@article {pmid31444931, year = {2019}, author = {Wu, F and Ma, C and Han, B and Meng, L and Hu, H and Fang, Y and Feng, M and Zhang, X and Rueppell, O and Li, J}, title = {Behavioral, physiological, and molecular changes in alloparental care givers may be responsible for selection response for female reproductive investment in honey bees.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15207}, pmid = {31444931}, issn = {1365-294X}, abstract = {Reproductive investment is a central life history variable that influences all aspects of life. Hormones coordinate reproduction in multicellular organisms, but the mechanisms controlling the collective reproductive investment of social insects are largely unexplored. One important aspect of honey bee (Apis mellifera) reproductive investment consists of raising female-destined larvae into new queens by alloparental care of nurse bees in form of royal jelly provisioning. Artificial selection for commercial royal jelly production over 40 years has increased this reproductive investment by an order of magnitude. In a cross-fostering experiment, we establish that this shift in social phenotype is caused by nurse bees. We find no evidence for changes in larval signaling. Instead, the antennae of the nurse bees of the selected stock are more responsive to brood pheromones than control bees. Correspondingly, the selected royal jelly bee nurses are more attracted to brood pheromones than unselected control nurses. Comparative proteomics of the antennae from the selected and unselected stocks indicate putative molecular mechanisms, primarily changes in chemosensation and energy metabolism. We report expression differences of several candidate genes that correlate with the differences in reproductive investment. The functional relevance of these genes is supported by demonstrating that the corresponding proteins can competitively bind one previously described and one newly discovered brood pheromone. Thus, we suggest several chemosensory genes, most prominently OBP16 and CSP4, as candidate mechanisms controlling queen rearing, a key reproductive investment, in honey bees. These findings reveal novel aspects of pheromonal communication in honey bees and explain how sensory changes affect communication and lead to a drastic shift in colony-level resource allocation to sexual reproduction. Thus, pheromonal and hormonal communication may play similar roles for reproductive investment in superorganisms and multicellular organisms, respectively. This article is protected by copyright. All rights reserved.}, }
@article {pmid31444229, year = {2019}, author = {Draper, GW and Shoemark, DK and Adams, JC}, title = {Modelling the early evolution of extracellular matrix from modern Ctenophores and Sponges.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20180048}, pmid = {31444229}, issn = {1744-1358}, abstract = {Animals (metazoans) include some of the most complex living organisms on Earth, with regard to their multicellularity, numbers of differentiated cell types, and lifecycles. The metazoan extracellular matrix (ECM) is well-known to have major roles in the development of tissues during embryogenesis and in maintaining homoeostasis throughout life, yet insight into the ECM proteins which may have contributed to the transition from unicellular eukaryotes to multicellular animals remains sparse. Recent phylogenetic studies place either ctenophores or poriferans as the closest modern relatives of the earliest emerging metazoans. Here, we review the literature and representative genomic and transcriptomic databases for evidence of ECM and ECM-affiliated components known to be conserved in bilaterians, that are also present in ctenophores and/or poriferans. Whereas an extensive set of related proteins are identifiable in poriferans, there is a strikingly lack of conservation in ctenophores. From this perspective, much remains to be learnt about the composition of ctenophore mesoglea. The principal ECM-related proteins conserved between ctenophores, poriferans, and bilaterians include collagen IV, laminin-like proteins, thrombospondin superfamily members, integrins, membrane-associated proteoglycans, and tissue transglutaminase. These are candidates for a putative ancestral ECM that may have contributed to the emergence of the metazoans.}, }
@article {pmid31430180, year = {2019}, author = {D'Ario, M and Sablowski, R}, title = {Cell Size Control in Plants.}, journal = {Annual review of genetics}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-genet-112618-043602}, pmid = {31430180}, issn = {1545-2948}, abstract = {The genetic control of the characteristic cell sizes of different species and tissues is a long-standing enigma. Plants are convenient for studying this question in a multicellular context, as their cells do not move and are easily tracked and measured from organ initiation in the meristems to subsequent morphogenesis and differentiation. In this article, we discuss cell size control in plants compared with other organisms. As seen from yeast cells to mammalian cells, size homeostasis is maintained cell autonomously in the shoot meristem. In developing organs, vacuolization contributes to cell size heterogeneity and may resolve conflicts between growth control at the cellular and organ levels. Molecular mechanisms for cell size control have implications for how cell size responds to changes in ploidy, which are particularly important in plant development and evolution. We also discuss comparatively the functional consequences of cell size and their potential repercussions at higher scales, including genome evolution. Expected final online publication date for the Annual Review of Genetics, Volume 53 is November 23, 2019. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid31427514, year = {2019}, author = {Kjeldsen, KU and Schreiber, L and Thorup, CA and Boesen, T and Bjerg, JT and Yang, T and Dueholm, MS and Larsen, S and Risgaard-Petersen, N and Nierychlo, M and Schmid, M and Bøggild, A and van de Vossenberg, J and Geelhoed, JS and Meysman, FJR and Wagner, M and Nielsen, PH and Nielsen, LP and Schramm, A}, title = {On the evolution and physiology of cable bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1903514116}, pmid = {31427514}, issn = {1091-6490}, abstract = {Cable bacteria of the family Desulfobulbaceae form centimeter-long filaments comprising thousands of cells. They occur worldwide in the surface of aquatic sediments, where they connect sulfide oxidation with oxygen or nitrate reduction via long-distance electron transport. In the absence of pure cultures, we used single-filament genomics and metagenomics to retrieve draft genomes of 3 marine Candidatus Electrothrix and 1 freshwater Ca. Electronema species. These genomes contain >50% unknown genes but still share their core genomic makeup with sulfate-reducing and sulfur-disproportionating Desulfobulbaceae, with few core genes lost and 212 unique genes (from 197 gene families) conserved among cable bacteria. Last common ancestor analysis indicates gene divergence and lateral gene transfer as equally important origins of these unique genes. With support from metaproteomics of a Ca. Electronema enrichment, the genomes suggest that cable bacteria oxidize sulfide by reversing the canonical sulfate reduction pathway and fix CO2 using the Wood-Ljungdahl pathway. Cable bacteria show limited organotrophic potential, may assimilate smaller organic acids and alcohols, fix N2, and synthesize polyphosphates and polyglucose as storage compounds; several of these traits were confirmed by cell-level experimental analyses. We propose a model for electron flow from sulfide to oxygen that involves periplasmic cytochromes, yet-unidentified conductive periplasmic fibers, and periplasmic oxygen reduction. This model proposes that an active cable bacterium gains energy in the anodic, sulfide-oxidizing cells, whereas cells in the oxic zone flare off electrons through intense cathodic oxygen respiration without energy conservation; this peculiar form of multicellularity seems unparalleled in the microbial world.}, }
@article {pmid31415772, year = {2019}, author = {Miller, WB and Torday, JS and Baluška, F}, title = {The N-Space Episenome Unifies Cellular Information Space-Time within Cognition-Based Evolution.}, journal = {Progress in biophysics and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pbiomolbio.2019.08.006}, pmid = {31415772}, issn = {1873-1732}, abstract = {Self-referential cellular homeostasis is maintained by the measured assessment of both internal status and external conditions based within an integrated cellular information field. This cellular field attachment to biologic information space-time coordinates environmental inputs by connecting the cellular senome, as the sum of the sensory experiences of the cell, with its genome and epigenome. In multicellular organisms, individual cellular information fields aggregate into a collective information architectural matrix, termed a N-space Episenome, that enables mutualized organism-wide information management. It is hypothesized that biological organization represents a dual heritable system constituted by both its biological materiality and a conjoining N-space Episenome. It is further proposed that morphogenesis derives from reciprocations between these inter-related facets to yield coordinated multicellular growth and development. The N-space Episenome is conceived as a whole cell informational projection that is heritable, transferable via cell division and essential for the synchronous integration of the diverse self-referential cells that constitute holobionts.}, }
@article {pmid31413788, year = {2019}, author = {Fields, C and Levin, M}, title = {Somatic multicellularity as a satisficing solution to the prediction-error minimization problem.}, journal = {Communicative & integrative biology}, volume = {12}, number = {1}, pages = {119-132}, doi = {10.1080/19420889.2019.1643666}, pmid = {31413788}, issn = {1942-0889}, abstract = {Adaptive success in the biosphere requires the dynamic ability to adjust physiological, transcriptional, and behavioral responses to environmental conditions. From chemical networks to organisms to whole communities, biological entities at all levels of organization seek to optimize their predictive power. Here, we argue that this fundamental drive provides a novel perspective on the origin of multicellularity. One way for unicellular organisms to minimize surprise with respect to external inputs is to be surrounded by reproductively-disabled, i.e. somatic copies of themselves - highly predictable agents which in effect reduce uncertainty in their microenvironments. We show that the transition to multicellularity can be modeled as a phase transition driven by environmental threats. We present modeling results showing how multicellular bodies can arise if non-reproductive somatic cells protect their reproductive parents from environmental lethality. We discuss how a somatic body can be interpreted as a Markov blanket around one or more reproductive cells, and how the transition to somatic multicellularity can be represented as a transition from exposure of reproductive cells to a high-uncertainty environment to their protection from environmental uncertainty by this Markov blanket. This is, effectively, a transition by the Markov blanket from transparency to opacity for the variational free energy of the environment. We suggest that the ability to arrest the cell cycle of daughter cells and redirect their resource utilization from division to environmental threat amelioration is the key innovation of obligate multicellular eukaryotes, that the nervous system evolved to exercise this control over long distances, and that cancer is an escape by somatic cells from the control of reproductive cells. Our quantitative model illustrates the evolutionary dynamics of this system, provides a novel hypothesis for the origin of multicellular animal bodies, and suggests a fundamental link between the architectures of complex organisms and information processing in proto-cognitive cellular agents.}, }
@article {pmid30256189, year = {2018}, author = {Almeida, LV and Coqueiro-Dos-Santos, A and Rodriguez-Luiz, GF and McCulloch, R and Bartholomeu, DC and Reis-Cunha, JL}, title = {Chromosomal copy number variation analysis by next generation sequencing confirms ploidy stability in Trypanosoma brucei subspecies.}, journal = {Microbial genomics}, volume = {4}, number = {10}, pages = {}, pmid = {30256189}, issn = {2057-5858}, support = {//Wellcome Trust/United Kingdom ; BB/K006495/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M028909/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N016165/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 206815/Z/17/Z//Wellcome Trust/United Kingdom ; 104111//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Chromosomes/*genetics/metabolism ; *DNA Copy Number Variations ; DNA Replication/physiology ; DNA, Protozoan/biosynthesis/genetics ; High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence ; Leishmania/genetics/metabolism ; *Phylogeny ; *Ploidies ; Species Specificity ; Trypanosoma brucei brucei/*genetics/metabolism ; Trypanosoma cruzi/*genetics/metabolism ; }, abstract = {Although aneuploidy usually results in severe abnormalities in multicellular eukaryotes, recent data suggest that it could be beneficial for unicellular eukaryotes, such as yeast and trypanosomatid parasites, providing increased survival under stressful conditions. Among characterized trypanosomatids, Trypanosoma cruzi, Trypanosoma brucei and species from the genus Leishmania stand out due to their importance in public health, infecting around 20 million people worldwide. The presence of aneuploidies in T. cruzi and Leishmania was recently confirmed by analysis based on next generation sequencing (NGS) and fluorescence in situ hybridization, where they have been associated with adaptation during transmission between their insect vectors and mammalian hosts and in promoting drug resistance. Although chromosomal copy number variations (CCNVs) are present in the aforementioned species, PFGE and fluorescence cytophotometry analyses suggest that aneuploidies are absent from T. brucei. A re-evaluation of CCNV in T. b gambiense based on NGS reads confirmed the absence of aneuploidies in this subspecies. However, the presence of aneuploidies in the other two T. brucei subspecies, T. b. brucei and T. b. rhodesiense, has not been evaluated using NGS approaches. In the present work, we tested for aneuploidies in 26 T. brucei isolates, including samples from the three T. brucei subspecies, by both allele frequency and read depth coverage analyses. These analyses showed that none of the T. brucei subspecies presents aneuploidies, which could be related to differences in the mechanisms of DNA replication and recombination in these parasites when compared with Leishmania.}, }
@article {pmid31410258, year = {2019}, author = {Kuzdzal-Fick, JJ and Chen, L and Balázsi, G}, title = {Disadvantages and benefits of evolved unicellularity versus multicellularity in budding yeast.}, journal = {Ecology and evolution}, volume = {9}, number = {15}, pages = {8509-8523}, doi = {10.1002/ece3.5322}, pmid = {31410258}, issn = {2045-7758}, abstract = {Multicellular organisms appeared on Earth through several independent major evolutionary transitions. Are such transitions reversible? Addressing this fundamental question entails understanding the benefits and costs of multicellularity versus unicellularity. For example, some wild yeast strains form multicellular clumps, which might be beneficial in stressful conditions, but this has been untested. Here, we show that unicellular yeast evolve from clump-forming ancestors by propagating samples from suspension after larger clumps have settled. Unicellular yeast strains differed from their clumping ancestors mainly by mutations in the AMN1 (Antagonist of Mitotic exit Network) gene. Ancestral yeast clumps were more resistant to freeze/thaw, hydrogen peroxide, and ethanol stressors than their unicellular counterparts, but they grew slower without stress. These findings suggest disadvantages and benefits to multicellularity and unicellularity that may have impacted the emergence of multicellular life forms.}, }
@article {pmid31409661, year = {2019}, author = {Small, CM and Currey, M and Beck, EA and Bassham, S and Cresko, WA}, title = {Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, doi = {10.1128/mSystems.00331-19}, pmid = {31409661}, issn = {2379-5077}, abstract = {Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.}, }
@article {pmid28687624, year = {2018}, author = {Tejos, R and Rodriguez-Furlán, C and Adamowski, M and Sauer, M and Norambuena, L and Friml, J}, title = {PATELLINS are regulators of auxin-mediated PIN1 relocation and plant development in Arabidopsis thaliana.}, journal = {Journal of cell science}, volume = {131}, number = {2}, pages = {}, doi = {10.1242/jcs.204198}, pmid = {28687624}, issn = {1477-9137}, mesh = {Arabidopsis/drug effects/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Body Patterning/drug effects ; Gene Expression Regulation, Plant/drug effects ; Indoleacetic Acids/pharmacology ; Membrane Transport Proteins/genetics/*metabolism ; Mutation/genetics ; Phenotype ; Phylogeny ; *Plant Development/drug effects ; Plant Epidermis/cytology ; Plant Roots/drug effects/genetics/growth & development/metabolism ; Seedlings/drug effects/metabolism ; Seeds/drug effects/genetics ; }, abstract = {Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We used a microarray-based approach to find regulators of the auxin-induced PIN relocation in Arabidopsis thaliana root, and identified a subset of a family of phosphatidylinositol transfer proteins (PITPs), the PATELLINs (PATLs). Here, we show that PATLs are expressed in partially overlapping cell types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests that PATLs play a redundant and crucial role in polarity and patterning in Arabidopsis.}, }
@article {pmid30912879, year = {2019}, author = {Aripovsky, AV and Titov, VN}, title = {[Biologocally active peptides in metabolism regulation. Peptons, peptides, amino acids, fatty acids, lipoproteins, lipids, and the effect of nutriceuticals.].}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {64}, number = {1}, pages = {14-23}, doi = {10.18821/0869-2084-2019-64-1-14-23}, pmid = {30912879}, issn = {0869-2084}, mesh = {Amino Acids ; Animals ; Dietary Proteins/metabolism ; *Dietary Supplements ; Fatty Acids ; Humans ; Lipids ; Lipoproteins ; Lysosomes ; Peptides/*metabolism ; Phylogeny ; Proteolysis ; }, abstract = {According to phylogenetic theory of general pathology, formation of multicellular organisms started when each cell (a unicellular organism) reached the first level of relative biological perfection. By that time the stimuli for perfection of the unicellular exhausted, and formation of the multicellular became a biological necessity. All cells, being associated, formed the second level of relative biological perfection within the principle of biological succession. The association included highly organized unicellular organisms with their specific autocrine biological functions and reactions. At the second level of relative biological perfection all humoral mediators in paracrine regulated cell communities (PC) and organs were predominantly hydrophilic and short living. They had a small molecular weight and were probably biologically active peptides (BAP). We believe that functional difference of PC and later of organs is based on differentiation of lysosomal function and production of various enzymes involved in proteolysis of dietary proteins. This allowed various PC and organs to form chemically and functionally different BAP pools from one protein upon proteolysis. Individual peptide pools in PC created the basis for morphologically and functionally different cells and organs. Cell that produces peptides can modify their concentration, chemical parameters and ratios by varying the selectivity of its proteases. In vivo regulation of metabolism by BAP has a common root in bacteria, plants and vertebrates, including Homo sapiens. The third level of relative biological perfection in the organism has formed in close association with cognitive biological function.}, }
@article {pmid31384725, year = {2019}, author = {Blum, P and Payne, S}, title = {Evidence of an Epigenetics System in Archaea.}, journal = {Epigenetics insights}, volume = {12}, number = {}, pages = {2516865719865280}, doi = {10.1177/2516865719865280}, pmid = {31384725}, issn = {2516-8657}, abstract = {Changes in the phenotype of a cell or organism that are heritable but do not involve changes in DNA sequence are referred to as epigenetic. They occur primarily through the gain or loss of chemical modification of chromatin protein or DNA. Epigenetics is therefore a non-Mendelian process. The study of epigenetics in eukaryotes is expanding with advances in knowledge about the relationship between mechanism and phenotype and as a requirement for multicellularity and cancer. However, life also includes other groups or domains, notably the bacteria and archaea. The occurrence of epigenetics in these deep lineages is an emerging topic accompanied by controversy. In these non-eukaryotic organisms, epigenetics is critically important because it stimulates new evolutionary theory and refines perspective about biological action.}, }
@article {pmid31380606, year = {2019}, author = {Newman, SA}, title = {Inherent forms and the evolution of evolution.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22895}, pmid = {31380606}, issn = {1552-5015}, abstract = {John Bonner presented a provocative conjecture that the means by which organisms evolve has itself evolved. The elements of his postulated nonuniformitarianism in the essay under discussion-the emergence of sex, the enhanced selection pressures on larger multicellular forms-center on a presumed close mapping of genotypic to phenotypic change. A different view emerges from delving into earlier work of Bonner's in which he proposed the concept of "neutral phenotypes" and "neutral morphologies" allied to D'Arcy Thompson's analysis of physical determinants of form and studied the conditional elicitation of intrinsic organizational properties of cell aggregates in social amoebae. By comparing the shared and disparate mechanistic bases of morphogenesis and developmental outcomes in the embryos of metazoans (animals), closely related nonmetazoan holozoans, more distantly related dictyostelids, and very distantly related volvocine algae, I conclude, in agreement with Bonner's earlier proposals, that understanding the evolution of multicellular evolution requires knowledge of the inherent forms of diversifying lineages, and that the relevant causative factors extend beyond genes and adaptation to the physics of materials.}, }
@article {pmid31370870, year = {2019}, author = {Yeoh, LM and Goodman, CD and Mollard, V and McHugh, E and Lee, VV and Sturm, A and Cozijnsen, A and McFadden, GI and Ralph, SA}, title = {Alternative splicing is required for stage differentiation in malaria parasites.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {151}, doi = {10.1186/s13059-019-1756-6}, pmid = {31370870}, issn = {1474-760X}, support = {DP160100389//Australian Research Council/ ; 628704//National Health and Medical Research Council/ ; }, abstract = {BACKGROUND: In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular identity is currently unknown in any unicellular organism.<br><br>RESULTS: To test whether alternative splicing in unicellular protists plays a role in cellular differentiation, we conduct RNA-seq to compare splicing in female and male sexual stages to asexual intraerythrocytic stages in the rodent malaria parasite Plasmodium berghei. We find extensive changes in alternative splicing between stages and a role for alternative splicing in sexual differentiation. Previously, general gametocyte differentiation was shown to be modulated by specific transcription factors. Here, we show that alternative splicing establishes a subsequent layer of regulation, controlling genes relating to consequent sex-specific differentiation of gametocytes.<br><br>CONCLUSIONS: We demonstrate that alternative splicing is reprogrammed during cellular differentiation of a unicellular protist. Disruption of an alternative splicing factor, PbSR-MG, perturbs sex-specific alternative splicing and decreases the ability of the parasites to differentiate into male gametes and oocysts, thereby reducing transmission between vertebrate and insect hosts. Our results reveal alternative splicing as an integral, stage-specific phenomenon in these protists and as a regulator of cellular differentiation that arose early in eukaryotic evolution.}, }
@article {pmid31367038, year = {2019}, author = {Olin-Sandoval, V and Yu, JSL and Miller-Fleming, L and Alam, MT and Kamrad, S and Correia-Melo, C and Haas, R and Segal, J and Peña Navarro, DA and Herrera-Dominguez, L and Méndez-Lucio, O and Vowinckel, J and Mülleder, M and Ralser, M}, title = {Lysine harvesting is an antioxidant strategy and triggers underground polyamine metabolism.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-019-1442-6}, pmid = {31367038}, issn = {1476-4687}, abstract = {Both single and multicellular organisms depend on anti-stress mechanisms that enable them to deal with sudden changes in the environment, including exposure to heat and oxidants. Central to the stress response are dynamic changes in metabolism, such as the transition from the glycolysis to the pentose phosphate pathway-a conserved first-line response to oxidative insults1,2. Here we report a second metabolic adaptation that protects microbial cells in stress situations. The role of the yeast polyamine transporter Tpo1p3-5 in maintaining oxidant resistance is unknown6. However, a proteomic time-course experiment suggests a link to lysine metabolism. We reveal a connection between polyamine and lysine metabolism during stress situations, in the form of a promiscuous enzymatic reaction in which the first enzyme of the polyamine pathway, Spe1p, decarboxylates lysine and forms an alternative polyamine, cadaverine. The reaction proceeds in the presence of extracellular lysine, which is taken up by cells to reach concentrations up to one hundred times higher than those required for growth. Such extensive harvest is not observed for the other amino acids, is dependent on the polyamine pathway and triggers a reprogramming of redox metabolism. As a result, NADPH-which would otherwise be required for lysine biosynthesis-is channelled into glutathione metabolism, leading to a large increase in glutathione concentrations, lower levels of reactive oxygen species and increased oxidant tolerance. Our results show that nutrient uptake occurs not only to enable cell growth, but when the nutrient availability is favourable it also enables cells to reconfigure their metabolism to preventatively mount stress protection.}, }
@article {pmid31354387, year = {2014}, author = {Herron, MD and Ghimire, S and Vinikoor, CR and Michod, RE}, title = {Fitness trade-offs and developmental constraints in the evolution of soma: an experimental study in a volvocine alga.}, journal = {Evolutionary ecology research}, volume = {16}, number = {3}, pages = {203-221}, pmid = {31354387}, issn = {1522-0613}, abstract = {Background: The evolution of mortal somatic cells was a critical step in the evolution of complex body plans and the major radiations of multicellular life. In the volvocine green algae, somatic cells are hypothesized to mitigate an increasing cost of reproduction as colony size increases, primarily by providing motility to the colony during reproduction.<br><br>Questions: Does selection on colony size cause an evolutionary response in proportion of somatic cells? Does the effect of selection on colony size differ in environments that differ in the importance of motility?<br><br>Methods: We subjected an outcrossed population of the volvocine alga Pleodorina starrii to selection on colony size in still and mixed environments. After approximately 40 generations with periodic selection, we estimated the relationship between colony size and proportion of soma in evolved colonies from both environments.<br><br>Results: In the largest size category, colonies selected in the still environment (in which motility is hypothesized to be more important) had a higher proportion of soma than those from the mixed environment. Within-strain variation in cell number was surprisingly large: up to 16-fold for some genotypes. The positive among-species relationship between colony size and proportion of soma was paralleled within the larger (16- to 64-celled) colonies of P. starrii, but not within the smaller (4- and 8-celled) colonies, which had the highest proportions of soma, suggesting the existence of an evolutionary constraint preventing optimization of soma in the smallest size classes.}, }
@article {pmid31347665, year = {2019}, author = {Lu, TM and Kanda, M and Furuya, H and Satoh, N}, title = {Dicyemid mesozoans: a unique parasitic lifestyle with reduced genome.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz157}, pmid = {31347665}, issn = {1759-6653}, abstract = {Dicyemids, previously called &quot;mesozoans&quot; (intermediates between unicellular protozoans and multicellular metazoans), are an enigmatic animal group. They have a highly simplified adult body, comprising only ∼30 cells, and they have a unique parasitic lifestyle. Recently, dicyemids were shown to be spiralians, with affinities to the Platyhelminthes. In order to understand molecular mechanisms involved in evolution of this odd animal, we sequenced the genome of Dicyema japonicum and a reference transcriptome assembly using mixed-stage samples. The D. japonicum genome features a high proportion of repetitive sequences that account for 49% of the genome. The dicyemid genome is reduced to approximately 67.5 Mb with 5,012 protein-coding genes. Only four Hox genes exist in the genome, with no clustering. Gene distribution in KEGG pathways shows that D. japonicum has fewer genes in most pathways. Instead of eliminating entire critical metabolic pathways, parasitic lineages likely simplify pathways by eliminating pathway-specific genes, while genes with fundamental functions may be retained in multiple pathways. In principle, parasites can stand to lose genes that are unnecessary, in order to conserve energy. However, whether retained genes in incomplete pathways serve intermediate functions and how parasites overcome the physiological needs served by lost genes, remain to be investigated in future studies.}, }
@article {pmid30915345, year = {2019}, author = {Zannier, F and Portero, LR and Ordoñez, OF and Martinez, LJ and Farías, ME and Albarracin, VH}, title = {Polyextremophilic Bacteria from High Altitude Andean Lakes: Arsenic Resistance Profiles and Biofilm Production.}, journal = {BioMed research international}, volume = {2019}, number = {}, pages = {1231975}, doi = {10.1155/2019/1231975}, pmid = {30915345}, issn = {2314-6141}, mesh = {Acinetobacter/drug effects/genetics/*growth &amp; development ; Adaptation, Physiological/*genetics ; Altitude ; Arsenic/toxicity ; Biodegradation, Environmental ; Biofilms/drug effects/growth &amp; development ; *Ecosystem ; Lakes/microbiology ; *Phylogeny ; Ultraviolet Rays ; }, abstract = {High levels of arsenic present in the High Altitude Andean Lakes (HAALs) ecosystems selected arsenic-resistant microbial communities which are of novel interest to study adaptations mechanisms potentially useful in bioremediation processes. We herein performed a detailed characterization of the arsenic tolerance profiles and the biofilm production of two HAAL polyextremophiles, Acinetobacter sp. Ver3 (Ver3) and Exiguobacterium sp. S17 (S17). Cellular adherence over glass and polypropylene surfaces were evaluated together with the effect of increasing doses and oxidative states of arsenic over the quality and quantity of their biofilm production. The arsenic tolerance outcomes showed that HAAL strains could tolerate higher arsenic concentrations than phylogenetic related strains belonging to the German collection of microorganisms and cell cultures (Deutsche Sammlung von Mikroorganismen und Zellkulturen, DSMZ), which suggest adaptations of HAAL strains to their original environment. On the other hand, the crystal violet method (CV) and SEM analysis showed that Ver3 and S17 were able to attach to solid surfaces and to form the biofilm. The quantification of biofilms production in 48 hours' cultures through CV shows that Ver3 yielded higher production in the treatment without arsenic cultured on a glass support, while S17 yield higher biofilm production under intermediate arsenic concentration on glass supports. Polypropylene supports had negative effects on the biofilm production of Ver3 and S17. SEM analysis shows that the highest biofilm yields could be associated with a larger number of attached cells as well as the development of more complex 3D multicellular structures.}, }
@article {pmid29133885, year = {2017}, author = {Yu, YN and Cooper, E and Velicer, GJ}, title = {A conserved stem of the Myxococcus xanthus sRNA Pxr controls sRNA accumulation and multicellular development.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15411}, pmid = {29133885}, issn = {2045-2322}, support = {R01 GM079690/GM/NIGMS NIH HHS/United States ; }, mesh = {Enhancer Elements, Genetic/*genetics ; Evolution, Molecular ; Genes, Bacterial/genetics ; Myxococcus xanthus/*physiology ; *Nucleic Acid Conformation ; RNA, Bacterial/chemistry/*genetics/metabolism ; Transcription, Genetic/*genetics ; }, abstract = {The small RNA (sRNA) Pxr negatively controls multicellular fruiting body formation in the bacterium Myxococcus xanthus, inhibiting the transition from growth to development when nutrients are abundant. Like many other prokaryotic sRNAs, Pxr is predicted to fold into three stem loops (SL1-SL3). SL1 and SL2 are highly conserved across the myxobacteria, whereas SL3 is much more variable. SL1 is necessary for the regulatory function of Pxr but the importance of SL3 in this regard is unknown. To test for cis genetic elements required for Pxr function, we deleted the entire pxr gene from a developmentally defective strain that fails to remove Pxr-mediated blockage of development and reintroduced variably truncated fragments of the pxr region to test for their ability to block development. These truncations demonstrated that SL3 is necessary for Pxr function in the defective strain. We further show that a highly conserved eight-base-pair segment of SL3 is not only necessary for Pxr to block development in the defective strain under starvation conditions, but is also required for Pxr to prevent fruiting body development by a developmentally proficient wild-type strain under high-nutrient conditions. This conserved segment of SL3 is also necessary for detectable levels of Pxr to accumulate, suggesting that this segment either stabilizes Pxr against premature degradation during vegetative growth or positively regulates its transcription.}, }
@article {pmid31325911, year = {2019}, author = {Perez-Lamarque, B and Morlon, H}, title = {Characterizing symbiont inheritance during host-microbiota evolution: application to the great apes gut microbiota.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13063}, pmid = {31325911}, issn = {1755-0998}, abstract = {Microbiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition), transmitted across generations with a faithful association with their hosts (i.e. strict vertical transmission), or transmitted with occasional host-switches (i.e. vertical transmission with horizontal switches). These different modes of inheritance affect microbes' diversification, which at the two extremes can be independent from that of their associated host or follow host diversification. The few existing quantitative tools for investigating the inheritance of symbiotic organisms rely on cophylogenetic approaches, which require knowledge of both host and symbiont phylogenies, and are therefore often not well adapted to DNA metabarcoding microbial data. Here, we develop a model-based framework for identifying vertically transmitted microbial taxa. We consider a model for the evolution of microbial sequences on a fixed host phylogeny that includes vertical transmission and horizontal host-switches. This model allows estimating the number of host-switches and testing for strict vertical transmission and independent evolution. We test our approach using simulations. Finally, we illustrate our framework on gut microbiota high-throughput sequencing data of the family Hominidae and identify several microbial taxonomic units, including fibrolytic bacteria involved in carbohydrate digestion, that tend to be vertically transmitted. This article is protected by copyright. All rights reserved.}, }
