cells and germ cells of diverse multicellular animals. Studies of Gcna-mutant C. elegans and mice indicate that GCNA has functioned in reproduction for at least 600 million years. Homology to IDR-containing proteins implicated in DNA damage repair suggests that GCNA proteins may protect the genomic integrity of cells carrying a heritable genome.}, }
@article {pmid27751769, year = {2016}, author = {Gadahi, JA and Ehsan, M and Wang, S and Zhang, Z and Wang, Y and Yan, R and Song, X and Xu, L and Li, X}, title = {Recombinant protein of Haemonchus contortus 14-3-3 isoform 2 (rHcftt-2) decreased the production of IL-4 and suppressed the proliferation of goat PBMCs in vitro.}, journal = {Experimental parasitology}, volume = {171}, number = {}, pages = {57-66}, doi = {10.1016/j.exppara.2016.10.014}, pmid = {27751769}, issn = {1090-2449}, mesh = {Amino Acid Sequence ; Animals ; Antibodies, Helminth/biosynthesis ; Cell Proliferation/drug effects ; Cloning, Molecular ; DNA, Complementary/metabolism ; DNA, Helminth/metabolism ; Dose-Response Relationship, Drug ; Female ; Goats ; Haemonchus/chemistry/genetics/*immunology ; Helminth Proteins/chemistry/*immunology/pharmacology ; Interleukin-4/*immunology/metabolism ; Neutrophils/*immunology/metabolism ; Nitric Oxide/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Protein Isoforms/immunology/pharmacology ; RNA, Helminth/genetics/isolation &amp; purification ; Rats ; Rats, Sprague-Dawley ; Recombinant Proteins/*immunology/pharmacology ; Sequence Alignment ; }, abstract = {14-3-3 proteins have been found to be an excreted/secreted antigen and assumed to be released into the host-parasite interface and described in several unicellular and multicellular parasites. However, little is known about the immunomodulatory effects of H. controtus 14-3-3 protein on host cell. In present study, 14-3-3 isoform 2 gene, designated as Hcftt-2, was amplified by reverse transcription-polymerase chain reaction (RT-PCR) from the adult H. contortus cDNA and cloned into expression plasmid pET32a (+) and expression of the recombinant protein (rHcftt-2) was induced by IPTG. Binding activity of rHcftt-2 to goat peripheral blood mononuclear cells (PBMCs) was confirmed by immunofluorescence assay (IFA) and modulatory effects on cytokine production, cell proliferation, cell migration and nitric oxide (NO) production were observed by co-incubation of rHcftt-2 with goat PBMCs. Sequence analysis showed that it had significant homology with the known 14-3-3 protein isoform 2. Results of IFA revealed that, the rHcftt-2 was bound to the cell surface. We found that, the productions of IL10, IL-17, IFN-γ and cell migration of PBMCs were increased after the cells were incubated with rHCftt-2. However, the productions of IL-4, NO and cell proliferation of the PBMCs were significantly decreased in dose depended manner. Our results showed that the Hcftt-2 played important suppressive regulatory effects on the goat PBMCs.}, }
@article {pmid27738200, year = {2016}, author = {Spatafora, JW and Chang, Y and Benny, GL and Lazarus, K and Smith, ME and Berbee, ML and Bonito, G and Corradi, N and Grigoriev, I and Gryganskyi, A and James, TY and O'Donnell, K and Roberson, RW and Taylor, TN and Uehling, J and Vilgalys, R and White, MM and Stajich, JE}, title = {A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.}, journal = {Mycologia}, volume = {108}, number = {5}, pages = {1028-1046}, doi = {10.3852/16-042}, pmid = {27738200}, issn = {0027-5514}, support = {S10 OD016290/OD/NIH HHS/United States ; }, mesh = {Fungi/*classification/*genetics ; *Genome, Fungal ; *Phylogeny ; }, abstract = {Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.}, }
@article {pmid27737633, year = {2016}, author = {Lumsden, AL and Young, RL and Pezos, N and Keating, DJ}, title = {Huntingtin-associated protein 1: Eutherian adaptation from a TRAK-like protein, conserved gene promoter elements, and localization in the human intestine.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {214}, doi = {10.1186/s12862-016-0780-3}, pmid = {27737633}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/genetics ; Conserved Sequence/*genetics ; Humans ; Intestines/*metabolism ; Mammals/*genetics ; Mitochondria/genetics ; Multigene Family ; Nerve Tissue Proteins/*metabolism ; Nucleotide Motifs/genetics ; Phylogeny ; *Promoter Regions, Genetic ; Protein Binding/genetics ; Protein Domains ; Protein Transport ; Reproducibility of Results ; Sequence Homology, Nucleic Acid ; Serotonin/metabolism ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Huntingtin-associated Protein 1 (HAP1) is expressed in neurons and endocrine cells, and is critical for postnatal survival in mice. HAP1 shares a conserved &quot;HAP1_N&quot; domain with TRAfficking Kinesin proteins TRAK1 and TRAK2 (vertebrate), Milton (Drosophila) and T27A3.1 (C. elegans). HAP1, TRAK1 and TRAK2 have a degree of common function, particularly regarding intracellular receptor trafficking. However, TRAK1, TRAK2 and Milton (which have a &quot;Milt/TRAK&quot; domain that is absent in human and rodent HAP1) differ in function to HAP1 in that they are mitochondrial transport proteins, while HAP1 has emerging roles in starvation response. We have investigated HAP1 function by examining its evolution, and upstream gene promoter sequences. We performed phylogenetic analyses of the HAP1_N domain family of proteins, incorporating HAP1 orthologues (identified by genomic synteny) from 5 vertebrate classes, and also searched the Dictyostelium proteome for a common ancestor. Computational analyses of mammalian HAP1 gene promoters were performed to identify phylogenetically conserved regulatory motifs.<br><br>RESULTS: We found that as recently as marsupials, HAP1 contained a Milt/TRAK domain and was more similar to TRAK1 and TRAK2 than to eutherian HAP1. The Milt/TRAK domain likely arose post multicellularity, as it was absent in the Dictyostelium proteome. It was lost from HAP1 in the eutherian lineage, and also from T27A3.1 in C. elegans. The HAP1 promoter from human, mouse, rat, rabbit, horse, dog, Tasmanian devil and opossum contained common sites for transcription factors involved in cell cycle, growth, differentiation, and stress response. A conserved arrangement of regulatory elements was identified, including sites for caudal-related homeobox transcription factors (CDX1 and CDX2), and myc-associated factor X (MAX) in the region of the TATA box. CDX1 and CDX2 are intestine-enriched factors, prompting investigation of HAP1 protein expression in the human duodenum. HAP1 was localized to singly dispersed mucosal cells, including a subset of serotonin-positive enterochromaffin cells.<br><br>CONCLUSION: We have identified eutherian HAP1 as an evolutionarily recent adaptation of a vertebrate TRAK protein-like ancestor, and found conserved CDX1/CDX2 and MAX transcription factor binding sites near the TATA box in mammalian HAP1 gene promoters. We also demonstrated that HAP1 is expressed in endocrine cells of the human gut.}, }
@article {pmid27733125, year = {2016}, author = {Höhn, S and Hallmann, A}, title = {Distinct shape-shifting regimes of bowl-shaped cell sheets - embryonic inversion in the multicellular green alga Pleodorina.}, journal = {BMC developmental biology}, volume = {16}, number = {1}, pages = {35}, doi = {10.1186/s12861-016-0134-9}, pmid = {27733125}, issn = {1471-213X}, mesh = {Biological Evolution ; Cell Division ; Chlorophyta/*cytology/*embryology/ultrastructure ; Microscopy, Electron, Transmission ; *Models, Biological ; *Morphogenesis ; Photogrammetry ; Time Factors ; }, abstract = {BACKGROUND: The multicellular volvocine alga Pleodorina is intermediate in organismal complexity between its unicellular relative, Chlamydomonas, and its multicellular relative, Volvox, which shows complete division of labor between different cell types. The volvocine green microalgae form a group of genera closely related to the genus Volvox within the order Volvocales (Chlorophyta). Embryos of multicellular volvocine algae consist of a cellular monolayer that, depending on the species, is either bowl-shaped or comprises a sphere. During embryogenesis, multicellular volvocine embryos turn their cellular monolayer right-side out to expose their flagella. This process is called 'inversion' and serves as simple model for epithelial folding in metazoa. While the development of spherical Volvox embryos has been the subject of detailed studies, the inversion process of bowl-shaped embryos is less well understood. Therefore, it has been unclear how the inversion of a sphere might have evolved from less complicated processes.<br><br>RESULTS: In this study we characterized the inversion of initially bowl-shaped embryos of the 64- to 128-celled volvocine species Pleodorina californica. We focused on the movement patterns of the cell sheet, cell shape changes and changes in the localization of cytoplasmic bridges (CBs) connecting the cells. The development of living embryos was recorded using time-lapse light microscopy. Moreover, fixed and sectioned embryos throughout inversion and at successive stages of development were analyzed by light and transmission electron microscopy. We generated three-dimensional models of the identified cell shapes including the localization of CBs.<br><br>CONCLUSIONS: In contrast to descriptions concerning volvocine embryos with lower cell numbers, the embryonic cells of P. californica undergo non-simultaneous and non-uniform cell shape changes. In P. californica, cell wedging in combination with a relocation of the CBs to the basal cell tips explains the curling of the cell sheet during inversion. In volvocine genera with lower organismal complexity, the cell shape changes and relocation of CBs are less pronounced in comparison to P. californica, while they are more pronounced in all members of the genus Volvox. This finding supports an increasing significance of the temporal and spatial regulation of cell shape changes and CB relocations with both increasing cell number and organismal complexity during evolution of differentiated multicellularity.}, }
@article {pmid27717470, year = {2016}, author = {Devic, M and Roscoe, T}, title = {Seed maturation: Simplification of control networks in plants.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {252}, number = {}, pages = {335-346}, doi = {10.1016/j.plantsci.2016.08.012}, pmid = {27717470}, issn = {1873-2259}, mesh = {Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Multigene Family ; Plant Development/*genetics ; Plant Proteins/genetics/metabolism/physiology ; Seeds/*genetics/growth &amp; development ; Transcription Factors/genetics/metabolism/physiology ; }, abstract = {Networks controlling developmental or metabolic processes in plants are often complex as a consequence of the duplication and specialisation of the regulatory genes as well as the numerous levels of transcriptional and post-transcriptional controls added during evolution. Networks serve to accommodate multicellular complexity and increase robustness to environmental changes. Mathematical simplification by regrouping genes or pathways in a limited number of hubs has facilitated the construction of models for complex traits. In a complementary approach, a biological simplification can be achieved by using genetic modification to understand the core and singular ancestral function of the network, which is likely to be more prevalent within the plant kingdom rather than specific to a species. With this viewpoint, we review examples of simplification successfully undertaken in yeast and other organisms. A strategy of progressive complementation of single, double and triple mutants of seed maturation confirmed the fundamental role of the AFL sub-family of B3 transcription factors as master regulators of seed maturation, illustrating that biological simplification of complex networks could be more widely applied in plants. Defining minimal control networks will facilitate evolutionary comparisons of regulatory processes and the identification of an essential gene set for synthetic biology.}, }
@article {pmid27708766, year = {2016}, author = {Fozard, JA and Bennett, MJ and King, JR and Jensen, OE}, title = {Hybrid vertex-midline modelling of elongated plant organs.}, journal = {Interface focus}, volume = {6}, number = {5}, pages = {20160043}, doi = {10.1098/rsfs.2016.0043}, pmid = {27708766}, issn = {2042-8898}, abstract = {We describe a method for the simulation of the growth of elongated plant organs, such as seedling roots. By combining a midline representation of the organ on a tissue scale and a vertex-based representation on the cell scale, we obtain a multiscale method, which is able to both simulate organ growth and incorporate cell-scale processes. Equations for the evolution of the midline are obtained, which depend on the cell-wall properties of individual cells through appropriate averages over the vertex-based representation. The evolution of the organ midline is used to deform the cellular-scale representation. This permits the investigation of the regulation of organ growth through the cell-scale transport of the plant hormone auxin. The utility of this method is demonstrated in simulating the early stages of the response of a root to gravity, using a vertex-based template acquired from confocal imaging. Asymmetries in the concentrations of auxin between the upper and lower sides of the root lead to bending of the root midline, reflecting a gravitropic response.}, }
@article {pmid27703714, year = {2016}, author = {Manjarrez-Casas, AM and Bagheri, HC and Dobay, A}, title = {Transition from one- to two-dimensional development facilitates maintenance of multicellularity.}, journal = {Royal Society open science}, volume = {3}, number = {9}, pages = {160554}, doi = {10.1098/rsos.160554}, pmid = {27703714}, issn = {2054-5703}, abstract = {Filamentous organisms represent an example where incomplete separation after cell division underlies the development of multicellular formations. With a view to understanding the evolution of more complex multicellular structures, we explore the transition of multicellular growth from one to two dimensions. We develop a computational model to simulate multicellular development in populations where cells exhibit density-dependent division and death rates. In both the one- and two-dimensional contexts, multicellular formations go through a developmental cycle of growth and subsequent decay. However, the model shows that a transition to a higher dimension increases the size of multicellular formations and facilitates the maintenance of large cell clusters for significantly longer periods of time. We further show that the turnover rate for cell division and death scales with the number of iterations required to reach the stationary multicellular size at equilibrium. Although size and life cycles of multicellular organisms are affected by other environmental and genetic factors, the model presented here evaluates the extent to which the transition of multicellular growth from one to two dimensions contributes to the maintenance of multicellular structures during development.}, }
@article {pmid27697546, year = {2017}, author = {Cai, W and Zhang, K and Li, P and Zhu, L and Xu, J and Yang, B and Hu, X and Lu, Z and Chen, J}, title = {Dysfunction of the neurovascular unit in ischemic stroke and neurodegenerative diseases: An aging effect.}, journal = {Ageing research reviews}, volume = {34}, number = {}, pages = {77-87}, doi = {10.1016/j.arr.2016.09.006}, pmid = {27697546}, issn = {1872-9649}, support = {R01 NS089534/NS/NINDS NIH HHS/United States ; R01 NS095671/NS/NINDS NIH HHS/United States ; I01 BX002495/BX/BLRD VA/United States ; I01 RX000420/RX/RRD VA/United States ; R01 NS036736/NS/NINDS NIH HHS/United States ; R01 NS045048/NS/NINDS NIH HHS/United States ; }, mesh = {Aging/*physiology ; Blood-Brain Barrier ; *Brain/blood supply/pathology/physiopathology ; Humans ; *Neurodegenerative Diseases/pathology/physiopathology ; Neurovascular Coupling/*physiology ; *Stroke/pathology/physiopathology ; }, abstract = {Current understanding on the mechanisms of brain injury and neurodegeneration highlights an appreciation of multicellular interactions within the neurovascular unit (NVU), which include the evolution of blood-brain barrier (BBB) damage, neuronal cell death or degeneration, glial reaction, and immune cell infiltration. Aging is an important factor that influences the integrity of the NVU. The age-related physiological or pathological changes in the cellular components of the NVU have been shown to increase the vulnerability of the NVU to ischemia/reperfusion injury or neurodegeneration, and to result in deteriorated brain damage. This review describes the impacts of aging on each NVU component and discusses the mechanisms by which aging increases NVU sensitivity to stroke and neurodegenerative diseases. Prophylactic or therapeutic perspectives that may delay or diminish aging and thus prevent the incidence of these neurological disorders will also be reviewed.}, }
@article {pmid27693864, year = {2016}, author = {Kuburich, NA and Adhikari, N and Hadwiger, JA}, title = {Acanthamoeba and Dictyostelium Use Different Foraging Strategies.}, journal = {Protist}, volume = {167}, number = {6}, pages = {511-525}, doi = {10.1016/j.protis.2016.08.006}, pmid = {27693864}, issn = {1618-0941}, support = {R15 GM097717/GM/NIGMS NIH HHS/United States ; }, mesh = {Acanthamoeba/classification/genetics/*physiology ; *Chemotaxis ; Dictyostelium/classification/genetics/*physiology ; Phylogeny ; Protozoan Proteins/genetics ; Signal Transduction ; }, abstract = {Amoeba often use cell movement as a mechanism to find food, such as bacteria, in their environment. The chemotactic movement of the soil amoeba Dictyostelium to folate or other pterin compounds released by bacteria is a well-documented foraging mechanism. Acanthamoeba can also feed on bacteria but relatively little is known about the mechanism(s) by which this amoeba locates bacteria. Acanthamoeba movement in the presence of folate or bacteria was analyzed in above agar assays and compared to that observed for Dictyostelium. The overall mobility of Acanthamoeba was robust like that of Dictyostelium but Acanthamoeba did not display a chemotactic response to folate. In the presence of bacteria, Acanthamoeba only showed a marginal bias in directed movement whereas Dictyostelium displayed a strong chemotactic response. A comparison of genomes revealed that Acanthamoeba and Dictyostelium share some similarities in G protein signaling components but that specific G proteins used in Dictyostelium chemotactic responses were not present in current Acanthamoeba genome sequence data. The results of this study suggest that Acanthamoeba does not use chemotaxis as the primary mechanism to find bacterial food sources and that the chemotactic responses of Dictyostelium to bacteria may have co-evolved with chemotactic responses that facilitate multicellular development.}, }
@article {pmid27686422, year = {2017}, author = {Mills, DB and Canfield, DE}, title = {A trophic framework for animal origins.}, journal = {Geobiology}, volume = {15}, number = {2}, pages = {197-210}, doi = {10.1111/gbi.12216}, pmid = {27686422}, issn = {1472-4669}, mesh = {Animals ; *Biological Evolution ; Feeding Behavior ; *Heterotrophic Processes ; Organic Chemicals/*metabolism ; *Phagocytosis ; }, abstract = {Metazoans emerged in a microbial world and play a unique role in the biosphere as the only complex multicellular eukaryotes capable of phagocytosis. While the bodyplan and feeding mode of the last common metazoan ancestor remain unresolved, the earliest multicellular stem-metazoans likely subsisted on picoplankton (planktonic microbes 0.2-2 μm in diameter) and dissolved organic matter (DOM), similarly to modern sponges. Once multicellular stem-metazoans emerged, they conceivably modulated both the local availability of picoplankton, which they preferentially removed from the water column for feeding, and detrital particles 2-100 μm in diameter, which they expelled and deposited into the benthos as waste products. By influencing the availability of these heterotrophic food sources, the earliest multicellular stem-metazoans would have acted as ecosystem engineers, helping create the ecological conditions under which other metazoans, namely detritivores and non-sponge suspension feeders incapable of subsisting on picoplankton and DOM, could emerge and diversify. This early style of metazoan feeding, specifically the phagocytosis of small eukaryotic prey, could have also encouraged the evolution of larger, even multicellular, eukaryotic forms less prone to metazoan consumption. Therefore, the first multicellular stem-metazoans, through their feeding, arguably helped bridge the strictly microbial food webs of the Proterozoic Eon (2.5-0.541 billion years ago) to the more macroscopic, metazoan-sustaining food webs of the Phanerozoic Eon (0.541-0 billion years ago).}, }
@article {pmid27686281, year = {2016}, author = {Wu, CI and Wang, HY and Ling, S and Lu, X}, title = {The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process.}, journal = {Annual review of genetics}, volume = {50}, number = {}, pages = {347-369}, doi = {10.1146/annurev-genet-112414-054842}, pmid = {27686281}, issn = {1545-2948}, mesh = {Animals ; *Biological Evolution ; Ecology ; Genetic Variation ; Genetics, Population ; Genome, Human ; Genotype ; Humans ; Neoplasms/*etiology/genetics ; Phenotype ; Population Growth ; *Selection, Genetic ; }, abstract = {Although tumorigenesis has been accepted as an evolutionary process (20 , 102), many forces may operate differently in cancers than in organisms, as they evolve at vastly different time scales. Among such forces, natural selection, here defined as differential cellular proliferation among distinct somatic cell genotypes, is particularly interesting because its action might be thwarted in multicellular organisms (20 , 29). In this review, selection is analyzed in two stages of cancer evolution: Stage I is the evolution between tumors and normal tissues, and Stage II is the evolution within tumors. The Cancer Genome Atlas (TCGA) data show a low degree of convergent evolution in Stage I, where genetic changes are not extensively shared among cases. An equally important, albeit much less highlighted, discovery using TCGA data is that there is almost no net selection in cancer evolution. Both positive and negative selection are evident but they neatly cancel each other out, rendering total selection ineffective in the absence of recombination. The efficacy of selection is even lower in Stage II, where neutral (non-Darwinian) evolution is increasingly supported by high-density sampling studies (81 , 123). Because natural selection is not a strong deterministic force, cancers usually evolve divergently even in similar tissue environments.}, }
@article {pmid27676437, year = {2016}, author = {Loh, KM and van Amerongen, R and Nusse, R}, title = {Generating Cellular Diversity and Spatial Form: Wnt Signaling and the Evolution of Multicellular Animals.}, journal = {Developmental cell}, volume = {38}, number = {6}, pages = {643-655}, doi = {10.1016/j.devcel.2016.08.011}, pmid = {27676437}, issn = {1878-1551}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Biological Evolution ; Cell Division/genetics ; Cell Lineage/*genetics ; Cell Polarity/genetics ; Embryonic Development/genetics ; Gene Expression Regulation, Developmental/genetics ; *Genetic Variation ; Signal Transduction ; Wnt Proteins/*genetics ; }, abstract = {There were multiple prerequisites to the evolution of multicellular animal life, including the generation of multiple cell fates (&quot;cellular diversity&quot;) and their patterned spatial arrangement (&quot;spatial form&quot;). Wnt proteins operate as primordial symmetry-breaking signals. By virtue of their short-range nature and their capacity to activate both lineage-specifying and cell-polarizing intracellular signaling cascades, Wnts can polarize cells at their site of contact, orienting the axis of cell division while simultaneously programming daughter cells to adopt diverging fates in a spatially stereotyped way. By coupling cell fate to position, symmetry-breaking Wnt signals were pivotal in constructing the metazoan body by generating cellular diversity and spatial form.}, }
@article {pmid27663838, year = {2017}, author = {Ageitos, JM and Sánchez-Pérez, A and Calo-Mata, P and Villa, TG}, title = {Antimicrobial peptides (AMPs): Ancient compounds that represent novel weapons in the fight against bacteria.}, journal = {Biochemical pharmacology}, volume = {133}, number = {}, pages = {117-138}, doi = {10.1016/j.bcp.2016.09.018}, pmid = {27663838}, issn = {1873-2968}, mesh = {Amino Acid Sequence ; Animals ; Antimicrobial Cationic Peptides/*chemistry/genetics/*pharmacology ; Biological Products/*chemistry/*pharmacology ; Cell Wall/drug effects/physiology ; Drug Resistance, Multiple, Bacterial/*drug effects/physiology ; Humans ; Methicillin-Resistant Staphylococcus aureus/drug effects/physiology ; Microbial Sensitivity Tests/methods ; Protein Structure, Secondary ; }, abstract = {Antimicrobial peptides (AMPs) are short peptidic molecules produced by most living creatures. They help unicellular organisms to successfully compete for nutrients with other organisms sharing their biological niche, while AMPs form part of the immune system of multicellular creatures. Thus, these molecules represent biological weapons that have evolved over millions of years as a result of an escalating arms race for survival among living organisms. All AMPs share common features, such as a small size, with cationic and hydrophobic sequences within a linear or cyclic structure. AMPs can inhibit or kill bacteria at micromolar concentrations, often by non-specific mechanisms; hence the appearance of resistance to these antimicrobials is rare. Moreover, AMPs can kill antibiotic-resistant bacteria, including insidious microbes such as Acinetobacter baumannii and the methicillin-resistant Staphylococcus aureus. This review gives a detailed insight into a selection of the most prominent and interesting AMPs with antibacterial activity. In the near future AMPs, due to their properties and despite their ancient origin, should represent a novel alternative to antibiotics in the struggle to control pathogenic microorganisms and maintain the current human life expectancy.}, }
@article {pmid27637882, year = {2016}, author = {Wong, M and Liang, X and Smart, M and Tang, L and Moore, R and Ingalls, B and Dong, TG}, title = {Microbial herd protection mediated by antagonistic interaction in polymicrobial communities.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.02210-16}, pmid = {27637882}, issn = {1098-5336}, abstract = {In the host and natural environments, microbes often exist in complex multispecies communities. The molecular mechanisms through which such communities develop and persist - despite significant antagonistic interactions between species - are not well understood. The type VI secretion system (T6SS) is a lethal weapon commonly employed by Gram-negative bacteria to inhibit neighboring species through delivery of toxic effectors. It is well established that intra-species protection is conferred by immunity proteins that neutralize effector toxicities. By contrast, the mechanisms for interspecies protection are not clear. Here we use two T6SS active antagonistic bacteria, Aeromonas hydrophila (AH) and Vibrio cholerae (VC), to demonstrate that interspecies protection is dependent on effectors. AH and VC do not share conserved immunity genes but could equally co-exist in a mixture. However, mutants lacking the T6SS or effectors were effectively eliminated by the other competing wild type. Time-lapse microscopy analyses show that mutually lethal interactions drive the segregation of mixed species into distinct single-species clusters by eliminating interspersed single cells. Cluster formation provides herd protection by abolishing lethal interaction inside each cluster and restricting it to the boundary. Using an agent-based modeling approach, we simulated the antagonistic interactions of two hypothetical species. The resulting simulations recapitulate our experimental observation. These results provide mechanistic insights for the general role of microbial weapons in determining the structures of complex multispecies communities.<br><br>IMPORTANCE: Investigating the warfare of microbes allows us to better understand the ecological relationships in complex microbial communities such as the human microbiota. Here we use the T6SS, a deadly bacterial weapon, as a model to demonstrate the importance of lethal interactions in determining community structures and exchange of genetic materials. This simplified model elucidates a mechanism of microbial herd protection by which competing antagonistic species coexist in the same niche despite their diverse mutually destructive activities. Our results also suggest that antagonistic interaction imposes a strong selection that could promote multicellular like social behaviors and contribute to the transition to multicellularity during evolution.}, }
@article {pmid27629030, year = {2016}, author = {Wensink, MJ}, title = {Size, longevity and cancer: age structure.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1838}, pages = {}, doi = {10.1098/rspb.2016.1510}, pmid = {27629030}, issn = {1471-2954}, mesh = {Animals ; *Body Size ; Humans ; *Longevity ; Models, Biological ; *Neoplasms ; Probability ; }, abstract = {There is significant recent interest in Peto's paradox and the related problem of the evolution of large, long-lived organisms in terms of cancer robustness. Peto's paradox refers to the expectation that large, long-lived organisms have a higher lifetime cancer risk, which is not the case: a paradox. This paradox, however, is circular: large, long-lived organisms are large and long-lived because they are cancer robust. Lifetime risk, meanwhile, depends on the age distributions of both cancer and competing risks: if cancer strikes before competing risks, then lifetime risk is high; if not, not. Because no set of competing risks is generally prevalent, it is instructive to temporarily dispose of competing risks and investigate the pure age dynamics of cancer under the multistage model of carcinogenesis. In addition to augmenting earlier results, I show that in terms of cancer-free lifespan large organisms reap greater benefits from an increase in cellular cancer robustness than smaller organisms. Conversely, a higher cellular cancer robustness renders cancer-free lifespan more resilient to an increase in size. This interaction may be an important driver of the evolution of large, cancer-robust organisms.}, }