@article {pmid31311477, year = {2019}, author = {Boscaro, V and Husnik, F and Vannini, C and Keeling, PJ}, title = {Symbionts of the ciliate Euplotes: diversity, patterns and potential as models for bacteria-eukaryote endosymbioses.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1907}, pages = {20190693}, doi = {10.1098/rspb.2019.0693}, pmid = {31311477}, issn = {1471-2954}, abstract = {Endosymbioses between bacteria and eukaryotes are enormously important in ecology and evolution, and as such are intensely studied. Despite this, the range of investigated hosts is narrow in the context of the whole eukaryotic tree of life: most of the information pertains to animal hosts, while most of the diversity is found in unicellular protists. A prominent case study is the ciliate Euplotes, which has repeatedly taken up the bacterium Polynucleobacter from the environment, triggering its transformation into obligate endosymbiont. This multiple origin makes the relationship an excellent model to understand recent symbioses, but Euplotes may host bacteria other than Polynucleobacter, and a more detailed knowledge of these additional interactions is needed in order to correctly interpret the system. Here, we present the first systematic survey of Euplotes endosymbionts, adopting a classical as well as a metagenomic approach, and review the state of knowledge. The emerging picture is indeed quite complex, with some Euplotes harbouring rich, stable prokaryotic communities not unlike those of multicellular animals. We provide insights into the distribution, evolution and diversity of these symbionts (including the establishment of six novel bacterial taxa), and outline differences and similarities with the most well-understood group of eukaryotic hosts: insects.}, }
@article {pmid29413517, year = {2018}, author = {Gavish, M and Veenman, L}, title = {Regulation of Mitochondrial, Cellular, and Organismal Functions by TSPO.}, journal = {Advances in pharmacology (San Diego, Calif.)}, volume = {82}, number = {}, pages = {103-136}, doi = {10.1016/bs.apha.2017.09.004}, pmid = {29413517}, issn = {1557-8925}, mesh = {Animals ; Evolution, Molecular ; Genes, Essential ; Homeostasis ; Humans ; Mitochondria/*metabolism ; Reactive Oxygen Species/metabolism ; Receptors, GABA/*metabolism ; }, abstract = {In 1999, the enigma of the 18kDa mitochondrial translocator protein (TSPO), also known as the peripheral-type benzodiazepine receptor, was the seeming disparity of the many functions attributed to TSPO, ranging from the potential of TSPO acting as a housekeeping gene at molecular biological levels to adaptations to stress, and even involvement in higher emotional and cognitive functioning, such as anxiety and depression. In the years since then, knowledge regarding the many functions modulated by TSPO has expanded, and understanding has deepened. In addition, new functions could be firmly associated with TSPO, such as regulation of programmed cell death and modulation of gene expression. Interestingly, control by the mitochondrial TSPO over both of these life and death functions appears to include Ca++ homeostasis, generation of reactive oxygen species (ROS), and ATP production. Other mitochondrial functions under TSPO control are considered to be steroidogenesis and tetrapyrrole metabolism. As TSPO effects on gene expression and on programmed cell death can be related to the wide range of functions that can be associated with TSPO, several of these five elements of Ca++, ROS, ATP, steroids, and tetrapyrroles may indeed form the basis of TSPO's capability to operate as a multifunctional housekeeping gene to maintain homeostasis of the cell and of the whole multicellular organism.}, }
@article {pmid31162574, year = {2018}, author = {McGrath, C}, title = {Highlight: Origins of Multicellularity Revealed by Single-Celled Amoebae.}, journal = {Genome biology and evolution}, volume = {10}, number = {2}, pages = {705-706}, doi = {10.1093/gbe/evy038}, pmid = {31162574}, issn = {1759-6653}, mesh = {*Amoeba ; Biological Evolution ; Phylogeny ; }, }
@article {pmid31302471, year = {2019}, author = {Newman, SA}, title = {Inherency and homomorphy in the evolution of development.}, journal = {Current opinion in genetics &amp; development}, volume = {57}, number = {}, pages = {1-8}, doi = {10.1016/j.gde.2019.05.006}, pmid = {31302471}, issn = {1879-0380}, abstract = {Organismal development occurs when expression of certain genes leads to the mobilization of physical forces and effects that shape and pattern multicellular clusters. All materials exhibit preferred forms, but the inherent morphological motifs of some, such as liquids and crystalline solids are well-characterized. Recent work has shown that the origin of the animals (Metazoa) was accompanied by the acquisition by their developing tissues of liquid-like and liquid-crystalline properties. This and the novel capacity to produce stiff internal substrata (basal laminae) set these organisms apart from their closest relatives by the propensity (predictable from their material nature) to form complex bodies and organs. Once functional forms became established, however, they were susceptible to further genetic change as well as partial or full supplanting of original physical determinants by different ones. This results in the increasingly recognized phenomenon of homomorphy, the presence of the same structure in descendent organisms, brought about by transformed developmental mechanisms.}, }
@article {pmid31295970, year = {2019}, author = {Joukov, V and De Nicolo, A}, title = {The Centrosome and the Primary Cilium: The Yin and Yang of a Hybrid Organelle.}, journal = {Cells}, volume = {8}, number = {7}, pages = {}, doi = {10.3390/cells8070701}, pmid = {31295970}, issn = {2073-4409}, abstract = {Centrosomes and primary cilia are usually considered as distinct organelles, although both are assembled with the same evolutionary conserved, microtubule-based templates, the centrioles. Centrosomes serve as major microtubule- and actin cytoskeleton-organizing centers and are involved in a variety of intracellular processes, whereas primary cilia receive and transduce environmental signals to elicit cellular and organismal responses. Understanding the functional relationship between centrosomes and primary cilia is important because defects in both structures have been implicated in various diseases, including cancer. Here, we discuss evidence that the animal centrosome evolved, with the transition to complex multicellularity, as a hybrid organelle comprised of the two distinct, but intertwined, structural-functional modules: the centriole/primary cilium module and the pericentriolar material/centrosome module. The evolution of the former module may have been caused by the expanding cellular diversification and intercommunication, whereas that of the latter module may have been driven by the increasing complexity of mitosis and the requirement for maintaining cell polarity, individuation, and adhesion. Through its unique ability to serve both as a plasma membrane-associated primary cilium organizer and a juxtanuclear microtubule-organizing center, the animal centrosome has become an ideal integrator of extracellular and intracellular signals with the cytoskeleton and a switch between the non-cell autonomous and the cell-autonomous signaling modes. In light of this hypothesis, we discuss centrosome dynamics during cell proliferation, migration, and differentiation and propose a model of centrosome-driven microtubule assembly in mitotic and interphase cells. In addition, we outline the evolutionary benefits of the animal centrosome and highlight the hierarchy and modularity of the centrosome biogenesis networks.}, }
@article {pmid31291955, year = {2019}, author = {Yang, YJ and Singh, RP and Lan, X and Zhang, CS and Sheng, DH and Li, YQ}, title = {Whole transcriptome analysis and gene deletion to understand the chloramphenicol resistance mechanism and develop a screening method for homologous recombination in Myxococcus xanthus.}, journal = {Microbial cell factories}, volume = {18}, number = {1}, pages = {123}, doi = {10.1186/s12934-019-1172-3}, pmid = {31291955}, issn = {1475-2859}, support = {ASTIP-TRIC07//Agricultural Science and Technology Innovation Program of China/ ; }, abstract = {BACKGROUND: Myxococcus xanthus DK1622 is a model system for studying multicellular development, predation, cellular differentiation, and evolution. Furthermore, it is a rich source of novel secondary metabolites and is widely used as heterologous expression host of exogenous biosynthetic gene clusters. For decades, genetic modification of M. xanthus DK1622 has mainly relied on kanamycin and tetracycline selection systems.<br><br>RESULTS: Here, we introduce an alternative selection system based on chloramphenicol (Cm) to broaden the spectrum of available molecular tools. A chloramphenicol-resistant growth phase and a chloramphenicol-susceptible growth phase before and after chloramphenicol-induction were prepared, and later sequenced to identify specific genes related to chloramphenicol-repercussion and drug-resistance. A total of 481 differentially expressed genes were revealed in chloramphenicol-resistant Cm5_36h and 1920 differentially expressed genes in chloramphenicol-dormant Cm_8h. Moreover, the gene expression profile in the chloramphenicol-dormant strain Cm_8h was quite different from that of Cm5_36 which had completely adapted to Cm, and 1513 differentially expression genes were identified between these two phenotypes. Besides upregulated acetyltransferases, several transporter encoding genes, including ABC transporters, major facilitator superfamily transporters (MFS), resistance-nodulation-cell division (RND) super family transporters and multidrug and toxic compound extrusion family transporters (MATE) were found to be involved in Cm resistance. After the knockout of the most highly upregulated MXAN_2566 MFS family gene, mutant strain DK-2566 was proved to be sensitive to Cm by measuring the growth curve in the Cm-added condition. A plasmid with a Cm resistance marker was constructed and integrated into chromosomes via homologous recombination and Cm screening. The integration efficiency was about 20% at different concentrations of Cm.<br><br>CONCLUSIONS: This study provides a new antibiotic-based selection system, and will help to understand antibiotic resistance mechanisms in M. xanthus DK1622.}, }
@article {pmid31286803, year = {2019}, author = {Rezaei-Lotfi, S and Hunter, N and Farahani, RM}, title = {Coupled cycling programs multicellular self-organization of neural progenitors.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/15384101.2019.1638692}, pmid = {31286803}, issn = {1551-4005}, abstract = {Self-organization is central to the morphogenesis of multicellular organisms. However, the molecular platform that coordinates the robust emergence of complex morphological patterns from local interactions between cells remains unresolved. Here we demonstrate that neural self- organization is driven by coupled cycling of progenitor cells. In a coupled cycling mode, intercellular contacts relay extrinsic cues to override the intrinsic cycling rhythm of an individual cell and synchronize the population. The stringency of coupling and hence the synchronicity of the population is programmed by recruitment of a key coupler, β-catenin, into junctional complexes. As such, multicellular self-organization is driven by the same basic mathematical principle that governs synchronized behavior of macro-scale biological systems as diverse as the synchronized chirping of crickets, flashing of fireflies and schooling of fish; that is synchronization by coupling. It is proposed that coupled cycling foreshadows a fundamental adaptive change that facilitated evolution and diversification of multicellular life forms.}, }
@article {pmid31285576, year = {2019}, author = {Staps, M and van Gestel, J and Tarnita, CE}, title = {Emergence of diverse life cycles and life histories at the origin of multicellularity.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41559-019-0940-0}, pmid = {31285576}, issn = {2397-334X}, abstract = {The evolution of multicellularity has given rise to a remarkable diversity of multicellular life cycles and life histories. Whereas some multicellular organisms are long-lived, grow through cell division, and repeatedly release single-celled propagules (for example, animals), others are short-lived, form by aggregation, and propagate only once, by generating large numbers of solitary cells (for example, cellular slime moulds). There are no systematic studies that explore how diverse multicellular life cycles can come about. Here, we focus on the origin of multicellularity and develop a mechanistic model to examine the primitive life cycles that emerge from a unicellular ancestor when an ancestral gene is co-opted for cell adhesion. Diverse life cycles readily emerge, depending on ecological conditions, group-forming mechanism, and ancestral constraints. Among these life cycles, we recapitulate both extremes of long-lived groups that propagate continuously and short-lived groups that propagate only once, with the latter type of life cycle being particularly favoured when groups can form by aggregation. Our results show how diverse life cycles and life histories can easily emerge at the origin of multicellularity, shaped by ancestral constraints and ecological conditions. Beyond multicellularity, this finding has similar implications for other major transitions, such as the evolution of sociality.}, }
@article {pmid31267819, year = {2019}, author = {Etxebeste, O and Otamendi, A and Garzia, A and Espeso, EA and Cortese, MS}, title = {Rewiring of transcriptional networks as a major event leading to the diversity of asexual multicellularity in fungi.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/1040841X.2019.1630359}, pmid = {31267819}, issn = {1549-7828}, abstract = {Complex multicellularity (CM) is characterized by the generation of three-dimensional structures that follow a genetically controlled program. CM emerged at least five times in evolution, one of them in fungi. There are two types of CM programs in fungi, leading, respectively, to the formation of sexual or asexual spores. Asexual spores foment the spread of mycoses, as they are the main vehicle for dispersion. In spite of this key dependence, there is great morphological diversity of asexual multicellular structures in fungi. To advance the understanding of the mechanisms that control initiation and progression of asexual CM and how they can lead to such a remarkable morphological diversification, we studied 503 fungal proteomes, representing all phyla and subphyla, and most known classes. Conservation analyses of 33 regulators of asexual development suggest stepwise emergence of transcription factors. While velvet proteins constitute one of the most ancient systems, the central regulator BrlA emerged late in evolution (with the class Eurotiomycetes). Some factors, such as MoConX4, seem to be species-specific. These observations suggest that the emergence and evolution of transcriptional regulators rewire transcriptional networks. This process could reach the species level, resulting in a vast diversity of morphologies.}, }
@article {pmid31254720, year = {2019}, author = {Falz, AL and Müller-Schüssele, SJ}, title = {Physcomitrella as a model system for plant cell biology and organelle-organelle communication.}, journal = {Current opinion in plant biology}, volume = {52}, number = {}, pages = {7-13}, doi = {10.1016/j.pbi.2019.05.007}, pmid = {31254720}, issn = {1879-0356}, abstract = {In multicellular eukaryotic cells, metabolism and growth are sustained by the cooperative functioning of organelles in combination with cell-to-cell communication at the organism level. In land plants, multiple strategies have evolved to adapt to life outside water. As basal land plant, the moss Physcomitrella patens is used for comparative genomics, allowing to study lineage-specific features, as well as to track the evolution of fundamental parameters of plant cell organisation and physiology. P. patens is a versatile model for cell biology research, especially to investigate adaptive growth, stress biology as well as organelle dynamics and interactions. Recent advances include the use of genetically encoded biosensors for in vivo imaging of physiological parameters.}, }
@article {pmid31246972, year = {2019}, author = {Aufrecht, JA and Fowlkes, JD and Bible, AN and Morrell-Falvey, J and Doktycz, MJ and Retterer, ST}, title = {Pore-scale hydrodynamics influence the spatial evolution of bacterial biofilms in a microfluidic porous network.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0218316}, doi = {10.1371/journal.pone.0218316}, pmid = {31246972}, issn = {1932-6203}, abstract = {Bacteria occupy heterogeneous environments, attaching and growing within pores in materials, living hosts, and matrices like soil. Systems that permit high-resolution visualization of dynamic bacterial processes within the physical confines of a realistic and tractable porous media environment are rare. Here we use microfluidics to replicate the grain shape and packing density of natural sands in a 2D platform to study the flow-induced spatial evolution of bacterial biofilms underground. We discover that initial bacterial dispersal and grain attachment is influenced by bacterial transport across pore space velocity gradients, a phenomenon otherwise known as rheotaxis. We find that gravity-driven flow conditions activate different bacterial cell-clustering phenotypes depending on the strain's ability to product extracellular polymeric substances (EPS). A wildtype, biofilm-producing bacteria formed compact, multicellular patches while an EPS-defective mutant displayed a linked-cell phenotype in the presence of flow. These phenotypes subsequently influenced the overall spatial distribution of cells across the porous media network as colonies grew and altered the fluid dynamics of their microenvironment.}, }
@article {pmid31239554, year = {2019}, author = {Ågren, JA and Davies, NG and Foster, KR}, title = {Enforcement is central to the evolution of cooperation.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41559-019-0907-1}, pmid = {31239554}, issn = {2397-334X}, abstract = {Cooperation occurs at all levels of life, from genomes, complex cells and multicellular organisms to societies and mutualisms between species. A major question for evolutionary biology is what these diverse systems have in common. Here, we review the full breadth of cooperative systems and find that they frequently rely on enforcement mechanisms that suppress selfish behaviour. We discuss many examples, including the suppression of transposable elements, uniparental inheritance of mitochondria and plastids, anti-cancer mechanisms, reciprocation and punishment in humans and other vertebrates, policing in eusocial insects and partner choice in mutualisms between species. To address a lack of accompanying theory, we develop a series of evolutionary models that show that the enforcement of cooperation is widely predicted. We argue that enforcement is an underappreciated, and often critical, ingredient for cooperation across all scales of biological organization.}, }
@article {pmid31236128, year = {2019}, author = {Robu, A and Mironov, V and Neagu, A}, title = {Using Sacrificial Cell Spheroids for the Bioprinting of Perfusable 3D Tissue and Organ Constructs: A Computational Study.}, journal = {Computational and mathematical methods in medicine}, volume = {2019}, number = {}, pages = {7853586}, doi = {10.1155/2019/7853586}, pmid = {31236128}, issn = {1748-6718}, abstract = {A long-standing problem in tissue engineering is the biofabrication of perfusable tissue constructs that can be readily connected to the patient's vasculature. It was partially solved by three-dimensional (3D) printing of sacrificial material (e.g., hydrogel) strands: upon incorporation in another cell-laden hydrogel, the strands were removed, leaving behind perfusable channels. Their complexity, however, did not match that of the native vasculature. Here, we propose to use multicellular spheroids as a sacrificial material and investigate their potential benefits in the context of 3D bioprinting of cell aggregates and/or cell-laden hydrogels. Our study is based on computer simulations of postprinting cellular rearrangements. The computational model of the biological system is built on a cubic lattice, whereas its evolution is simulated using the Metropolis Monte Carlo algorithm. The simulations describe structural changes in three types of tissue constructs: a tube made of a single cell type, a tube made of two cell types, and a cell-laden hydrogel slab that incorporates a branching tube. In all three constructs, the lumen is obtained after the elimination of the sacrificial cell population. Our study suggests that sacrificial cell spheroids (sacrospheres) enable one to print tissue constructs outfitted with a finer and more complex network of channels than the ones obtained so far. Moreover, cellular interactions might give rise to a tissue microarchitecture that lies beyond the bioprinter's resolution. Although more expensive than inert materials, sacrificial cells have the potential to bring further progress towards the biofabrication of fully vascularized tissue substitutes.}, }
@article {pmid31227860, year = {2019}, author = {Tian, L and Zhang, B and Zhang, J and Zhang, T and Cai, Y and Qin, H and Metzner, W and Pan, Y}, title = {A magnetic compass guides the direction of foraging in a bat.}, journal = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00359-019-01353-1}, pmid = {31227860}, issn = {1432-1351}, support = {41674071//National Natural Science Foundation of China/ ; 41621004//National Natural Science Foundation of China/ ; QYZDJ-SSW-DQC024//the Chinese Academy of Sciences project/ ; }, abstract = {Previously, two studies have provided evidence that bats can use magnetic field cues for homing or roosting. For insectivorous bats, it is well established that foraging represents one of the most fundamental behaviors in animals relies on their ability to echolocate. Whether echolocating bats can also use magnetic cues during foraging remains unknown, however. Here, we tested the orientation behavior of Chinese noctules (Nyctalus plancyi) during foraging in a plus-shaped, 4-channel apparatus under different magnetic field conditions. To minimize the effects of spatial memory on orientation from repeated experiments, naïve bats were tested only once in each experimental condition. As expected, under geomagnetic field and a food resource offered conditions, the bats significantly preferred to enter the channel containing food, indicating that they primarily relied on direct sensory signals unrelated to magnetic cues. In contrast, when we offered food simultaneously in all four channels and minimized any differences in all other sensory signals available, the bats exhibited a clear directional preference to forage along the magnetic field direction under either geomagnetic field or a magnetic field in which the horizontal component was rotated by 90°. Our study offers a novel evidence for the importance of a geomagnetic field during foraging.}, }
@article {pmid31214991, year = {2019}, author = {Muras, V and Toulouse, C and Fritz, G and Steuber, J}, title = {Respiratory Membrane Protein Complexes Convert Chemical Energy.}, journal = {Sub-cellular biochemistry}, volume = {92}, number = {}, pages = {301-335}, doi = {10.1007/978-3-030-18768-2_10}, pmid = {31214991}, issn = {0306-0225}, abstract = {The invention of a biological membrane which is used as energy storage system to drive the metabolism of a primordial, unicellular organism represents a key event in the evolution of life. The innovative, underlying principle of this key event is respiration. In respiration, a lipid bilayer with insulating properties is chosen as the site for catalysis of an exergonic redox reaction converting substrates offered from the environment, using the liberated Gibbs free energy (ΔG) for the build-up of an electrochemical H+ (proton motive force, PMF) or Na+ gradient (sodium motive force, SMF) across the lipid bilayer. Very frequently , several redox reactions are performed in a consecutive manner, with the first reaction delivering a product which is used as substrate for the second redox reaction, resulting in a respiratory chain. From today's perspective, the (mostly) unicellular bacteria and archaea seem to be much simpler and less evolved when compared to multicellular eukaryotes. However, they are overwhelmingly complex with regard to the various respiratory chains which permit survival in very different habitats of our planet, utilizing a plethora of substances to drive metabolism. This includes nitrogen, sulfur and carbon compounds which are oxidized or reduced by specialized, respiratory enzymes of bacteria and archaea which lie at the heart of the geochemical N, S and C-cycles. This chapter gives an overview of general principles of microbial respiration considering thermodynamic aspects, chemical reactions and kinetic restraints. The respiratory chains of Escherichia coli and Vibrio cholerae are discussed as models for PMF- versus SMF-generating processes, respectively. We introduce main redox cofactors of microbial respiratory enzymes, and the concept of intra-and interelectron transfer. Since oxygen is an electron acceptor used by many respiratory chains, the formation and removal of toxic oxygen radicals is described. Promising directions of future research are respiratory enzymes as novel bacterial targets, and biotechnological applications relying on respiratory complexes.}, }
@article {pmid31209997, year = {2019}, author = {Bonner, JT}, title = {The evolution of evolution.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22859}, pmid = {31209997}, issn = {1552-5015}, abstract = {In the past, most biologists, myself included, did not think of evolution as changing over time. The wonders of natural selection were always at hand and went into operation once there was life. However, with a little reflection it becomes obvious that evolution has changed-there has been an evolution of evolution. Evolution can be separated into four phases, or eras, that may or may not overlap. The first era starts with the evolution of life on earth, which led to single cells that multiply asexually. The second era takes advantage of the invention of sexual reproduction as evolution could now gallop forward because of a richer fare of diverse offspring for natural selection. The third era begins with the introduction of multicellularity. In the fourth era there is a radical innovation: the nervous system that arises animals by standard Darwinian selection. This has allowed major rapid changes to proceed, such as language that led to all the rapid progress we call civilization; a true revolution, and one that does not depend on the slow genetic changes of all other standard gene-controlled evolutionary steps.}, }
@article {pmid30668717, year = {2019}, author = {Belato, FA and Schrago, CG and Coates, CJ and Halanych, KM and Costa-Paiva, EM}, title = {Newly Discovered Occurrences and Gene Tree of the Extracellular Globins and Linker Chains from the Giant Hexagonal Bilayer Hemoglobin in Metazoans.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {597-612}, doi = {10.1093/gbe/evz012}, pmid = {30668717}, issn = {1759-6653}, mesh = {Animals ; Globins/*genetics ; Invertebrates/*genetics ; *Phylogeny ; }, abstract = {Multicellular organisms depend on oxygen-carrying proteins to transport oxygen throughout the body; therefore, proteins such as hemoglobins (Hbs), hemocyanins, and hemerythrins are essential for maintenance of tissues and cellular respiration. Vertebrate Hbs are among the most extensively studied proteins; however, much less is known about invertebrate Hbs. Recent studies of hemocyanins and hemerythrins have demonstrated that they have much wider distributions than previously thought, suggesting that oxygen-binding protein diversity is underestimated across metazoans. Hexagonal bilayer hemoglobin (HBL-Hb), a blood pigment found exclusively in annelids, is a polymer comprised up to 144 extracellular globins and 36 linker chains. To further understand the evolutionary history of this protein complex, we explored the diversity of linkers and extracellular globins from HBL-Hbs using in silico approaches on 319 metazoan and one choanoflagellate transcriptomes. We found 559 extracellular globin and 414 linker genes transcribed in 171 species from ten animal phyla with new records in Echinodermata, Hemichordata, Brachiopoda, Mollusca, Nemertea, Bryozoa, Phoronida, Platyhelminthes, and Priapulida. Contrary to previous suggestions that linkers and extracellular globins emerged in the annelid ancestor, our findings indicate that they have putatively emerged before the protostome-deuterostome split. For the first time, we unveiled the comprehensive evolutionary history of metazoan HBL-Hb components, which consists of multiple episodes of gene gains and losses. Moreover, because our study design surveyed linkers and extracellular globins independently, we were able to cross-validate our results, significantly reducing the rate of false positives. We confirmed that the distribution of HBL-Hb components has until now been underestimated among animals.}, }
@article {pmid31196608, year = {2019}, author = {Pirkmajer, S and Chibalin, AV}, title = {Hormonal regulation of Na+-K+-ATPase from the evolutionary perspective.}, journal = {Current topics in membranes}, volume = {83}, number = {}, pages = {315-351}, doi = {10.1016/bs.ctm.2019.01.009}, pmid = {31196608}, issn = {1063-5823}, abstract = {Na+-K+-ATPase, an α/β heterodimer, is an ancient enzyme that maintains Na+ and K+ gradients, thus preserving cellular ion homeostasis. In multicellular organisms, this basic housekeeping function is integrated to fulfill the needs of specialized organs and preserve whole-body homeostasis. In vertebrates, Na+-K+-ATPase is essential for many fundamental physiological processes, such as nerve conduction, muscle contraction, nutrient absorption, and urine excretion. During vertebrate evolution, three key developments contributed to diversification and integration of Na+-K+-ATPase functions. Generation of novel α- and β-subunits led to formation of multiple Na+-K+-ATPase isoenyzmes with distinct functional characteristics. Development of a complex endocrine system enabled efficient coordination of diverse Na+-K+-ATPase functions. Emergence of FXYDs, small transmembrane proteins that regulate Na+-K+-ATPase, opened new ways to modulate its function. FXYDs are a vertebrate innovation and an important site of hormonal action, suggesting they played an especially prominent role in evolving interaction between Na+-K+-ATPase and the endocrine system in vertebrates.}, }
@article {pmid31189954, year = {2019}, author = {Sogabe, S and Hatleberg, WL and Kocot, KM and Say, TE and Stoupin, D and Roper, KE and Fernandez-Valverde, SL and Degnan, SM and Degnan, BM}, title = {Pluripotency and the origin of animal multicellularity.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-019-1290-4}, pmid = {31189954}, issn = {1476-4687}, abstract = {A widely held-but rarely tested-hypothesis for the origin of animals is that they evolved from a unicellular ancestor, with an apical cilium surrounded by a microvillar collar, that structurally resembled modern sponge choanocytes and choanoflagellates1-4. Here we test this view of animal origins by comparing the transcriptomes, fates and behaviours of the three primary sponge cell types-choanocytes, pluripotent mesenchymal archaeocytes and epithelial pinacocytes-with choanoflagellates and other unicellular holozoans. Unexpectedly, we find that the transcriptome of sponge choanocytes is the least similar to the transcriptomes of choanoflagellates and is significantly enriched in genes unique to either animals or sponges alone. By contrast, pluripotent archaeocytes upregulate genes that control cell proliferation and gene expression, as in other metazoan stem cells and in the proliferating stages of two unicellular holozoans, including a colonial choanoflagellate. Choanocytes in the sponge Amphimedon queenslandica exist in a transient metastable state and readily transdifferentiate into archaeocytes, which can differentiate into a range of other cell types. These sponge cell-type conversions are similar to the temporal cell-state changes that occur in unicellular holozoans5. Together, these analyses argue against homology of sponge choanocytes and choanoflagellates, and the view that the first multicellular animals were simple balls of cells with limited capacity to differentiate. Instead, our results are consistent with the first animal cell being able to transition between multiple states in a manner similar to modern transdifferentiating and stem cells.}, }
@article {pmid31187926, year = {2019}, author = {Qian, XX and Santini, CL and Kosta, A and Menguy, N and Le Guenno, H and Zhang, W and Li, J and Chen, YR and Liu, J and Alberto, F and Espinosa, L and Xiao, T and Wu, LF}, title = {Juxtaposed membranes underpin cellular adhesion and display unilateral cell division of multicellular magnetotactic prokaryotes.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14710}, pmid = {31187926}, issn = {1462-2920}, abstract = {Multicellular magnetotactic prokaryotes (MMPs) exhibit peculiar coordination of swimming along geomagnetic field lines. Approximate 40-80 cells assemble, with a helical geometry or axisymmetry, into spherical or ellipsoidal MMPs, respectively. To contribute to a comprehensive understanding of bacterial multicellularity here we took multiple microscopic approaches to study the diversity, assembly, reproduction and motility of ellipsoidal MMPs. Using correlative fluorescence in situ hybridization and scanning electron microscopy analysis, we found an unexpected diversity in populations of ellipsoidal MMPs in the Mediterranean Sea. The high-pressure freezing/freeze substitution fixation technique allowed us to show, for the first time, that cells adhere via juxtaposed membranes and are held together by a rimming lattice. Fluorescence confocal microscopy and ultra-thin section images revealed not only the one-layer hollow three-dimensional architecture, but also periphery-core unilateral constriction of constituent cells and unidirectional binary fission of the ellipsoidal MMPs. This finding suggests the evolution toward MMPs multicellularity via the mechanism of incomplete separation of offspring. Remarkably, thousands of flagellar at the periphery surface of cells underpin the coordinated swimming of MMPs in response to mechanical, chemical, magnetic and optical stimuli, including a magnetotactic photokinesis behavior. Together these results unveil the unique structure and function property of ellipsoidal MMPs. This article is protected by copyright. All rights reserved.}, }
@article {pmid31185890, year = {2019}, author = {Yamashita, S and Nozaki, H}, title = {Embryogenesis of flattened colonies implies the innovation required for the evolution of spheroidal colonies in volvocine green algae.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {120}, doi = {10.1186/s12862-019-1452-x}, pmid = {31185890}, issn = {1471-2148}, support = {17J03439//Japan Society for the Promotion of Science/ ; 16H02518//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: Volvocine algae provide a suitable model for investigation of the evolution of multicellular organisms. Within this group, evolution of the body plan from flattened to spheroidal colonies is thought to have occurred independently in two different lineages, Volvocaceae and Astrephomene. Volvocacean species undergo inversion to form a spheroidal cell layer following successive cell divisions during embryogenesis. During inversion, the daughter protoplasts change their shape and develop acute chloroplast ends (opposite to basal bodies). By contrast, Astrephomene does not undergo inversion; rather, its daughter protoplasts rotate during successive cell divisions to form a spheroidal colony. However, the evolutionary pathways of these cellular events involved in the two tactics for formation of spheroidal colony are unclear, since the embryogenesis of extant volvocine genera with ancestral flattened colonies, such as Gonium and Tetrabaena, has not previously been investigated in detail.<br><br>RESULTS: We conducted time-lapse imaging by light microscopy and indirect immunofluorescence microscopy with staining of basal bodies, nuclei, and microtubules to observe embryogenesis in G. pectorale and T. socialis, which form 16-celled or 4-celled flattened colonies, respectively. In G. pectorale, a cup-shaped cell layer of the 16-celled embryo underwent gradual expansion after successive cell divisions, with the apical ends (position of basal bodies) of the square embryo's peripheral protoplasts separated from each other. In T. socialis, on the other hand, there was no apparent expansion of the daughter protoplasts in 4-celled embryos after successive cell divisions, however the two pairs of diagonally opposed daughter protoplasts shifted slightly and flattened after hatching. Neither of these two species exhibited rotation of daughter protoplasts during successive cell divisions as in Astrephomene or the formation of acute chloroplast ends of daughter protoplasts as in volvocacean inversion.<br><br>CONCLUSIONS: The present results indicate that the ancestor of Astrephomene might have newly acquired the rotation of daughter protoplasts after it diverged from the ancestor of Gonium, while the ancestor of Volvocaceae might have newly acquired the formation of acute chloroplast ends to complete inversion after divergence from the ancestor of Goniaceae (Gonium and Astrephomene).}, }
@article {pmid31185009, year = {2019}, author = {Roy, M and Finley, SD}, title = {Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model.}, journal = {PLoS computational biology}, volume = {15}, number = {6}, pages = {e1007053}, doi = {10.1371/journal.pcbi.1007053}, pmid = {31185009}, issn = {1553-7358}, abstract = {Mathematical modeling provides the predictive ability to understand the metabolic reprogramming and complex pathways that mediate cancer cells' proliferation. We present a mathematical model using a multiscale, multicellular approach to simulate avascular tumor growth, applied to pancreatic cancer. The model spans three distinct spatial and temporal scales. At the extracellular level, reaction diffusion equations describe nutrient concentrations over a span of seconds. At the cellular level, a lattice-based energy driven stochastic approach describes cellular phenomena including adhesion, proliferation, viability and cell state transitions, occurring on the timescale of hours. At the sub-cellular level, we incorporate a detailed kinetic model of intracellular metabolite dynamics on the timescale of minutes, which enables the cells to uptake and excrete metabolites and use the metabolites to generate energy and building blocks for cell growth. This is a particularly novel aspect of the model. Certain defined criteria for the concentrations of intracellular metabolites lead to cancer cell growth, proliferation or death. Overall, we model the evolution of the tumor in both time and space. Starting with a cluster of tumor cells, the model produces an avascular tumor that quantitatively and qualitatively mimics experimental measurements of multicellular tumor spheroids. Through our model simulations, we can investigate the response of individual intracellular species under a metabolic perturbation and investigate how that response contributes to the response of the tumor as a whole. The predicted response of intracellular metabolites under various targeted strategies are difficult to resolve with experimental techniques. Thus, the model can give novel predictions as to the response of the tumor as a whole, identifies potential therapies to impede tumor growth, and predicts the effects of those therapeutic strategies. In particular, the model provides quantitative insight into the dynamic reprogramming of tumor cells at the intracellular level in response to specific metabolic perturbations. Overall, the model is a useful framework to study targeted metabolic strategies for inhibiting tumor growth.}, }
@article {pmid31183520, year = {2019}, author = {Chaplain, MAJ and Lorenzi, T and Macfarlane, FR}, title = {Bridging the gap between individual-based and continuum models of growing cell populations.}, journal = {Journal of mathematical biology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00285-019-01391-y}, pmid = {31183520}, issn = {1432-1416}, support = {EP/N014642/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations that describe the evolution of cellular densities in response to pressure gradients generated by population growth. Little prior work has explored the relation between such continuum models and related single-cell-based models. We present here a simple stochastic individual-based model for the spatial dynamics of multicellular systems whereby cells undergo pressure-driven movement and pressure-dependent proliferation. We show that nonlinear partial differential equations commonly used to model the spatial dynamics of growing cell populations can be formally derived from the branching random walk that underlies our discrete model. Moreover, we carry out a systematic comparison between the individual-based model and its continuum counterparts, both in the case of one single cell population and in the case of multiple cell populations with different biophysical properties. The outcomes of our comparative study demonstrate that the results of computational simulations of the individual-based model faithfully mirror the qualitative and quantitative properties of the solutions to the corresponding nonlinear partial differential equations. Ultimately, these results illustrate how the simple rules governing the dynamics of single cells in our individual-based model can lead to the emergence of complex spatial patterns of population growth observed in continuum models.}, }
@article {pmid31175188, year = {2019}, author = {Kees, ED and Pendleton, AR and Paquete, CM and Arriola, MB and Kane, AL and Kotloski, NJ and Intile, PJ and Gralnick, JA}, title = {On the Cost and Role of Secreted Flavin Cofactors for Anaerobic Respiration of Fumarate and Urocanate by Shewanella oneidensis.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00852-19}, pmid = {31175188}, issn = {1098-5336}, abstract = {Shewanella oneidensis strain MR-1, a facultative anaerobe and model organism for dissimilatory metal reduction, uses a periplasmic flavocytochrome, FccA, as both a terminal fumarate reductase and as a periplasmic electron transfer hub for extracellular respiration of a variety of substrates. It is currently unclear how maturation of FccA and other periplasmic flavoproteins is achieved, specifically in the context of flavin cofactor loading nor has the fitness cost of flavin secretion been quantified. We demonstrate that deletion of the inner membrane flavin adenine dinucleotide (FAD) exporter Bfe results in a 23% slower growth rate than wild-type during fumarate respiration, and an 80-90% loss in fumarate reductase activity. Exogenous flavin supplementation does not restore FccA activity in a Δbfe mutant unless the gene encoding the periplasmic FAD hydrolase UshA is also deleted. We demonstrate that the small Bfe-independent pool of FccA is sufficient for anaerobic growth with fumarate. Strains lacking Bfe were unable to grow using urocanate as the sole electron acceptor, which relies on the periplasmic flavoprotein UrdA. We show that periplasmic flavoprotein maturation occurs in careful balance with periplasmic FAD hydrolysis, and that the current model for periplasmic flavin cofactor loading must account for a Bfe-independent mechanism for flavin transport. Finally, we determine that the metabolic burden of flavin secretion is not significant during growth with flavin-independent anaerobic electron acceptors. Our work helps frame the physiological motivations that drove evolution of flavin secretion by ShewanellaImportanceShewanella species are prevalent in marine and aquatic environments, throughout stratified water columns, mineral rich sediments and in association with multicellular marine and aquatic organisms. The diversity of niches Shewanellae can occupy are due largely to their respiratory versatility. Shewanella oneidensis is a model organism for dissimilatory metal reduction and can respire a diverse array of organic and inorganic compounds including dissolved and solid metal oxides. The fumarate reductase FccA is a highly abundant multifunctional periplasmic protein that acts to bridge the periplasm and temporarily store electrons in a variety of respiratory nodes including metal, nitrate and dimethyl sulfoxide respiration. However, maturation of this central protein, particularly flavin cofactor acquisition, is poorly understood. Here we quantify the fitness cost of flavin secretion and describe how free flavins are acquired by FccA and a homologous periplasmic flavoprotein UrdA.}, }
@article {pmid31172192, year = {2019}, author = {St-Georges-Robillard, A and Cahuzac, M and Péant, B and Fleury, H and Lateef, MA and Ricard, A and Sauriol, A and Leblond, F and Mes-Masson, AM and Gervais, T}, title = {Long-term fluorescence hyperspectral imaging of on-chip treated co-culture tumour spheroids to follow clonal evolution.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {}, number = {}, pages = {}, doi = {10.1093/intbio/zyz012}, pmid = {31172192}, issn = {1757-9708}, abstract = {Multicellular tumour spheroids are an ideal in vitro tumour model to study clonal heterogeneity and drug resistance in cancer research because different cell types can be mixed at will. However, measuring the individual response of each cell population over time is challenging: current methods are either destructive, such as flow cytometry, or cannot image throughout a spheroid, such as confocal microscopy. Our group previously developed a wide-field fluorescence hyperspectral imaging system to study spheroids formed and cultured in microfluidic chips. In the present study, two subclones of a single parental ovarian cancer cell line transfected to express different fluorophores were produced and co-culture spheroids were formed on-chip using ratios forming highly asymmetric subpopulations. We performed a 3D proliferation assay on each cell population forming the spheroids that matched the 2D growth behaviour. Response assays to PARP inhibitors and platinum-based drugs were also performed to follow the clonal evolution of mixed populations. Our experiments show that hyperspectral imaging can detect spheroid response before observing a decrease in spheroid diameter. Hyperspectral imaging and microfluidic-based spheroid assays provide a versatile solution to study clonal heterogeneity, able to measure response in subpopulations presenting as little as 10% of the initial spheroid.}, }
@article {pmid31171786, year = {2019}, author = {Rossy, T and Nadell, CD and Persat, A}, title = {Cellular advective-diffusion drives the emergence of bacterial surface colonization patterns and heterogeneity.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {2471}, doi = {10.1038/s41467-019-10469-6}, pmid = {31171786}, issn = {2041-1723}, support = {31003A_169377//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_169377//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; MCB 1817342//National Science Foundation (NSF)/ ; STANTO15RO//Cystic Fibrosis Foundation (CF Foundation)/ ; P20-GM113132//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {Microorganisms navigate and divide on surfaces to form multicellular structures called biofilms, the most widespread survival strategy found in the bacterial world. One common assumption is that cellular components guide the spatial architecture and arrangement of multiple species in a biofilm. However, bacteria must contend with mechanical forces generated through contact with surfaces and under fluid flow, whose contributions to colonization patterns are poorly understood. Here, we show how the balance between motility and flow promotes the emergence of morphological patterns in Caulobacter crescentus biofilms. By modeling transport of single cells by flow and Brownian-like swimming, we show that the emergence of these patterns is guided by an effective Péclet number. By analogy with transport phenomena we show that, counter-intuitively, fluid flow represses mixing of distinct clonal lineages, thereby affecting the interaction landscapes between biofilm-dwelling bacteria. This demonstrates that hydrodynamics influence species interaction and evolution within surface-associated communities.}, }
@article {pmid31170405, year = {2019}, author = {Edgar, JA}, title = {L-Ascorbic Acid and the Evolution of Multicellular Eukaryotes.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtbi.2019.06.001}, pmid = {31170405}, issn = {1095-8541}, abstract = {The lifeless earth was formed around 4.5 billion years ago and the first anaerobic unicellular &quot;organisms&quot; may have appeared half a billion years later. Despite subsequent prokaryotes (bacteria and archaea) evolving quite complex biochemistry and some eukaryote characteristics, the transition from unicellular prokaryotes to multicellular, aerobic eukaryotes took a further 2.5 billion years to begin. The key factor or factors that eventually caused this long-delayed transition is a question that has been a focus of considerable research and a topic of discussion over many years. On the basis of the extensive literature available and consideration of some of the characteristics that distinguish multicellular eukaryotes from prokaryotes, it is proposed that, as well as the development of oxygenic photosynthesis producing high levels of environmental oxygen and the formation of vital organelles such as aerobic adenosine triphosphate-generating mitochondria, the concurrent evolution of the L-ascorbic acid redox system should be considered as a key factor that led to the evolution of multicellular eukaryotes and it remains vitally involved in the maintenance of multicellularity and many other eukaryote characteristics.}, }
@article {pmid31170137, year = {2019}, author = {Thomas, F and Madsen, T and Giraudeau, M and Misse, D and Hamede, R and Vincze, O and Renaud, F and Roche, B and Ujvari, B}, title = {Transmissible cancer and the evolution of sex.}, journal = {PLoS biology}, volume = {17}, number = {6}, pages = {e3000275}, doi = {10.1371/journal.pbio.3000275}, pmid = {31170137}, issn = {1545-7885}, abstract = {The origin and subsequent maintenance of sex and recombination are among the most elusive and controversial problems in evolutionary biology. Here, we propose a novel hypothesis, suggesting that sexual reproduction not only evolved to reduce the negative effects of the accumulation of deleterious mutations and processes associated with pathogen and/or parasite resistance but also to prevent invasion by transmissible selfish neoplastic cheater cells, henceforth referred to as transmissible cancer cells. Sexual reproduction permits systematic change of the multicellular organism's genotype and hence an enhanced detection of transmissible cancer cells by immune system. Given the omnipresence of oncogenic processes in multicellular organisms, together with the fact that transmissible cancer cells can have dramatic effects on their host fitness, our scenario suggests that the benefits of sex and concomitant recombination will be large and permanent, explaining why sexual reproduction is, despite its costs, the dominant mode of reproduction among eukaryotes.}, }
@article {pmid31169232, year = {2019}, author = {Siddiqui, S and Singh, A and Faizi, N and Khalid, A}, title = {Cell cannibalism in oral cancer: A sign of aggressiveness, de-evolution, and retroversion of multicellularity.}, journal = {Journal of cancer research and therapeutics}, volume = {15}, number = {3}, pages = {631-637}, doi = {10.4103/jcrt.JCRT_504_17}, pmid = {31169232}, issn = {1998-4138}, abstract = {Background: According to Darwin's theory of evolution, complex creatures evolve from more simplistic ancestors. Dollo's law of irreversibility states that evolution is irreversible. However, cancer cells tend to follow anti-Dollo's law. Unfavorable conditions such as hypoxia, acidic pH and low nutrients cause the cancer cells to switch their lifestyle atavistically in order to survive. They start behaving like a unicellular organism. There is a switch from normal metabolism to Warburg effect and finally cannibalism. Cannibalism is a cell eating cell phenomenon. It is defined as a large cell enclosing a smaller one within its cytoplasm and is known by odd names such as &quot;bird's eye cells&quot; or &quot;signet ring cells.&quot; Smaller tumor cells are found in the cytoplasm of larger tumor cells with crescent-shaped nucleus. Cannibalistic cells (CCs) are a feature of aggressive tumors. These cell types are vulnerable to metastasis.<br><br>Aim: The aim of this study is to identify CCs in various histological grades of oral squamous cell carcinoma (OSCC) and to relate them with the pattern of invasion, lymphocytic response (LR), and mitotic figures (Mfs). The purpose of the article is to establish it as a marker of aggressiveness and metastasis and as an evidence of de-evolution and retroversion of multicellularity.<br><br>Materials and Methods: Sixty-five histologically confirmed cases of OSCC were studied. Pattern of invasion, LR, number of CCs, and Mfs were recorded on 5 μ hematoxylin and eosin-stained tissue sections. ANOVA and t-test were applied; P < 0.05 was considered statistically significant.<br><br>Results: CCs were more in sections with patchy LR, increased Mfs, and grade IV pattern of invasion.<br><br>Conclusion: With increase in dedifferentiation, tumor cells start behaving like unicellular organisms with cell eating cell characteristics.}, }
@article {pmid31163162, year = {2019}, author = {Ostrowski, EA}, title = {Enforcing Cooperation in the Social Amoebae.}, journal = {Current biology : CB}, volume = {29}, number = {11}, pages = {R474-R484}, doi = {10.1016/j.cub.2019.04.022}, pmid = {31163162}, issn = {1879-0445}, abstract = {Cooperation has been essential to the evolution of biological complexity, but many societies struggle to overcome internal conflicts and divisions. Dictyostelium discoideum, or the social amoeba, has been a useful model system for exploring these conflicts and how they can be resolved. When starved, these cells communicate, gather into groups, and build themselves into a multicellular fruiting body. Some cells altruistically die to form the rigid stalk, while the remainder sit atop the stalk, become spores, and disperse. Evolutionary theory predicts that conflict will arise over which cells die to form the stalk and which cells become spores and survive. The power of the social amoeba lies in the ability to explore how cooperation and conflict work across multiple levels, ranging from proximate mechanisms (how does it work?) to ultimate evolutionary answers (why does it work?). Recent studies point to solutions to the problem of ensuring fairness, such as the ability to suppress selfishness and to recognize and avoid unrelated individuals. This work confirms a central role for kin selection, but also suggests new explanations for how social amoebae might enforce cooperation. New approaches based on genomics are also enabling researchers to decipher for the first time the evolutionary history of cooperation and conflict and to determine its role in shaping the biology of multicellular organisms.}, }
@article {pmid31163154, year = {2019}, author = {Smith, P and Schuster, M}, title = {Public goods and cheating in microbes.}, journal = {Current biology : CB}, volume = {29}, number = {11}, pages = {R442-R447}, doi = {10.1016/j.cub.2019.03.001}, pmid = {31163154}, issn = {1879-0445}, abstract = {Communication and cooperation are not restricted to complex, higher organisms. Microbes, too, perform a variety of collective, multicellular behaviors, including biofilm formation, quorum sensing, nutrient acquisition, and dispersal. The products of these microbial cooperative behaviors are generally referred to as public goods. Here we describe the nature of microbial public goods, the associated problem of cheating, and ways in which microbes maintain public goods in the face of cheating. We highlight work in a growing field at the interface of microbiology, evolution, and ecology that combines multiple approaches in experimental evolution, genetics, and mathematical modeling.}, }
@article {pmid31155362, year = {2019}, author = {Russell, SL and Chappell, L and Sullivan, W}, title = {A symbiont's guide to the germline.}, journal = {Current topics in developmental biology}, volume = {135}, number = {}, pages = {315-351}, doi = {10.1016/bs.ctdb.2019.04.007}, pmid = {31155362}, issn = {1557-8933}, abstract = {Microbial symbioses exhibit astounding adaptations, yet all symbionts face the problem of how to reliably associate with host offspring every generation. A common strategy is vertical transmission, in which symbionts are directly transmitted from the female to her offspring. The diversity of symbionts and vertical transmission mechanisms is as expansive as the diversity of eukaryotic host taxa that house them. However, there are several common themes among these mechanisms based on the degree to which symbionts associate with the host germline during transmission. In this review, we detail three distinct vertical transmission strategies, starting with associations that are transmitted from host somatic cells to offspring somatic cells, either due to lacking a germline or avoiding it. A second strategy involves somatically-localized symbionts that migrate into the germline during host development. The third strategy we discuss is one in which the symbiont maintains continuous association with the germline throughout development. Unexpectedly, the vast majority of documented vertically inherited symbionts rely on the second strategy: soma-to-germline migration. Given that not all eukaryotes contain a sequestered germline and instead produce offspring from somatic stem cell lineages, this soma-to-germline migration is discussed in the context of multicellular evolution. Lastly, as recent genomics data have revealed an abundance of horizontal gene transfer events from symbiotic and non-symbiotic bacteria to host genomes, we discuss their impact on eukaryotic host evolution.}, }
@article {pmid31150287, year = {2019}, author = {Moreno, MA and Ofria, C}, title = {Toward Open-Ended Fraternal Transitions in Individuality.}, journal = {Artificial life}, volume = {25}, number = {2}, pages = {117-133}, doi = {10.1162/artl_a_00284}, pmid = {31150287}, issn = {1530-9185}, abstract = {The emergence of new replicating entities from the union of simpler entities characterizes some of the most profound events in natural evolutionary history. Such transitions in individuality are essential to the evolution of the most complex forms of life. Thus, understanding these transitions is critical to building artificial systems capable of open-ended evolution. Alas, these transitions are challenging to induce or detect, even with computational organisms. Here, we introduce the DISHTINY (Distributed Hierarchical Transitions in Individuality) platform, which provides simple cell-like organisms with the ability and incentive to unite into new individuals in a manner that can continue to scale to subsequent transitions. The system is designed to encourage these transitions so that they can be studied: Organisms that coordinate spatiotemporally can maximize the rate of resource harvest, which is closely linked to their reproductive ability. We demonstrate the hierarchical emergence of multiple levels of individuality among simple cell-like organisms that evolve parameters for manually designed strategies. During evolution, we observe reproductive division of labor and close cooperation among cells, including resource-sharing, aggregation of resource endowments for propagules, and emergence of an apoptosis response to somatic mutation. Many replicate populations evolved to direct their resources toward low-level groups (behaving like multicellular individuals), and many others evolved to direct their resources toward high-level groups (acting as larger-scale multicellular individuals).}, }
@article {pmid31142622, year = {2019}, author = {Sweeney, EG and Nishida, A and Weston, A and Bañuelos, MS and Potter, K and Conery, J and Guillemin, K}, title = {Agent-Based Modeling Demonstrates How Local Chemotactic Behavior Can Shape Biofilm Architecture.}, journal = {mSphere}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/mSphere.00285-19}, pmid = {31142622}, issn = {2379-5042}, abstract = {Bacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms of Helicobacter pylori, a common bacterial resident of human stomachs. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterized H. pylori strains with various AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis-defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger-scale emergent properties of biofilms.IMPORTANCE Most bacteria exist in aggregated, three-dimensional structures called biofilms. Although biofilms play important ecological roles in natural and engineered settings, they can also pose societal problems, for example, when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown that Helicobacter pylori bacteria are repulsed by high concentrations of a self-produced molecule, AI-2, and that H. pylori mutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here, we used computer simulations of biofilm formation to show that local H. pylori behavior of repulsion from high AI-2 could explain the overall architecture of H. pylori biofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.}, }
@article {pmid31118944, year = {2019}, author = {Liu, T and Wang, X and Wang, G and Jia, S and Liu, G and Shan, G and Chi, S and Zhang, J and Yu, Y and Xue, T and Yu, J}, title = {Evolution of Complex Thallus Alga: Genome Sequencing of Saccharina japonica.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {378}, doi = {10.3389/fgene.2019.00378}, pmid = {31118944}, issn = {1664-8021}, abstract = {Saccharina, as one of the most important brown algae (Phaeophyceae) with multicellular thallus, has a very remarkable evolutionary history, and globally accounts for most of the economic marine aquaculture production worldwide. Here, we present the 580.5 million base pairs of genome sequence of Saccharina japonica, whose current assembly contains 35,725 protein-coding genes. In a comparative analysis with Ectocarpus siliculosus, the integrated virus sequence suggested the genome evolutionary footprints, which derived from their co-ancestry and experienced genomic arrangements. Furthermore, the gene expansion was found to be an important strategy for functional evolution, especially with regard to extracelluar components, stress-related genes, and vanadium-dependent haloperoxidases, and we proposed a hypothesis that gene duplication events were the main driving force for the evolution history from multicellular filamentous algae to thallus algae. The sequenced Saccharina genome paves the way for further molecular studies and is useful for genome-assisted breeding of S. japonica and other related algae species.}, }
@article {pmid31118507, year = {2019}, author = {Loron, CC and François, C and Rainbird, RH and Turner, EC and Borensztajn, S and Javaux, EJ}, title = {Early fungi from the Proterozoic era in Arctic Canada.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-019-1217-0}, pmid = {31118507}, issn = {1476-4687}, abstract = {Fungi are crucial components of modern ecosystems. They may have had an important role in the colonization of land by eukaryotes, and in the appearance and success of land plants and metazoans1-3. Nevertheless, fossils that can unambiguously be identified as fungi are absent from the fossil record until the middle of the Palaeozoic era4,5. Here we show, using morphological, ultrastructural and spectroscopic analyses, that multicellular organic-walled microfossils preserved in shale of the Grassy Bay Formation (Shaler Supergroup, Arctic Canada), which dates to approximately 1,010-890 million years ago, have a fungal affinity. These microfossils are more than half a billion years older than previously reported unambiguous occurrences of fungi, a date which is consistent with data from molecular clocks for the emergence of this clade6,7. In extending the fossil record of the fungi, this finding also pushes back the minimum date for the appearance of eukaryotic crown group Opisthokonta, which comprises metazoans, fungi and their protist relatives8,9.}, }
@article {pmid31113629, year = {2019}, author = {Ballinger, MJ and Perlman, SJ}, title = {The defensive Spiroplasma.}, journal = {Current opinion in insect science}, volume = {32}, number = {}, pages = {36-41}, doi = {10.1016/j.cois.2018.10.004}, pmid = {31113629}, issn = {2214-5753}, abstract = {Defensive microbes are of great interest for their roles in arthropod health, disease transmission, and biocontrol efforts. Obligate bacterial passengers of arthropods, such as Spiroplasma, confer protection against the natural enemies of their hosts to improve their own fitness. Although known for less than a decade, Spiroplasma's defensive reach extends to diverse parasites, both microbial and multicellular. We provide an overview of known defensive phenotypes against nematodes, parasitoid wasps, and fungi, and highlight recent studies supporting the role of Spiroplasma-encoded ribosome-inactivating proteins in protection. With cellular features well-suited for life in the hemolymph, broad distribution among invertebrate hosts, and the capacity to repeatedly evolve vertical transmission, Spiroplasma may be uniquely equipped to form intimate, defensive associations to combat extracellular parasites. Along with insights into defensive mechanisms, recent significant advances have been made in male-killing - a phenotype with interesting evolutionary ties to defense. Finally, we look forward to an exciting decade using the genetic tools of Drosophila, and the rapidly-advancing tractability of Spiroplasma itself, to better understand mechanisms and evolution in defensive symbiosis.}, }
@article {pmid31095603, year = {2019}, author = {Khan, MAW and Stephens, WZ and Mohammed, AD and Round, JL and Kubinak, JL}, title = {Does MHC heterozygosity influence microbiota form and function?.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215946}, doi = {10.1371/journal.pone.0215946}, pmid = {31095603}, issn = {1932-6203}, abstract = {MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host's microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.}, }
@article {pmid31088261, year = {2019}, author = {Pichugin, Y and Park, HJ and Traulsen, A}, title = {Evolution of simple multicellular life cycles in dynamic environments.}, journal = {Journal of the Royal Society, Interface}, volume = {16}, number = {154}, pages = {20190054}, doi = {10.1098/rsif.2019.0054}, pmid = {31088261}, issn = {1742-5662}, abstract = {The mode of reproduction is a critical characteristic of any species, as it has a strong effect on its evolution. As any other trait, the reproduction mode is subject to natural selection and may adapt to the environment. When the environment varies over time, different reproduction modes could be optimal at different times. The natural response to a dynamic environment seems to be bet hedging, where multiple reproductive strategies are stochastically executed. Here, we develop a framework for the evolution of simple multicellular life cycles in a dynamic environment. We use a matrix population model of undifferentiated multicellular groups undergoing fragmentation and ask which mode maximizes the population growth rate. Counterintuitively, we find that natural selection in dynamic environments generally tends to promote deterministic, not stochastic, reproduction modes.}, }
@article {pmid31086369, year = {2019}, author = {Gao, Y and Traulsen, A and Pichugin, Y}, title = {Interacting cells driving the evolution of multicellular life cycles.}, journal = {PLoS computational biology}, volume = {15}, number = {5}, pages = {e1006987}, doi = {10.1371/journal.pcbi.1006987}, pmid = {31086369}, issn = {1553-7358}, abstract = {Evolution of complex multicellular life began from the emergence of a life cycle involving the formation of cell clusters. The opportunity for cells to interact within clusters provided them with an advantage over unicellular life forms. However, what kind of interactions may lead to the evolution of multicellular life cycles? Here, we combine evolutionary game theory with a model for the emergence of multicellular groups to investigate how cell interactions can influence reproduction modes during the early stages of the evolution of multicellularity. In our model, the presence of both cell types is maintained by stochastic phenotype switching during cell division. We identify evolutionary optimal life cycles as those which maximize the population growth rate. Among all interactions captured by two-player games, the vast majority promotes two classes of life cycles: (i) splitting into unicellular propagules or (ii) fragmentation into two offspring clusters of equal (or almost equal) size. Our findings indicate that the three most important characteristics, determining whether multicellular life cycles will evolve, are the average performance of homogeneous groups, heterogeneous groups, and solitary cells.}, }
@article {pmid31077747, year = {2019}, author = {Vinogradov, AE and Anatskaya, OV}, title = {Evolutionary framework of the human interactome: Unicellular and multicellular giant clusters.}, journal = {Bio Systems}, volume = {181}, number = {}, pages = {82-87}, doi = {10.1016/j.biosystems.2019.05.004}, pmid = {31077747}, issn = {1872-8324}, abstract = {The main contradiction of multicellularity (MCM) is between the unicellular (UC) and multicellular (MC) levels. In human interactome we revealed two giant clusters with MC and UC medians (and several smaller ones with MC medians). The enrichment of these clusters by phylostrata and by functions support the MC versus UC division. The total interactome and the giant clusters show a core-periphery evolutionary growth. From viewpoint of the MCM, the most important is the placement of genes, appearing at UC evolutionary stage, in the MC clusters. Thus, genes involved in vesicle-mediated transport, cell cycle, cellular responses to stress, post-translational modifications and many diseases appeared at UC evolutionary stage but are placed mostly in MC clusters. Genes downregulated with age are enriched in UC cluster, whereas the upregulated genes are preferentially placed in MC giant cluster. The tumor suppressor and pluripotency regulating pathways are also enriched in MC giant cluster. Therefore, this cluster probably operates as 'internal manager' constraining runaway unicellularity. The clusters have denser interactions within than between them, therefore they can serve as attractors (stable states of dynamic systems) of cellular programs. Importantly, the UC cluster have a higher inside/outside connection ratio compared with MC clusters, which suggests a stronger attractor effect and may explain why cells of MC organisms are prone to oncogenesis. The evolutionary clustering of human interactome elucidates the MC control over functions appearing at UC evolutionary stage and can build a framework for biosystems studies focusing on the interplay between UC and MC levels.}, }
@article {pmid31069269, year = {2019}, author = {Erkenbrack, EM and Thompson, JR}, title = {Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {160}, doi = {10.1038/s42003-019-0417-3}, pmid = {31069269}, issn = {2399-3642}, abstract = {The multiplicity of cell types comprising multicellular organisms begs the question as to how cell type identities evolve over time. Cell type phylogenetics informs this question by comparing gene expression of homologous cell types in distantly related taxa. We employ this approach to inform the identity of larval skeletogenic cells of echinoderms, a clade for which there are phylogenetically diverse datasets of spatial gene expression patterns. We determined ancestral spatial expression patterns of alx1, ets1, tbr, erg, and vegfr, key components of the skeletogenic gene regulatory network driving identity of the larval skeletogenic cell. Here we show ancestral state reconstructions of spatial gene expression of extant eleutherozoan echinoderms support homology and common ancestry of echinoderm larval skeletogenic cells. We propose larval skeletogenic cells arose in the stem lineage of eleutherozoans during a cell type duplication event that heterochronically activated adult skeletogenic cells in a topographically distinct tissue in early development.}, }