@article {pmid27628442, year = {2016}, author = {Li, S and Hauser, F and Skadborg, SK and Nielsen, SV and Kirketerp-Møller, N and Grimmelikhuijzen, CJ}, title = {Adipokinetic hormones and their G protein-coupled receptors emerged in Lophotrochozoa.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {32789}, doi = {10.1038/srep32789}, pmid = {27628442}, issn = {2045-2322}, mesh = {Adipokines/*metabolism ; Animals ; *Biological Evolution ; CHO Cells ; Cloning, Molecular ; Computational Biology ; Crassostrea/metabolism ; Cricetinae ; Cricetulus ; Drosophila melanogaster ; Gonadotropin-Releasing Hormone/metabolism ; Humans ; Insect Hormones/*metabolism ; Insect Proteins/metabolism ; Insecta ; Invertebrates/*metabolism ; Ligands ; Neuropeptides/metabolism ; Oligopeptides/*metabolism ; Peptides/metabolism ; Phylogeny ; Pyrrolidonecarboxylic Acid/*analogs &amp; derivatives/metabolism ; Receptors, G-Protein-Coupled/*metabolism ; Signal Transduction ; }, abstract = {Most multicellular animals belong to two evolutionary lineages, the Proto- and Deuterostomia, which diverged 640-760 million years (MYR) ago. Neuropeptide signaling is abundant in animals belonging to both lineages, but it is often unclear whether there exist evolutionary relationships between the neuropeptide systems used by proto- or deuterostomes. An exception, however, are members of the gonadotropin-releasing hormone (GnRH) receptor superfamily, which occur in both evolutionary lineages, where GnRHs are the ligands in Deuterostomia and GnRH-like peptides, adipokinetic hormone (AKH), corazonin, and AKH/corazonin-related peptide (ACP) are the ligands in Protostomia. AKH is a well-studied insect neuropeptide that mobilizes lipids and carbohydrates from the insect fat body during flight. In our present paper, we show that AKH is not only widespread in insects, but also in other Ecdysozoa and in Lophotrochozoa. Furthermore, we have cloned and deorphanized two G protein-coupled receptors (GPCRs) from the oyster Crassostrea gigas (Mollusca) that are activated by low nanomolar concentrations of oyster AKH (pQVSFSTNWGSamide). Our discovery of functional AKH receptors in molluscs is especially significant, because it traces the emergence of AKH signaling back to about 550 MYR ago and brings us closer to a more complete understanding of the evolutionary origins of the GnRH receptor superfamily.}, }
@article {pmid27621281, year = {2016}, author = {Yu, YN and Kleiner, M and Velicer, GJ}, title = {Spontaneous Reversions of an Evolutionary Trait Loss Reveal Regulators of a Small RNA That Controls Multicellular Development in Myxobacteria.}, journal = {Journal of bacteriology}, volume = {198}, number = {23}, pages = {3142-3151}, doi = {10.1128/JB.00389-16}, pmid = {27621281}, issn = {1098-5530}, mesh = {Bacterial Proteins/genetics/metabolism ; Biological Evolution ; *Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Developmental ; Histidine Kinase/genetics/metabolism ; Mutation ; Myxococcus xanthus/*genetics/*growth &amp; development/metabolism ; RNA, Bacterial/genetics/*metabolism ; }, abstract = {Lost traits can reevolve, but the probability of trait reversion depends partly on a trait's genetic complexity. Myxobacterial fruiting body development is a complex trait controlled by the small RNA (sRNA) Pxr, which blocks development under conditions of nutrient abundance. In developmentally proficient strains of Myxococcus xanthus, starvation relaxes the inhibition by Pxr, thereby allowing development to proceed. In contrast, the lab-evolved strain OC does not develop because it fails to relay an early starvation signal that alleviates inhibition by Pxr. A descendant of OC, strain PX, previously reevolved developmental proficiency via a mutation in pxr that inactivates its function. A single-colony screen was used to test whether reversion of OC to developmental proficiency occurs only by mutation of pxr or might also occur through alternative regulatory loci. Five spontaneous mutants of OC that exhibited restored development were isolated, and all five showed defects in Pxr synthesis, structure, or processing, including one that incurred an eight-nucleotide deletion in pxr Two mutations occurred in the σ54 response regulator (RR) gene MXAN_1078 (named pxrR here), immediately upstream of pxr PxrR was found to positively regulate pxr transcription, presumably via the σ54 promoter of pxr Two other mutations were identified in a histidine kinase (HK) gene (MXAN_1077; named pxrK here) immediately upstream of pxrR Evolutionarily, the rate of trait restoration documented in this study suggests that reversion of social defects in natural microbial populations may be common. Molecularly, these results suggest a mechanism by which the regulatory functions of an HK-RR two-component signaling system and an sRNA are integrated to control initiation of myxobacterial development.<br><br>IMPORTANCE: Many myxobacteria initiate a process of multicellular fruiting body development upon starvation, but key features of the regulatory network controlling the transition from growth to development remain obscure. Previous work with Myxococcus xanthus identified the first small RNA (sRNA) regulator (Pxr) known to serve as a gatekeeper in this life history transition, as it blocks development when nutrients are abundant. In the present study, a screen for spontaneous mutants of M. xanthus was developed that revealed a two-component system operon (encoding a histidine kinase and a σ54 response regulator) associated with the production and processing of Pxr sRNA. This discovery broadens our knowledge of early developmental gene regulation and also represents an evolutionary integration of two-component signaling and sRNA gene regulation to control a bacterial social trait.}, }
@article {pmid27619696, year = {2016}, author = {Lehtonen, J and Kokko, H and Parker, GA}, title = {What do isogamous organisms teach us about sex and the two sexes?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1706}, pages = {}, doi = {10.1098/rstb.2015.0532}, pmid = {27619696}, issn = {1471-2970}, mesh = {*Biological Evolution ; Eukaryota/*physiology ; Germ Cells/*physiology ; Reproduction ; *Sex ; }, abstract = {Isogamy is a reproductive system where all gametes are morphologically similar, especially in terms of size. Its importance goes beyond specific cases: to this day non-anisogamous systems are common outside of multicellular animals and plants, they can be found in all eukaryotic super-groups, and anisogamous organisms appear to have isogamous ancestors. Furthermore, because maleness is synonymous with the production of small gametes, an explanation for the initial origin of males and females is synonymous with understanding the transition from isogamy to anisogamy. As we show here, this transition may also be crucial for understanding why sex itself remains common even in taxa with high costs of male production (the twofold cost of sex). The transition to anisogamy implies the origin of male and female sexes, kickstarts the subsequent evolution of sex roles, and has a major impact on the costliness of sexual reproduction. Finally, we combine some of the consequences of isogamy and anisogamy in a thought experiment on the maintenance of sexual reproduction. We ask what happens if there is a less than twofold benefit to sex (not an unlikely scenario as large short-term benefits have proved difficult to find), and argue that this could lead to a situation where lineages that evolve anisogamy-and thus the highest costs of sex-end up being associated with constraints that make invasion by asexual reproduction unlikely (the 'anisogamy gateway' hypothesis).This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.}, }
@article {pmid27617970, year = {2016}, author = {Bowman, JL and Sakakibara, K and Furumizu, C and Dierschke, T}, title = {Evolution in the Cycles of Life.}, journal = {Annual review of genetics}, volume = {50}, number = {}, pages = {133-154}, doi = {10.1146/annurev-genet-120215-035227}, pmid = {27617970}, issn = {1545-2948}, mesh = {*Biological Evolution ; Bryophyta/genetics ; Chlorophyta/genetics ; Diploidy ; Eukaryota ; Fungi/genetics ; Haploidy ; Homeodomain Proteins/genetics ; Magnoliopsida/genetics ; Phaeophyta/genetics ; Phylogeny ; Plants/*genetics ; Rhodophyta/genetics ; }, abstract = {The life cycles of eukaryotes alternate between haploid and diploid phases, which are initiated by meiosis and gamete fusion, respectively. In both ascomycete and basidiomycete fungi and chlorophyte algae, the haploid-to-diploid transition is regulated by a pair of paralogous homeodomain protein encoding genes. That a common genetic program controls the haploid-to-diploid transition in phylogenetically disparate eukaryotic lineages suggests this may be the ancestral function for homeodomain proteins. Multicellularity has evolved independently in many eukaryotic lineages in either one or both phases of the life cycle. Organisms, such as land plants, exhibiting a life cycle whereby multicellular bodies develop in both the haploid and diploid phases are often referred to as possessing an alternation of generations. We review recent progress on understanding the genetic basis for the land plant alternation of generations and highlight the roles that homeodomain-encoding genes may have played in the evolution of complex multicellularity in this lineage.}, }
@article {pmid27595342, year = {2017}, author = {Ishizaki, K}, title = {Evolution of land plants: insights from molecular studies on basal lineages.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {81}, number = {1}, pages = {73-80}, doi = {10.1080/09168451.2016.1224641}, pmid = {27595342}, issn = {1347-6947}, mesh = {Embryophyta/*genetics/metabolism ; *Evolution, Molecular ; Introduced Species ; }, abstract = {The invasion of the land by plants, or terrestrialization, was one of the most critical events in the history of the Earth. The evolution of land plants included significant transformations in body plans: the emergence of a multicellular diploid sporophyte, transition from gametophyte-dominant to sporophyte-dominant life histories, and development of many specialized tissues and organs, such as stomata, vascular tissues, roots, leaves, seeds, and flowers. Recent advances in molecular genetics in two model basal plants, bryophytes Physcomitrella patens and Marchantia polymorpha, have begun to provide answers to several key questions regarding land plant evolution. This paper discusses the evolution of the genes and regulatory mechanisms that helped drive such significant morphological innovations among land-based plants.}, }
@article {pmid27589960, year = {2016}, author = {Lee, J and Cho, CH and Park, SI and Choi, JW and Song, HS and West, JA and Bhattacharya, D and Yoon, HS}, title = {Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants.}, journal = {BMC biology}, volume = {14}, number = {}, pages = {75}, doi = {10.1186/s12915-016-0299-5}, pmid = {27589960}, issn = {1741-7007}, mesh = {Conserved Sequence/*genetics ; Cycadopsida/*genetics ; *Evolution, Molecular ; Genetic Variation ; *Genome, Plastid ; Magnoliopsida/*genetics ; Multigene Family ; Phylogeny ; Rhodophyta/*genetics ; Seeds/*genetics ; Synteny/genetics ; }, abstract = {BACKGROUND: The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles.<br><br>RESULTS: We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms.<br><br>CONCLUSIONS: Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages.}, }
@article {pmid27579832, year = {2016}, author = {Xu, Y and Yu, XL and Hu, CM and Hao, G}, title = {Morphological and Molecular Phylogenetic Data Reveal a New Species of Primula (Primulaceae) from Hunan, China.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0161172}, doi = {10.1371/journal.pone.0161172}, pmid = {27579832}, issn = {1932-6203}, mesh = {China ; Genetic Markers ; *Phylogeny ; Plant Proteins/*genetics ; *Primula/anatomy &amp; histology/classification/genetics ; }, abstract = {A new species of Primulaceae, Primula undulifolia, is described from the hilly area of Hunan province in south-central China. Its morphology and distributional range suggest that it is allied to P. kwangtungensis, both adapted to subtropical climate, having contiguous distribution and similar habitat, growing on shady and moist cliffs. Petioles, scapes and pedicels of them are densely covered with rusty multicellular hairs, but the new species can be easily distinguished by its smaller flowers and narrowly oblong leaves with undulate margins. Molecular phylogenetic analysis based on four DNA markers (ITS, matK, trnL-F and rps16) confirmed the new species as an independent lineage and constitutes a main clade together with P. kwangtungensis, P. kweichouensis, P. wangii and P. hunanensis of Primula sect. Carolinella.}, }
@article {pmid27571751, year = {2016}, author = {Leducq, JB and Nielly-Thibault, L and Charron, G and Eberlein, C and Verta, JP and Samani, P and Sylvester, K and Hittinger, CT and Bell, G and Landry, CR}, title = {Speciation driven by hybridization and chromosomal plasticity in a wild yeast.}, journal = {Nature microbiology}, volume = {1}, number = {}, pages = {15003}, doi = {10.1038/nmicrobiol.2015.3}, pmid = {27571751}, issn = {2058-5276}, mesh = {*Chromosomes, Fungal ; Forests ; *Genetic Speciation ; *Genetic Variation ; *Hybridization, Genetic ; North America ; *Recombination, Genetic ; Saccharomyces/*classification/*genetics/isolation &amp; purification ; }, abstract = {Hybridization is recognized as a powerful mechanism of speciation and a driving force in generating biodiversity. However, only few multicellular species, limited to a handful of plants and animals, have been shown to fulfil all the criteria of homoploid hybrid speciation. This lack of evidence could lead to the interpretation that speciation by hybridization has a limited role in eukaryotes, particularly in single-celled organisms. Laboratory experiments have revealed that fungi such as budding yeasts can rapidly develop reproductive isolation and novel phenotypes through hybridization, showing that in principle homoploid speciation could occur in nature. Here, we report a case of homoploid hybrid speciation in natural populations of the budding yeast Saccharomyces paradoxus inhabiting the North American forests. We show that the rapid evolution of chromosome architecture and an ecological context that led to secondary contact between nascent species drove the formation of an incipient hybrid species with a potentially unique ecological niche.}, }