@article {pmid31069245, year = {2018}, author = {Wang, P and Liang, J and Shi, LZ and Wang, Y and Zhang, P and Ouyang, M and Preece, D and Peng, Q and Shao, L and Fan, J and Sun, J and Li, SS and Berns, MW and Zhao, H and Wang, Y}, title = {Visualizing Spatiotemporal Dynamics of Intercellular Mechanotransmission upon Wounding.}, journal = {ACS photonics}, volume = {5}, number = {9}, pages = {3565-3574}, doi = {10.1021/acsphotonics.8b00383}, pmid = {31069245}, issn = {2330-4022}, support = {R01 GM126016/GM/NIGMS NIH HHS/United States ; R01 GM125379/GM/NIGMS NIH HHS/United States ; R33 CA204704/CA/NCI NIH HHS/United States ; R01 HL121365/HL/NHLBI NIH HHS/United States ; R21 CA209629/CA/NCI NIH HHS/United States ; }, abstract = {During cell-to-cell communications, the interplay between physical and biochemical cues is essential for informational exchange and functional coordination, especially in multicellular organisms. However, it remains a challenge to visualize intercellular signaling dynamics in single live cells. Here, we report a photonic approach, based on laser microscissors and Förster resonance energy transfer (FRET) microscopy, to study intercellular signaling transmission. First, using our high-throughput screening platform, we developed a highly sensitive FRET-based biosensor (SCAGE) for Src kinase, a key regulator of intercellular interactions and signaling cascades. Notably, SCAGE showed a more than 40-fold sensitivity enhancement than the original biosensor in live mammalian cells. Next, upon local severance of physical intercellular connections by femtosecond laser pulses, SCAGE enabled the visualization of a transient Src activation across neighboring cells. Lastly, we found that this observed transient Src activation following the loss of cell-cell contacts depends on the passive structural support of cytoskeleton but not on the active actomyosin contractility. Hence, by precisely introducing local physical perturbations and directly visualizing spatiotemporal transmission of ensuing signaling events, our integrated approach could be broadly applied to mimic and investigate the wounding process at single-cell resolutions. This integrated approach with highly sensitive FRET-based biosensors provides a unique system to advance our in-depth understanding of molecular mechanisms underlying the physical-biochemical basis of intercellular coupling and wounding processes.}, }
@article {pmid31062469, year = {2019}, author = {Turan, ZG and Parvizi, P and Dönertaş, HM and Tung, J and Khaitovich, P and Somel, M}, title = {Molecular footprint of Medawar's mutation accumulation process in mammalian aging.}, journal = {Aging cell}, volume = {}, number = {}, pages = {e12965}, doi = {10.1111/acel.12965}, pmid = {31062469}, issn = {1474-9726}, support = {//Science Academy/ ; 114C040//Scientific and Technological Research Council of Turkey/ ; 215Z495//Scientific and Technological Research Council of Turkey/ ; //Middle East Technical University (METU)/ ; }, abstract = {Medawar's mutation accumulation hypothesis explains aging by the declining force of natural selection with age: Slightly deleterious germline mutations expressed in old age can drift to fixation and thereby lead to aging-related phenotypes. Although widely cited, empirical evidence for this hypothesis has remained limited. Here, we test one of its predictions that genes relatively highly expressed in old adults should be under weaker purifying selection than genes relatively highly expressed in young adults. Combining 66 transcriptome datasets (including 16 tissues from five mammalian species) with sequence conservation estimates across mammals, here we report that the overall conservation level of expressed genes is lower at old age compared to young adulthood. This age-related decrease in transcriptome conservation (ADICT) is systematically observed in diverse mammalian tissues, including the brain, liver, lung, and artery, but not in others, most notably in the muscle and heart. Where observed, ADICT is driven partly by poorly conserved genes being up-regulated during aging. In general, the more often a gene is found up-regulated with age among tissues and species, the lower its evolutionary conservation. Poorly conserved and up-regulated genes have overlapping functional properties that include responses to age-associated tissue damage, such as apoptosis and inflammation. Meanwhile, these genes do not appear to be under positive selection. Hence, genes contributing to old age phenotypes are found to harbor an excess of slightly deleterious alleles, at least in certain tissues. This supports the notion that genetic drift shapes aging in multicellular organisms, consistent with Medawar's mutation accumulation hypothesis.}, }
@article {pmid31055860, year = {2019}, author = {Singer, D and Mitchell, EAD and Payne, RJ and Blandenier, Q and Duckert, C and Fernández, LD and Fournier, B and Hernández, CE and Granath, G and Rydin, H and Bragazza, L and Koronatova, NG and Goia, I and Harris, LI and Kajukało, K and Kosakyan, A and Lamentowicz, M and Kosykh, NP and Vellak, K and Lara, E}, title = {Dispersal limitations and historical factors determine the biogeography of specialized terrestrial protists.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15117}, pmid = {31055860}, issn = {1365-294X}, abstract = {Recent studies show that soil eukaryotic diversity is immense and dominated by microorganisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to microorganisms. Major diversification events in multicellular organisms have often been attributed to long-term climatic and geological processes, but the impact of such processes on protist diversity has received much less attention as their distribution has often been believed to be largely cosmopolitan. Here, we quantified phylogeographic patterns in Hyalosphenia papilio, a large testate amoeba restricted to Holarctic Sphagnum-dominated peatlands, to test if the current distribution of its genetic diversity can be explained by historical factors or by the current distribution of suitable habitat. Phylogenetic diversity was higher in Western North America, corresponding to the inferred geographical origin of the H. papilio complex, and was lower in Eurasia despite extensive suitable habitat. These results suggest that patterns of phylogenetic diversity and distribution can be explained by the history of Holarctic Sphagnum peatland range expansions and contractions in response to Quaternary glaciations that promoted cladogenetic range evolution, rather than the contemporary distribution of suitable habitats. Species distributions were positively correlated with climatic niche breadth, suggesting that climatic tolerance is key to dispersal ability in H. papilio. This implies that, at least for large and specialized terrestrial microorganisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographic patterns and may partly explain their very high overall diversity. This article is protected by copyright. All rights reserved.}, }
@article {pmid31053584, year = {2019}, author = {Li, J and Zhang, H and Liu, P and Menguy, N and Roberts, AP and Chen, H and Wang, Y and Pan, Y}, title = {Phylogenetic and structural identification of a novel magnetotactic Deltaproteobacterium strain WYHR-1 from a freshwater lake.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00731-19}, pmid = {31053584}, issn = {1098-5336}, abstract = {Magnetotactic bacteria (MTB) are phylogenetically diverse prokaryotes that are able to biomineralize intracellular, magnetic chains of magnetite or greigite nanocrystals called magnetosomes. Simultaneous characterization of MTB phylogeny and biomineralization is crucial but challenging because most MTB are extremely difficult to culture. We identify a large rod, bean-like MTB (tentatively named WYHR-1) from freshwater sediments of Weiyang Lake, Xi'an, China, using a coupled fluorescence and scanning electron microscopy approach at the single-cell scale. Phylogenetic analysis of 16S rRNA gene sequences indicates that WYHR-1 is a novel genus from the Deltaproteobacteria class. Transmission electron microscope observations reveal that WYHR-1 cells contain tens of magnetite magnetosomes that are organized into a single chain bundle along the cell long axis. Mature WYHR-1 magnetosomes are bullet-shaped, straight and elongated along the (001) direction, with a large flat end terminated by a {100} face at the base and a conical top. This crystal morphology is distinctively different from bullet-shaped magnetosomes produced by other MTB in the Deltaproteobacteria class and the Nitrospirae phylum. This indicates that WYHR-1 may have a different crystal growth process and mechanism from other species, which results from species-specific magnetosome biomineralization in MTB.IMPORTANCE Magnetotactic bacteria (MTB) are a model system for understanding biomineralization, and are also studied intensively in biogeomagnetic and paleomagnetic research. However, many uncultured MTB strains have not been identified phylogenetically or investigated structurally at the single-cell level, which limits comprehensive understanding of MTB diversity and their role in biomineralization. We have identified a novel MTB strain WYHR-1 from a freshwater lake using a coupled fluorescence and scanning electron microscopy approach at the single-cell scale. Our analyses further indicate that strain WYHR-1 represents a novel genus from the Deltaproteobacteria class. In contrast to bullet-shaped magnetosomes produced by other MTB in the Deltaproteobacteria class and the Nitrospirae phylum, WYHR-1 magnetosomes are bullet-shaped, straight, and highly elongated along the (001) direction, and are terminated by a large {100} face at their base and have a conical top. Our findings imply that, consistent with phylogenetic diversity of MTB, bullet-shaped magnetosomes have diverse crystal habits and growth patterns.}, }
@article {pmid31046194, year = {2019}, author = {Biscotti, MA and Barucca, M and Carducci, F and Forconi, M and Canapa, A}, title = {The p53 gene family in vertebrates: Evolutionary considerations.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22856}, pmid = {31046194}, issn = {1552-5015}, support = {467-2014//Ministero della Ricerca e dell'Istruzione/ ; }, abstract = {The origin of the p53 gene family predates multicellular life since TP53 members of this gene family have been found in unicellular eukaryotes. In invertebrates one or two genes attributable to a TP53-like or TP63/73-like gene are present. The radiation into three genes, TP53, TP63, and TP73, has been reported as a vertebrate invention. TP53 is considered the &quot;guardian of the genome&quot; given its role in protecting cells against the DNA damage and cellular stressors. TP63 and TP73 play a role in epithelial development and neurogenesis, respectively. The evolution of the p53 gene family has been the subject of considerable analyses even if several questions remain still open. In this study we addressed the evolutionary history of the p53 gene family in vertebrates performing an extended microsyntenic investigation coupled with a phylogenetic analysis, together with protein domain organization and structure assessment. On the basis of our results we discussed a possible evolutionary scenario according to which a TP53/63/73 ancestor form gave rise to the current TP53 and a TP63/73 form, which in turn independently duplicated into two genes in agnathe and gnathostome lineages.}, }
@article {pmid31040327, year = {2019}, author = {Salvi, M and Morbiducci, U and Amadeo, F and Santoro, R and Angelini, F and Chimenti, I and Massai, D and Messina, E and Giacomello, A and Pesce, M and Molinari, F}, title = {Automated Segmentation of Fluorescence Microscopy Images for 3D Cell Detection in human-derived Cardiospheres.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6644}, doi = {10.1038/s41598-019-43137-2}, pmid = {31040327}, issn = {2045-2322}, abstract = {The 'cardiosphere' is a 3D cluster of cardiac progenitor cells recapitulating a stem cell niche-like microenvironment with a potential for disease and regeneration modelling of the failing human myocardium. In this multicellular 3D context, it is extremely important to decrypt the spatial distribution of cell markers for dissecting the evolution of cellular phenotypes by direct quantification of fluorescent signals in confocal microscopy. In this study, we present a fully automated method, named CARE ('CARdiosphere Evaluation'), for the segmentation of membranes and cell nuclei in human-derived cardiospheres. The proposed method is tested on twenty 3D-stacks of cardiospheres, for a total of 1160 images. Automatic results are compared with manual annotations and two open-source software designed for fluorescence microscopy. CARE performance was excellent in cardiospheres membrane segmentation and, in cell nuclei detection, the algorithm achieved the same performance as two expert operators. To the best of our knowledge, CARE is the first fully automated algorithm for segmentation inside in vitro 3D cell spheroids, including cardiospheres. The proposed approach will provide, in the future, automated quantitative analysis of markers distribution within the cardiac niche-like environment, enabling predictive associations between cell mechanical stresses and dynamic phenotypic changes.}, }
@article {pmid31036299, year = {2019}, author = {Borisenko, I and Podgornaya, OI and Ereskovsky, AV}, title = {From traveler to homebody: Which signaling mechanisms sponge larvae use to become adult sponges?.}, journal = {Advances in protein chemistry and structural biology}, volume = {116}, number = {}, pages = {421-449}, doi = {10.1016/bs.apcsb.2019.02.002}, pmid = {31036299}, issn = {1876-1631}, abstract = {Cell-to-cell signaling is responsible for regulation of many developmental processes such as proliferation, cell migration, survival, cell fate specification and axis patterning. In this article we discussed the role of signaling in the metamorphosis of sponges with a focus on epithelial-mesenchymal transition (EMT) accompanying this event. Sponges (Porifera) are an ancient lineage of morphologically simple animals occupying a basal position on the tree of life. The study of these animals is necessary for understanding the origin of multicellularity and the evolution of developmental processes. Development of sponges is quite diverse. It finishes with the metamorphosis of a free-swimming larva into a young settled sponge. The outer surface of sponge larvae consists of a ciliated epithelial sheath, which ensures locomotion, while their internal structure varies from genus to genus. The fate of larval ciliated cells is the most intriguing aspect of metamorphosis. In this review we discuss the fate of larval ciliated cells, the processes going on in cells during metamorphosis at the molecular level and the regulation of this process. The review is based on information about several sponge species with a focus on Halisarca dujardini, Sycon ciliatum and Amphimedon queenslandica. In our model sponge, H. dujardini, ciliated cells leave the larval epithelium during metamorphosis and migrate to the internal cell mass as amoeboid cells to be differentiated into choanocytes of the juvenile sponge. Ciliated cells undergo EMT and internalize within minutes. As EMT involves the disappearance of adherens junctions and as cadherin, the main adherens junction protein, was identified in the transcriptome of several sponges, we suppose that EMT is regulated through cadherin-containing adherens junctions between ciliated cells. We failed to identify the master genes of EMT in the H. dujardini transcriptome, possibly because transcription was absent in the sequenced stages. They may be revealed by a search in the genome. The master genes themselves are controlled by various signaling pathways. Sponges have all the six signaling pathways conserved in Metazoa: Wnt, TGF-beta, Hedgehog, Notch, FGF and NO-dependent pathways. Summarizing the new data about intercellular communication in sponges, we can put forward two main questions regarding metamorphosis: (1) Which of the signaling pathways and in what hierarchical order are involved in metamorphosis? (2) How is the organization of a young sponge related to that of the larva or, in other words, is there a heredity of axes between the larva and the adult sponge?}, }
@article {pmid31032028, year = {2019}, author = {Rivera-Yoshida, N and Arzola, AV and Arias Del Angel, JA and Franci, A and Travisano, M and Escalante, AE and Benítez, M}, title = {Plastic multicellular development of Myxococcus xanthus: genotype-environment interactions in a physical gradient.}, journal = {Royal Society open science}, volume = {6}, number = {3}, pages = {181730}, doi = {10.1098/rsos.181730}, pmid = {31032028}, issn = {2054-5703}, abstract = {In order to investigate the contribution of the physical environment to variation in multicellular development of Myxococcus xanthus, phenotypes developed by different genotypes in a gradient of substrate stiffness conditions were quantitatively characterized. Statistical analysis showed that plastic phenotypes result from the genotype, the substrate conditions and the interaction between them. Also, phenotypes were expressed in two distinguishable scales, the individual and the population levels, and the interaction with the environment showed scale and trait specificity. Overall, our results highlight the constructive role of the physical context in the development of microbial multicellularity, with both ecological and evolutionary implications.}, }
@article {pmid31031789, year = {2019}, author = {Hajheidari, M and Koncz, C and Bucher, M}, title = {Chromatin Evolution-Key Innovations Underpinning Morphological Complexity.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {454}, doi = {10.3389/fpls.2019.00454}, pmid = {31031789}, issn = {1664-462X}, abstract = {The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.}, }
@article {pmid31023220, year = {2019}, author = {Krishnan, A and Degnan, BM and Degnan, SM}, title = {The first identification of complete Eph-ephrin signalling in ctenophores and sponges reveals a role for neofunctionalization in the emergence of signalling domains.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {96}, doi = {10.1186/s12862-019-1418-z}, pmid = {31023220}, issn = {1471-2148}, abstract = {BACKGROUND: Animals have a greater diversity of signalling pathways than their unicellular relatives, consistent with the evolution and expansion of these pathways occurring in parallel with the origin of animal multicellularity. However, the genomes of sponges and ctenophores - non-bilaterian basal animals - typically encode no, or far fewer, recognisable signalling ligands compared to bilaterians and cnidarians. For instance, the largest subclass of receptor tyrosine kinases (RTKs) in bilaterians, the Eph receptors (Ephs), are present in sponges and ctenophores, but their cognate ligands, the ephrins, have not yet been detected.<br><br>RESULTS: Here, we use an iterative HMM analysis to identify for the first time membrane-bound ephrins in sponges and ctenophores. We also expand the number of Eph-receptor subtypes identified in these animals and in cnidarians. Both sequence and structural analyses are consistent with the Eph ligand binding domain (LBD) and the ephrin receptor binding domain (RBD) having evolved via the co-option of ancient galactose-binding (discoidin-domain)-like and monodomain cupredoxin domains, respectively. Although we did not detect a complete Eph-ephrin signalling pathway in closely-related unicellular holozoans or in other non-metazoan eukaryotes, truncated proteins with Eph receptor LBDs and ephrin RBDs are present in some choanoflagellates. Together, these results indicate that Eph-ephrin signalling was present in the last common ancestor of extant metazoans, and perhaps even in the last common ancestor of animals and choanoflagellates. Either scenario pushes the origin of Eph-ephrin signalling back much earlier than previously reported.<br><br>CONCLUSIONS: We propose that the Eph-LBD and ephrin-RBD, which were ancestrally localised in the cytosol, became linked to the extracellular parts of two cell surface proteins before the divergence of sponges and ctenophores from the rest of the animal kingdom. The ephrin-RBD lost the ancestral capacity to bind copper, and the Eph-LBD became linked to an ancient RTK. The identification of divergent ephrin ligands in sponges and ctenophores suggests that these ligands evolve faster than their cognate receptors. As this may be a general phenomena, we propose that the sequence-structure approach used in this study may be usefully applied to other signalling systems where no, or a small number of, ligands have been identified.}, }
@article {pmid31012964, year = {2019}, author = {Gunaratne, PH and Pan, Y and Rao, AK and Lin, C and Hernandez-Herrera, A and Liang, K and Rait, AS and Venkatanarayan, A and Benham, AL and Rubab, F and Kim, SS and Rajapakshe, K and Chan, CK and Mangala, LS and Lopez-Berestein, G and Sood, AK and Rowat, AC and Coarfa, C and Pirollo, KF and Flores, ER and Chang, EH}, title = {Activating p53 family member TAp63: A novel therapeutic strategy for targeting p53-altered tumors.}, journal = {Cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/cncr.32053}, pmid = {31012964}, issn = {1097-0142}, support = {1 S10 RR 15768-01//U.S. Public Health Service/ ; RP110355//Cancer Prevention and Research Institute of Texas/ ; RP120124//Cancer Prevention and Research Institute of Texas/ ; RP150094//Cancer Prevention and Research Institute of Texas/ ; DBI-1254185//National Science Foundation/ ; HU0001//National Foundation for Cancer Research/ ; 1R01 CA218025-01//National Cancer Institute/ ; 1R01CA160394-01A1//National Cancer Institute/ ; 2P30-CA-51008//National Cancer Institute/ ; 5R01CA132012-02//National Cancer Institute/ ; 5T32CA009686-19//National Institutes of Health/ ; C06RR14567//National Institutes of Health/ ; R00DK094981//National Institutes of Health/ ; }, abstract = {BACKGROUND: Over 96% of high-grade ovarian carcinomas and 50% of all cancers are characterized by alterations in the p53 gene. Therapeutic strategies to restore and/or reactivate the p53 pathway have been challenging. By contrast, p63, which shares many of the downstream targets and functions of p53, is rarely mutated in cancer.<br><br>METHODS: A novel strategy is presented for circumventing alterations in p53 by inducing the tumor-suppressor isoform TAp63 (transactivation domain of tumor protein p63) through its direct downstream target, microRNA-130b (miR-130b), which is epigenetically silenced and/or downregulated in chemoresistant ovarian cancer.<br><br>RESULTS: Treatment with miR-130b resulted in: 1) decreased migration/invasion in HEYA8 cells (p53 wild-type) and disruption of multicellular spheroids in OVCAR8 cells (p53-mutant) in vitro, 2) sensitization of HEYA8 and OVCAR8 cells to cisplatin (CDDP) in vitro and in vivo, and 3) transcriptional activation of TAp63 and the B-cell lymphoma (Bcl)-inhibitor B-cell lymphoma 2-like protein 11 (BIM). Overexpression of TAp63 was sufficient to decrease cell viability, suggesting that it is a critical downstream effector of miR-130b. In vivo, combined miR-130b plus CDDP exhibited greater therapeutic efficacy than miR-130b or CDDP alone. Mice that carried OVCAR8 xenograft tumors and were injected with miR-130b in 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) liposomes had a significant decrease in tumor burden at rates similar to those observed in CDDP-treated mice, and 20% of DOPC-miR-130b plus CDDP-treated mice were living tumor free. Systemic injections of scL-miR-130b plus CDDP in a clinically tested, tumor-targeted nanocomplex (scL) improved survival in 60% and complete remissions in 40% of mice that carried HEYA8 xenografts.<br><br>CONCLUSIONS: The miR-130b/TAp63 axis is proposed as a new druggable pathway that has the potential to uncover broad-spectrum therapeutic options for the majority of p53-altered cancers.}, }
@article {pmid31006855, year = {2019}, author = {Sudianto, E}, title = {Digest: Banding together to battle adversaries has its consequences.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {6}, pages = {1320-1321}, doi = {10.1111/evo.13750}, pmid = {31006855}, issn = {1558-5646}, abstract = {Why did life evolve from single-celled to multicellular organisms? Could there be advantages to this transition? What about associated fitness costs? Kapsetaki and West found that although multicellularity allows Chlorella sorokiniana to avoid predation from similarly-sized predators, it also reduces their competitiveness when resources are limited.}, }
@article {pmid31002575, year = {2019}, author = {Lehtonen, J and Parker, GA}, title = {Evolution of the Two Sexes under Internal Fertilization and Alternative Evolutionary Pathways.}, journal = {The American naturalist}, volume = {193}, number = {5}, pages = {702-716}, doi = {10.1086/702588}, pmid = {31002575}, issn = {1537-5323}, abstract = {Transition from isogamy to anisogamy, hence males and females, leads to sexual selection, sexual conflict, sexual dimorphism, and sex roles. Gamete dynamics theory links biophysics of gamete limitation, gamete competition, and resource requirements for zygote survival and assumes broadcast spawning. It makes testable predictions, but most comparative tests use volvocine algae, which feature internal fertilization. We broaden this theory by comparing broadcast-spawning predictions with two plausible internal-fertilization scenarios: gamete casting/brooding (one mating type retains gametes internally, the other broadcasts them) and packet casting/brooding (one type retains gametes internally, the other broadcasts packets containing gametes, which are released for fertilization). Models show that predictions are remarkably robust to these radical changes, yielding (1) isogamy under low gamete limitation, low gamete competition, and similar required resources for gametes and zygotes, (2) anisogamy when gamete competition and/or limitation are higher and when zygotes require more resources than gametes, as is likely as multicellularity develops, (3) a positive correlation between multicellular complexity and anisogamy ratio, and (4) under gamete competition, only brooders becoming female. Thus, gamete dynamics theory represents a potent rationale for isogamy/anisogamy and makes similar testable predictions for broadcast spawners and internal fertilizers, regardless of whether anisogamy or internal fertilization evolved first.}, }
@article {pmid31002570, year = {2019}, author = {Olito, C and Connallon, T}, title = {Sexually Antagonistic Variation and the Evolution of Dimorphic Sexual Systems.}, journal = {The American naturalist}, volume = {193}, number = {5}, pages = {688-701}, doi = {10.1086/702847}, pmid = {31002570}, issn = {1537-5323}, abstract = {Multicellular Eukaryotes use a broad spectrum of sexual reproduction strategies, ranging from simultaneous hermaphroditism to complete dioecy (separate sexes). The evolutionary pathway from hermaphroditism to dioecy involves the spread of sterility alleles that eliminate female or male reproductive functions, producing unisexual individuals. Classical theory predicts that evolutionary transitions to dioecy are feasible when female and male sex functions genetically trade off with one another (allocation to sex functions is sexually antagonistic) and rates of self-fertilization and inbreeding depression are high within the ancestral hermaphrodite population. We show that genetic linkage between sterility alleles and loci under sexually antagonistic selection significantly alters these classical predictions. We identify three specific consequences of linkage for the evolution of dimorphic sexual systems. First, linkage broadens conditions for the invasion of unisexual sterility alleles, facilitating transitions to sexual systems that are intermediate between hermaphroditism and dioecy (androdioecy and gynodioecy). Second, linkage elevates the equilibrium frequencies of unisexual individuals within androdioecious and gynodioecious populations, which promotes subsequent transitions to full dioecy. Third, linkage dampens the role of inbreeding during transitions to androdioecy and gynodioecy, making these transitions feasible in outbred populations. We discuss implications of these results for the evolution of dimorphic reproductive systems and sex chromosomes.}, }
@article {pmid30989357, year = {2019}, author = {Pérez, P and Soto, T and Gómez-Gil, E and Cansado, J}, title = {Functional interaction between Cdc42 and the stress MAPK signaling pathway during the regulation of fission yeast polarized growth.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10123-019-00072-6}, pmid = {30989357}, issn = {1618-1905}, support = {BIO2015-69958-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; BFU2017-82423-P//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; CSI068P17//Consejería de Educación, Junta de Castilla y León/ ; CLU-2017-03//Consejería de Educación, Junta de Castilla y León/ ; }, abstract = {Cell polarization can be defined as the generation and maintenance of directional cellular organization. The spatial distribution and protein or lipid composition of the cell are not symmetric but organized in specialized domains which allow cells to grow and acquire a certain shape that is closely linked to their physiological function. The establishment and maintenance of polarized growth requires the coordination of diverse processes including cytoskeletal dynamics, membrane trafficking, and signaling cascade regulation. Some of the major players involved in the selection and maintenance of sites for polarized growth are Rho GTPases, which recognize the polarization site and transmit the signal to regulatory proteins of the cytoskeleton. Additionally, cytoskeletal organization, polarized secretion, and endocytosis are controlled by signaling pathways including those mediated by mitogen-activated protein kinases (MAPKs). Rho GTPases and the MAPK signaling pathways are strongly conserved from yeast to mammals, suggesting that the basic mechanisms of polarized growth have been maintained throughout evolution. For this reason, the study of how polarized growth is established and regulated in simple organisms such as the fission yeast Schizosaccharomyces pombe has contributed to broaden our knowledge about these processes in multicellular organisms. We review here the function of the Cdc42 GTPase and the stress activated MAPK (SAPK) signaling pathways during fission yeast polarized growth, and discuss the relevance of the crosstalk between both pathways.}, }
@article {pmid30980502, year = {2019}, author = {Qian, XX and Liu, J and Menguy, N and Li, J and Alberto, F and Teng, Z and Xiao, T and Zhang, W and Wu, LF}, title = {Identification of novel species of marine magnetotactic bacteria affiliated with Nitrospirae phylum.}, journal = {Environmental microbiology reports}, volume = {11}, number = {3}, pages = {330-337}, doi = {10.1111/1758-2229.12755}, pmid = {30980502}, issn = {1758-2229}, support = {//CNRS/ ; 41522402//NSFC/ ; U1706208//NSFC/ ; 41776131//NSFC/ ; }, abstract = {Magnetotactic bacteria (MTB) are a group of Gram-negative bacteria characterized by synthesizing magnetosomes and swimming along geomagnetic field lines. Phylogenetically, they belong to different taxonomic lineages including Proteobacteria, Nitrospirae, Omnitrophica, Latescibacteria and Planctomycetes phyla on the phylogenetic tree. To date, six Nitrospirae MTB phylotypes have been identified from freshwater or low-salinity environments and described in the literature. Here, we report the identification of two Nitrospirae MTB phylotypes collected, for the first time, from the marine environment. Both have a spherical morphology with a cell size of ~ 5 μM and similar motility but are different colours (black-brown and ivory-white) under the optic microscope. They synthesized bullet-shaped iron-oxide magnetosomes that were arranged in multiple bundles of chains. Moreover, the cytoplasm of the black-brown Nitrospirae MTB contained sulphur inclusions that conferred on cells a rough, granular appearance. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they are two novel species and cluster with the previously reported MTB affiliated with the phylum Nitrospirae, thus extending the distribution of Nitrospirae MTB from freshwater to the marine environment.}, }
@article {pmid30978201, year = {2019}, author = {Laundon, D and Larson, BT and McDonald, K and King, N and Burkhardt, P}, title = {The architecture of cell differentiation in choanoflagellates and sponge choanocytes.}, journal = {PLoS biology}, volume = {17}, number = {4}, pages = {e3000226}, doi = {10.1371/journal.pbio.3000226}, pmid = {30978201}, issn = {1545-7885}, abstract = {Although collar cells are conserved across animals and their closest relatives, the choanoflagellates, little is known about their ancestry, their subcellular architecture, or how they differentiate. The choanoflagellate Salpingoeca rosetta expresses genes necessary for animal development and can alternate between unicellular and multicellular states, making it a powerful model for investigating the origin of animal multicellularity and mechanisms underlying cell differentiation. To compare the subcellular architecture of solitary collar cells in S. rosetta with that of multicellular 'rosette' colonies and collar cells in sponges, we reconstructed entire cells in 3D through transmission electron microscopy on serial ultrathin sections. Structural analysis of our 3D reconstructions revealed important differences between single and colonial choanoflagellate cells, with colonial cells exhibiting a more amoeboid morphology consistent with higher levels of macropinocytotic activity. Comparison of multiple reconstructed rosette colonies highlighted the variable nature of cell sizes, cell-cell contact networks, and colony arrangement. Importantly, we uncovered the presence of elongated cells in some rosette colonies that likely represent a distinct and differentiated cell type, pointing toward spatial cell differentiation. Intercellular bridges within choanoflagellate colonies displayed a variety of morphologies and connected some but not all neighbouring cells. Reconstruction of sponge choanocytes revealed ultrastructural commonalities but also differences in major organelle composition in comparison to choanoflagellates. Together, our comparative reconstructions uncover the architecture of cell differentiation in choanoflagellates and sponge choanocytes and constitute an important step in reconstructing the cell biology of the last common ancestor of animals.}, }
@article {pmid30963641, year = {2019}, author = {Rêgo, A and Messina, FJ and Gompert, Z}, title = {Dynamics of genomic change during evolutionary rescue in the seed beetle Callosobruchus maculatus.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.15085}, pmid = {30963641}, issn = {1365-294X}, abstract = {Rapid adaptation can prevent extinction when populations are exposed to extremely marginal or stressful environments. Factors that affect the likelihood of evolutionary rescue from extinction have been identified, but much less is known about the evolutionary dynamics (e.g., rates and patterns of allele frequency change) and genomic basis of successful rescue, particularly in multicellular organisms. We conducted an evolve-and-resequence experiment to investigate the dynamics of evolutionary rescue at the genetic level in the cowpea seed beetle, Callosobruchus maculatus, when it is experimentally shifted to a stressful host plant, lentil. Low survival (~1%) at the onset of the experiment caused population decline. But adaptive evolution quickly rescued the population, with survival rates climbing to 69% by the F5 generation and 90% by the F10 generation. Population genomic data showed that rescue likely was caused by rapid evolutionary change at multiple loci, with many alleles fixing or nearly fixing within five generations of selection on lentil. Selection on these loci was only moderately consistent in time, but parallel evolutionary changes were evident in sublines formed after the lentil line had passed through a bottleneck. By comparing estimates of selection and genomic change on lentil across five independent C. maculatus lines (the new lentil-adapted line, three long-established lines and one case of failed evolutionary rescue), we found that adaptation on lentil occurred via somewhat idiosyncratic evolutionary changes. Overall, our results suggest that evolutionary rescue in this system can be caused by very strong selection on multiple loci driving rapid and pronounced genomic change.}, }