@article {pmid27559062, year = {2016}, author = {Schoustra, S and Hwang, S and Krug, J and de Visser, JA}, title = {Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1837}, pages = {}, doi = {10.1098/rspb.2016.1376}, pmid = {27559062}, issn = {1471-2954}, mesh = {Aspergillus nidulans/*genetics ; *Epistasis, Genetic ; *Genetic Fitness ; Genotype ; Models, Genetic ; *Mutation ; }, abstract = {Adaptive evolution ultimately is fuelled by mutations generating novel genetic variation. Non-additivity of fitness effects of mutations (called epistasis) may affect the dynamics and repeatability of adaptation. However, understanding the importance and implications of epistasis is hampered by the observation of substantial variation in patterns of epistasis across empirical studies. Interestingly, some recent studies report increasingly smaller benefits of beneficial mutations once genotypes become better adapted (called diminishing-returns epistasis) in unicellular microbes and single genes. Here, we use Fisher's geometric model (FGM) to generate analytical predictions about the relationship between the effect size of mutations and the extent of epistasis. We then test these predictions using the multicellular fungus Aspergillus nidulans by generating a collection of 108 strains in either a poor or a rich nutrient environment that each carry a beneficial mutation and constructing pairwise combinations using sexual crosses. Our results support the predictions from FGM and indicate negative epistasis among beneficial mutations in both environments, which scale with mutational effect size. Hence, our findings show the importance of diminishing-returns epistasis among beneficial mutations also for a multicellular organism, and suggest that this pattern reflects a generic constraint operating at diverse levels of biological organization.}, }
@article {pmid27549405, year = {2016}, author = {Rödelsperger, C and Menden, K and Serobyan, V and Witte, H and Baskaran, P}, title = {First insights into the nature and evolution of antisense transcription in nematodes.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {165}, doi = {10.1186/s12862-016-0740-y}, pmid = {27549405}, issn = {1471-2148}, abstract = {BACKGROUND: The development of multicellular organisms is coordinated by various gene regulatory mechanisms that ensure correct spatio-temporal patterns of gene expression. Recently, the role of antisense transcription in gene regulation has moved into focus of research. To characterize genome-wide patterns of antisense transcription and to study their evolutionary conservation, we sequenced a strand-specific RNA-seq library of the nematode Pristionchus pacificus.<br><br>RESULTS: We identified 1112 antisense configurations of which the largest group represents 465 antisense transcripts (ASTs) that are fully embedded in introns of their host genes. We find that most ASTs show homology to protein-coding genes and are overrepresented in proteomic data. Together with the finding, that expression levels of ASTs and host genes are uncorrelated, this indicates that most ASTs in P. pacificus do not represent non-coding RNAs and do not exhibit regulatory functions on their host genes. We studied the evolution of antisense gene pairs across 20 nematode genomes, showing that the majority of pairs is lineage-specific and even the highly conserved vps-4, ddx-27, and sel-2 loci show abundant structural changes including duplications, deletions, intron gains and loss of antisense transcription. In contrast, host genes in general, are remarkably conserved and encode exceptionally long introns leading to unusually large blocks of conserved synteny.<br><br>CONCLUSIONS: Our study has shown that in P. pacificus antisense transcription as such does not define non-coding RNAs but is rather a feature of highly conserved genes with long introns. We hypothesize that the presence of regulatory elements imposes evolutionary constraint on the intron length, but simultaneously, their large size makes them a likely target for translocation of genomic elements including protein-coding genes that eventually end up as ASTs.}, }
@article {pmid27534782, year = {2016}, author = {Šmardová, J and Koptíková, J}, title = {[Two Approaches to Cancer Development].}, journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti}, volume = {29}, number = {4}, pages = {259-266}, pmid = {27534782}, issn = {0862-495X}, mesh = {Carcinogenesis/*genetics ; Cell Proliferation/*genetics ; Epigenesis, Genetic/genetics ; Humans ; Mutation/*genetics ; Neoplasms/*genetics ; Tumor Microenvironment ; }, abstract = {BACKGROUND: The somatic mutation theory explaining the process of carcinogenesis is generally accepted. The theory postulates that carcinogenesis begins in a first renegade cell that undergoes gradual transformation from a healthy to a fully malignant state through the accumulation of genetic and epigenetic &quot;hits&quot;. This theory focuses specifically on mutations and genetic aberrations, and their impact on cells. It considers tumors as populations of sick cells that lose control of their own proliferation. The theory was put forward by Robert Weinberg and Douglas Hanahan, and is the predominant view in current cancer biology. By contrast, the tissue organization field theory proposed by Carlos Sonnenschein and Ana Soto considers loss of physiological structure and function by a tissue as key events in tumor development. According to this theory, tumors arise at a tissue rather than at a cellular level. It is based on a presumption that proliferation status, rather than quiescence, is the default position of cells in multicellular organisms.<br><br>AIM: The article aims to provide answers to following questions: Are the views of proponents of the somatic mutation theory (the reductionists) and proponents of the tissue organization field theory (the organicists) incompatible and incommensurable, even when the mainstream of tumor biology has shifted its attention from tumor cells toward the tumor microenvironment? Where to find a third interconnecting systemic approach? Is it useful to be aware of the controversy between reductionists and organicists? What this awareness contributes to? How do these alternative views influence practical oncology and tumor biology in general?<br><br>CONCLUSION: Whether the true position is held by reductionists or organicists is unimportant. What is important is to be aware of the existence of these two concepts because this knowledge makes the way we think about tumor origin and development, and how we set up and interpret our experiments, more precise.<br><br>KEY WORDS: carcinogenesis - mutation - cell - tissues - cell proliferation - cell quiescenceThis study was supported by grant of Internal Grant Agency of the Czech ministry of Health No. NT/13784-4/2012.The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.Submitted: 29. 7. 2015Accepted: 27. 4. 2016.}, }
@article {pmid27534726, year = {2016}, author = {Torday, JS}, title = {The Emergence of Physiology and Form: Natural Selection Revisited.}, journal = {Biology}, volume = {5}, number = {2}, pages = {}, doi = {10.3390/biology5020015}, pmid = {27534726}, issn = {2079-7737}, support = {R01 HL055268/HL/NHLBI NIH HHS/United States ; }, abstract = {Natural Selection describes how species have evolved differentially, but it is descriptive, non-mechanistic. What mechanisms does Nature use to accomplish this feat? One known way in which ancient natural forces affect development, phylogeny and physiology is through gravitational effects that have evolved as mechanotransduction, seen in the lung, kidney and bone, linking as molecular homologies to skin and brain. Tracing the ontogenetic and phylogenetic changes that have facilitated mechanotransduction identifies specific homologous cell-types and functional molecular markers for lung homeostasis that reveal how and why complex physiologic traits have evolved from the unicellular to the multicellular state. Such data are reinforced by their reverse-evolutionary patterns in chronic degenerative diseases. The physiologic responses of model organisms like Dictyostelium and yeast to gravity provide deep comparative molecular phenotypic homologies, revealing mammalian Target of Rapamycin (mTOR) as the final common pathway for vertical integration of vertebrate physiologic evolution; mTOR integrates calcium/lipid epistatic balance as both the proximate and ultimate positive selection pressure for vertebrate physiologic evolution. The commonality of all vertebrate structure-function relationships can be reduced to calcium/lipid homeostatic regulation as the fractal unit of vertebrate physiology, demonstrating the primacy of the unicellular state as the fundament of physiologic evolution.}, }
@article {pmid27518838, year = {2016}, author = {El Kafsi, H and Gorochov, G and Larsen, M}, title = {Host genetics affect microbial ecosystems via host immunity.}, journal = {Current opinion in allergy and clinical immunology}, volume = {16}, number = {5}, pages = {413-420}, doi = {10.1097/ACI.0000000000000302}, pmid = {27518838}, issn = {1473-6322}, mesh = {Animals ; Biological Evolution ; Ecosystem ; *Gene-Environment Interaction ; *Genetic Phenomena ; Homeostasis ; *Host-Pathogen Interactions ; Humans ; Immunity/*genetics ; Mice ; *Microbiota ; Symbiosis ; }, abstract = {PURPOSE OF REVIEW: Genetic evolution of multicellular organisms has occurred in response to environmental challenges, including competition for nutrients, climate change, physical and chemical stressors, and pathogens. However, fitness of an organism is dependent not only on defense efficacy, but also on the ability to take advantage of symbiotic organisms. Indeed, microbes not only encompass pathogenicity, but also enable efficient nutrient uptake from diets nondegradable by the host itself. Moreover, microbes play important roles in the development of host immunity. Here we review associations between specific host genes and variance in microbiota composition and compare with interactions between microbes and host immunity.<br><br>RECENT FINDINGS: Recent genome-wide association studies reveal that symbiosis between host and microbiota is the exquisite result of genetic coevolution. Moreover, a subset of microbes from human and mouse microbiota have been identified to interact with humoral and cellular immunity. Interestingly, microbes associated with both host genetics and host immunity are taxonomically related. Most involved are Bifidobacterium, Lactobacillus, and Akkermansia, which are dually associated with both host immunity and host genetics.<br><br>SUMMARY: We conclude that future therapeutics targeting microbiota in the context of chronic inflammatory diseases need to consider both immune and genetic host features associated with microbiota homeostasis.}, }
@article {pmid27512113, year = {2016}, author = {Derelle, R and López-García, P and Timpano, H and Moreira, D}, title = {A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts).}, journal = {Molecular biology and evolution}, volume = {33}, number = {11}, pages = {2890-2898}, doi = {10.1093/molbev/msw168}, pmid = {27512113}, issn = {1537-1719}, support = {322669//European Research Council/International ; }, mesh = {*Biological Evolution ; DNA, Ribosomal/genetics ; Diatoms/genetics ; Evolution, Molecular ; Heterotrophic Processes ; Phylogeny ; Sequence Analysis, DNA/methods ; Stramenopiles/*genetics ; }, abstract = {Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of protists. It includes ecologically important algae (such as diatoms or large multicellular brown seaweeds), as well as heterotrophic (e.g., bicosoecids, MAST groups) and parasitic (e.g., Blastocystis, oomycetes) species. Despite their evolutionary and ecological relevance, deep phylogenetic relationships among stramenopile groups, inferred mostly from small-subunit rDNA phylogenies, remain unresolved, especially for the heterotrophic taxa. Taking advantage of recently released stramenopile transcriptome and genome sequences, as well as data from the genomic assembly of the MAST-3 species Incisomonas marina generated in our laboratory, we have carried out the first extensive phylogenomic analysis of stramenopiles, including representatives of most major lineages. Our analyses, based on a large data set of 339 widely distributed proteins, strongly support a root of stramenopiles lying between two clades, Bigyra and Gyrista (Pseudofungi plus Ochrophyta). Additionally, our analyses challenge the Phaeista-Khakista dichotomy of photosynthetic stramenopiles (ochrophytes) as two groups previously considered to be part of the Phaeista (Pelagophyceae and Dictyochophyceae), branch with strong support with the Khakista (Bolidophyceae and Diatomeae). We propose a new classification of ochrophytes within the two groups Chrysista and Diatomista to reflect the new phylogenomic results. Our stramenopile phylogeny provides a robust phylogenetic framework to investigate the evolution and diversification of this group of ecologically relevant protists.}, }
@article {pmid27510329, year = {2017}, author = {Pesce, M and Santoro, R}, title = {Feeling the right force: How to contextualize the cell mechanical behavior in physiologic turnover and pathologic evolution of the cardiovascular system.}, journal = {Pharmacology &amp; therapeutics}, volume = {171}, number = {}, pages = {75-82}, doi = {10.1016/j.pharmthera.2016.08.002}, pmid = {27510329}, issn = {1879-016X}, mesh = {Animals ; Cardiovascular Diseases/*physiopathology ; Cardiovascular System/*cytology/metabolism/physiopathology ; Cell Differentiation/*physiology ; Cell Engineering/methods ; Embryonic Development/physiology ; Gene Expression/physiology ; Humans ; }, abstract = {Although traditionally linked to the physiology of tissues in 'motion', the ability of the cells to transduce external forces into coordinated gene expression programs is emerging as an integral component of the fundamental structural organization of multicellular organisms with consequences for cell differentiation even from the beginning of embryonic development. The ability of the cells to 'feel' the surrounding mechanical environment, even in the absence of tissue motion, is then translated into 'positional' or 'social' sensing that instructs, before the organ renewal, the correct patterning of the embryos. In the present review, we will highlight how these basic concepts, emerging from the employment of novel cell engineering tools, can be linked to pathophysiology of the cardiovascular system, and may contribute to understanding the molecular bases of some of the major cardiovascular diseases like heart failure, heart valve stenosis and failure of the venous aorto-coronary bypass.}, }