@article {pmid30958167, year = {2019}, author = {Nguyen, H and Koehl, MAR and Oakes, C and Bustamante, G and Fauci, L}, title = {Effects of cell morphology and attachment to a surface on the hydrodynamic performance of unicellular choanoflagellates.}, journal = {Journal of the Royal Society, Interface}, volume = {16}, number = {150}, pages = {20180736}, doi = {10.1098/rsif.2018.0736}, pmid = {30958167}, issn = {1742-5662}, abstract = {Choanoflagellates, eukaryotes that are important predators on bacteria in aquatic ecosystems, are closely related to animals and are used as a model system to study the evolution of animals from protozoan ancestors. The choanoflagellate Salpingoeca rosetta has a complex life cycle with different morphotypes, some unicellular and some multicellular. Here we use computational fluid dynamics to study the hydrodynamics of swimming and feeding by different unicellular stages of S. rosetta: a swimming cell with a collar of prey-capturing microvilli surrounding a single flagellum, a thecate cell attached to a surface and a dispersal-stage cell with a slender body, long flagellum and short collar. We show that a longer flagellum increases swimming speed, longer microvilli reduce speed and cell shape only affects speed when the collar is very short. The flux of prey-carrying water into the collar capture zone is greater for swimming than sessile cells, but this advantage decreases with collar size. Stalk length has little effect on flux for sessile cells. We show that ignoring the collar, as earlier models have done, overestimates flux and greatly overestimates the benefit to feeding performance of swimming versus being attached, and of a longer stalk for attached cells.}, }
@article {pmid30952878, year = {2019}, author = {Baade, T and Paone, C and Baldrich, A and Hauck, CR}, title = {Clustering of integrin β cytoplasmic domains triggers nascent adhesion formation and reveals a protozoan origin of the integrin-talin interaction.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5728}, doi = {10.1038/s41598-019-42002-6}, pmid = {30952878}, issn = {2045-2322}, support = {CRC969 B06//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Integrins and integrin-dependent cell-matrix adhesions are essential for a number of physiological processes. Integrin function is tightly regulated via binding of cytoplasmic proteins to integrin intracellular domains. Yet, the complexity of cell-matrix adhesions in mammals, with more than 150 core adhesome proteins, complicates the analysis of integrin-associated protein complexes. Interestingly, the evolutionary origin of integrins dates back before the transition from unicellular life to complex multicellular animals. Though unicellular relatives of metazoa have a less complex adhesome, nothing is known about the initial steps of integrin activation and adhesion complex assembly in protozoa. Therefore, we developed a minimal, microscope-based system using chimeric integrins to investigate receptor-proximal events during focal adhesion assembly. Clustering of the human integrin β1 tail led to recruitment of talin, kindlin, and paxillin and mutation of the known talin binding site abolished recruitment of this protein. Proteins indirectly linked to integrins, such as vinculin, migfilin, p130CAS, or zyxin were not enriched around the integrin β1 tail. With the exception of integrin β4 and integrin β8, the cytoplasmic domains of all human integrin β subunits supported talin binding. Likewise, the cytoplasmic domains of integrin β subunits expressed by the protozoan Capsaspora owczarzaki readily recruited talin and this interaction was based on an evolutionary conserved NPXY/F amino acid motif. The results we present here validate the use of our novel microscopic assay to uncover details of integrin-based protein-protein interactions in a cellular context and suggest that talin binding to integrin β cytoplasmic tails is an ancient feature of integrin regulation.}, }
@article {pmid30949307, year = {2019}, author = {Bohlin, J and Pettersson, JH}, title = {Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals.}, journal = {Computational and structural biotechnology journal}, volume = {17}, number = {}, pages = {362-370}, doi = {10.1016/j.csbj.2019.03.001}, pmid = {30949307}, issn = {2001-0370}, abstract = {Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.}, }
@article {pmid30941746, year = {2019}, author = {Gulli, JG and Herron, MD and Ratcliff, WC}, title = {Evolution of altruistic cooperation among nascent multicellular organisms.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {5}, pages = {1012-1024}, doi = {10.1111/evo.13727}, pmid = {30941746}, issn = {1558-5646}, support = {NNA17BB05A//National Aeronautics and Space Administration/ ; DGE-1148903//Division of Graduate Education/ ; DEB-1723293//National Science Foundation/ ; }, abstract = {Cooperation is a classic solution to hostile environments that limit individual survival. In extreme cases this may lead to the evolution of new types of biological individuals (e.g., eusocial super-organisms). We examined the potential for interindividual cooperation to evolve via experimental evolution, challenging nascent multicellular &quot;snowflake yeast&quot; with an environment in which solitary multicellular clusters experienced low survival. In response, snowflake yeast evolved to form cooperative groups composed of thousands of multicellular clusters that typically survive selection. Group formation occurred through the creation of protein aggregates, only arising in strains with high (>2%) rates of cell death. Nonetheless, it was adaptive and repeatable, although ultimately evolutionarily unstable. Extracellular protein aggregates act as a common good, as they can be exploited by cheats that do not contribute to aggregate production. These results highlight the importance of group formation as a mechanism for surviving environmental stress, and underscore the remarkable ease with which even simple multicellular entities may evolve-and lose-novel social traits.}, }
@article {pmid30923125, year = {2019}, author = {Pedchenko, V and Bauer, R and Pokidysheva, EN and Al-Shaer, A and Forde, NR and Fidler, AL and Hudson, BG and Boudko, SP}, title = {A chloride ring is an ancient evolutionary innovation mediating the assembly of the collagen IV scaffold of basement membranes.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {20}, pages = {7968-7981}, doi = {10.1074/jbc.RA119.007426}, pmid = {30923125}, issn = {1083-351X}, support = {R01 DK018381/DK/NIDDK NIH HHS/United States ; }, abstract = {Collagen IV scaffold is a principal component of the basement membrane (BM), a specialized extracellular matrix that is essential for animal multicellularity and tissue evolution. Scaffold assembly begins with the trimerization of α-chains into protomers inside the cell, which then are secreted and undergo oligomerization outside the cell. For the ubiquitous scaffold composed of α1- and α2-chains, both intracellular and extracellular stages are mediated by the noncollagenous domain (NC1). The association of protomers is chloride-dependent, whereby chloride ions induce interactions of the protomers' trimeric NC1 domains leading to NC1 hexamer formation. Here, we investigated the mechanisms, kinetics, and functionality of the chloride ion-mediated protomer assembly by using a single-chain technology to produce a stable NC1 trimer comprising α1, α2, and α1 NC1 monomers. We observed that in the presence of chloride, the single-chain NC1-trimer self-assembles into a hexamer, for which the crystal structure was determined. We discovered that a chloride ring, comprising 12 ions, induces the assembly of and stabilizes the NC1 hexamer. Furthermore, we found that the chloride ring is evolutionarily conserved across all animals, first appearing in cnidarians. These findings reveal a fundamental role for the chloride ring in the assembly of collagen IV scaffolds of BMs, a critical event enabling tissue evolution and development. Moreover, the single-chain technology is foundational for generating trimeric NC1 domains of other α-chain compositions to investigate the α121, α345, and α565 collagen IV scaffolds and to develop therapies for managing Alport syndrome, Goodpasture's disease, and cancerous tumor growth.}, }
@article {pmid30919568, year = {2019}, author = {Zhu, SQ and Zhang, YJ and Abbas, MN and Hao, XW and Zhao, YZ and Liang, HH and Cui, HJ and Yang, LQ}, title = {Hedgehog promotes cell proliferation in the midgut of silkworm, Bombyx mori.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.12672}, pmid = {30919568}, issn = {1744-7917}, support = {No. XDJK2015C129//Fundamental Research Funds for the Central Universities/ ; No. 2362015XK09//Fundamental Research Funds for the Central Universities/ ; No. XDJK2013B020//Fundamental Research Funds for the Central Universities/ ; No. 20120524//Fundamental Research Funds for the Central Universities/ ; CXTDX201601010//Chongqing University Innovation Team Building Program funded projects/ ; 2017ZBX10//Scientific Research Foundation of the Chongqing University of Arts and Sciences/ ; No. 31672496//National Natural Science Foundation of China/ ; cstc2016jcyjA0425//Natural Science Foundation of Chongqing/ ; }, abstract = {The Hedgehog (Hh) signaling pathway is one of the major regulators of embryonic development and tissue homeostasis in multicellular organisms. However, the role of this pathway in the silkworm, especially in the silkworm midgut, remains poorly understood. Here, we report that Bombyx mori Hedgehog (BmHh) is expressed in most tissues of silkworm larvae and that its functions are well-conserved throughout evolution. We further demonstrate that the messenger RNA of four Hh signaling components, BmHh ligand, BmPtch receptor, signal transducer BmSmo and transcription factor BmCi, are all upregulated following Escherichia coli or Bacillus thuringiensis infection, indicating the activation of the Hh pathway. Simultaneously, midgut cell proliferation is strongly promoted. Conversely, the repression of Hh signal transduction with double-stranded RNA or cyclopamine inhibits the expression of BmHh and BmCi and reduces cell proliferation. Overall, these findings provide new insights into the Hh signaling pathway in the silkworm, B. mori.}, }
@article {pmid30918953, year = {2019}, author = {Arimoto, A and Nishitsuji, K and Higa, Y and Arakaki, N and Hisata, K and Shinzato, C and Satoh, N and Shoguchi, E}, title = {A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {}, number = {}, pages = {}, doi = {10.1093/dnares/dsz002}, pmid = {30918953}, issn = {1756-1663}, abstract = {Genome evolution and development of unicellular, multinucleate macroalgae (siphonous algae) are poorly known, although various multicellular organisms have been studied extensively. To understand macroalgal developmental evolution, we assembled the ∼26 Mb genome of a siphonous green alga, Caulerpa lentillifera, with high contiguity, containing 9,311 protein-coding genes. Molecular phylogeny using 107 nuclear genes indicates that the diversification of the class Ulvophyceae, including C. lentillifera, occurred before the split of the Chlorophyceae and Trebouxiophyceae. Compared with other green algae, the TALE superclass of homeobox genes, which expanded in land plants, shows a series of lineage-specific duplications in this siphonous macroalga. Plant hormone signalling components were also expanded in a lineage-specific manner. Expanded transport regulators, which show spatially different expression, suggest that the structural patterning strategy of a multinucleate cell depends on diversification of nuclear pore proteins. These results not only imply functional convergence of duplicated genes among green plants, but also provide insight into evolutionary roots of green plants. Based on the present results, we propose cellular and molecular mechanisms involved in the structural differentiation in the siphonous alga.}, }
@article {pmid30918448, year = {2019}, author = {Stucky, BJ and Balhoff, JP and Barve, N and Barve, V and Brenskelle, L and Brush, MH and Dahlem, GA and Gilbert, JDJ and Kawahara, AY and Keller, O and Lucky, A and Mayhew, PJ and Plotkin, D and Seltmann, KC and Talamas, E and Vaidya, G and Walls, R and Yoder, M and Zhang, G and Guralnick, R}, title = {Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions.}, journal = {Biodiversity data journal}, volume = {7}, number = {}, pages = {e33303}, doi = {10.3897/BDJ.7.e33303}, pmid = {30918448}, issn = {1314-2828}, abstract = {Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.}, }
@article {pmid30915518, year = {2019}, author = {Kolasa, M and Ścibior, R and Mazur, MA and Kubisz, D and Dudek, K and Kajtoch, Ł}, title = {How Hosts Taxonomy, Trophy, and Endosymbionts Shape Microbiome Diversity in Beetles.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01358-y}, pmid = {30915518}, issn = {1432-184X}, support = {DEC-2013/11/D/NZ8/00583//National Science Centre, Poland/ ; small grants for young researchers//Polish Ministry of Science and Higher Education/ ; }, abstract = {Bacterial communities play a crucial role in the biology, ecology, and evolution of multicellular organisms. In this research, the microbiome of 24 selected beetle species representing five families (Carabidae, Staphylinidae, Curculionidae, Chrysomelidae, Scarabaeidae) and three trophic guilds (carnivorous, herbivorous, detrivorous) was examined using 16S rDNA sequencing on the Illumina platform. The aim of the study was to compare diversity within and among species on various levels of organization, including evaluation of the impact of endosymbiotic bacteria. Collected data showed that beetles possess various bacterial communities and that microbiota of individuals of particular species hosts are intermixed. The most diverse microbiota were found in Carabidae and Scarabaeidae; the least diverse, in Staphylinidae. On higher organization levels, the diversity of bacteria was more dissimilar between families, while the most distinct with respect to their microbiomes were trophic guilds. Moreover, eight taxa of endosymbiotic bacteria were detected including common genera such as Wolbachia, Rickettsia, and Spiroplasma, as well as the rarely detected Cardinium, Arsenophonus, Buchnera, Sulcia, Regiella, and Serratia. There were no correlations among the abundance of the most common Wolbachia and Rickettsia; a finding that does not support the hypothesis that these bacteria occur interchangeably. The abundance of endosymbionts only weakly and negatively correlates with diversity of the whole microbiome in beetles. Overall, microbiome diversity was found to be more dependent on host phylogeny than on the abundance of endosymbionts. This is the first study in which bacteria diversity is compared between numerous species of beetles in a standardized manner.}, }
@article {pmid30911363, year = {2019}, author = {Bielska, E and Birch, PRJ and Buck, AH and Abreu-Goodger, C and Innes, RW and Jin, H and Pfaffl, MW and Robatzek, S and Regev-Rudzki, N and Tisserant, C and Wang, S and Weiberg, A}, title = {Highlights of the mini-symposium on extracellular vesicles in inter-organismal communication, held in Munich, Germany, August 2018.}, journal = {Journal of extracellular vesicles}, volume = {8}, number = {1}, pages = {1590116}, doi = {10.1080/20013078.2019.1590116}, pmid = {30911363}, issn = {2001-3078}, abstract = {All living organisms secrete molecules for intercellular communication. Recent research has revealed that extracellular vesicles (EVs) play an important role in inter-organismal cell-to-cell communication by transporting diverse messenger molecules, including RNA, DNA, lipids and proteins. These discoveries have raised fundamental questions regarding EV biology. How are EVs biosynthesized and loaded with messenger/cargo molecules? How are EVs secreted into the extracellular matrix? What are the EV uptake mechanisms of recipient cells? As EVs are produced by all kind of organisms, from unicellular bacteria and protists, filamentous fungi and oomycetes, to complex multicellular life forms such as plants and animals, basic research in diverse model systems is urgently needed to shed light on the multifaceted biology of EVs and their role in inter-organismal communications. To help catalyse progress in this emerging field, a mini-symposium was held in Munich, Germany in August 2018. This report highlights recent progress and major questions being pursued across a very diverse group of model systems, all united by the question of how EVs contribute to inter-organismal communication.}, }
@article {pmid30909510, year = {2019}, author = {Moffitt, L and Karimnia, N and Stephens, A and Bilandzic, M}, title = {Therapeutic Targeting of Collective Invasion in Ovarian Cancer.}, journal = {International journal of molecular sciences}, volume = {20}, number = {6}, pages = {}, doi = {10.3390/ijms20061466}, pmid = {30909510}, issn = {1422-0067}, abstract = {Ovarian cancer is the seventh most commonly diagnosed cancer amongst women and has the highest mortality rate of all gynaecological malignancies. It is a heterogeneous disease attributed to one of three cell types found within the reproductive milieu: epithelial, stromal, and germ cell. Each histotype differs in etiology, pathogenesis, molecular biology, risk factors, and prognosis. Furthermore, the origin of ovarian cancer remains unclear, with ovarian involvement secondary to the contribution of other gynaecological tissues. Despite these complexities, the disease is often treated as a single entity, resulting in minimal improvement to survival rates since the introduction of platinum-based chemotherapy over 30 years ago. Despite concerted research efforts, ovarian cancer remains one of the most difficult cancers to detect and treat, which is in part due to the unique mode of its dissemination. Ovarian cancers tend to invade locally to neighbouring tissues by direct extension from the primary tumour, and passively to pelvic and distal organs within the peritoneal fluid or ascites as multicellular spheroids. Once at their target tissue, ovarian cancers, like most epithelial cancers including colorectal, melanoma, and breast, tend to invade as a cohesive unit in a process termed collective invasion, driven by specialized cells termed &quot;leader cells&quot;. Emerging evidence implicates leader cells as essential drivers of collective invasion and metastasis, identifying collective invasion and leader cells as a viable target for the management of metastatic disease. However, the development of targeted therapies specifically against this process and this subset of cells is lacking. Here, we review our understanding of metastasis, collective invasion, and the role of leader cells in ovarian cancer. We will discuss emerging research into the development of novel therapies targeting collective invasion and the leader cell population.}, }
@article {pmid30902897, year = {2019}, author = {Krizsán, K and Almási, É and Merényi, Z and Sahu, N and Virágh, M and Kószó, T and Mondo, S and Kiss, B and Bálint, B and Kües, U and Barry, K and Cseklye, J and Hegedüs, B and Henrissat, B and Johnson, J and Lipzen, A and Ohm, RA and Nagy, I and Pangilinan, J and Yan, J and Xiong, Y and Grigoriev, IV and Hibbett, DS and Nagy, LG}, title = {Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {15}, pages = {7409-7418}, doi = {10.1073/pnas.1817822116}, pmid = {30902897}, issn = {1091-6490}, mesh = {*Agaricales/genetics/growth &amp; development ; *Databases, Nucleic Acid ; *Fruiting Bodies, Fungal/genetics/growth &amp; development ; *Fungal Proteins/biosynthesis/genetics ; Gene Expression Regulation, Fungal/physiology ; *Genes, Fungal ; Transcriptome/*physiology ; }, abstract = {The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including animals, embryophytes, red and brown algae, and fungi. Despite being a key step toward the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. The development of fungal fruiting bodies from a hyphal thallus represents a transition from simple to complex multicellularity that is inducible under laboratory conditions. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall remodeling, targeted protein degradation, signal transduction, adhesion, and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, many of which convergently expanded in multicellular plants and/or animals too, reflecting convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides an entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.}, }
@article {pmid30898932, year = {2019}, author = {Wielgoss, S and Wolfensberger, R and Sun, L and Fiegna, F and Velicer, GJ}, title = {Social genes are selection hotspots in kin groups of a soil microbe.}, journal = {Science (New York, N.Y.)}, volume = {363}, number = {6433}, pages = {1342-1345}, doi = {10.1126/science.aar4416}, pmid = {30898932}, issn = {1095-9203}, abstract = {The composition of cooperative systems, including animal societies, organismal bodies, and microbial groups, reflects their past and shapes their future evolution. However, genomic diversity within many multiunit systems remains uncharacterized, limiting our ability to understand and compare their evolutionary character. We have analyzed genomic and social-phenotype variation among 120 natural isolates of the cooperative bacterium Myxococcus xanthus derived from six multicellular fruiting bodies. Each fruiting body was composed of multiple lineages radiating from a unique recent ancestor. Genomic evolution was concentrated in selection hotspots associated with evolutionary change in social phenotypes. Synonymous mutations indicated that kin lineages within the same fruiting body often first diverged from a common ancestor more than 100 generations ago. Thus, selection appears to promote endemic diversification of kin lineages that remain together over long histories of local interaction, thereby potentiating social coevolution.}, }
@article {pmid30886348, year = {2019}, author = {Talbert, PB and Meers, MP and Henikoff, S}, title = {Old cogs, new tricks: the evolution of gene expression in a chromatin context.}, journal = {Nature reviews. Genetics}, volume = {20}, number = {5}, pages = {283-297}, doi = {10.1038/s41576-019-0105-7}, pmid = {30886348}, issn = {1471-0064}, abstract = {Sophisticated gene-regulatory mechanisms probably evolved in prokaryotes billions of years before the emergence of modern eukaryotes, which inherited the same basic enzymatic machineries. However, the epigenomic landscapes of eukaryotes are dominated by nucleosomes, which have acquired roles in genome packaging, mitotic condensation and silencing parasitic genomic elements. Although the molecular mechanisms by which nucleosomes are displaced and modified have been described, just how transcription factors, histone variants and modifications and chromatin regulators act on nucleosomes to regulate transcription is the subject of considerable ongoing study. We explore the extent to which these transcriptional regulatory components function in the context of the evolutionarily ancient role of chromatin as a barrier to processes acting on DNA and how chromatin proteins have diversified to carry out evolutionarily recent functions that accompanied the emergence of differentiation and development in multicellular eukaryotes.}, }
@article {pmid30886148, year = {2019}, author = {Xu, S and Stapley, J and Gablenz, S and Boyer, J and Appenroth, KJ and Sree, KS and Gershenzon, J and Widmer, A and Huber, M}, title = {Low genetic variation is associated with low mutation rate in the giant duckweed.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1243}, doi = {10.1038/s41467-019-09235-5}, pmid = {30886148}, issn = {2041-1723}, mesh = {Africa ; Americas ; Araceae/classification/*genetics ; Asia ; DNA Mutational Analysis ; Europe ; *Genetic Variation ; *Genome, Plant ; *Mutation Rate ; Phylogeography ; Plant Dispersal/*genetics ; }, abstract = {Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. Here we investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals reveals extremely low intraspecific genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels. This study also highlights that accurate estimates of mutation rate can help to explain seemingly unexpected patterns of genome-wide variation.}, }
@article {pmid30883720, year = {2019}, author = {Kapsetaki, SE and West, SA}, title = {The costs and benefits of multicellular group formation in algae.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {6}, pages = {1296-1308}, doi = {10.1111/evo.13712}, pmid = {30883720}, issn = {1558-5646}, support = {//Alexander S. Onassis Public Benefit Foundation/ ; //European Research Council/ ; //A.G. Leventis Foundation/ ; }, abstract = {The first step in the evolution of complex multicellular organisms involves single cells forming a cooperative group. Consequently, to understand multicellularity, we need to understand the costs and benefits associated with multicellular group formation. We found that in the facultatively multicellular algae Chlorella sorokiniana: (1) the presence of the flagellate Ochromonas danica or the crustacean Daphnia magna leads to the formation of multicellular groups; (2) the formation of multicellular groups reduces predation by O. danica, but not by the larger predator D. magna; (3) under conditions of relatively low light intensity, where competition for light is greater, multicellular groups grow slower than single cells; (4) in the absence of live predators, the proportion of cells in multicellular groups decreases at a rate that does not vary with light intensity. These results can explain why, in cases such as this algae species, multicellular group formation is facultative, in response to the presence of predators.}, }
@article {pmid30875767, year = {2019}, author = {Goh, GH and Maloney, SK and Mark, PJ and Blache, D}, title = {Episodic Ultradian Events-Ultradian Rhythms.}, journal = {Biology}, volume = {8}, number = {1}, pages = {}, doi = {10.3390/biology8010015}, pmid = {30875767}, issn = {2079-7737}, abstract = {In the fast lane of chronobiology, ultradian events are short-term rhythms that have been observed since the beginning of modern biology and were quantified about a century ago. They are ubiquitous in all biological systems and found in all organisms, from unicellular organisms to mammals, and from single cells to complex biological functions in multicellular animals. Since these events are aperiodic and last for a few minutes to a few hours, they are better classified as episodic ultradian events (EUEs). Their origin is unclear. However, they could have a molecular basis and could be controlled by hormonal inputs-in vertebrates, they originate from the activity of the central nervous system. EUEs are receiving increasing attention but their aperiodic nature requires specific sampling and analytic tools. While longer scale rhythms are adaptations to predictable changes in the environment, in theory, EUEs could contribute to adaptation by preparing organisms and biological functions for unpredictability.}, }
@article {pmid30863851, year = {2019}, author = {Shoemark, DK and Ziegler, B and Watanabe, H and Strompen, J and Tucker, RP and Özbek, S and Adams, JC}, title = {Emergence of a Thrombospondin Superfamily at the Origin of Metazoans.}, journal = {Molecular biology and evolution}, volume = {36}, number = {6}, pages = {1220-1238}, doi = {10.1093/molbev/msz060}, pmid = {30863851}, issn = {1537-1719}, abstract = {Extracellular matrix (ECM) is considered central to the evolution of metazoan multicellularity; however, the repertoire of ECM proteins in nonbilaterians remains unclear. Thrombospondins (TSPs) are known to be well conserved from cnidarians to vertebrates, yet to date have been considered a unique family, principally studied for matricellular functions in vertebrates. Through searches utilizing the highly conserved C-terminal region of TSPs, we identify undisclosed new families of TSP-related proteins in metazoans, designated mega-TSP, sushi-TSP, and poriferan-TSP, each with a distinctive phylogenetic distribution. These proteins share the TSP C-terminal region domain architecture, as determined by domain composition and analysis of molecular models against known structures. Mega-TSPs, the only form identified in ctenophores, are typically >2,700 aa and are also characterized by N-terminal leucine-rich repeats and central cadherin/immunoglobulin domains. In cnidarians, which have a well-defined ECM, Mega-TSP was expressed throughout embryogenesis in Nematostella vectensis, with dynamic endodermal expression in larvae and primary polyps and widespread ectodermal expression in adult Nematostella vectensis and Hydra magnipapillata polyps. Hydra Mega-TSP was also expressed during regeneration and siRNA-silencing of Mega-TSP in Hydra caused specific blockade of head regeneration. Molecular phylogenetic analyses based on the conserved TSP C-terminal region identified each of the TSP-related groups to form clades distinct from the canonical TSPs. We discuss models for the evolution of the newly defined TSP superfamily by gene duplications, radiation, and gene losses from a debut in the last metazoan common ancestor. Together, the data provide new insight into the evolution of ECM and tissue organization in metazoans.}, }
@article {pmid30862622, year = {2019}, author = {Lenhart, BA and Meeks, B and Murphy, HA}, title = {Variation in Filamentous Growth and Response to Quorum-Sensing Compounds in Environmental Isolates of Saccharomyces cerevisiae.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {5}, pages = {1533-1544}, doi = {10.1534/g3.119.400080}, pmid = {30862622}, issn = {2160-1836}, abstract = {In fungi, filamentous growth is a major developmental transition that occurs in response to environmental cues. In diploid Saccharomyces cerevisiae, it is known as pseudohyphal growth and presumed to be a foraging mechanism. Rather than unicellular growth, multicellular filaments composed of elongated, attached cells spread over and into surfaces. This morphogenetic switch can be induced through quorum sensing with the aromatic alcohols phenylethanol and tryptophol. Most research investigating pseudohyphal growth has been conducted in a single lab background, Σ1278b. To investigate the natural variation in this phenotype and its induction, we assayed the diverse 100-genomes collection of environmental isolates. Using computational image analysis, we quantified the production of pseudohyphae and observed a large amount of variation. Population origin was significantly associated with pseudohyphal growth, with the West African population having the most. Surprisingly, most strains showed little or no response to exogenous phenylethanol or tryptophol. We also investigated the amount of natural genetic variation in pseudohyphal growth using a mapping population derived from a highly-heterozygous clinical isolate that contained as much phenotypic variation as the environmental panel. A bulk-segregant analysis uncovered five major peaks with candidate loci that have been implicated in the Σ1278b background. Our results indicate that the filamentous growth response is a generalized, highly variable phenotype in natural populations, while response to quorum sensing molecules is surprisingly rare. These findings highlight the importance of coupling studies in tractable lab strains with natural isolates in order to understand the relevance and distribution of well-studied traits.}, }
@article {pmid30857590, year = {2019}, author = {Sicard, A and Pirolles, E and Gallet, R and Vernerey, MS and Yvon, M and Urbino, C and Peterschmitt, M and Gutierrez, S and Michalakis, Y and Blanc, S}, title = {A multicellular way of life for a multipartite virus.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.43599}, pmid = {30857590}, issn = {2050-084X}, support = {ANR-14-CE02-0014//Agence Nationale de la Recherche/ ; }, abstract = {A founding paradigm in virology is that the spatial unit of the viral replication cycle is an individual cell. Multipartite viruses have a segmented genome where each segment is encapsidated separately. In this situation the viral genome is not recapitulated in a single virus particle but in the viral population. How multipartite viruses manage to efficiently infect individual cells with all segments, thus with the whole genome information, is a long-standing but perhaps deceptive mystery. By localizing and quantifying the genome segments of a nanovirus in host plant tissues we show that they rarely co-occur within individual cells. We further demonstrate that distinct segments accumulate independently in different cells and that the viral system is functional through complementation across cells. Our observation deviates from the classical conceptual framework in virology and opens an alternative possibility (at least for nanoviruses) where the infection can operate at a level above the individual cell level, defining a viral multicellular way of life.}, }
@article {pmid30839008, year = {2019}, author = {Ruiz, MC and Kljun, J and Turel, I and Di Virgilio, AL and León, IE}, title = {Comparative antitumor studies of organoruthenium complexes with 8-hydroxyquinolines on 2D and 3D cell models of bone, lung and breast cancer.}, journal = {Metallomics : integrated biometal science}, volume = {11}, number = {3}, pages = {666-675}, doi = {10.1039/c8mt00369f}, pmid = {30839008}, issn = {1756-591X}, abstract = {The purpose of this work was to screen the antitumor actions of two metal organoruthenium-8-hydroxyquinolinato (Ru-hq) complexes to find a potential novel agent for bone, lung and breast chemotherapies. We showed that ruthenium compounds (1 and 2) impaired the cell viability of human bone (MG-63), lung (A549) and breast (MCF7) cancer cells with greater selectivity and specificity than cisplatin. Besides, complexes 1 and 2 decreased proliferation, migration and invasion on cell monolayers at lower concentrations (2.5-10 μM). In addition, both compounds induced genotoxicity revealed by the micronucleus test, which led to G2/M cell cycle arrest and induced the tumor cells to undergo apoptosis. On the other hand, in multicellular 3D models (multicellular spheroids; MCS), 1 and 2 overcame CDDP presenting lower IC50 values only in MCS of lung origin. Moreover, 1 outperformed 2 in MCS of bone and breast origin. Finally, our findings revealed that both compounds inhibited the cell invasion of multicellular spheroids, showing that complex 1 exhibited the most important antimetastatic action. Taken together, these results indicate that compound 1 is an interesting candidate to be tested on in vivo models as a novel strategy for anticancer therapy.}, }
@article {pmid30826447, year = {2019}, author = {Fillinger, RJ and Anderson, MZ}, title = {Seasons of change: Mechanisms of genome evolution in human fungal pathogens.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {70}, number = {}, pages = {165-174}, doi = {10.1016/j.meegid.2019.02.031}, pmid = {30826447}, issn = {1567-7257}, abstract = {Fungi are a diverse kingdom of organisms capable of thriving in various niches across the world including those in close association with multicellular eukaryotes. Fungal pathogens that contribute to human disease reside both within the host as commensal organisms of the microbiota and the environment. Their niche of origin dictates how infection initiates but also places specific selective pressures on the fungal pathogen that contributes to its genome organization and genetic repertoire. Recent efforts to catalogue genomic variation among major human fungal pathogens have unveiled evolutionary themes that shape the fungal genome. Mechanisms ranging from large scale changes such as aneuploidy and ploidy cycling as well as more targeted mutations like base substitutions and gene copy number variations contribute to the evolution of these species, which are often under multiple competing selective pressures with their host, environment, and other microbes. Here, we provide an overview of the major selective pressures and mechanisms acting to evolve the genome of clinically important fungal pathogens of humans.}, }
@article {pmid30824779, year = {2019}, author = {Kabir, M and Wenlock, S and Doig, AJ and Hentges, KE}, title = {The Essentiality Status of Mouse Duplicate Gene Pairs Correlates with Developmental Co-Expression Patterns.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3224}, doi = {10.1038/s41598-019-39894-9}, pmid = {30824779}, issn = {2045-2322}, support = {BB/L018276/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/L018276/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, abstract = {During the evolution of multicellular eukaryotes, gene duplication occurs frequently to generate new genes and/or functions. A duplicated gene may have a similar function to its ancestral gene. Therefore, it may be expected that duplicated genes are less likely to be critical for the survival of an organism, since there are multiple copies of the gene rendering each individual copy redundant. In this study, we explored the developmental expression patterns of duplicate gene pairs and the relationship between development co-expression and phenotypes resulting from the knockout of duplicate genes in the mouse. We define genes that generate lethal phenotypes in single gene knockout experiments as essential genes. We found that duplicate gene pairs comprised of two essential genes tend to be expressed at different stages of development, compared to duplicate gene pairs with at least one non-essential member, showing that the timing of developmental expression affects the ability of one paralogue to compensate for the loss of the other. Gene essentiality, developmental expression and gene duplication are thus closely linked.}, }
@article {pmid30824706, year = {2019}, author = {Lurgi, M and Thomas, T and Wemheuer, B and Webster, NS and Montoya, JM}, title = {Modularity and predicted functions of the global sponge-microbiome network.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {992}, doi = {10.1038/s41467-019-08925-4}, pmid = {30824706}, issn = {2041-1723}, mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Biological Evolution ; Ecology ; Host Microbial Interactions/*physiology ; Microbiota/genetics/*physiology ; Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis ; }, abstract = {Defining the organisation of species interaction networks and unveiling the processes behind their assembly is fundamental to understanding patterns of biodiversity, community stability and ecosystem functioning. Marine sponges host complex communities of microorganisms that contribute to their health and survival, yet the mechanisms behind microbiome assembly are largely unknown. We present the global marine sponge-microbiome network and reveal a modular organisation in both community structure and function. Modules are linked by a few sponge species that share microbes with other species around the world. Further, we provide evidence that abiotic factors influence the structuring of the sponge microbiome when considering all microbes present, but biotic interactions drive the assembly of more intimately associated 'core' microorganisms. These findings suggest that both ecological and evolutionary processes are at play in host-microbe network assembly. We expect mechanisms behind microbiome assembly to be consistent across multicellular hosts throughout the tree of life.}, }
@article {pmid30808737, year = {2019}, author = {El Albani, A and Mangano, MG and Buatois, LA and Bengtson, S and Riboulleau, A and Bekker, A and Konhauser, K and Lyons, T and Rollion-Bard, C and Bankole, O and Lekele Baghekema, SG and Meunier, A and Trentesaux, A and Mazurier, A and Aubineau, J and Laforest, C and Fontaine, C and Recourt, P and Chi Fru, E and Macchiarelli, R and Reynaud, JY and Gauthier-Lafaye, F and Canfield, DE}, title = {Organism motility in an oxygenated shallow-marine environment 2.1 billion years ago.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {9}, pages = {3431-3436}, doi = {10.1073/pnas.1815721116}, pmid = {30808737}, issn = {1091-6490}, mesh = {Atmosphere ; *Biological Evolution ; Biota/physiology ; *Fossils ; Gabon ; Geologic Sediments/*chemistry ; Oxidation-Reduction ; Oxygen/*chemistry ; }, abstract = {Evidence for macroscopic life in the Paleoproterozoic Era comes from 1.8 billion-year-old (Ga) compression fossils [Han TM, Runnegar B (1992) Science 257:232-235; Knoll et al. (2006) Philos Trans R Soc Lond B 361:1023-1038], Stirling biota [Bengtson S et al. (2007) Paleobiology 33:351-381], and large colonial organisms exhibiting signs of coordinated growth from the 2.1-Ga Francevillian series, Gabon. Here we report on pyritized string-shaped structures from the Francevillian Basin. Combined microscopic, microtomographic, geochemical, and sedimentologic analyses provide evidence for biogenicity, and syngenicity and suggest that the structures underwent fossilization during early diagenesis close to the sediment-water interface. The string-shaped structures are up to 6 mm across and extend up to 170 mm through the strata. Morphological and 3D tomographic reconstructions suggest that the producer may have been a multicellular or syncytial organism able to migrate laterally and vertically to reach food resources. A possible modern analog is the aggregation of amoeboid cells into a migratory slug phase in cellular slime molds at times of starvation. This unique ecologic window established in an oxygenated, shallow-marine environment represents an exceptional record of the biosphere following the crucial changes that occurred in the atmosphere and ocean in the aftermath of the great oxidation event (GOE).}, }
@article {pmid30803482, year = {2019}, author = {Trigos, AS and Pearson, RB and Papenfuss, AT and Goode, DL}, title = {Somatic mutations in early metazoan genes disrupt regulatory links between unicellular and multicellular genes in cancer.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.40947}, pmid = {30803482}, issn = {2050-084X}, abstract = {Extensive transcriptional alterations are observed in cancer, many of which activate core biological processes established in unicellular organisms or suppress differentiation pathways formed in metazoans. Through rigorous, integrative analysis of genomics data from a range of solid tumors, we show many transcriptional changes in tumors are tied to mutations disrupting regulatory interactions between unicellular and multicellular genes within human gene regulatory networks (GRNs). Recurrent point mutations were enriched in regulator genes linking unicellular and multicellular subnetworks, while copy-number alterations affected downstream target genes in distinctly unicellular and multicellular regions of the GRN. Our results depict drivers of tumourigenesis as genes that created key regulatory links during the evolution of early multicellular life, whose dysfunction creates widespread dysregulation of primitive elements of the GRN. Several genes we identified as important in this process were associated with drug response, demonstrating the potential clinical value of our approach.}, }
@article {pmid30799483, year = {2019}, author = {Xie, P and Gao, M and Wang, C and Zhang, J and Noel, P and Yang, C and Von Hoff, D and Han, H and Zhang, MQ and Lin, W}, title = {SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkz116}, pmid = {30799483}, issn = {1362-4962}, abstract = {Characterization of individual cell types is fundamental to the study of multicellular samples. Single-cell RNAseq techniques, which allow high-throughput expression profiling of individual cells, have significantly advanced our ability of this task. Currently, most of the scRNA-seq data analyses are commenced with unsupervised clustering. Clusters are often assigned to different cell types based on the enriched canonical markers. However, this process is inefficient and arbitrary. In this study, we present a technical framework of training the expandable supervised-classifier in order to reveal the single-cell identities as soon as the single-cell expression profile is input. Using multiple scRNA-seq datasets we demonstrate the superior accuracy, robustness, compatibility and expandability of this new solution compared to the traditional methods. We use two examples of the model upgrade to demonstrate how the projected evolution of the cell-type classifier is realized.}, }
@article {pmid30796309, year = {2019}, author = {Zhang, L and Tan, Y and Fan, S and Zhang, X and Zhang, Z}, title = {Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2623}, doi = {10.1038/s41598-019-40023-9}, pmid = {30796309}, issn = {2045-2322}, support = {31800185//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31800185//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Ovarian cancer (OV) is an extremely lethal disease. However, the evolutionary machineries of OV are still largely unknown. Here, we used a method that combines phylostratigraphy information with gene co-expression networks to extensively study the evolutionary compositions of OV. The present co-expression network construction yielded 18,549 nodes and 114,985 edges based on 307 OV expression samples obtained from the Genome Data Analysis Centers database. A total of 20 modules were identified as OV related clusters. The human genome sequences were divided into 19 phylostrata (PS), the majority (67.45%) of OV genes was already present in the eukaryotic ancestor. There were two strong peaks of the emergence of OV genes screened by hypergeometric test: the evolution of the multicellular metazoan organisms (PS5 and PS6, P value = 0.002) and the emergence of bony fish (PS11 and PS12, P value = 0.009). Hence, the origin of OV is far earlier than its emergence. The integrated analysis of the topology of OV modules and the phylogenetic data revealed an evolutionary pattern of OV in human, namely, OV modules have arisen step by step during the evolution of the respective lineages. New genes have evolved and become locked into a pathway, where more and more biological pathways are fixed into OV modules by recruiting new genes during human evolution.}, }
@article {pmid30787483, year = {2019}, author = {Herron, MD and Borin, JM and Boswell, JC and Walker, J and Chen, IK and Knox, CA and Boyd, M and Rosenzweig, F and Ratcliff, WC}, title = {De novo origins of multicellularity in response to predation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2328}, doi = {10.1038/s41598-019-39558-8}, pmid = {30787483}, issn = {2045-2322}, support = {DEB-1457701//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1456652//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1457701//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1456652//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1456652//NSF | BIO | Division of Environmental Biology (DEB)/ ; NNA17BB05A//National Aeronautics and Space Administration (NASA)/ ; NNA17BB05A//National Aeronautics and Space Administration (NASA)/ ; 43285//John Templeton Foundation (JTF)/ ; Packard Foundation Fellowship//David and Lucile Packard Foundation (David &amp; Lucile Packard Foundation)/ ; }, abstract = {The transition from unicellular to multicellular life was one of a few major events in the history of life that created new opportunities for more complex biological systems to evolve. Predation is hypothesized as one selective pressure that may have driven the evolution of multicellularity. Here we show that de novo origins of simple multicellularity can evolve in response to predation. We subjected outcrossed populations of the unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia. Two of five experimental populations evolved multicellular structures not observed in unselected control populations within ~750 asexual generations. Considerable variation exists in the evolved multicellular life cycles, with both cell number and propagule size varying among isolates. Survival assays show that evolved multicellular traits provide effective protection against predation. These results support the hypothesis that selection imposed by predators may have played a role in some origins of multicellularity.}, }
@article {pmid30787193, year = {2019}, author = {Dunning, LT and Olofsson, JK and Parisod, C and Choudhury, RR and Moreno-Villena, JJ and Yang, Y and Dionora, J and Quick, WP and Park, M and Bennetzen, JL and Besnard, G and Nosil, P and Osborne, CP and Christin, PA}, title = {Lateral transfers of large DNA fragments spread functional genes among grasses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1810031116}, pmid = {30787193}, issn = {1091-6490}, support = {638333//European Research Council/International ; }, abstract = {A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.}, }
@article {pmid30775966, year = {2019}, author = {Nakahara, N and Nobu, MK and Takaki, Y and Miyazaki, M and Tasumi, E and Sakai, S and Ogawara, M and Yoshida, N and Tamaki, H and Yamanaka, Y and Katayama, A and Yamaguchi, T and Takai, K and Imachi, H}, title = {Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {4}, pages = {1185-1194}, doi = {10.1099/ijsem.0.003291}, pmid = {30775966}, issn = {1466-5034}, mesh = {Bacterial Typing Techniques ; Base Composition ; Bioreactors/*microbiology ; Chloroflexi/*classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Geologic Sediments/*microbiology ; Japan ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {A novel slow-growing, facultatively anaerobic, filamentous bacterium, strain MO-CFX2T, was isolated from a methanogenic microbial community in a continuous-flow bioreactor that was established from subseafloor sediment collected off the Shimokita Peninsula of Japan. Cells were multicellular filamentous, non-motile and Gram-stain-negative. The filaments were generally more than 20 µm (up to approximately 200 µm) long and 0.5-0.6 µm wide. Cells possessed pili-like structures on the cell surface and a multilayer structure in the cytoplasm. Growth of the strain was observed at 20-37 °C (optimum, 30 °C), pH 5.5-8.0 (pH 6.5-7.0), and 0-30 g l-1 NaCl (5 g l-1 NaCl). Under optimum growth conditions, doubling time and maximum cell density were estimated to be approximately 19 days and ~105 cells ml-1, respectively. Strain MO-CFX2T grew chemoorganotrophically on a limited range of organic substrates in anaerobic conditions. The major cellular fatty acids were saturated C16 : 0 (47.9 %) and C18 : 0 (36.9 %), and unsaturated C18 : 1ω9c (6.0 %) and C16 : 1ω7 (5.1 %). The G+C content of genomic DNA was 63.2 mol%. 16S rRNA gene-based phylogenetic analysis showed that strain MO-CFX2T shares a notably low sequence identity with its closest relatives, which were Thermanaerothrix daxensis GNS-1T and Thermomarinilinea lacunifontana SW7T (both 85.8 % sequence identity). Based on these phenotypic and genomic properties, we propose the name Aggregatilinea lenta gen. nov., sp. nov. for strain MO-CFX2T (=KCTC 15625T, =JCM 32065T). In addition, we also propose the associated family and order as Aggregatilineaceae fam. nov. and Aggregatilineales ord. nov., respectively.}, }
@article {pmid30764885, year = {2019}, author = {Lipinska, AP and Serrano-Serrano, ML and Cormier, A and Peters, AF and Kogame, K and Cock, JM and Coelho, SM}, title = {Rapid turnover of life-cycle-related genes in the brown algae.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {35}, doi = {10.1186/s13059-019-1630-6}, pmid = {30764885}, issn = {1474-760X}, support = {638240//European Research Council/International ; }, mesh = {*Evolution, Molecular ; Gene Duplication ; *Gene Expression ; Germ Cells, Plant ; Life Cycle Stages/*genetics ; Phaeophyta/*genetics/growth &amp; development/metabolism ; Phenotype ; *Selection, Genetic ; }, abstract = {BACKGROUND: Sexual life cycles in eukaryotes involve a cyclic alternation between haploid and diploid phases. While most animals possess a diploid life cycle, many plants and algae alternate between multicellular haploid (gametophyte) and diploid (sporophyte) generations. In many algae, gametophytes and sporophytes are independent and free-living and may present dramatic phenotypic differences. The same shared genome can therefore be subject to different, even conflicting, selection pressures during each of the life cycle generations. Here, we analyze the nature and extent of genome-wide, generation-biased gene expression in four species of brown algae with contrasting levels of dimorphism between life cycle generations.<br><br>RESULTS: We show that the proportion of the transcriptome that is generation-specific is broadly associated with the level of phenotypic dimorphism between the life cycle stages. Importantly, our data reveals a remarkably high turnover rate for life-cycle-related gene sets across the brown algae and highlights the importance not only of co-option of regulatory programs from one generation to the other but also of a role for newly emerged, lineage-specific gene expression patterns in the evolution of the gametophyte and sporophyte developmental programs in this major eukaryotic group. Moreover, we show that generation-biased genes display distinct evolutionary modes, with gametophyte-biased genes evolving rapidly at the coding sequence level whereas sporophyte-biased genes tend to exhibit changes in their patterns of expression.<br><br>CONCLUSION: Our analysis uncovers the characteristics, expression patterns, and evolution of generation-biased genes and underlines the selective forces that shape this previously underappreciated source of phenotypic diversity.}, }
@article {pmid30763317, year = {2019}, author = {Raza, Q and Choi, JY and Li, Y and O'Dowd, RM and Watkins, SC and Chikina, M and Hong, Y and Clark, NL and Kwiatkowski, AV}, title = {Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila.}, journal = {PLoS genetics}, volume = {15}, number = {2}, pages = {e1007720}, doi = {10.1371/journal.pgen.1007720}, pmid = {30763317}, issn = {1553-7404}, support = {R01 HG009299/HG/NHGRI NIH HHS/United States ; R01 HL127711/HL/NHLBI NIH HHS/United States ; R01 GM086423/GM/NIGMS NIH HHS/United States ; }, mesh = {Actin Cytoskeleton/metabolism ; Actins/*metabolism ; Adherens Junctions/metabolism ; Animals ; Cadherins/*metabolism ; Cell Adhesion/*physiology ; Cell Membrane/metabolism ; Cell Movement/physiology ; Circadian Rhythm Signaling Peptides and Proteins/*metabolism ; Drosophila/*metabolism ; Drosophila Proteins/*metabolism ; Signal Transduction/physiology ; }, abstract = {The adherens junction couples the actin cytoskeletons of neighboring cells to provide the foundation for multicellular organization. The core of the adherens junction is the cadherin-catenin complex that arose early in the evolution of multicellularity to link actin to intercellular adhesions. Over time, evolutionary pressures have shaped the signaling and mechanical functions of the adherens junction to meet specific developmental and physiological demands. Evolutionary rate covariation (ERC) identifies proteins with correlated fluctuations in evolutionary rate that can reflect shared selective pressures and functions. Here we use ERC to identify proteins with evolutionary histories similar to the Drosophila E-cadherin (DE-cad) ortholog. Core adherens junction components α-catenin and p120-catenin displayed positive ERC correlations with DE-cad, indicating that they evolved under similar selective pressures during evolution between Drosophila species. Further analysis of the DE-cad ERC profile revealed a collection of proteins not previously associated with DE-cad function or cadherin-mediated adhesion. We then analyzed the function of a subset of ERC-identified candidates by RNAi during border cell (BC) migration and identified novel genes that function to regulate DE-cad. Among these, we found that the gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates BC migration and adhesion. We named CG42684 raskol (&quot;to split&quot; in Russian) and show that it regulates DE-cad levels and actin protrusions in BCs. We propose that Raskol functions with DE-cad to restrict Ras/Rho signaling and help guide BC migration. Our results demonstrate that a coordinated selective pressure has shaped the adherens junction and this can be leveraged to identify novel components of the complexes and signaling pathways that regulate cadherin-mediated adhesion.}, }
@article {pmid30762281, year = {2019}, author = {Chen, IK and Satinsky, BM and Velicer, GJ and Yu, YN}, title = {sRNA-pathway genes regulating myxobacterial development exhibit clade-specific evolution.}, journal = {Evolution &amp; development}, volume = {21}, number = {2}, pages = {82-95}, doi = {10.1111/ede.12281}, pmid = {30762281}, issn = {1525-142X}, support = {GM079690/NH/NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; Genome, Bacterial ; Mutagenesis, Insertional ; Myxococcus xanthus/*genetics/growth &amp; development ; Phenotype ; Phylogeny ; RNA, Small Untranslated/*genetics ; }, abstract = {Small non-coding RNAs (sRNAs) control bacterial gene expression involved in a wide range of important cellular processes. In the highly social bacterium Myxococcus xanthus, the sRNA Pxr prevents multicellular fruiting-body development when nutrients are abundant. Pxr was discovered from the evolution of a developmentally defective strain (OC) into a developmentally proficient strain (PX). In OC, Pxr is constitutively expressed and blocks development even during starvation. In PX, one mutation deactivates Pxr allowing development to proceed. We screened for transposon mutants that suppress the OC defect and thus potentially reveal new Pxr-pathway components. Insertions significantly restoring development were found in four genes-rnd, rnhA, stkA and Mxan_5793-not previously associated with an sRNA activity. Phylogenetic analysis suggests that the Pxr pathway was constructed within the Cystobacterineae suborder both by co-option of genes predating the Myxococcales order and incorporation of a novel gene (Mxan_5793). Further, the sequence similarity of rnd, rnhA and stkA homologs relative to M. xanthus alleles was found to decrease greatly among species beyond the Cystobacterineae suborder compared to the housekeeping genes examined. Finally, ecological context differentially affected the developmental phenotypes of distinct mutants, with implications for the evolution of development in variable environments.}, }
@article {pmid30761165, year = {2019}, author = {Dipp-Álvarez, M and Cruz-Ramírez, A}, title = {A Phylogenetic Study of the ANT Family Points to a preANT Gene as the Ancestor of Basal and euANT Transcription Factors in Land Plants.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {17}, doi = {10.3389/fpls.2019.00017}, pmid = {30761165}, issn = {1664-462X}, abstract = {Comparative genomics has revealed that members of early divergent lineages of land plants share a set of highly conserved transcription factors (TFs) with flowering plants. While gene copy numbers have expanded through time, it has been predicted that diversification, co-option, and reassembly of gene regulatory networks implicated in development are directly related to morphological innovations that led to more complex land plant bodies. Examples of key networks have been deeply studied in Arabidopsis thaliana, such as those involving the AINTEGUMENTA (ANT) gene family that encodes AP2-type TFs. These TFs play significant roles in plant development such as the maintenance of stem cell niches, the correct development of the embryo and the formation of lateral organs, as well as fatty acid metabolism. Previously, it has been hypothesized that the common ancestor of mosses and vascular plants encoded two ANT genes that later diversified in seed plants. However, algae and bryophyte sequences have been underrepresented from such phylogenetic analyses. To understand the evolution of ANT in a complete manner, we performed phylogenetic analyses of ANT protein sequences of representative species from across the Streptophyta clade, including algae, liverworts, and hornworts, previously unrepresented. Moreover, protein domain architecture, selection analyses, and regulatory cis elements prediction, allowed us to propose a scenario of how the evolution of ANT genes occurred. In this study we show that a duplication of a preANT-like gene in the ancestor of embryophytes may have given rise to the land plant-exclusive basalANT and euANT lineages. We hypothesize that the absence of euANT-type and basalANT-type sequences in algae, and its presence in extant land plant species, suggests that the divergence of pre-ANT into basal and eu-ANT clades in embryophytes may have influenced the conquest of land by plants, as ANT TFs play important roles in tolerance to desiccation and the establishment, maintenance, and development of complex multicellular structures which either became more complex or appeared in land plants.}, }
@article {pmid30760850, year = {2019}, author = {Junqueira Alves, C and Yotoko, K and Zou, H and Friedel, RH}, title = {Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1970}, doi = {10.1038/s41598-019-38512-y}, pmid = {30760850}, issn = {2045-2322}, support = {R01 NS092735/NS/NINDS NIH HHS/United States ; R01 NS092735/NS/NINDS NIH HHS/United States ; }, abstract = {The transition from unicellular to multicellular organisms poses the question as to when genes that regulate cell-cell interactions emerged during evolution. The receptor and ligand pairing of plexins and semaphorins regulates cellular interactions in a wide range of developmental and physiological contexts. We surveyed here genomes of unicellular eukaryotes and of non-bilaterian and bilaterian Metazoa and performed phylogenetic analyses to gain insight into the evolution of plexin and semaphorin families. Remarkably, we detected plexins and semaphorins in unicellular choanoflagellates, indicating their evolutionary origin in a common ancestor of Choanoflagellida and Metazoa. The plexin domain structure is conserved throughout all clades; in contrast, semaphorins are structurally diverse. Choanoflagellate semaphorins are transmembrane proteins with multiple fibronectin type III domains following the N-terminal Sema domain (termed Sema-FN). Other previously not yet described semaphorin classes include semaphorins of Ctenophora with tandem immunoglobulin domains (Sema-IG) and secreted semaphorins of Echinoderamata (Sema-SP, Sema-SI). Our study also identified Met receptor tyrosine kinases (RTKs), which carry a truncated plexin extracellular domain, in several bilaterian clades, indicating evolutionary origin in a common ancestor of Bilateria. In addition, a novel type of Met-like RTK with a complete plexin extracellular domain was detected in Lophotrochozoa and Echinodermata (termed Met-LP RTK). Our findings are consistent with an ancient function of plexins and semaphorins in regulating cytoskeletal dynamics and cell adhesion that predates their role as axon guidance molecules.}, }
@article {pmid30760717, year = {2019}, author = {Ferrari, C and Proost, S and Janowski, M and Becker, J and Nikoloski, Z and Bhattacharya, D and Price, D and Tohge, T and Bar-Even, A and Fernie, A and Stitt, M and Mutwil, M}, title = {Kingdom-wide comparison reveals the evolution of diurnal gene expression in Archaeplastida.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {737}, doi = {10.1038/s41467-019-08703-2}, pmid = {30760717}, issn = {2041-1723}, mesh = {Chlorophyta/genetics ; *Circadian Rhythm ; Embryophyta/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Gene Expression Profiling/*methods ; Photosynthesis/genetics ; Phylogeny ; Rhodophyta/genetics ; Transcriptome/*genetics ; }, abstract = {Plants have adapted to the diurnal light-dark cycle by establishing elaborate transcriptional programs that coordinate many metabolic, physiological, and developmental responses to the external environment. These transcriptional programs have been studied in only a few species, and their function and conservation across algae and plants is currently unknown. We performed a comparative transcriptome analysis of the diurnal cycle of nine members of Archaeplastida, and we observed that, despite large phylogenetic distances and dramatic differences in morphology and lifestyle, diurnal transcriptional programs of these organisms are similar. Expression of genes related to cell division and the majority of biological pathways depends on the time of day in unicellular algae but we did not observe such patterns at the tissue level in multicellular land plants. Hence, our study provides evidence for the universality of diurnal gene expression and elucidates its evolutionary history among different photosynthetic eukaryotes.}, }
@article {pmid30740458, year = {2019}, author = {Oborník, M}, title = {In the beginning was the word: How terminology drives our understanding of endosymbiotic organelles.}, journal = {Microbial cell (Graz, Austria)}, volume = {6}, number = {2}, pages = {134-141}, doi = {10.15698/mic2019.02.669}, pmid = {30740458}, issn = {2311-2638}, abstract = {The names we give objects of research, to some extent, predispose our ways of thinking about them. Misclassifications of Oomycota, Microsporidia, Myxosporidia, and Helicosporidia have obviously affected not only their formal taxonomic names, but also the methods and approaches with which they have been investigated. Therefore, it is important to name biological entities with accurate terms in order to avoid discrepancies in researching them. The endosymbiotic origin of mitochondria and plastids is now the most accepted scenario for their evolution. Since it is apparent that there is no natural definitive border between bacteria and semiautonomous organelles, I propose that mitochondria and plastids should be called bacteria and classified accordingly, in the bacterial classification system. I discuss some consequences of this approach, including: i) the resulting &quot;changes&quot; in the abundances of bacteria, ii) the definitions of terms like microbiome or multicellularity, and iii) the concept of endosymbiotic domestication.}, }
@article {pmid30729842, year = {2019}, author = {Tan, J and He, Q and Pentz, JT and Peng, C and Yang, X and Tsai, MH and Chen, Y and Ratcliff, WC and Jiang, L}, title = {Copper oxide nanoparticles promote the evolution of multicellularity in yeast.}, journal = {Nanotoxicology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/17435390.2018.1553253}, pmid = {30729842}, issn = {1743-5404}, abstract = {Engineered nanomaterials are rapidly becoming an essential component of modern technology. Thousands of tons of nanomaterials are manufactured, used, and subsequently released into the environment annually. While the presence of these engineered nanomaterials in the environment has profound effects on various biological systems in the short term, little work has been done to understand their consequences over long, evolutionary timescales. The evolution of multicellularity is a critical step in the origin of complex life on Earth and a unique strategy for microorganisms to alleviate adverse environmental impacts, yet the selective pressures that favor the evolution of multicellular groups remain poorly understood. Here, we show that engineered nanomaterials, specifically copper oxide nanoparticles (CuO NPs), promote the evolution of undifferentiated multicellularity in Baker's yeast (Saccharomyces cerevisiae strain Y55). Transcriptomic analysis suggests that multicellularity mitigates the negative effects of CuO NPs in yeast cells and shifts their metabolism from alcoholic fermentation towards aerobic respiration, potentially increasing resource efficiency and providing a fitness benefit during CuO NP exposure. Competition assays also confirm that the multicellular yeast possesses a fitness advantage when exposed to CuO NPs. Our results, therefore, demonstrate that nanoparticles can have profound and unexpected evolutionary consequences, underscoring the need for a more comprehensive understanding of the long-term biological impacts of nanomaterial pollution.}, }
@article {pmid30728304, year = {2019}, author = {Peyraud, R and Mbengue, M and Barbacci, A and Raffaele, S}, title = {Intercellular cooperation in a fungal plant pathogen facilitates host colonization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {8}, pages = {3193-3201}, doi = {10.1073/pnas.1811267116}, pmid = {30728304}, issn = {1091-6490}, support = {336808//European Research Council/International ; }, mesh = {Arabidopsis/genetics/growth &amp; development/*microbiology ; Ascomycota/genetics/*pathogenicity ; Genome, Plant/genetics ; Host-Pathogen Interactions/*genetics ; Hyphae/genetics/pathogenicity ; Plant Diseases/*genetics/microbiology ; }, abstract = {Cooperation is associated with major transitions in evolution such as the emergence of multicellularity. It is central to the evolution of many complex traits in nature, including growth and virulence in pathogenic bacteria. Whether cells of multicellular parasites function cooperatively during infection remains, however, largely unknown. Here, we show that hyphal cells of the fungal pathogen Sclerotinia sclerotiorum reprogram toward division of labor to facilitate the colonization of host plants. Using global transcriptome sequencing, we reveal that gene expression patterns diverge markedly in cells at the center and apex of hyphae during Arabidopsis thaliana colonization compared with in vitro growth. We reconstructed a genome-scale metabolic model for S. sclerotiorum and used flux balance analysis to demonstrate metabolic heterogeneity supporting division of labor between hyphal cells. Accordingly, continuity between the central and apical compartments of invasive hyphae was required for optimal growth in planta Using a multicell model of fungal hyphae, we show that this cooperative functioning enhances fungal growth predominantly during host colonization. Our work identifies cooperation in fungal hyphae as a mechanism emerging at the multicellular level to support host colonization and virulence.}, }
@article {pmid30718271, year = {2019}, author = {Fischer, MS and Jonkers, W and Glass, NL}, title = {Integration of Self and Non-self Recognition Modulates Asexual Cell-to-Cell Communication in Neurospora crassa.}, journal = {Genetics}, volume = {211}, number = {4}, pages = {1255-1267}, doi = {10.1534/genetics.118.301780}, pmid = {30718271}, issn = {1943-2631}, support = {P01 GM068087/GM/NIGMS NIH HHS/United States ; S10 OD021828/OD/NIH HHS/United States ; T32 GM007127/GM/NIGMS NIH HHS/United States ; }, mesh = {*Chemotaxis ; Fungal Proteins/genetics/metabolism ; MAP Kinase Signaling System ; Neurospora crassa/genetics/*physiology ; *Quorum Sensing ; }, abstract = {Cells rarely exist alone, which drives the evolution of diverse mechanisms for identifying and responding appropriately to the presence of other nearby cells. Filamentous fungi depend on somatic cell-to-cell communication and fusion for the development and maintenance of a multicellular, interconnected colony that is characteristic of this group of organisms. The filamentous fungus Neurospora crassa is a model for investigating the mechanisms of somatic cell-to-cell communication and fusion. N. crassa cells chemotropically grow toward genetically similar cells, which ultimately make physical contact and undergo cell fusion. Here, we describe the development of a Pprm1-luciferase reporter system that differentiates whether genes function upstream or downstream of a conserved MAP kinase (MAPK) signaling complex, by using a set of mutants required for communication and cell fusion. The vast majority of these mutants are deficient for self-fusion and for fusion when paired with wild-type cells. However, the Δham-11 mutant is unique in that it fails to undergo self-fusion, but chemotropic interactions and cell fusion are restored in Δham-11 + wild-type interactions. In genetically dissimilar cells, chemotropic interactions are regulated by genetic differences at doc-1 and doc-2, which regulate prefusion non-self recognition; cells with dissimilar doc-1 and doc-2 alleles show greatly reduced cell-fusion frequencies. Here, we show that HAM-11 functions in parallel with the DOC-1 and DOC-2 proteins to regulate the activity of the MAPK signaling complex. Together, our data support a model of integrated self and non-self recognition processes that modulate somatic cell-to-cell communication in N. crassa.}, }