@article {pmid27504112, year = {2016}, author = {Beilby, MJ}, title = {Multi-Scale Characean Experimental System: From Electrophysiology of Membrane Transporters to Cell-to-Cell Connectivity, Cytoplasmic Streaming and Auxin Metabolism.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {1052}, doi = {10.3389/fpls.2016.01052}, pmid = {27504112}, issn = {1664-462X}, abstract = {The morphology of characean algae could be mistaken for a higher plant: stem-like axes with leaf-like branchlets anchored in the soil by root-like rhizoids. However, all of these structures are made up of giant multinucleate cells separated by multicellular nodal complexes. The excised internodal cells survive long enough for the nodes to give rise to new thallus. The size of the internodes and their thick cytoplasmic layer minimize impalement injury and allow specific micro-electrode placement. The cell structure can be manipulated by centrifugation, perfusion of cell contents or creation of cytoplasmic droplets, allowing access to both vacuolar and cytoplasmic compartments and both sides of the cell membranes. Thousands of electrical measurements on intact or altered cells and cytoplasmic droplets laid down basis to modern plant electrophysiology. Furthermore, the giant internodal cells and whole thalli facilitate research into many other plant properties. As nutrients have to be transported from rhizoids to growing parts of the thallus and hormonal signals need to pass from cell to cell, Characeae possess very fast cytoplasmic streaming. The mechanism was resolved in the characean model. Plasmodesmata between the internodal cells and nodal complexes facilitate transport of ions, nutrients and photosynthates across the nodes. The internal structure was found to be similar to those of higher plants. Recent experiments suggest a strong circadian influence on metabolic pathways producing indole-3-acetic acid (IAA) and serotonin/melatonin. The review will discuss the impact of the characean models arising from fragments of cells, single cells, cell-to-cell transport or whole thalli on understanding of plant evolution and physiology.}, }
@article {pmid27501943, year = {2016}, author = {Sojo, V and Dessimoz, C and Pomiankowski, A and Lane, N}, title = {Membrane Proteins Are Dramatically Less Conserved than Water-Soluble Proteins across the Tree of Life.}, journal = {Molecular biology and evolution}, volume = {33}, number = {11}, pages = {2874-2884}, doi = {10.1093/molbev/msw164}, pmid = {27501943}, issn = {1537-1719}, support = {BB/L018241/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Biological ; Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; Databases, Protein ; Eukaryota/genetics ; Evolution, Molecular ; Homeostasis ; Membrane Proteins/*genetics/metabolism ; Phylogeny ; Prokaryotic Cells ; Proteins/*genetics/metabolism ; Sequence Analysis, Protein/*methods ; Solubility ; Water/metabolism ; }, abstract = {Membrane proteins are crucial in transport, signaling, bioenergetics, catalysis, and as drug targets. Here, we show that membrane proteins have dramatically fewer detectable orthologs than water-soluble proteins, less than half in most species analyzed. This sparse distribution could reflect rapid divergence or gene loss. We find that both mechanisms operate. First, membrane proteins evolve faster than water-soluble proteins, particularly in their exterior-facing portions. Second, we demonstrate that predicted ancestral membrane proteins are preferentially lost compared with water-soluble proteins in closely related species of archaea and bacteria. These patterns are consistent across the whole tree of life, and in each of the three domains of archaea, bacteria, and eukaryotes. Our findings point to a fundamental evolutionary principle: membrane proteins evolve faster due to stronger adaptive selection in changing environments, whereas cytosolic proteins are under more stringent purifying selection in the homeostatic interior of the cell. This effect should be strongest in prokaryotes, weaker in unicellular eukaryotes (with intracellular membranes), and weakest in multicellular eukaryotes (with extracellular homeostasis). We demonstrate that this is indeed the case. Similarly, we show that extracellular water-soluble proteins exhibit an even stronger pattern of low homology than membrane proteins. These striking differences in conservation of membrane proteins versus water-soluble proteins have important implications for evolution and medicine.}, }
@article {pmid27490201, year = {2016}, author = {Denver, DR and Brown, AM and Howe, DK and Peetz, AB and Zasada, IA}, title = {Genome Skimming: A Rapid Approach to Gaining Diverse Biological Insights into Multicellular Pathogens.}, journal = {PLoS pathogens}, volume = {12}, number = {8}, pages = {e1005713}, doi = {10.1371/journal.ppat.1005713}, pmid = {27490201}, issn = {1553-7374}, mesh = {Animals ; Genome ; Humans ; Nematoda/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, }
@article {pmid27476447, year = {2017}, author = {Jubin, T and Kadam, A and Gani, AR and Singh, M and Dwivedi, M and Begum, R}, title = {Poly ADP-ribose polymerase-1: Beyond transcription and towards differentiation.}, journal = {Seminars in cell &amp; developmental biology}, volume = {63}, number = {}, pages = {167-179}, doi = {10.1016/j.semcdb.2016.07.027}, pmid = {27476447}, issn = {1096-3634}, mesh = {Animals ; Cell Differentiation/*genetics ; Embryonic Development/genetics ; Gene Expression Regulation ; Humans ; Models, Biological ; Poly(ADP-ribose) Polymerases/*metabolism ; *Transcription, Genetic ; }, abstract = {Gene regulation mediates the processes of cellular development and differentiation leading to the origin of different cell types each having their own signature gene expression profile. However, the compact chromatin structure and the timely recruitment of molecules involved in various signaling pathways are of prime importance for temporal and spatial gene regulation that eventually contribute towards cell type and specificity. Poly (ADP-ribose) polymerase-1 (PARP-1), a 116-kDa nuclear multitasking protein is involved in modulation of chromatin condensation leading to altered gene expression. In response to activation signals, it adds ADP-ribose units to various target proteins including itself, thus regulating various key cellular processes like DNA repair, cell death, transcription, mRNA splicing etc. This review provides insights into the role of PARP-1 in gene regulation, cell differentiation and multicellular morphogenesis. In addition, the review also explores involvement of PARP-1 in immune cells development and therapeutic possibilities to treat various human diseases.}, }
@article {pmid27458581, year = {2016}, author = {Pietak, A and Levin, M}, title = {Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {4}, number = {}, pages = {55}, doi = {10.3389/fbioe.2016.00055}, pmid = {27458581}, issn = {2296-4185}, support = {R01 AR055993/AR/NIAMS NIH HHS/United States ; }, abstract = {Bioelectric cell properties have been revealed as powerful targets for modulating stem cell function, regenerative response, developmental patterning, and tumor reprograming. Spatio-temporal distributions of endogenous resting potential, ion flows, and electric fields are influenced not only by the genome and external signals but also by their own intrinsic dynamics. Ion channels and electrical synapses (gap junctions) both determine, and are themselves gated by, cellular resting potential. Thus, the origin and progression of bioelectric patterns in multicellular tissues is complex, which hampers the rational control of voltage distributions for biomedical interventions. To improve understanding of these dynamics and facilitate the development of bioelectric pattern control strategies, we developed the BioElectric Tissue Simulation Engine (BETSE), a finite volume method multiphysics simulator, which predicts bioelectric patterns and their spatio-temporal dynamics by modeling ion channel and gap junction activity and tracking changes to the fundamental property of ion concentration. We validate performance of the simulator by matching experimentally obtained data on membrane permeability, ion concentration and resting potential to simulated values, and by demonstrating the expected outcomes for a range of well-known cases, such as predicting the correct transmembrane voltage changes for perturbation of single cell membrane states and environmental ion concentrations, in addition to the development of realistic transepithelial potentials and bioelectric wounding signals. In silico experiments reveal factors influencing transmembrane potential are significantly different in gap junction-networked cell clusters with tight junctions, and identify non-linear feedback mechanisms capable of generating strong, emergent, cluster-wide resting potential gradients. The BETSE platform will enable a deep understanding of local and long-range bioelectrical dynamics in tissues, and assist the development of specific interventions to achieve greater control of pattern during morphogenesis and remodeling.}, }
@article {pmid27458458, year = {2016}, author = {Zhang, X and Soldati, T}, title = {Of Amoebae and Men: Extracellular DNA Traps as an Ancient Cell-Intrinsic Defense Mechanism.}, journal = {Frontiers in immunology}, volume = {7}, number = {}, pages = {269}, doi = {10.3389/fimmu.2016.00269}, pmid = {27458458}, issn = {1664-3224}, abstract = {Since the discovery of the formation of DNA-based extracellular traps (ETs) by neutrophils as an innate immune defense mechanism (1), hundreds of articles describe the involvement of ETs in physiological and pathological human and animal conditions [reviewed in Ref. (2), and the previous Frontiers Research Topic on NETosis: http://www.frontiersin.org/books/NETosis_At_the_Intersection_of_Cell_Biology_Microbiology_and_Immunology/195]. Interestingly, a few reports reveal that ETs can be formed by immune cells of more ancient organisms, as far back as the common ancestor of vertebrates and invertebrates (3). Recently, we reported that the Sentinel cells of the multicellular slug of the social amoeba Dictyostelium discoideum also produce ETs to trap and kill slug-invading bacteria [see Box 1; and Figure 1 Ref. (4)]. This is a strong evidence that DNA-based cell-intrinsic defense mechanisms emerged much earlier than thought, about 1.3 billion years ago. Amazingly, using extrusion of DNA as a weapon to capture and kill uningestable microbes has its rationale. During the emergence of multicellularity, a primitive innate immune system developed in the form of a dedicated set of specialized phagocytic cells. This professionalization of immunity allowed the evolution of sophisticated defense mechanisms including the sacrifice of a small set of cells by a mechanism related to NETosis. This altruistic behavior likely emerged in steps, starting from the release of &quot;dispensable&quot; mitochondrial DNA by D. discoideum Sentinel cells. Grounded in this realization, one can anticipate that in the near future, many more examples of the invention and fine-tuning of ETs by early metazoan ancestors will be identified. Consequently, it can be expected that this more complete picture of the evolution of ETs will impact our views of the involvement and pathologies linked to ETs in human and animals.}, }
@article {pmid27452234, year = {2016}, author = {Kulkarni, A and Pandey, P and Rao, P and Mahmoud, A and Goldman, A and Sabbisetti, V and Parcha, S and Natarajan, SK and Chandrasekar, V and Dinulescu, D and Roy, S and Sengupta, S}, title = {Algorithm for Designing Nanoscale Supramolecular Therapeutics with Increased Anticancer Efficacy.}, journal = {ACS nano}, volume = {10}, number = {9}, pages = {8154-8168}, doi = {10.1021/acsnano.6b00241}, pmid = {27452234}, issn = {1936-086X}, support = {R01 CA135242/CA/NCI NIH HHS/United States ; }, mesh = {*Algorithms ; Molecular Dynamics Simulation ; *Nanoparticles ; Nanostructures ; Neoplasms/*therapy ; }, abstract = {In the chemical world, evolution is mirrored in the origin of nanoscale supramolecular structures from molecular subunits. The complexity of function acquired in a supramolecular system over a molecular subunit can be harnessed in the treatment of cancer. However, the design of supramolecular nanostructures is hindered by a limited atomistic level understanding of interactions between building blocks. Here, we report the development of a computational algorithm, which we term Volvox after the first multicellular organism, that sequentially integrates quantum mechanical energy-state- and force-field-based models with large-scale all-atomistic explicit water molecular dynamics simulations to design stable nanoscale lipidic supramolecular structures. In one example, we demonstrate that Volvox enables the design of a nanoscale taxane supramolecular therapeutic. In another example, we demonstrate that Volvox can be extended to optimizing the ratio of excipients to form a stable nanoscale supramolecular therapeutic. The nanoscale taxane supramolecular therapeutic exerts greater antitumor efficacy than a clinically used taxane in vivo. Volvox can emerge as a powerful tool in the design of nanoscale supramolecular therapeutics for effective treatment of cancer.}, }
@article {pmid27451296, year = {2016}, author = {Matt, G and Umen, J}, title = {Volvox: A simple algal model for embryogenesis, morphogenesis and cellular differentiation.}, journal = {Developmental biology}, volume = {419}, number = {1}, pages = {99-113}, doi = {10.1016/j.ydbio.2016.07.014}, pmid = {27451296}, issn = {1095-564X}, support = {R01 GM078376/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Cycle ; Cell Lineage ; Cell Size ; Cellular Senescence ; *Models, Biological ; Morphogenesis ; Mutation ; Phylogeny ; Reproduction, Asexual ; Seeds ; Volvox/*cytology/genetics/physiology ; }, abstract = {Patterning of a multicellular body plan involves a coordinated set of developmental processes that includes cell division, morphogenesis, and cellular differentiation. These processes have been most intensively studied in animals and land plants; however, deep insight can also be gained by studying development in simpler multicellular organisms. The multicellular green alga Volvox carteri (Volvox) is an excellent model for the investigation of developmental mechanisms and their evolutionary origins. Volvox has a streamlined body plan that contains only a few thousand cells and two distinct cell types: reproductive germ cells and terminally differentiated somatic cells. Patterning of the Volvox body plan is achieved through a stereotyped developmental program that includes embryonic cleavage with asymmetric cell division, morphogenesis, and cell-type differentiation. In this review we provide an overview of how these three developmental processes give rise to the adult form in Volvox and how developmental mutants have provided insights into the mechanisms behind these events. We highlight the accessibility and tractability of Volvox and its relatives that provide a unique opportunity for studying development.}, }