@article {pmid30717103, year = {2019}, author = {Gonçalves, DS and Ferreira, MDS and Guimarães, AJ}, title = {Extracellular Vesicles from the Protozoa Acanthamoeba castellanii: Their Role in Pathogenesis, Environmental Adaptation and Potential Applications.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {6}, number = {1}, pages = {}, doi = {10.3390/bioengineering6010013}, pmid = {30717103}, issn = {2306-5354}, support = {JCNE 2018//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro - FAPERJ./ ; }, abstract = {Extracellular vesicles (EVs) are membranous compartments of distinct cellular origin and biogenesis, displaying different sizes and include exosomes, microvesicles, and apoptotic bodies. The EVs have been described in almost every living organism, from simple unicellular to higher evolutionary scale multicellular organisms, such as mammals. Several functions have been attributed to these structures, including roles in energy acquisition, cell-to-cell communication, gene expression modulation and pathogenesis. In this review, we described several aspects of the recently characterized EVs of the protozoa Acanthamoeba castellanii, a free-living amoeba (FLA) of emerging epidemiological importance, and compare their features to other parasites' EVs. These A. castellanii EVs are comprised of small microvesicles and exosomes and carry a wide range of molecules involved in many biological processes like cell signaling, carbohydrate metabolism and proteolytic activity, such as kinases, glucanases, and proteases, respectively. Several biomedical applications of these EVs have been proposed lately, including their use in vaccination, biofuel production, and the pharmaceutical industry, such as platforms for drug delivery.}, }
@article {pmid30714631, year = {2019}, author = {Baluška, F and Reber, A}, title = {Sentience and Consciousness in Single Cells: How the First Minds Emerged in Unicellular Species.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {3}, pages = {e1800229}, doi = {10.1002/bies.201800229}, pmid = {30714631}, issn = {1521-1878}, abstract = {A reductionistic, bottom-up, cellular-based concept of the origins of sentience and consciousness has been put forward. Because all life is based on cells, any evolutionary theory of the emergence of sentience and consciousness must be grounded in mechanisms that take place in prokaryotes, the simplest unicellular species. It has been posited that subjective awareness is a fundamental property of cellular life. It emerges as an inherent feature of, and contemporaneously with, the very first life-forms. All other varieties of mentation are the result of evolutionary mechanisms based on this singular event. Therefore, all forms of sentience and consciousness evolve from this original instantiation in prokaryotes. It has also been identified that three cellular structures and mechanisms that likely play critical roles here are excitable membranes, oscillating cytoskeletal polymers, and structurally flexible proteins. Finally, basic biophysical principles are proposed to guide those processes that underly the emergence of supracellular sentience from cellular sentience in multicellular organisms.}, }
@article {pmid30705751, year = {2018}, author = {Kosach, V and Shkarina, K and Kravchenko, A and Tereshchenko, Y and Kovalchuk, E and Skoroda, L and Krotevych, M and Khoruzhenko, A}, title = {Nucleocytoplasmic distribution of S6K1 depends on the density and motility of MCF-7 cells in vitro.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {1332}, doi = {10.12688/f1000research.15447.2}, pmid = {30705751}, issn = {2046-1402}, abstract = {Background: The ribosomal protein S6 kinase 1 (S6K1) is one of the main components of the mTOR/S6K signal transduction pathway, which controls cellular metabolism, autophagy, growth, and proliferation. Overexpression of S6K1 was detected in tumors of different origin including breast cancer, and correlated with the worse disease outcome. In addition, significant accumulation of S6K1 was found in the nuclei of breast carcinoma cells suggesting the implication of kinase nuclear substrates in tumor progression. However, this aspect of S6K1 functioning is still poorly understood. The main aim of the present work was to study the subcellular localization of S6K1 in breast cancer cells with the focus on cell migration. Methods: Multicellular spheroids of MCF-7 cells were generated using agarose-coated Petri dishes. Cell migration was induced by spheroids seeding onto adhesive growth surface and subsequent cultivation for 24 to 72 hours. The subcellular localization of S6K1 was studied in human normal breast and cancer tissue samples, 2D and 3D MCF-7 cell cultures using immunofluorescence analysis and confocal microscopy. Results: Analysis of histological sections of human breast tissue samples revealed predominantly nuclear localization of S6K1 in breast malignant cells and its mainly cytoplasmic localization in conditionally normal cells. In vitro studies of MCF-7 cells demonstrated that the subcellular localization of S6K1 depends on the cell density in the monolayer culture. S6K1 relocalization from the cytoplasm into the nucleus was detected in MCF-7 cells migrating from multicellular spheroids onto growth surface. Immunofluorescence analysis of S6K1 and immunocoprecipitation assay revealed the colocalization and interaction between S6K1 and transcription factor TBR2 (T-box brain protein 2) in MCF-7 cells. Conclusions: Subcellular localization of S6K1 depends on the density and locomotor activity of the MCF-7 cells.}, }
@article {pmid30699103, year = {2019}, author = {Helsen, J and Frickel, J and Jelier, R and Verstrepen, KJ}, title = {Network hubs affect evolvability.}, journal = {PLoS biology}, volume = {17}, number = {1}, pages = {e3000111}, doi = {10.1371/journal.pbio.3000111}, pmid = {30699103}, issn = {1545-7885}, abstract = {The regulatory processes in cells are typically organized into complex genetic networks. However, it is still unclear how this network structure modulates the evolution of cellular regulation. One would expect that mutations in central and highly connected modules of a network (so-called hubs) would often result in a breakdown and therefore be an evolutionary dead end. However, a new study by Koubkova-Yu and colleagues finds that in some circumstances, altering a hub can offer a quick evolutionary advantage. Specifically, changes in a hub can induce significant phenotypic changes that allow organisms to move away from a local fitness peak, whereas the fitness defects caused by the perturbed hub can be mitigated by mutations in its interaction partners. Together, the results demonstrate how network architecture shapes and facilitates evolutionary adaptation.}, }
@article {pmid30698789, year = {2019}, author = {Muley, VY and Akhter, Y and Galande, S}, title = {PDZ Domains Across the Microbial World: Molecular Link to the Proteases, Stress Response, and Protein Synthesis.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {644-659}, doi = {10.1093/gbe/evz023}, pmid = {30698789}, issn = {1759-6653}, abstract = {The PSD-95/Dlg-A/ZO-1 (PDZ) domain is highly expanded, diversified, and well distributed across metazoa where it assembles diverse signaling components by virtue of interactions with other proteins in a sequence-specific manner. In contrast, in the microbial world they are reported to be involved in protein quality control during stress response. The distribution, functions, and origins of PDZ domain-containing proteins in the prokaryotic organisms remain largely unexplored. We analyzed 7,852 PDZ domain-containing proteins in 1,474 microbial genomes in this context. PDZ domain-containing proteins from planctomycetes, myxobacteria, and other eubacteria occupying terrestrial and aquatic niches are found to be in multiple copies within their genomes. Over 93% of the 7,852 PDZ domain-containing proteins were classified into 12 families including six novel families based on additional structural and functional domains present in these proteins. The higher PDZ domain encoding capacity of the investigated organisms was observed to be associated with adaptation to the ecological niche where multicellular life might have originated and flourished. Predicted subcellular localization of PDZ domain-containing proteins and their genomic context argue in favor of crucial roles in translation and membrane remodeling during stress response. Based on rigorous sequence, structure, and phylogenetic analyses, we propose that the highly diverse PDZ domain of the uncharacterized Fe-S oxidoreductase superfamily, exclusively found in gladobacteria and several anaerobes and acetogens, might represent the most ancient form among all the existing PDZ domains.}, }
@article {pmid30689829, year = {2019}, author = {Parey, E and Crombach, A}, title = {Evolution of the Drosophila melanogaster Chromatin Landscape and Its Associated Proteins.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {660-677}, doi = {10.1093/gbe/evz019}, pmid = {30689829}, issn = {1759-6653}, abstract = {In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin-associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. These five types were given color names in reference to the Greek word chroma. They are defined by distinct but overlapping combinations of proteins and differ in biological and biochemical properties, including transcriptional activity, replication timing, and histone modifications. In this work, we assess the evolutionary relationships of chromatin-associated proteins and present an integrated view of the evolution and conservation of the fruit fly Drosophila melanogaster chromatin landscape. We combine homology prediction across a wide range of species with gene age inference methods to determine the origin of each chromatin-associated protein. This provides insight into the evolution of the different chromatin types. Our results indicate that for the euchromatic types, YELLOW and RED, young associated proteins are more specialized than old ones; and for genes found in either chromatin type, intron/exon structure is lineage-specific. Next, we provide evidence that a subset of GREEN-associated proteins is involved in a centromere drive in D. melanogaster. Our results on BLUE chromatin support the hypothesis that the emergence of Polycomb Group proteins is linked to eukaryotic multicellularity. In light of these results, we discuss how the regulatory complexification of chromatin links to the origins of eukaryotic multicellularity.}, }
@article {pmid30685797, year = {2019}, author = {Nedelcu, AM}, title = {Independent evolution of complex development in animals and plants: deep homology and lateral gene transfer.}, journal = {Development genes and evolution}, volume = {229}, number = {1}, pages = {25-34}, doi = {10.1007/s00427-019-00626-8}, pmid = {30685797}, issn = {1432-041X}, mesh = {Animals ; Conserved Sequence ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Plant Proteins/chemistry/genetics ; Plants/genetics ; Protein Domains ; *Sequence Homology ; Transcription Factors/chemistry/genetics ; }, abstract = {The evolution of multicellularity is a premier example of phenotypic convergence: simple multicellularity evolved independently many times, and complex multicellular phenotypes are found in several distant groups. Furthermore, both animal and plant lineages have independently reached extreme levels of morphological, functional, and developmental complexity. This study explores the genetic basis for the parallel evolution of complex multicellularity and development in the animal and green plant (i.e., green algae and land plants) lineages. Specifically, the study (i) identifies the SAND domain-a DNA-binding domain with important roles in the regulation of cell proliferation and differentiation, as unique to animals, green algae, and land plants; and (ii) suggests that the parallel deployment of this ancestral domain in similar regulatory roles could have contributed to the independent evolution of complex development in these distant groups. Given the deep animal-green plant divergence, the limited distribution of the SAND domain is best explained by invoking a lateral gene transfer (LGT) event from a green alga to an early metazoan. The presence of a sequence motif specifically shared by a family of SAND-containing transcription factors involved in the evolution of complex multicellularity in volvocine algae and two types of SAND proteins that emerged early in the evolution of animals is consistent with this scenario. Overall, these findings imply that (i) in addition to be involved in the evolution of similar phenotypes, deep homologous sequences can also contribute to shaping parallel evolutionary trajectories in distant lineages, and (ii) LGT could provide an additional source of latent homologous sequences that can be deployed in analogous roles and affect the evolutionary potentials of distantly related groups.}, }
@article {pmid30668691, year = {2019}, author = {Passow, CN and Bronikowski, AM and Blackmon, H and Parsai, S and Schwartz, TS and McGaugh, SE}, title = {Contrasting Patterns of Rapid Molecular Evolution within the p53 Network across Mammal and Sauropsid Lineages.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {629-643}, doi = {10.1093/gbe/evy273}, pmid = {30668691}, issn = {1759-6653}, support = {R01 AG049416/AG/NIA NIH HHS/United States ; }, abstract = {Cancer is a threat to multicellular organisms, yet the molecular evolution of pathways that prevent the accumulation of genetic damage has been largely unexplored. The p53 network regulates how cells respond to DNA-damaging stressors. We know little about p53 network molecular evolution as a whole. In this study, we performed comparative genetic analyses of the p53 network to quantify the number of genes within the network that are rapidly evolving and constrained, and the association between lifespan and the patterns of evolution. Based on our previous published data set, we used genomes and transcriptomes of 34 sauropsids and 32 mammals to analyze the molecular evolution of 45 genes within the p53 network. We found that genes in the network exhibited evidence of positive selection and divergent molecular evolution in mammals and sauropsids. Specifically, we found more evidence of positive selection in sauropsids than mammals, indicating that sauropsids have different targets of selection. In sauropsids, more genes upstream in the network exhibited positive selection, and this observation is driven by positive selection in squamates, which is consistent with previous work showing rapid divergence and adaptation of metabolic and stress pathways in this group. Finally, we identified a negative correlation between maximum lifespan and the number of genes with evidence of divergent molecular evolution, indicating that species with longer lifespans likely experienced less variation in selection across the network. In summary, our study offers evidence that comparative genomic approaches can provide insights into how molecular networks have evolved across diverse species.}, }
@article {pmid30667071, year = {2019}, author = {Coelho, SM and Mignerot, L and Cock, JM}, title = {Origin and evolution of sex-determination systems in the brown algae.}, journal = {The New phytologist}, volume = {222}, number = {4}, pages = {1751-1756}, doi = {10.1111/nph.15694}, pmid = {30667071}, issn = {1469-8137}, support = {//Sorbonne Universités/ ; //CNRS/ ; //ANR/ ; 638240//European Research Council/International ; }, abstract = {Sexual reproduction is a nearly universal feature of eukaryotic organisms. Meiosis appears to have had a single ancient origin, but the mechanisms underlying male or female sex determination are diverse and have emerged repeatedly and independently in the different eukaryotic groups. The brown algae are a group of multicellular photosynthetic eukaryotes that have a distinct evolutionary history compared with animals and plants, as they have been evolving independently for over 1 billion yr. Here, we review recent work using the brown alga Ectocarpus as a model organism to study haploid sex chromosomes, and highlight how the diversity of reproductive and life cycle features of the brown algae offer unique opportunities to characterize the evolutionary forces and the mechanisms underlying the evolution of sex determination.}, }
@article {pmid30663729, year = {2019}, author = {Peel, S and Corrigan, AM and Ehrhardt, B and Jang, KJ and Caetano-Pinto, P and Boeckeler, M and Rubins, JE and Kodella, K and Petropolis, DB and Ronxhi, J and Kulkarni, G and Foster, AJ and Williams, D and Hamilton, GA and Ewart, L}, title = {Introducing an automated high content confocal imaging approach for Organs-on-Chips.}, journal = {Lab on a chip}, volume = {19}, number = {3}, pages = {410-421}, doi = {10.1039/c8lc00829a}, pmid = {30663729}, issn = {1473-0189}, abstract = {Organ-Chips are micro-engineered systems that aim to recapitulate the organ microenvironment. Implementation of Organ-Chips within the pharmaceutical industry aims to improve the probability of success of drugs reaching late stage clinical trial by generating models for drug discovery that are of human origin and have disease relevance. We are adopting the use of Organ-Chips for enhancing pre-clinical efficacy and toxicity evaluation and prediction. Whilst capturing cellular phenotype via imaging in response to drug exposure is a useful readout in these models, application has been limited due to difficulties in imaging the chips at scale. Here we created an end-to-end, automated workflow to capture and analyse confocal images of multicellular Organ-Chips to assess detailed cellular phenotype across large batches of chips. By automating this process, we not only reduced acquisition time, but we also minimised process variability and user bias. This enabled us to establish, for the first time, a framework of statistical best practice for Organ-Chip imaging, creating the capability of using Organ-Chips and imaging for routine testing in drug discovery applications that rely on quantitative image data for decision making. We tested our approach using benzbromarone, whose mechanism of toxicity has been linked to mitochondrial damage with subsequent induction of apoptosis and necrosis, and staurosporine, a tool inducer of apoptosis. We also applied this workflow to assess the hepatotoxic effect of an active AstraZeneca drug candidate illustrating its applicability in drug safety assessment beyond testing tool compounds. Finally, we have demonstrated that this approach could be adapted to Organ-Chips of different shapes and sizes through application to a Kidney-Chip.}, }
@article {pmid30662758, year = {2018}, author = {Bogdan, MJ and Savin, T}, title = {Fingering instabilities in tissue invasion: an active fluid model.}, journal = {Royal Society open science}, volume = {5}, number = {12}, pages = {181579}, doi = {10.1098/rsos.181579}, pmid = {30662758}, issn = {2054-5703}, abstract = {Metastatic tumours often invade healthy neighbouring tissues by forming multicellular finger-like protrusions emerging from the cancer mass. To understand the mechanical context behind this phenomenon, we here develop a minimalist fluid model of a self-propelled, growing biological tissue. The theory involves only four mechanical parameters and remains analytically trackable in various settings. As an application of the model, we study the evolution of a two-dimensional circular droplet made of our active and expanding fluid, and embedded in a passive non-growing tissue. This system could be used to model the evolution of a carcinoma in an epithelial layer. We find that our description can explain the propensity of tumour tissues to fingering instabilities, as conditioned by the magnitude of active traction and the growth kinetics. We are also able to derive predictions for the tumour size at the onset of metastasis, and for the number of subsequent invasive fingers. Our active fluid model may help describe a wider range of biological processes, including wound healing and developmental patterning.}, }
@article {pmid30659161, year = {2019}, author = {Rodríguez-Pascual, F}, title = {How evolution made the matrix punch at the multicellularity party.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {3}, pages = {770-771}, doi = {10.1074/jbc.H118.006972}, pmid = {30659161}, issn = {1083-351X}, mesh = {Animals ; Basement Membrane/*metabolism ; *Evolution, Molecular ; Humans ; Protein-Serine-Threonine Kinases/*genetics/*metabolism ; }, abstract = {The basement membrane is a specialized sheet-like form of the extracellular matrix that provides structural support to epithelial cells and tissues, while influencing multiple biological functions, and was essential in the transition to multicellularity. By exploring a variety of genomes, Darris et al. provide evidence that the emergence and divergence of a multifunctional Goodpasture antigen-binding protein (GPBP), a basement membrane constituent, played a role in this transition. These findings help to explain how GPBP contributed to the formation of these extracellular matrices and to more precisely define the transition to multicellular organisms.}, }
@article {pmid30653459, year = {2019}, author = {Yoshida, T and Prudent, M and D'alessandro, A}, title = {Red blood cell storage lesion: causes and potential clinical consequences.}, journal = {Blood transfusion = Trasfusione del sangue}, volume = {17}, number = {1}, pages = {27-52}, doi = {10.2450/2019.0217-18}, pmid = {30653459}, issn = {1723-2007}, mesh = {*Blood Preservation ; Erythrocyte Transfusion/adverse effects/methods ; Erythrocytes/cytology/*metabolism ; Humans ; Oxygen/metabolism ; Pharmaceutical Solutions/pharmacology ; Time Factors ; }, abstract = {Red blood cells (RBCs) are a specialised organ that enabled the evolution of multicellular organisms by supplying a sufficient quantity of oxygen to cells that cannot obtain oxygen directly from ambient air via diffusion, thereby fueling oxidative phosphorylation for highly efficient energy production. RBCs have evolved to optimally serve this purpose by packing high concentrations of haemoglobin in their cytosol and shedding nuclei and other organelles. During their circulatory lifetimes in humans of approximately 120 days, RBCs are poised to transport oxygen by metabolic/redox enzymes until they accumulate damage and are promptly removed by the reticuloendothelial system. These elaborate evolutionary adaptions, however, are no longer effective when RBCs are removed from the circulation and stored hypothermically in blood banks, where they develop storage-induced damages (&quot;storage lesions&quot;) that accumulate over the shelf life of stored RBCs. This review attempts to provide a comprehensive view of the literature on the subject of RBC storage lesions and their purported clinical consequences by incorporating the recent exponential growth in available data obtained from &quot;omics&quot; technologies in addition to that published in more traditional literature. To summarise this vast amount of information, the subject is organised in figures with four panels: i) root causes; ii) RBC storage lesions; iii) physiological effects; and iv) reported outcomes. The driving forces for the development of the storage lesions can be roughly classified into two root causes: i) metabolite accumulation/depletion, the target of various interventions (additive solutions) developed since the inception of blood banking; and ii) oxidative damages, which have been reported for decades but not addressed systemically until recently. Downstream physiological consequences of these storage lesions, derived mainly by in vitro studies, are described, and further potential links to clinical consequences are discussed. Interventions to postpone the onset and mitigate the extent of the storage lesion development are briefly reviewed. In addition, we briefly discuss the results from recent randomised controlled trials on the age of stored blood and clinical outcomes of transfusion.}, }
@article {pmid30651122, year = {2019}, author = {Patthy, L}, title = {Exon skipping-rich transcriptomes of animals reflect the significance of exon-shuffling in metazoan proteome evolution.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {2}, doi = {10.1186/s13062-019-0231-3}, pmid = {30651122}, issn = {1745-6150}, abstract = {ᅟ: Animals are known to have higher rates of exon skipping than other eukaryotes. In a recent study, Grau-Bové et al. (Genome Biology 19:135, 2018) have used RNA-seq data across 65 eukaryotic species to investigate when and how this high prevalence of exon skipping evolved. They have found that bilaterian Metazoa have significantly increased exon skipping frequencies compared to all other eukaryotic groups and that exon skipping in nearly all animals, including non-bilaterians, is strongly enriched for frame-preserving events. The authors have hypothesized that &quot;the increase of exon skipping rates in animals followed a two-step process. First, exon skipping in early animals became enriched for frame-preserving events. Second, bilaterian ancestors dramatically increased their exon skipping frequencies, likely driven by the interplay between a shift in their genome architectures towards more exon definition and recruitment of frame-preserving exon skipping events to functionally diversify their cell-specific proteomes.&quot; Here we offer a different explanation for the higher frequency of frame-preserving exon skipping in Metzoa than in all other eukaryotes. In our view these observations reflect the fact that the majority of multidomain proteins unique to metazoa and indispensable for metazoan type multicellularity were assembled by exon-shuffling from 'symmetrical' modules (i.e. modules flanked by introns of the same phase), whereas this type of protein evolution played a minor role in other groups of eukaryotes, including plants. The higher frequency of 'symmetrical' exons in Metazoan genomes provides an explanation for the enrichment for frame-preserving events since skipping or inclusion of 'symmetrical' modules during alternative splicing does not result in a reading-frame shift. REVIEWERS: This article was reviewed by Manuel Irimia, Ashish Lal and Erez Levanon. The reviewers were nominated by the Editorial Board.}, }
@article {pmid30649338, year = {2019}, author = {Russell, SL}, title = {Transmission mode is associated with environment type and taxa across bacteria-eukaryote symbioses: a systematic review and meta-analysis.}, journal = {FEMS microbiology letters}, volume = {366}, number = {3}, pages = {}, doi = {10.1093/femsle/fnz013}, pmid = {30649338}, issn = {1574-6968}, abstract = {Symbiotic associations between bacteria and eukaryotes exhibit a range of transmission strategies. The rates and distributions of transmission modes have not been thoroughly investigated across associations, despite their consequences on symbiont and host evolution. To address this empirically, I compiled data from the literature on bacteria-multicellular eukaryote associations for which transmission mode data was available. Of the total 528 analyzed symbioses, 21.2% were strictly horizontally transmitted, 36.0% exhibited some form of mixed mode transmission and 42.8% were strictly vertically transmitted. Controlling for phylogenetically independent symbiosis events revealed modes were approximately equally distributed among the 113 independent associations, at 32.1%+/-0.57% horizontal, 37.8%+/-1.4% mixed mode and 31.1%+/-1.3% vertical transmission. Binning symbioses by environment revealed an abundance of vertical transmission on land and a lack of it in aquatic environments. The naturally occurring uneven distribution of taxa among environments prevented controlling for host/symbiont phylogeny. However, the results were robust over a large number of independently evolved associations, suggesting that many vertically transmitted bacteria are capable of mixed mode transmission and barriers exist that reduce the rate of horizontal transmission events. Thus, both the environment type and host/symbiont taxa influence symbiont transmission mode evolution.}, }
@article {pmid30644818, year = {2019}, author = {Arun, A and Coelho, SM and Peters, AF and Bourdareau, S and Pérès, L and Scornet, D and Strittmatter, M and Lipinska, AP and Yao, H and Godfroy, O and Montecinos, GJ and Avia, K and Macaisne, N and Troadec, C and Bendahmane, A and Cock, JM}, title = {Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.43101}, pmid = {30644818}, issn = {2050-084X}, support = {ANR-10-BLAN-1727//Agence Nationale de la Recherche/ ; Marinexus//Interreg Program France (Channel)-England/ ; 638240//European Research Council/International ; European Erasmus Mundus program//European Commission/ ; ANR-10-BTBR-04-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-40//Agence Nationale de la Recherche/ ; ERC-SEXYPARTH//European Research Council/International ; Marinexus//Interreg Program France -England/ ; }, abstract = {Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.}, }
@article {pmid30626024, year = {2019}, author = {Oxford, JT and Reeck, JC and Hardy, MJ}, title = {Extracellular Matrix in Development and Disease.}, journal = {International journal of molecular sciences}, volume = {20}, number = {1}, pages = {}, doi = {10.3390/ijms20010205}, pmid = {30626024}, issn = {1422-0067}, mesh = {Animals ; *Disease ; Extracellular Matrix/*metabolism ; *Growth and Development ; Humans ; Integrins/metabolism ; Muscles/metabolism ; Reproduction ; Tissue Engineering ; }, abstract = {The evolution of multicellular metazoan organisms was marked by the inclusion of an extracellular matrix (ECM), a multicomponent, proteinaceous network between cells that contributes to the spatial arrangement of cells and the resulting tissue organization. [...].}, }
@article {pmid30622525, year = {2018}, author = {Li, XG and Zhang, WJ and Xiao, X and Jian, HH and Jiang, T and Tang, HZ and Qi, XQ and Wu, LF}, title = {Pressure-Regulated Gene Expression and Enzymatic Activity of the Two Periplasmic Nitrate Reductases in the Deep-Sea Bacterium Shewanella piezotolerans WP3.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3173}, doi = {10.3389/fmicb.2018.03173}, pmid = {30622525}, issn = {1664-302X}, abstract = {Shewanella species are widely distributed in marine environments, from the shallow coasts to the deepest sea bottom. Most Shewanella species possess two isoforms of periplasmic nitrate reductases (NAP-α and NAP-β) and are able to generate energy through nitrate reduction. However, the contributions of the two NAP systems to bacterial deep-sea adaptation remain unclear. In this study, we found that the deep-sea denitrifier Shewanella piezotolerans WP3 was capable of performing nitrate respiration under high hydrostatic pressure (HHP) conditions. In the wild-type strain, NAP-β played a dominant role and was induced by both the substrate and an elevated pressure, whereas NAP-α was constitutively expressed at a relatively lower level. Genetic studies showed that each NAP system alone was sufficient to fully sustain nitrate-dependent growth and that both NAP systems exhibited substrate and pressure inducible expression patterns when the other set was absent. Biochemical assays further demonstrated that NAP-α had a higher tolerance to elevated pressure. Collectively, we report for the first time the distinct properties and contributions of the two NAP systems to nitrate reduction under different pressure conditions. The results will shed light on the mechanisms of bacterial HHP adaptation and nitrogen cycling in the deep-sea environment.}, }
@article {pmid30618841, year = {2018}, author = {Huitzil, S and Sandoval-Motta, S and Frank, A and Aldana, M}, title = {Modeling the Role of the Microbiome in Evolution.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {1836}, doi = {10.3389/fphys.2018.01836}, pmid = {30618841}, issn = {1664-042X}, abstract = {There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.}, }
@article {pmid30612623, year = {2019}, author = {Bowman, JL and Briginshaw, LN and Florent, SN}, title = {Evolution and co-option of developmental regulatory networks in early land plants.}, journal = {Current topics in developmental biology}, volume = {131}, number = {}, pages = {35-53}, doi = {10.1016/bs.ctdb.2018.10.001}, pmid = {30612623}, issn = {1557-8933}, abstract = {Land plants evolved from an ancestral alga from which they inherited developmental and physiological characters. A key innovation of land plants is a life cycle with an alternation of generations, with both haploid gametophyte and diploid sporophyte generations having complex multicellular bodies. The origins of the developmental genetic programs patterning these bodies, whether inherited from an algal ancestor or evolved de novo, and whether programs were co-opted between generations, are largely open questions. We first provide a framework for land plant evolution and co-option of developmental regulatory pathways and then examine two cases in more detail.}, }
@article {pmid30612620, year = {2019}, author = {Hackenberg, D and Twell, D}, title = {The evolution and patterning of male gametophyte development.}, journal = {Current topics in developmental biology}, volume = {131}, number = {}, pages = {257-298}, doi = {10.1016/bs.ctdb.2018.10.008}, pmid = {30612620}, issn = {1557-8933}, support = {BB/N005090/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The reproductive adaptations of land plants have played a key role in their terrestrial colonization and radiation. This encompasses mechanisms used for the production, dispersal and union of gametes to support sexual reproduction. The production of small motile male gametes and larger immotile female gametes (oogamy) in specialized multicellular gametangia evolved in the charophyte algae, the closest extant relatives of land plants. Reliance on water and motile male gametes for sexual reproduction was retained by bryophytes and basal vascular plants, but was overcome in seed plants by the dispersal of pollen and the guided delivery of non-motile sperm to the female gametes. Here we discuss the evolutionary history of male gametogenesis in streptophytes (green plants) and the underlying developmental biology, including recent advances in bryophyte and angiosperm models. We conclude with a perspective on research trends that promise to deliver a deeper understanding of the evolutionary and developmental mechanisms of male gametogenesis in plants.}, }
@article {pmid30612613, year = {2019}, author = {Szövényi, P and Waller, M and Kirbis, A}, title = {Evolution of the plant body plan.}, journal = {Current topics in developmental biology}, volume = {131}, number = {}, pages = {1-34}, doi = {10.1016/bs.ctdb.2018.11.005}, pmid = {30612613}, issn = {1557-8933}, abstract = {Land plants evolved about 470 million years ago or even earlier, in a biological crust-dominated terrestrial flora. The origin of land plants was probably one of the most significant events in Earth's history, which ultimately contributed to the greening of the terrestrial environment and opened up the way for the diversification of both plant and non-plant lineages. Fossil and phylogenetic evidence suggest that land plants have evolved from fresh-water charophycean algae, which were physiologically, genetically, and developmentally potentiated to make the transition to land. Since all land plants have biphasic life cycles, in contrast to the haplontic life cycle of Charophytes, the evolution of land plants was linked to the origin of a multicellular sporophytic phase. Land plants have evolved complex body plans in a way that overall complexity increased toward the tip of the land plant tree of life. Early forms were unbranched, with terminal sporangia and simple rhizoid rooting structures but without vasculature and leaves. Later on, branched forms with lateral sporangia appeared and paved the route for the evolution for indeterminacy. Finally, leaves and roots evolved to enable efficient nutrient transport to support a large plant body. The fossil record also suggests that almost all plant organs, such as leaves and roots, evolved multiple times independently over the course of land plant evolution. In this review, we summarize the current knowledge on the evolution of the land plant body plan by combining evidence of the fossil record, phylogenetics, and developmental biology.}, }