@article {pmid27431528, year = {2016}, author = {Solé, R}, title = {The major synthetic evolutionary transitions.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1701}, pages = {}, doi = {10.1098/rstb.2016.0175}, pmid = {27431528}, issn = {1471-2970}, mesh = {*Artificial Intelligence ; *Biological Evolution ; Cells, Cultured/*physiology ; *Language ; Robotics ; *Synthetic Biology ; }, abstract = {Evolution is marked by well-defined events involving profound innovations that are known as 'major evolutionary transitions'. They involve the integration of autonomous elements into a new, higher-level organization whereby the former isolated units interact in novel ways, losing their original autonomy. All major transitions, which include the origin of life, cells, multicellular systems, societies or language (among other examples), took place millions of years ago. Are these transitions unique, rare events? Have they instead universal traits that make them almost inevitable when the right pieces are in place? Are there general laws of evolutionary innovation? In order to approach this problem under a novel perspective, we argue that a parallel class of evolutionary transitions can be explored involving the use of artificial evolutionary experiments where alternative paths to innovation can be explored. These 'synthetic' transitions include, for example, the artificial evolution of multicellular systems or the emergence of language in evolved communicating robots. These alternative scenarios could help us to understand the underlying laws that predate the rise of major innovations and the possibility for general laws of evolved complexity. Several key examples and theoretical approaches are summarized and future challenges are outlined.This article is part of the themed issue 'The major synthetic evolutionary transitions'.}, }
@article {pmid27431524, year = {2016}, author = {Moses, M and Bezerra, G and Edwards, B and Brown, J and Forrest, S}, title = {Energy and time determine scaling in biological and computer designs.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1701}, pages = {}, doi = {10.1098/rstb.2015.0446}, pmid = {27431524}, issn = {1471-2970}, support = {T32 EB009414/EB/NIBIB NIH HHS/United States ; }, mesh = {Animals ; *Basal Metabolism ; Biological Evolution ; *Electric Power Supplies ; Mammals/*physiology ; *Microcomputers ; Models, Biological ; Models, Theoretical ; Selection, Genetic ; }, abstract = {Metabolic rate in animals and power consumption in computers are analogous quantities that scale similarly with size. We analyse vascular systems of mammals and on-chip networks of microprocessors, where natural selection and human engineering, respectively, have produced systems that minimize both energy dissipation and delivery times. Using a simple network model that simultaneously minimizes energy and time, our analysis explains empirically observed trends in the scaling of metabolic rate in mammals and power consumption and performance in microprocessors across several orders of magnitude in size. Just as the evolutionary transitions from unicellular to multicellular animals in biology are associated with shifts in metabolic scaling, our model suggests that the scaling of power and performance will change as computer designs transition to decentralized multi-core and distributed cyber-physical systems. More generally, a single energy-time minimization principle may govern the design of many complex systems that process energy, materials and information.This article is part of the themed issue 'The major synthetic evolutionary transitions'.}, }
@article {pmid27431523, year = {2016}, author = {Lachmann, M and Libby, E}, title = {Epigenetic inheritance systems contribute to the evolution of a germline.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1701}, pages = {}, doi = {10.1098/rstb.2015.0445}, pmid = {27431523}, issn = {1471-2970}, mesh = {*Biological Evolution ; *Cell Lineage ; *Epigenesis, Genetic ; Germ Cells/*physiology ; Heredity ; Models, Genetic ; }, abstract = {Differentiation within multicellular organisms is controlled by epigenetic markers transmitted across cell division. The process of differentiation will modify these epigenetic markers so that information that one cell type possesses can be lost in the transition to another. Many of the systems that encode these markers also exist in unicellular organisms but do not control differentiation. Thus, during the evolution of multicellularity, epigenetic inheritance systems were probably exapted for their current use in differentiation. We show that the simultaneous use of an information carrier for differentiation and transmission across generations can lead to the evolution of cell types that do not directly contribute to the progeny of the organism and ergo a germ-soma distinction. This shows that an intrinsic instability during a transition from unicellularity to multicellularity may contribute to widespread evolution of a germline and its maintenance, a phenomenon also relevant to the evolution of eusociality. The difference in epigenetic information contents between different cell lines in a multicellular organism is also relevant for the full-success cloning of higher animals, as well as for the maintenance of single germlines over evolutionary timescales.This article is part of the themed issue 'The major synthetic evolutionary transitions'.}, }
@article {pmid27431522, year = {2016}, author = {Libby, E and Conlin, PL and Kerr, B and Ratcliff, WC}, title = {Stabilizing multicellularity through ratcheting.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1701}, pages = {}, doi = {10.1098/rstb.2015.0444}, pmid = {27431522}, issn = {1471-2970}, mesh = {*Adaptation, Biological ; *Biological Evolution ; Eukaryota/genetics/*physiology ; Models, Genetic ; *Selection, Genetic ; }, abstract = {The evolutionary transition to multicellularity probably began with the formation of simple undifferentiated cellular groups. Such groups evolve readily in diverse lineages of extant unicellular taxa, suggesting that there are few genetic barriers to this first key step. This may act as a double-edged sword: labile transitions between unicellular and multicellular states may facilitate the evolution of simple multicellularity, but reversion to a unicellular state may inhibit the evolution of increased complexity. In this paper, we examine how multicellular adaptations can act as evolutionary 'ratchets', limiting the potential for reversion to unicellularity. We consider a nascent multicellular lineage growing in an environment that varies between favouring multicellularity and favouring unicellularity. The first type of ratcheting mutations increase cell-level fitness in a multicellular context but are costly in a single-celled context, reducing the fitness of revertants. The second type of ratcheting mutations directly decrease the probability that a mutation will result in reversion (either as a pleiotropic consequence or via direct modification of switch rates). We show that both types of ratcheting mutations act to stabilize the multicellular state. We also identify synergistic effects between the two types of ratcheting mutations in which the presence of one creates the selective conditions favouring the other. Ratcheting mutations may play a key role in diverse evolutionary transitions in individuality, sustaining selection on the new higher-level organism by constraining evolutionary reversion.This article is part of the themed issue 'The major synthetic evolutionary transitions'.}, }
@article {pmid27431521, year = {2016}, author = {Newman, SA}, title = {'Biogeneric' developmental processes: drivers of major transitions in animal evolution.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1701}, pages = {}, doi = {10.1098/rstb.2015.0443}, pmid = {27431521}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Evolution, Molecular ; Extremities/anatomy &amp; histology ; Fishes/anatomy &amp; histology/*physiology ; Invertebrates/*physiology ; *Morphogenesis ; }, abstract = {Using three examples drawn from animal systems, I advance the hypothesis that major transitions in multicellular evolution often involved the constitution of new cell-based materials with unprecedented morphogenetic capabilities. I term the materials and formative processes that arise when highly evolved cells are incorporated into mesoscale matter 'biogeneric', to reflect their commonality with, and distinctiveness from, the organizational properties of non-living materials. The first transition arose by the innovation of classical cell-adhesive cadherins with transmembrane linkage to the cytoskeleton and the appearance of the morphogen Wnt, transforming some ancestral unicellular holozoans into 'liquid tissues', and thereby originating the metazoans. The second transition involved the new capabilities, within a basal metazoan population, of producing a mechanically stable basal lamina, and of planar cell polarization. This gave rise to the eumetazoans, initially diploblastic (two-layered) forms, and then with the addition of extracellular matrices promoting epithelial-mesenchymal transformation, three-layered triploblasts. The last example is the fin-to-limb transition. Here, the components of a molecular network that promoted the development of species-idiosyncratic endoskeletal elements in gnathostome ancestors are proposed to have evolved to a dynamical regime in which they constituted a Turing-type reaction-diffusion system capable of organizing the stereotypical arrays of elements of lobe-finned fish and tetrapods. The contrasting implications of the biogeneric materials-based and neo-Darwinian perspectives for understanding major evolutionary transitions are discussed.This article is part of the themed issue 'The major synthetic evolutionary transitions'.}, }
@article {pmid27431520, year = {2016}, author = {Koonin, EV}, title = {Viruses and mobile elements as drivers of evolutionary transitions.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1701}, pages = {}, doi = {10.1098/rstb.2015.0442}, pmid = {27431520}, issn = {1471-2970}, mesh = {*Biological Evolution ; Interspersed Repetitive Sequences/*genetics ; Viruses/*genetics ; }, abstract = {The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions include the origin of prokaryotic and then eukaryotic cells, multicellular organisms and eusocial animals. All or nearly all cellular life forms are hosts to diverse selfish genetic elements with various levels of autonomy including plasmids, transposons and viruses. I present evidence that, at least up to and including the origin of multicellularity, evolutionary transitions are driven by the coevolution of hosts with these genetic parasites along with sharing of 'public goods'. Selfish elements drive evolutionary transitions at two distinct levels. First, mathematical modelling of evolutionary processes, such as evolution of primitive replicator populations or unicellular organisms, indicates that only increasing organizational complexity, e.g. emergence of multicellular aggregates, can prevent the collapse of the host-parasite system under the pressure of parasites. Second, comparative genomic analysis reveals numerous cases of recruitment of genes with essential functions in cellular life forms, including those that enable evolutionary transitions.This article is part of the themed issue 'The major synthetic evolutionary transitions'.}, }
@article {pmid27431519, year = {2016}, author = {Elena, SF}, title = {Evolutionary transitions during RNA virus experimental evolution.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1701}, pages = {}, doi = {10.1098/rstb.2015.0441}, pmid = {27431519}, issn = {1471-2970}, mesh = {*Biological Evolution ; Coinfection/virology ; Evolution, Molecular ; *Genome, Viral ; *Microbial Interactions ; RNA Viruses/*genetics/physiology ; }, abstract = {In their search to understand the evolution of biological complexity, John Maynard Smith and Eörs Szathmáry put forward the notion of major evolutionary transitions as those in which elementary units get together to generate something new, larger and more complex. The origins of chromosomes, eukaryotic cells, multicellular organisms, colonies and, more recently, language and technological societies are examples that clearly illustrate this notion. However, a transition may be considered as anecdotal or as major depending on the specific level of biological organization under study. In this contribution, I will argue that transitions may also be occurring at a much smaller scale of biological organization: the viral world. Not only that, but also that we can observe in real time how these major transitions take place during experimental evolution. I will review the outcome of recent evolution experiments with viruses that illustrate four major evolutionary transitions: (i) the origin of a new virus that infects an otherwise inaccessible host and completely changes the way it interacts with the host regulatory and metabolic networks, (ii) the incorporation and loss of genes, (iii) the origin of segmented genomes from a non-segmented one, and (iv) the evolution of cooperative behaviour and cheating between different viruses or strains during co-infection of the same host.This article is part of the themed issue 'The major synthetic evolutionary transitions'.}, }
@article {pmid27431516, year = {2016}, author = {Solé, R}, title = {Synthetic transitions: towards a new synthesis.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1701}, pages = {}, doi = {10.1098/rstb.2015.0438}, pmid = {27431516}, issn = {1471-2970}, mesh = {Biological Evolution ; Computer Simulation ; *Life ; *Physics ; *Robotics ; *Synthetic Biology ; }, abstract = {The evolution of life in our biosphere has been marked by several major innovations. Such major complexity shifts include the origin of cells, genetic codes or multicellularity to the emergence of non-genetic information, language or even consciousness. Understanding the nature and conditions for their rise and success is a major challenge for evolutionary biology. Along with data analysis, phylogenetic studies and dedicated experimental work, theoretical and computational studies are an essential part of this exploration. With the rise of synthetic biology, evolutionary robotics, artificial life and advanced simulations, novel perspectives to these problems have led to a rather interesting scenario, where not only the major transitions can be studied or even reproduced, but even new ones might be potentially identified. In both cases, transitions can be understood in terms of phase transitions, as defined in physics. Such mapping (if correct) would help in defining a general framework to establish a theory of major transitions, both natural and artificial. Here, we review some advances made at the crossroads between statistical physics, artificial life, synthetic biology and evolutionary robotics.This article is part of the themed issue 'The major synthetic evolutionary transitions'.}, }
@article {pmid27412854, year = {2016}, author = {Smeds, L and Qvarnström, A and Ellegren, H}, title = {Direct estimate of the rate of germline mutation in a bird.}, journal = {Genome research}, volume = {26}, number = {9}, pages = {1211-1218}, doi = {10.1101/gr.204669.116}, pmid = {27412854}, issn = {1549-5469}, mesh = {Animals ; *Evolution, Molecular ; Genome ; Germ-Line Mutation/*genetics ; High-Throughput Nucleotide Sequencing ; Mutation Rate ; Pedigree ; Songbirds/*genetics ; }, abstract = {The fidelity of DNA replication together with repair mechanisms ensure that the genetic material is properly copied from one generation to another. However, on extremely rare occasions when damages to DNA or replication errors are not repaired, germline mutations can be transmitted to the next generation. Because of the rarity of these events, studying the rate at which new mutations arise across organisms has been a great challenge, especially in multicellular nonmodel organisms with large genomes. We sequenced the genomes of 11 birds from a three-generation pedigree of the collared flycatcher (Ficedula albicollis) and used highly stringent bioinformatic criteria for mutation detection and used several procedures to validate mutations, including following the stable inheritance of new mutations to subsequent generations. We identified 55 de novo mutations with a 10-fold enrichment of mutations at CpG sites and with only a modest male mutation bias. The estimated rate of mutation per site per generation was 4.6 × 10(-9), which corresponds to 2.3 × 10(-9) mutations per site per year. Compared to mammals, this is similar to mouse but about half of that reported for humans, which may be due to the higher frequency of male mutations in humans. We confirm that mutation rate scales positively with genome size and that there is a strong negative relationship between mutation rate and effective population size, in line with the drift-barrier hypothesis. Our study illustrates that it should be feasible to obtain direct estimates of the rate of mutation in essentially any organism from which family material can be obtained.}, }
@article {pmid27411810, year = {2016}, author = {Cook, LM and Araujo, A and Pow-Sang, JM and Budzevich, MM and Basanta, D and Lynch, CC}, title = {Predictive computational modeling to define effective treatment strategies for bone metastatic prostate cancer.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29384}, doi = {10.1038/srep29384}, pmid = {27411810}, issn = {2045-2322}, support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA143094/CA/NCI NIH HHS/United States ; U01 CA151924/CA/NCI NIH HHS/United States ; U01 CA202958/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bone Neoplasms/*secondary/*therapy ; Bone and Bones/pathology ; Cell Differentiation ; Cell Survival ; *Computer Simulation ; Humans ; Male ; Mice ; Mice, SCID ; Neoplasm Metastasis ; Osteoblasts/cytology ; Osteoclasts/cytology ; Osteolysis ; Prostate/pathology ; Prostatic Neoplasms/*pathology/*therapy ; Transforming Growth Factor beta1/antagonists &amp; inhibitors/*metabolism ; }, abstract = {The ability to rapidly assess the efficacy of therapeutic strategies for incurable bone metastatic prostate cancer is an urgent need. Pre-clinical in vivo models are limited in their ability to define the temporal effects of therapies on simultaneous multicellular interactions in the cancer-bone microenvironment. Integrating biological and computational modeling approaches can overcome this limitation. Here, we generated a biologically driven discrete hybrid cellular automaton (HCA) model of bone metastatic prostate cancer to identify the optimal therapeutic window for putative targeted therapies. As proof of principle, we focused on TGFβ because of its known pleiotropic cellular effects. HCA simulations predict an optimal effect for TGFβ inhibition in a pre-metastatic setting with quantitative outputs indicating a significant impact on prostate cancer cell viability, osteoclast formation and osteoblast differentiation. In silico predictions were validated in vivo with models of bone metastatic prostate cancer (PAIII and C4-2B). Analysis of human bone metastatic prostate cancer specimens reveals heterogeneous cancer cell use of TGFβ. Patient specific information was seeded into the HCA model to predict the effect of TGFβ inhibitor treatment on disease evolution. Collectively, we demonstrate how an integrated computational/biological approach can rapidly optimize the efficacy of potential targeted therapies on bone metastatic prostate cancer.}, }
@article {pmid27404254, year = {2016}, author = {Durand, PM and Sym, S and Michod, RE}, title = {Programmed Cell Death and Complexity in Microbial Systems.}, journal = {Current biology : CB}, volume = {26}, number = {13}, pages = {R587-R593}, doi = {10.1016/j.cub.2016.05.057}, pmid = {27404254}, issn = {1879-0445}, mesh = {*Apoptosis ; Archaea/*physiology ; *Bacterial Physiological Phenomena ; }, abstract = {Programmed cell death (PCD) is central to organism development and for a long time was considered a hallmark of multicellularity. Its discovery, therefore, in unicellular organisms presents compelling questions. Why did PCD evolve? What is its ecological effect on communities? To answer these questions, one is compelled to consider the impacts of PCD beyond the cell, for death obviously lowers the fitness of the cell. Here, we examine the ecological effects of PCD in different microbial scenarios and conclude that PCD can increase biological complexity. In mixed microbial communities, the mode of death affects the microenvironment, impacting the interactions between taxa. Where the population comprises groups of relatives, death has a more explicit effect. Death by lysis or other means can be harmful, while PCD can evolve by providing advantages to relatives. The synchronization of death between individuals suggests a group level property is being maintained and the mode of death also appears to have had an impact during the origin of multicellularity. PCD can result in the export of fitness from the cell to the group level via re-usable resources and PCD may also provide a mechanism for how groups beget new groups comprising kin. Furthermore, PCD is a means for solving a central problem of group living - the toxic effects of death - by making resources in dying cells beneficial to others. What emerges from the data reviewed here is that while PCD carries an obvious cost to the cell, it can be a driver of complexity in microbial communities.}, }
@article {pmid27402737, year = {2016}, author = {Wahl, ME and Murray, AW}, title = {Multicellularity makes somatic differentiation evolutionarily stable.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {30}, pages = {8362-8367}, doi = {10.1073/pnas.1608278113}, pmid = {27402737}, issn = {1091-6490}, support = {P50 GM068763/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; *Cell Differentiation ; Cell Division/genetics ; *Cell Lineage ; Cell Survival/genetics ; Genetic Engineering/methods ; Germ Cells/*cytology/metabolism ; *Models, Biological ; Mutation ; Saccharomyces cerevisiae/cytology/genetics ; }, abstract = {Many multicellular organisms produce two cell lineages: germ cells, whose descendants produce the next generation, and somatic cells, which support, protect, and disperse the germ cells. This germ-soma demarcation has evolved independently in dozens of multicellular taxa but is absent in unicellular species. A common explanation holds that in these organisms, inefficient intercellular nutrient exchange compels the fitness cost of producing nonreproductive somatic cells to outweigh any potential benefits. We propose instead that the absence of unicellular, soma-producing populations reflects their susceptibility to invasion by nondifferentiating mutants that ultimately eradicate the soma-producing lineage. We argue that multicellularity can prevent the victory of such mutants by giving germ cells preferential access to the benefits conferred by somatic cells. The absence of natural unicellular, soma-producing species previously prevented these hypotheses from being directly tested in vivo: to overcome this obstacle, we engineered strains of the budding yeast Saccharomyces cerevisiae that differ only in the presence or absence of multicellularity and somatic differentiation, permitting direct comparisons between organisms with different lifestyles. Our strains implement the essential features of irreversible conversion from germ line to soma, reproductive division of labor, and clonal multicellularity while maintaining sufficient generality to permit broad extension of our conclusions. Our somatic cells can provide fitness benefits that exceed the reproductive costs of their production, even in unicellular strains. We find that nondifferentiating mutants overtake unicellular populations but are outcompeted by multicellular, soma-producing strains, suggesting that multicellularity confers evolutionary stability to somatic differentiation.}, }
@article {pmid27401232, year = {2016}, author = {Francois, CM and Duret, L and Simon, L and Mermillod-Blondin, F and Malard, F and Konecny-Dupré, L and Planel, R and Penel, S and Douady, CJ and Lefébure, T}, title = {No Evidence That Nitrogen Limitation Influences the Elemental Composition of Isopod Transcriptomes and Proteomes.}, journal = {Molecular biology and evolution}, volume = {33}, number = {10}, pages = {2605-2620}, doi = {10.1093/molbev/msw131}, pmid = {27401232}, issn = {1537-1719}, mesh = {Amino Acids/genetics/metabolism ; Animals ; Ecosystem ; Isopoda/*genetics/*metabolism ; Nitrogen/*deficiency/*metabolism ; Nucleotides/genetics/metabolism ; Phylogeny ; Proteome ; Selection, Genetic ; Transcriptome ; }, abstract = {The field of stoichiogenomics aims at understanding the influence of nutrient limitations on the elemental composition of the genome, transcriptome, and proteome. The 20 amino acids and the 4 nt differ in the number of nutrients they contain, such as nitrogen (N). Thus, N limitation shall theoretically select for changes in the composition of proteins or RNAs through preferential use of N-poor amino acids or nucleotides, which will decrease the N-budget of an organism. While these N-saving mechanisms have been evidenced in microorganisms, they remain controversial in multicellular eukaryotes. In this study, we used 13 surface and subterranean isopod species pairs that face strongly contrasted N limitations, either in terms of quantity or quality. We combined in situ nutrient quantification and transcriptome sequencing to test if N limitation selected for N-savings through changes in the expression and composition of the transcriptome and proteome. No evidence of N-savings was found in the total N-budget of transcriptomes or proteomes or in the average protein N-cost. Nevertheless, subterranean species evolving in N-depleted habitats displayed lower N-usage at their third codon positions. To test if this convergent compositional change was driven by natural selection, we developed a method to detect the strand-asymmetric signature that stoichiogenomic selection should leave in the substitution pattern. No such signature was evidenced, indicating that the observed stoichiogenomic-like patterns were attributable to nonadaptive processes. The absence of stoichiogenomic signal despite strong N limitation within a powerful phylogenetic framework casts doubt on the existence of stoichiogenomic mechanisms in metazoans.}, }
@article {pmid27391808, year = {2016}, author = {Jeong, SY and Lee, JH and Shin, Y and Chung, S and Kuh, HJ}, title = {Co-Culture of Tumor Spheroids and Fibroblasts in a Collagen Matrix-Incorporated Microfluidic Chip Mimics Reciprocal Activation in Solid Tumor Microenvironment.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0159013}, doi = {10.1371/journal.pone.0159013}, pmid = {27391808}, issn = {1932-6203}, mesh = {Coculture Techniques/instrumentation/methods ; Collagen/*chemistry ; Colorectal Neoplasms/*metabolism/pathology ; Extracellular Matrix/chemistry ; Fibroblasts/*metabolism/pathology ; Humans ; *Lab-On-A-Chip Devices ; Spheroids, Cellular/*metabolism/pathology ; *Tumor Microenvironment ; }, abstract = {Multicellular 3D culture and interaction with stromal components are considered essential elements in establishing a 'more clinically relevant' tumor model. Matrix-embedded 3D cultures using a microfluidic chip platform can recapitulate the microscale interaction within tumor microenvironments. As a major component of tumor microenvironment, cancer-associated fibroblasts (CAFs) play a role in cancer progression and drug resistance. Here, we present a microfluidic chip-based tumor tissue culture model that integrates 3D tumor spheroids (TSs) with CAF in proximity within a hydrogel scaffold. HT-29 human colorectal carcinoma cells grew into 3D TSs and the growth was stimulated when co-cultured with fibroblasts as shown by 1.5-folds increase of % changes in diameter over 5 days. TS cultured for 6 days showed a reduced expression of Ki-67 along with increased expression of fibronectin when co-cultured with fibroblasts compared to mono-cultured TSs. Fibroblasts were activated under co-culture conditions, as demonstrated by increases in α-SMA expression and migratory activity. When exposed to paclitaxel, a survival advantage was observed in TSs co-cultured with activated fibroblasts. Overall, we demonstrated the reciprocal interaction between TSs and fibroblasts in our 7-channel microfluidic chip. The co-culture of 3D TS-CAF in a collagen matrix-incorporated microfluidic chip may be useful to study the tumor microenvironment and for evaluation of drug screening and evaluation.}, }
@article {pmid27383475, year = {2016}, author = {Baek, SY and Jang, KH and Choi, EH and Ryu, SH and Kim, SK and Lee, JH and Lim, YJ and Lee, J and Jun, J and Kwak, M and Lee, YS and Hwang, JS and Venmathi Maran, BA and Chang, CY and Kim, IH and Hwang, UW}, title = {DNA Barcoding of Metazoan Zooplankton Copepods from South Korea.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0157307}, doi = {10.1371/journal.pone.0157307}, pmid = {27383475}, issn = {1932-6203}, mesh = {Animals ; Copepoda/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genes, Mitochondrial ; Genetic Variation ; Geography ; Phylogeny ; Republic of Korea ; Sequence Analysis, DNA ; Species Specificity ; Zooplankton/*genetics ; }, abstract = {Copepods, small aquatic crustaceans, are the most abundant metazoan zooplankton and outnumber every other group of multicellular animals on earth. In spite of ecological and biological importance in aquatic environment, their morphological plasticity, originated from their various lifestyles and their incomparable capacity to adapt to a variety of environments, has made the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of cryptic or sibling species based on DNA sequence data. We examined sequence variation of a partial mitochondrial cytochrome C oxidase I gene (COI) from 133 copepod individuals collected from the Korean Peninsula, in order to identify and discriminate 94 copepod species covering six copepod orders of Calanoida, Cyclopoida, Harpacticoida, Monstrilloida, Poecilostomatoida and Siphonostomatoida. The results showed that there exists a clear gap with ca. 20 fold difference between the averages of within-specific sequence divergence (2.42%) and that of between-specific sequence divergence (42.79%) in COI, suggesting the plausible utility of this gene in delimitating copepod species. The results showed, with the COI barcoding data among 94 copepod species, that a copepod species could be distinguished from the others very clearly, only with four exceptions as followings: Mesocyclops dissimilis-Mesocyclops pehpeiensis (0.26% K2P distance in percent) and Oithona davisae-Oithona similis (1.1%) in Cyclopoida, Ostrincola japonica-Pseudomyicola spinosus (1.5%) in Poecilostomatoida, and Hatschekia japonica-Caligus quadratus (5.2%) in Siphonostomatoida. Thus, it strongly indicated that COI may be a useful tool in identifying various copepod species and make an initial progress toward the construction of a comprehensive DNA barcode database for copepods inhabiting the Korean Peninsula.}, }
@article {pmid27379901, year = {2016}, author = {Olson, BJ and Nedelcu, AM}, title = {Co-option during the evolution of multicellular and developmental complexity in the volvocine green algae.}, journal = {Current opinion in genetics &amp; development}, volume = {39}, number = {}, pages = {107-115}, doi = {10.1016/j.gde.2016.06.003}, pmid = {27379901}, issn = {1879-0380}, mesh = {Cell Differentiation/*genetics ; Chlamydomonas/classification/genetics/growth &amp; development ; Chlorophyta/classification/*genetics/growth &amp; development ; *Evolution, Molecular ; Germ Cells/growth &amp; development ; *Phylogeny ; Volvox/classification/genetics/growth &amp; development ; }, abstract = {Despite its major impact on the evolution of Life on Earth, the transition to multicellularity remains poorly understood, especially in terms of its genetic basis. The volvocine algae are a group of closely related species that range in morphology from unicellular individuals (Chlamydomonas) to undifferentiated multicellular forms (Gonium) and complex organisms with distinct developmental programs and one (Pleodorina) or two (Volvox) specialized cell types. Modern genetic approaches, complemented by the recent sequencing of genomes from several key species, revealed that co-option of existing genes and pathways is the primary driving force for the evolution of multicellularity in this lineage. The initial transition to undifferentiated multicellularity, as typified by the extant Gonium, was driven primarily by the co-option of cell cycle regulation. Further morphological and developmental innovations in the lineage leading to Volvox resulted from additional co-option events involving genes important for embryonic inversion, asymmetric cell division, somatic and germ cell differentiation and the structure and function of the extracellular matrix. Because of their relatively low but variable levels of morphological and developmental complexity, simple underlying genetics and recent evolutionary history, the volvocine algae are providing significant insight into our understanding of the genetics and evolution of major developmental and morphological traits.}, }
@article {pmid27376334, year = {2016}, author = {Bains, W and Schulze-Makuch, D}, title = {The Cosmic Zoo: The (Near) Inevitability of the Evolution of Complex, Macroscopic Life.}, journal = {Life (Basel, Switzerland)}, volume = {6}, number = {3}, pages = {}, doi = {10.3390/life6030025}, pmid = {27376334}, issn = {2075-1729}, abstract = {Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily. The conclusion for other worlds is that if the origin of life can occur rather easily, we should live in a cosmic zoo, as the innovations necessary to lead to complex life will occur with high probability given sufficient time and habitat. On the other hand, if the origin of life is rare, then we might live in a rather empty universe.}, }
@article {pmid27374341, year = {2016}, author = {Mikhailov, KV and Slyusarev, GS and Nikitin, MA and Logacheva, MD and Penin, AA and Aleoshin, VV and Panchin, YV}, title = {The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians.}, journal = {Current biology : CB}, volume = {26}, number = {13}, pages = {1768-1774}, doi = {10.1016/j.cub.2016.05.007}, pmid = {27374341}, issn = {1879-0445}, mesh = {Animals ; Female ; *Genome ; Host-Parasite Interactions ; Invertebrates/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Orthonectids are rare parasites of marine invertebrates [1] that are commonly treated in textbooks as a taxon of uncertain affinity [2]. Trophic forms of orthonectids reside in the tissues of their hosts as multinucleated plasmodia, generating short-lived, worm-like ciliated female and male organisms that exit into the environment for copulation [3]. These ephemeral males and females are composed of just several hundred somatic cells and are deprived of digestive, circulatory, or excretory systems. Since their discovery in the 19(th) century, the orthonectids were described as organisms with no differentiated cell types and considered as part of Mesozoa, a putative link between multicellular animals and their unicellular relatives. More recently, this view was challenged as the new data suggested that orthonectids are animals that became simplified due to their parasitic way of life [3, 4]. Here, we report the genomic sequence of Intoshia linei, one of about 20 known species of orthonectids. The genomic data confirm recent morphological analysis asserting that orthonectids are members of Spiralia and possess muscular and nervous systems [5]. The 43-Mbp genome of I. linei encodes about 9,000 genes and retains those essential for the development and activity of muscular and nervous systems. The simplification of orthonectid body plan is associated with considerable reduction of metazoan developmental genes, leaving what might be viewed as the minimal gene set necessary to retain critical bilaterian features.}, }
@article {pmid27357338, year = {2016}, author = {Glöckner, G and Lawal, HM and Felder, M and Singh, R and Singer, G and Weijer, CJ and Schaap, P}, title = {The multicellularity genes of dictyostelid social amoebas.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12085}, doi = {10.1038/ncomms12085}, pmid = {27357338}, issn = {2041-1723}, support = {BB/G020426/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {*Biological Evolution ; Cell Differentiation/genetics ; Dictyostelium/*genetics ; Gene Expression Profiling ; Gene Transfer, Horizontal ; *Genes, Essential ; Whole Genome Sequencing ; }, abstract = {The evolution of multicellularity enabled specialization of cells, but required novel signalling mechanisms for regulating cell differentiation. Early multicellular organisms are mostly extinct and the origins of these mechanisms are unknown. Here using comparative genome and transcriptome analysis across eight uni- and multicellular amoebozoan genomes, we find that 80% of proteins essential for the development of multicellular Dictyostelia are already present in their unicellular relatives. This set is enriched in cytosolic and nuclear proteins, and protein kinases. The remaining 20%, unique to Dictyostelia, mostly consists of extracellularly exposed and secreted proteins, with roles in sensing and recognition, while several genes for synthesis of signals that induce cell-type specialization were acquired by lateral gene transfer. Across Dictyostelia, changes in gene expression correspond more strongly with phenotypic innovation than changes in protein functional domains. We conclude that the transition to multicellularity required novel signals and sensors rather than novel signal processing mechanisms.}, }
@article {pmid27356975, year = {2016}, author = {Yerramsetty, P and Stata, M and Siford, R and Sage, TL and Sage, RF and Wong, GK and Albert, VA and Berry, JO}, title = {Evolution of RLSB, a nuclear-encoded S1 domain RNA binding protein associated with post-transcriptional regulation of plastid-encoded rbcL mRNA in vascular plants.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {141}, doi = {10.1186/s12862-016-0713-1}, pmid = {27356975}, issn = {1471-2148}, mesh = {Chloroplasts/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Plant ; Magnoliopsida/*genetics ; Photosynthesis ; Phylogeny ; Plant Leaves/genetics ; Plant Proteins/*genetics/metabolism ; Plastids/*genetics/metabolism ; Poaceae/genetics ; RNA Processing, Post-Transcriptional ; RNA, Messenger/metabolism ; RNA-Binding Proteins/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; Zea mays/genetics ; }, abstract = {BACKGROUND: RLSB, an S-1 domain RNA binding protein of Arabidopsis, selectively binds rbcL mRNA and co-localizes with Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) within chloroplasts of C3 and C4 plants. Previous studies using both Arabidopsis (C3) and maize (C4) suggest RLSB homologs are post-transcriptional regulators of plastid-encoded rbcL mRNA. While RLSB accumulates in all Arabidopsis leaf chlorenchyma cells, in C4 leaves RLSB-like proteins accumulate only within Rubisco-containing bundle sheath chloroplasts of Kranz-type species, and only within central compartment chloroplasts in the single cell C4 plant Bienertia. Our recent evidence implicates this mRNA binding protein as a primary determinant of rbcL expression, cellular localization/compartmentalization, and photosynthetic function in all multicellular green plants. This study addresses the hypothesis that RLSB is a highly conserved Rubisco regulatory factor that occurs in the chloroplasts all higher plants.<br><br>RESULTS: Phylogenetic analysis has identified RLSB orthologs and paralogs in all major plant groups, from ancient liverworts to recent angiosperms. RLSB homologs were also identified in algae of the division Charophyta, a lineage closely related to land plants. RLSB-like sequences were not identified in any other algae, suggesting that it may be specific to the evolutionary line leading to land plants. The RLSB family occurs in single copy across most angiosperms, although a few species with two copies were identified, seemingly randomly distributed throughout the various taxa, although perhaps correlating in some cases with known ancient whole genome duplications. Monocots of the order Poales (Poaceae and Cyperaceae) were found to contain two copies, designated here as RLSB-a and RLSB-b, with only RLSB-a implicated in the regulation of rbcL across the maize developmental gradient. Analysis of microsynteny in angiosperms revealed high levels of conservation across eudicot species and for both paralogs in grasses, highlighting the possible importance of maintaining this gene and its surrounding genomic regions.<br><br>CONCLUSIONS: Findings presented here indicate that the RLSB family originated as a unique gene in land plant evolution, perhaps in the common ancestor of charophytes and higher plants. Purifying selection has maintained this as a highly conserved single- or two-copy gene across most extant species, with several conserved gene duplications. Together with previous findings, this study suggests that RLSB has been sustained as an important regulatory protein throughout the course of land plant evolution. While only RLSB-a has been directly implicated in rbcL regulation in maize, RLSB-b could have an overlapping function in the co-regulation of rbcL, or may have diverged as a regulator of one or more other plastid-encoded mRNAs. This analysis confirms that RLSB is an important and unique photosynthetic regulatory protein that has been continuously expressed in land plants as they emerged and diversified from their ancient common ancestor.}, }
@article {pmid29368868, year = {2016}, author = {Zakharov, IA}, title = {[Horizontal gene transfer into the genomes of insects].}, journal = {Genetika}, volume = {52}, number = {7}, pages = {804-809}, pmid = {29368868}, issn = {0016-6758}, mesh = {Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal/*physiology ; Insecta/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is widespread in the world of prokaryotes, but the examples of this phenomenon among multicellular animals, particularly insects, are few. This review examines the transfer of genetic material to the nuclear genomes of insects from the mitochondrial genome (intracellular HGT), as well as from the genomes of viruses, bacteria, fungi, and unrelated insects. In most cases, the mechanisms of this transfer are unknown. Many pro- and eukaryotic genes that moved through the HGT are expressed in the insect genome and in some cases can provide the evolutionary innovations that are considered as aromorphoses.}, }
@article {pmid27339473, year = {2016}, author = {Chisholm, RH and Lorenzi, T and Clairambault, J}, title = {Cell population heterogeneity and evolution towards drug resistance in cancer: Biological and mathematical assessment, theoretical treatment optimisation.}, journal = {Biochimica et biophysica acta}, volume = {1860}, number = {11 Pt B}, pages = {2627-2645}, doi = {10.1016/j.bbagen.2016.06.009}, pmid = {27339473}, issn = {0006-3002}, mesh = {Drug Resistance, Neoplasm/*drug effects ; Humans ; Immunotherapy/methods ; Models, Biological ; Models, Theoretical ; Neoplasms/*drug therapy/*pathology ; Phenotype ; }, abstract = {BACKGROUND: Drug-induced drug resistance in cancer has been attributed to diverse biological mechanisms at the individual cell or cell population scale, relying on stochastically or epigenetically varying expression of phenotypes at the single cell level, and on the adaptability of tumours at the cell population level.<br><br>SCOPE OF REVIEW: We focus on intra-tumour heterogeneity, namely between-cell variability within cancer cell populations, to account for drug resistance. To shed light on such heterogeneity, we review evolutionary mechanisms that encompass the great evolution that has designed multicellular organisms, as well as smaller windows of evolution on the time scale of human disease. We also present mathematical models used to predict drug resistance in cancer and optimal control methods that can circumvent it in combined therapeutic strategies.<br><br>MAJOR CONCLUSIONS: Plasticity in cancer cells, i.e., partial reversal to a stem-like status in individual cells and resulting adaptability of cancer cell populations, may be viewed as backward evolution making cancer cell populations resistant to drug insult. This reversible plasticity is captured by mathematical models that incorporate between-cell heterogeneity through continuous phenotypic variables. Such models have the benefit of being compatible with optimal control methods for the design of optimised therapeutic protocols involving combinations of cytotoxic and cytostatic treatments with epigenetic drugs and immunotherapies.<br><br>GENERAL SIGNIFICANCE: Gathering knowledge from cancer and evolutionary biology with physiologically based mathematical models of cell population dynamics should provide oncologists with a rationale to design optimised therapeutic strategies to circumvent drug resistance, that still remains a major pitfall of cancer therapeutics. This article is part of a Special Issue entitled &quot;System Genetics&quot; Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.}, }
@article {pmid27338490, year = {2016}, author = {Shapiro, JA}, title = {Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.}, journal = {Biology}, volume = {5}, number = {2}, pages = {}, doi = {10.3390/biology5020027}, pmid = {27338490}, issn = {2079-7737}, abstract = {The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather tha