@article {pmid30602438, year = {2019}, author = {Murre, C}, title = {Helix-loop-helix proteins and the advent of cellular diversity: 30 years of discovery.}, journal = {Genes &amp; development}, volume = {33}, number = {1-2}, pages = {6-25}, doi = {10.1101/gad.320663.118}, pmid = {30602438}, issn = {1549-5477}, support = {R01 AI082850/AI/NIAID NIH HHS/United States ; Z01 AI000880/AI/NIAID NIH HHS/United States ; }, mesh = {Basic Helix-Loop-Helix Transcription Factors/metabolism ; Cell Lineage/genetics ; Enhancer Elements, Genetic/physiology ; *Evolution, Molecular ; Gene Expression Regulation, Developmental ; Helix-Loop-Helix Motifs/physiology ; Promoter Regions, Genetic/physiology ; }, abstract = {Helix-loop-helix (HLH) proteins are dimeric transcription factors that control lineage- and developmental-specific gene programs. Genes encoding for HLH proteins arose in unicellular organisms >600 million years ago and then duplicated and diversified from ancestral genes across the metazoan and plant kingdoms to establish multicellularity. Hundreds of HLH proteins have been identified with diverse functions in a wide variety of cell types. HLH proteins orchestrate lineage specification, commitment, self-renewal, proliferation, differentiation, and homing. HLH proteins also regulate circadian clocks, protect against hypoxic stress, promote antigen receptor locus assembly, and program transdifferentiation. HLH proteins deposit or erase epigenetic marks, activate noncoding transcription, and sequester chromatin remodelers across the chromatin landscape to dictate enhancer-promoter communication and somatic recombination. Here the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed.}, }
@article {pmid30590727, year = {2018}, author = {Tsitsekian, D and Daras, G and Alatzas, A and Templalexis, D and Hatzopoulos, P and Rigas, S}, title = {Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/ery440}, pmid = {30590727}, issn = {1460-2431}, abstract = {The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.}, }
@article {pmid30590062, year = {2019}, author = {Måløy, M and Måløy, F and Lahoz-Beltrá, R and Carlos Nuño, J and Bru, A}, title = {An extended Moran process that captures the struggle for fitness.}, journal = {Mathematical biosciences}, volume = {308}, number = {}, pages = {81-104}, doi = {10.1016/j.mbs.2018.12.014}, pmid = {30590062}, issn = {1879-3134}, abstract = {When a new type of individual appears in a stable population, the newcomer is typically not advantageous. Due to stochasticity, the new type can grow in numbers, but the newcomers can only become advantageous if they manage to change the environment in such a way that they increase their fitness. This dynamics is observed in several situations in which a relatively stable population is invaded by an alternative strategy, for instance the evolution of cooperation among bacteria, the invasion of cancer in a multicellular organism and the evolution of ideas that contradict social norms. These examples also show that, by generating different versions of itself, the new type increases the probability of winning the struggle for fitness. Our model captures the imposed cooperation whereby the first generation of newcomers dies while changing the environment such that the next generations become more advantageous.}, }
@article {pmid30585312, year = {2019}, author = {Denbo, S and Aono, K and Kai, T and Yagasaki, R and Ruiz-Trillo, I and Suga, H}, title = {Revision of the Capsaspora genome using read mating information adjusts the view on premetazoan genome.}, journal = {Development, growth &amp; differentiation}, volume = {61}, number = {1}, pages = {34-42}, doi = {10.1111/dgd.12587}, pmid = {30585312}, issn = {1440-169X}, support = {16K07468//JSPS KAKENHI/ ; //NOVARTIS Foundation/ ; //ITOH Science Foundation/ ; //Naito Foundation/ ; //Prefectural University of Hiroshima JUTEN Grant/ ; ERC-2012-Co-616960//European Research Council Consolidator Grant/ ; BFU2014-57779-P//European Research Council Consolidator Grant/ ; BFU2017-90114-P//European Research Council Consolidator Grant/ ; //Ministerio de Economía y Competitividad (MINECO)/ ; //Agencia Estatal de Investigación (AEI)/ ; //Fondo Europeo de Desarrollo Regional (FEDER)/ ; }, mesh = {Animals ; Chromosomes/genetics ; Eukaryota/enzymology/*genetics/metabolism ; Genome/*genetics ; Phylogeny ; Protein-Tyrosine Kinases/genetics ; }, abstract = {The genome sequences of unicellular holozoans, the closest relatives to animals, are shedding light on the evolution of animal multicellularity, shaping the genetic contents of the putative premetazoans. However, the assembly quality of the genomes remains poor compared to the major model organisms such as human and fly. Improving the assembly is critical for precise comparative genomics studies and further molecular biological studies requiring accurate sequence information such as enhancer analysis and genome editing. In this report, we present a new strategy to improve the assembly by fully exploiting the information of Illumina mate-pair reads. By visualizing the distance and orientation of the mapped read pairs, we could highlight the regions where possible assembly errors exist in the genome sequence of Capsaspora, a lineage of unicellular holozoans. Manual modification of these errors repaired 590 assembly problems in total and reassembled 84 supercontigs into 55. Our telomere prediction analysis using the read pairs containing the pan-eukaryotic telomere-like sequence identified at least 13 chromosomes. The resulting new assembly posed us a re-annotation of 112 genes, including 15 putative receptor protein tyrosine kinases. Our strategy thus provides a useful approach for improving assemblies of draft genomes, and the new Capsaspora genome offers us an opportunity to adjust the view on the genome of the unicellular animal ancestor.}, }
@article {pmid30576875, year = {2019}, author = {Ortega-Escalante, JA and Kwok, O and Miller, SM}, title = {New Selectable Markers for Volvox carteri Transformation.}, journal = {Protist}, volume = {170}, number = {1}, pages = {52-63}, doi = {10.1016/j.protis.2018.11.002}, pmid = {30576875}, issn = {1618-0941}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacillus cereus/genetics ; Cinnamates/*pharmacology ; Coccidioides/genetics ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Genetic Markers/genetics ; Hygromycin B/*analogs &amp; derivatives/pharmacology ; Microorganisms, Genetically-Modified/genetics ; Nucleosides/pharmacology ; Transformation, Genetic/drug effects/*genetics ; Volvox/drug effects/*genetics ; }, abstract = {Volvox carteri is an excellent model for investigating the evolution of multicellularity and cell differentiation, and the rate of future progress with this system will depend on improved molecular genetic tools. Several selectable markers for nuclear transformation of V. carteri have been developed, including the nitrate reductase (nitA) gene, but it would be useful to have additional markers to multiplex transgenes in this species. To further facilitate molecular genetic analyses of V. carteri, we developed two new selectable markers that provide rapid, easily selected, and stable resistance to the antibiotics hygromycin and blasticidin. We generated constructs with Volvox-specific regulatory sequences and codon-optimized hygromycin (VcHyg) and blasticidin (VcBlast) resistance genes from Coccidioides posadasii and Bacillus cereus, respectively. With these constructs, transformants were obtained via biolistic bombardment at rates of 0.5-13 per million target cells bombarded. Antibiotic-resistant survivors were readily isolated 7days post bombardment. VcHyg and VcBlast transgenes and transcripts were detected in transformants. Co-transformation rates using the VcHyg or VcBlast markers with unselected genes were comparable to those obtained with nitA. These results indicate that the pVcHyg and pVcBlast plasmids are highly efficient and convenient for transforming and co-transforming a broad range of V. carteri strains.}, }
@article {pmid30568302, year = {2019}, author = {Chen, Y and Ikeda, K and Yoneshiro, T and Scaramozza, A and Tajima, K and Wang, Q and Kim, K and Shinoda, K and Sponton, CH and Brown, Z and Brack, A and Kajimura, S}, title = {Thermal stress induces glycolytic beige fat formation via a myogenic state.}, journal = {Nature}, volume = {565}, number = {7738}, pages = {180-185}, doi = {10.1038/s41586-018-0801-z}, pmid = {30568302}, issn = {1476-4687}, support = {R56 AR060868/AR/NIAMS NIH HHS/United States ; R01 AR061002/AR/NIAMS NIH HHS/United States ; R01 DK097441/DK/NIDDK NIH HHS/United States ; R01 AR060868/AR/NIAMS NIH HHS/United States ; R01 DK108822/DK/NIDDK NIH HHS/United States ; R01 DK112268/DK/NIDDK NIH HHS/United States ; }, abstract = {Environmental cues profoundly affect cellular plasticity in multicellular organisms. For instance, exercise promotes a glycolytic-to-oxidative fibre-type switch in skeletal muscle, and cold acclimation induces beige adipocyte biogenesis in adipose tissue. However, the molecular mechanisms by which physiological or pathological cues evoke developmental plasticity remain incompletely understood. Here we report a type of beige adipocyte that has a critical role in chronic cold adaptation in the absence of β-adrenergic receptor signalling. This beige fat is distinct from conventional beige fat with respect to developmental origin and regulation, and displays enhanced glucose oxidation. We therefore refer to it as glycolytic beige fat. Mechanistically, we identify GA-binding protein α as a regulator of glycolytic beige adipocyte differentiation through a myogenic intermediate. Our study reveals a non-canonical adaptive mechanism by which thermal stress induces progenitor cell plasticity and recruits a distinct form of thermogenic cell that is required for energy homeostasis and survival.}, }
@article {pmid30564256, year = {2018}, author = {Solórzano-Cascante, P and Sánchez-Chiang, N and Jiménez, VM}, title = {Explant Type, Culture System, 6-Benzyladenine, Meta-Topolin and Encapsulation Affect Indirect Somatic Embryogenesis and Regeneration in Carica papaya L.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1769}, doi = {10.3389/fpls.2018.01769}, pmid = {30564256}, issn = {1664-462X}, abstract = {A protocol to propagate papaya hybrid plants through indirect somatic embryogenesis was developed considering the effect of explant type, culture system, particular cytokinins and encapsulation, in different stages of the process. Optimal 2,4-dichlorophenoxyacetic acid (2,4-D) concentrations for non-embryogenic callus formation ranged between 9.0 and 27.1 μM in half-cut seeds, while higher concentrations were harmful. Non-embryogenic callus was also obtained with 22-158 μM 2,4-D from hypocotyl segments. Callus with embryogenic structures was only obtained in half-cut seeds cultured in the darkness on half-strength Murashige and Skoog culture medium supplemented with 2,4-D, while hypocotyl segments and isolated zygotic embryos failed to produce this type of callus regardless of the 2,4-D and sucrose (30 and 70 g l-1) concentrations tested in this study. Both, embryogenic callus development and quantity of somatic embryos formed per embryogenic callus, which ranged between 11 and 31 units after 14 months, required 2,4-D, but without any effect of the concentration. Histological studies confirmed the multicellular origin of the somatic embryos. In further steps, liquid medium induced over four times more somatic embryos than agar-gelled medium and showed significantly higher production of globular somatic embryos (85 vs. 57%). Both, 6-benzyladenine (BA) and meta-topolin (Mtop) stimulated sprouting (40-45%) of the somatic embryos (development of shoots only) in concentrations of up to 2.7 and 10 μM, respectively. Sprouting probability showed a 2nd order polynomial trend despite the range of concentration used for each cytokinin. This is the first report about the positive effect of Mtop on the apical shoot development of Carica papaya somatic embryos known to the authors. Radicle growth was observed in 5% or less of the cultivated embryos, regardless of the BA concentration. Finally, all encapsulation conditions tested (2.5, 3.5, and 4.5% sodium alginate, combined with 50 and 100 mM CaCl2) reduced sprouting of somatic embryos when compared to the non-encapsulated ones, whereas capsule hardness showed low correlation with embryo sprouting. Embryos were further cultivated until they became plantlets approximately 5 cm long. They were acclimatized and afterward planted in the field, where they flowered and produced fruit.}, }
@article {pmid30563248, year = {2018}, author = {Wang, Z and Zhou, W and Hameed, MS and Liu, J and Zeng, X}, title = {Characterization and Expression Profiling of Neuropeptides and G-Protein-Coupled Receptors (GPCRs) for Neuropeptides in the Asian Citrus Psyllid, Diaphorina citri (Hemiptera: Psyllidae).}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, doi = {10.3390/ijms19123912}, pmid = {30563248}, issn = {1422-0067}, support = {31572314//National Natural Science Foundation of China/ ; 2017YFD0202005//National Key Research and Development Program of China/ ; 2015B090903076//Department of Science and Technology of Guangdong Province/ ; }, mesh = {Animals ; Citrus/*parasitology ; Evolution, Molecular ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Developmental ; Hemiptera/genetics/*growth &amp; development ; Insect Proteins/genetics ; Neuropeptides/*genetics ; Organ Specificity ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Receptors, G-Protein-Coupled/*genetics ; Sequence Analysis, RNA ; }, abstract = {Neuropeptides are endogenous active substances that widely exist in multicellular biological nerve tissue and participate in the function of the nervous system, and most of them act on neuropeptide receptors. In insects, neuropeptides and their receptors play important roles in controlling a multitude of physiological processes. In this project, we sequenced the transcriptome from twelve tissues of the Asian citrus psyllid, Diaphorina citri Kuwayama. A total of 40 candidate neuropeptide genes and 42 neuropeptide receptor genes were identified. Among the neuropeptide receptor genes, 35 of them belong to the A-family (or rhodopsin-like), four of them belong to the B-family (or secretin-like), and three of them are leucine-rich repeat-containing G-protein-coupled receptors. The expression profile of the 82 genes across developmental stages was determined by qRT-PCR. Our study provides the first investigation on the genes of neuropeptides and their receptors in D. citri, which may play key roles in regulating the physiology and behaviors of D. citri.}, }
@article {pmid30558164, year = {2018}, author = {Millán, I and Piñero-Ramos, JD and Lara, I and Parra-Llorca, A and Torres-Cuevas, I and Vento, M}, title = {Oxidative Stress in the Newborn Period: Useful Biomarkers in the Clinical Setting.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {7}, number = {12}, pages = {}, doi = {10.3390/antiox7120193}, pmid = {30558164}, issn = {2076-3921}, support = {PI17/0131//Instituto de Investigación en Salud Carlos III/ ; APOSTD/2018/A/172//CONSELLERIA EDUCAÇIÓ, INVESTIGAÇIÓ, CULTURA I ESPORT/ ; }, abstract = {Aerobic metabolism is highly efficient in providing energy for multicellular organisms. However, even under physiological conditions, an incomplete reduction of oxygen produces reactive oxygen species and, subsequently, oxidative stress. Some of these chemical species are highly reactive free radicals capable of causing functional and structural damage to cell components (protein, lipids, or nucleotides). Oxygen is the most used drug in ill-adapted patients during the newborn period. The use of oxygen may cause oxidative stress-related diseases that increase mortality and cause morbidity with adverse long-term outcomes. Conditions such as prematurity or birth asphyxia are frequently treated with oxygen supplementation. Both pathophysiological situations of hypoxia⁻reoxygenation in asphyxia and hyperoxia in premature infants cause a burst of reactive oxygen species and oxidative stress. Recently developed analytical assays using mass spectrometry have allowed us to determine highly specific biomarkers with minimal samples. The detection of these metabolites will help improve the diagnosis, evolution, and response to therapy in oxidative stress-related conditions during the newborn period.}, }
@article {pmid30554805, year = {2019}, author = {Stein, WD}, title = {The ages of the cancer-associated genes.}, journal = {Seminars in oncology}, volume = {46}, number = {1}, pages = {10-18}, doi = {10.1053/j.seminoncol.2018.11.001}, pmid = {30554805}, issn = {1532-8708}, mesh = {Carcinoma/genetics ; *Evolution, Molecular ; Genome, Human/*genetics ; Humans ; Lymphoma/genetics ; Mutation/genetics ; Neoplasms/*genetics/pathology ; Open Reading Frames/*genetics ; Sarcoma/genetics ; }, abstract = {In the accompanying manuscript (Litman and Stein, 2018) we list the ages of all the protein-coding genes and of many of the noncoding genes of the human genome. The present manuscript uses those results to derive the ages of the genes on the COSMIC list of somatic mutations in cancer. The lymphoma-associated genes in the COSMIC list are younger than the sarcoma-associated or the carcinoma-associated genes, or the genes shared by lymphomas and carcinomas. Genes that accreted to the evolving genome with the appearance of the fish are major contributors to the sarcoma-, lymphoma-, or carcinoma-associated gene sets, but it is genes accreted during the development of multicellularity that contribute most to the genes common to the classes. Genes arising with the evolution of the fish are also dominant in a list of noncoding genes associated with cancer. A list is provided of the COSMIC genes which have not yet been reported as drug targets.}, }
@article {pmid30553725, year = {2018}, author = {Taggart, JC and Li, GW}, title = {Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes.}, journal = {Cell systems}, volume = {7}, number = {6}, pages = {580-589.e4}, doi = {10.1016/j.cels.2018.11.003}, pmid = {30553725}, issn = {2405-4712}, abstract = {Constituents of multiprotein complexes are required at well-defined levels relative to each other. However, it remains unknown whether eukaryotic cells typically produce precise amounts of subunits, or instead rely on degradation to mitigate imprecise production. Here, we quantified the production rates of multiprotein complexes in unicellular and multicellular eukaryotes using ribosome profiling. By resolving read-mapping ambiguities, which occur for a large fraction of ribosome footprints and distort quantitation accuracy in eukaryotes, we found that obligate components of multiprotein complexes are produced in proportion to their stoichiometry, indicating that their abundances are already precisely tuned at the synthesis level. By systematically interrogating the impact of gene dosage variations in budding yeast, we found a general lack of negative feedback regulation protecting the normally precise rates of subunit synthesis. These results reveal a core principle of proteome homeostasis and highlight the evolution toward quantitative control at every step in the central dogma.}, }
@article {pmid30545356, year = {2018}, author = {Herron, MD and Zamani-Dahaj, SA and Ratcliff, WC}, title = {Trait heritability in major transitions.}, journal = {BMC biology}, volume = {16}, number = {1}, pages = {145}, doi = {10.1186/s12915-018-0612-6}, pmid = {30545356}, issn = {1741-7007}, mesh = {*Biological Evolution ; *Heredity ; Models, Genetic ; *Phenotype ; Selection, Genetic ; }, abstract = {BACKGROUND: Increases in biological complexity and the origins of life's hierarchical organization are described by the &quot;major transitions&quot; framework. A crucial component of this paradigm is that after the transition in complexity or organization, adaptation occurs primarily at the level of the new, higher-level unit. For collective-level adaptations to occur, though, collective-level traits-properties of the group, such as collective size-must be heritable. Since collective-level trait values are functions of lower-level trait values, collective-level heritability is related to particle-level heritability. However, the nature of this relationship has rarely been explored in the context of major transitions.<br><br>RESULTS: We examine relationships between particle-level heritability and collective-level heritability for several functions that express collective-level trait values in terms of particle-level trait values. For clonal populations, when a collective-level trait value is a linear function of particle-level trait values and the number of particles per collective is fixed, the heritability of a collective-level trait is never less than that of the corresponding particle-level trait and is higher under most conditions. For more complicated functions, collective-level heritability is higher under most conditions, but can be lower when the environment experienced by collectives is heterogeneous. Within-genotype variation in collective size reduces collective-level heritability, but it can still exceed particle-level heritability when phenotypic variance among particles within collectives is large. These results hold for a diverse sample of biologically relevant traits.<br><br>CONCLUSIONS: Rather than being an impediment to major transitions, we show that, under a wide range of conditions, the heritability of collective-level traits is actually higher than that of the corresponding particle-level traits. High levels of collective-level trait heritability thus arise &quot;for free,&quot; with important implications not only for major transitions but for multilevel selection in general.}, }
@article {pmid30541961, year = {2018}, author = {Hayakawa, IS and Inouye, K}, title = {Species recognition in social amoebae.}, journal = {Journal of biosciences}, volume = {43}, number = {5}, pages = {1025-1036}, pmid = {30541961}, issn = {0973-7138}, mesh = {Biological Evolution ; Dictyostelium/classification/*genetics ; *Genes, Protozoan ; *Genome, Protozoan ; Phylogeny ; Reproduction ; Species Specificity ; }, abstract = {Aggregative multicellularity requires the ability of cells to recognise conspecifics. Social amoebae are among the best studied of such organisms, but the mechanism and evolutionary background of species recognition remained to be investigated. Here we show that heterologous expression of a single Dictyostelium purpureum gene is sufficient for D. discoideum cells to efficiently make chimaeric fruiting bodies with D. purpureum cells. This gene forms a bidirectional pair with another gene on the D. purpureum genome, and they are both highly polymorphic among independent wild isolates of the same mating group that do not form chimaeric fruiting bodies with each other. These paired genes are both structurally similar to D. discoideum tgrB1/C1 pair, which is responsible for clonal discrimination within that species, suggesting that these tgr genes constitute the species recognition system that has attained a level of precision capable of discriminating between clones within a species. Analysis of the available genome sequences of social amoebae revealed that such gene pairs exist only within the clade composed of species that produce precursors of sterile stalk cells (prestalk cells), suggesting concurrent evolution of a precise allorecognition system and a new 'worker' cell-type dedicated to transporting and supporting the reproductive cells.}, }
@article {pmid30538242, year = {2018}, author = {Higo, A and Kawashima, T and Borg, M and Zhao, M and López-Vidriero, I and Sakayama, H and Montgomery, SA and Sekimoto, H and Hackenberg, D and Shimamura, M and Nishiyama, T and Sakakibara, K and Tomita, Y and Togawa, T and Kunimoto, K and Osakabe, A and Suzuki, Y and Yamato, KT and Ishizaki, K and Nishihama, R and Kohchi, T and Franco-Zorrilla, JM and Twell, D and Berger, F and Araki, T}, title = {Transcription factor DUO1 generated by neo-functionalization is associated with evolution of sperm differentiation in plants.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5283}, pmid = {30538242}, issn = {2041-1723}, mesh = {Cell Differentiation ; Chlorophyta/classification/genetics/growth &amp; development/metabolism ; *Evolution, Molecular ; Germ Cells, Plant/*cytology/metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants/classification/genetics/*metabolism ; Transcription Factors/genetics/*metabolism ; }, abstract = {Evolutionary mechanisms underlying innovation of cell types have remained largely unclear. In multicellular eukaryotes, the evolutionary molecular origin of sperm differentiation is unknown in most lineages. Here, we report that in algal ancestors of land plants, changes in the DNA-binding domain of the ancestor of the MYB transcription factor DUO1 enabled the recognition of a new cis-regulatory element. This event led to the differentiation of motile sperm. After neo-functionalization, DUO1 acquired sperm lineage-specific expression in the common ancestor of land plants. Subsequently the downstream network of DUO1 was rewired leading to sperm with distinct morphologies. Conjugating green algae, a sister group of land plants, accumulated mutations in the DNA-binding domain of DUO1 and lost sperm differentiation. Our findings suggest that the emergence of DUO1 was the defining event in the evolution of sperm differentiation and the varied modes of sexual reproduction in the land plant lineage.}, }
@article {pmid30532226, year = {2018}, author = {Shan, M and Dai, D and Vudem, A and Varner, JD and Stroock, AD}, title = {Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors.}, journal = {PLoS computational biology}, volume = {14}, number = {12}, pages = {e1006584}, doi = {10.1371/journal.pcbi.1006584}, pmid = {30532226}, issn = {1553-7358}, mesh = {Cell Line, Tumor ; Cell Proliferation ; Citric Acid Cycle/physiology ; Glucose/metabolism ; Glutamine/*metabolism ; Glycolysis/*physiology ; Humans ; Kinetics ; Lactic Acid/metabolism ; Metabolic Networks and Pathways/physiology ; Metabolome ; Neoplasms/metabolism ; Oxygen/metabolism ; Tumor Microenvironment/*physiology ; }, abstract = {Cancer metabolism has received renewed interest as a potential target for cancer therapy. In this study, we use a multi-scale modeling approach to interrogate the implications of three metabolic scenarios of potential clinical relevance: the Warburg effect, the reverse Warburg effect and glutamine addiction. At the intracellular level, we construct a network of central metabolism and perform flux balance analysis (FBA) to estimate metabolic fluxes; at the cellular level, we exploit this metabolic network to calculate parameters for a coarse-grained description of cellular growth kinetics; and at the multicellular level, we incorporate these kinetic schemes into the cellular automata of an agent-based model (ABM), iDynoMiCS. This ABM evaluates the reaction-diffusion of the metabolites, cellular division and motion over a simulation domain. Our multi-scale simulations suggest that the Warburg effect provides a growth advantage to the tumor cells under resource limitation. However, we identify a non-monotonic dependence of growth rate on the strength of glycolytic pathway. On the other hand, the reverse Warburg scenario provides an initial growth advantage in tumors that originate deeper in the tissue. The metabolic profile of stromal cells considered in this scenario allows more oxygen to reach the tumor cells in the deeper tissue and thus promotes tumor growth at earlier stages. Lastly, we suggest that glutamine addiction does not confer a selective advantage to tumor growth with glutamine acting as a carbon source in the tricarboxylic acid (TCA) cycle, any advantage of glutamine uptake must come through other pathways not included in our model (e.g., as a nitrogen donor). Our analysis illustrates the importance of accounting explicitly for spatial and temporal evolution of tumor microenvironment in the interpretation of metabolic scenarios and hence provides a basis for further studies, including evaluation of specific therapeutic strategies that target metabolism.}, }
@article {pmid30532131, year = {2018}, author = {Khasin, M and Cahoon, RR and Nickerson, KW and Riekhof, WR}, title = {Molecular machinery of auxin synthesis, secretion, and perception in the unicellular chlorophyte alga Chlorella sorokiniana UTEX 1230.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0205227}, doi = {10.1371/journal.pone.0205227}, pmid = {30532131}, issn = {1932-6203}, mesh = {Biological Transport, Active/physiology ; Chlorella/genetics/*metabolism ; *Evolution, Molecular ; Indoleacetic Acids/*metabolism ; Plant Proteins/genetics/*metabolism ; Receptors, Cell Surface/genetics/*metabolism ; Signal Transduction/*physiology ; }, abstract = {Indole-3-acetic acid is a ubiquitous small molecule found in all domains of life. It is the predominant and most active auxin in seed plants, where it coordinates a variety of complex growth and development processes. The potential origin of auxin signaling in algae remains a matter of some controversy. In order to clarify the evolutionary context of algal auxin signaling, we undertook a genomic survey to assess whether auxin acts as a signaling molecule in the emerging model chlorophyte Chlorella sorokiniana UTEX 1230. C. sorokiniana produces the auxin indole-3-acetic acid (IAA), which was present in both the cell pellet and in the supernatant at a concentration of ~ 1 nM, and its genome encodes orthologs of genes related to auxin synthesis, transport, and signaling in higher plants. Candidate orthologs for the canonical AUX/IAA signaling pathway were not found; however, auxin-binding protein 1 (ABP1), an alternate auxin receptor, is present and highly conserved at essential auxin binding and zinc coordinating residues. Additionally, candidate orthologs for PIN proteins, responsible for intercellular, vectorial auxin transport in higher plants, were not found, but PILs (PIN-Like) proteins, a recently discovered family that mediates intracellular auxin transport, were identified. The distribution of auxin related gene in this unicellular chlorophyte demonstrates that a core suite of auxin signaling components was present early in the evolution of plants. Understanding the simplified auxin signaling pathways in chlorophytes will aid in understanding phytohormone signaling and crosstalk in seed plants, and in understanding the diversification and integration of developmental signals during the evolution of multicellular plants.}, }
@article {pmid30520011, year = {2019}, author = {Rebolleda-Gómez, M and Travisano, M}, title = {Adaptation, chance, and history in experimental evolution reversals to unicellularity.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {1}, pages = {73-83}, doi = {10.1111/evo.13654}, pmid = {30520011}, issn = {1558-5646}, support = {//John Templeton Foundation/ ; 1051115//Division of Environmental Biology/ ; }, abstract = {Evolution is often deemed irreversible. The evolution of complex traits that require many mutations makes their reversal unlikely. Even in simpler traits, reversals might become less likely as neutral or beneficial mutations, with deleterious effects in the ancestral context, become fixed in the novel background. This is especially true in changes that involve large reorganizations of the organism and its interactions with the environment. The evolution of multicellularity involves the reorganization of previously autonomous cells into a more complex organism; despite the complexity of this change, single cells have repeatedly evolved from multicellular ancestors. These repeated reversals to unicellularity undermine the generality of Dollo's law. In this article, we evaluated the dynamics of reversals to unicellularity from recently evolved multicellular phenotypes of the brewers yeast Saccharomyces cerevisae. Even though multicellularity in this system evolved recently, it involves the evolution of new levels of selection. Strong selective pressures against multicellularity lead to rapid reversibility to single cells in all of our replicate lines, whereas counterselection favoring multicellularity led to minimal reductions to the rates of reversal. History and chance played an important role in the tempo and mode of reversibility, highlighting the interplay of deterministic and stochastic events in evolutionary reversals.}, }
@article {pmid30519187, year = {2018}, author = {Fux, JE and Mehta, A and Moffat, J and Spafford, JD}, title = {Eukaryotic Voltage-Gated Sodium Channels: On Their Origins, Asymmetries, Losses, Diversification and Adaptations.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {1406}, pmid = {30519187}, issn = {1664-042X}, abstract = {The appearance of voltage-gated, sodium-selective channels with rapid gating kinetics was a limiting factor in the evolution of nervous systems. Two rounds of domain duplications generated a common 24 transmembrane segment (4 × 6 TM) template that is shared amongst voltage-gated sodium (Nav1 and Nav2) and calcium channels (Cav1, Cav2, and Cav3) and leak channel (NALCN) plus homologs from yeast, different single-cell protists (heterokont and unikont) and algae (green and brown). A shared architecture in 4 × 6 TM channels include an asymmetrical arrangement of extended extracellular L5/L6 turrets containing a 4-0-2-2 pattern of cysteines, glycosylated residues, a universally short III-IV cytoplasmic linker and often a recognizable, C-terminal PDZ binding motif. Six intron splice junctions are conserved in the first domain, including a rare U12-type of the minor spliceosome provides support for a shared heritage for sodium and calcium channels, and a separate lineage for NALCN. The asymmetrically arranged pores of 4x6 TM channels allows for a changeable ion selectivity by means of a single lysine residue change in the high field strength site of the ion selectivity filter in Domains II or III. Multicellularity and the appearance of systems was an impetus for Nav1 channels to adapt to sodium ion selectivity and fast ion gating. A non-selective, and slowly gating Nav2 channel homolog in single cell eukaryotes, predate the diversification of Nav1 channels from a basal homolog in a common ancestor to extant cnidarians to the nine vertebrate Nav1.x channel genes plus Nax. A close kinship between Nav2 and Nav1 homologs is evident in the sharing of most (twenty) intron splice junctions. Different metazoan groups have lost their Nav1 channel genes altogether, while vertebrates rapidly expanded their gene numbers. The expansion in vertebrate Nav1 channel genes fills unique functional niches and generates overlapping properties contributing to redundancies. Specific nervous system adaptations include cytoplasmic linkers with phosphorylation sites and tethered elements to protein assemblies in First Initial Segments and nodes of Ranvier. Analogous accessory beta subunit appeared alongside Nav1 channels within different animal sub-phyla. Nav1 channels contribute to pace-making as persistent or resurgent currents, the former which is widespread across animals, while the latter is a likely vertebrate adaptation.}, }
@article {pmid30518860, year = {2018}, author = {Rosental, B and Kowarsky, M and Seita, J and Corey, DM and Ishizuka, KJ and Palmeri, KJ and Chen, SY and Sinha, R and Okamoto, J and Mantalas, G and Manni, L and Raveh, T and Clarke, DN and Tsai, JM and Newman, AM and Neff, NF and Nolan, GP and Quake, SR and Weissman, IL and Voskoboynik, A}, title = {Complex mammalian-like haematopoietic system found in a colonial chordate.}, journal = {Nature}, volume = {564}, number = {7736}, pages = {425-429}, doi = {10.1038/s41586-018-0783-x}, pmid = {30518860}, issn = {1476-4687}, support = {T32 AI007290/AI/NIAID NIH HHS/United States ; R01 AG037968/AG/NIA NIH HHS/United States ; T32 AR050942/AR/NIAMS NIH HHS/United States ; T32HL120824-03/HL/NHLBI NIH HHS/United States ; R01 GM100315/GM/NIGMS NIH HHS/United States ; R56 AI089968/AI/NIAID NIH HHS/United States ; T32 HL120824/HL/NHLBI NIH HHS/United States ; 5T32AI07290-28/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cell Differentiation ; Cell Lineage ; Cytotoxicity, Immunologic ; Female ; Flow Cytometry ; *Hematopoiesis ; Hematopoietic Stem Cells/cytology/immunology ; Hematopoietic System/*cytology ; Immunity, Cellular ; Isoantigens/immunology ; Male ; Mammals/anatomy &amp; histology/*blood ; Myeloid Cells/cytology/immunology ; Phagocytosis/immunology ; *Phylogeny ; Stem Cell Niche ; Transcriptome/genetics ; Urochordata/anatomy &amp; histology/*cytology/genetics/immunology ; }, abstract = {Haematopoiesis is an essential process that evolved in multicellular animals. At the heart of this process are haematopoietic stem cells (HSCs), which are multipotent and self-renewing, and generate the entire repertoire of blood and immune cells throughout an animal's life1. Although there have been comprehensive studies on self-renewal, differentiation, physiological regulation and niche occupation in vertebrate HSCs, relatively little is known about the evolutionary origin and niches of these cells. Here we describe the haematopoietic system of Botryllus schlosseri, a colonial tunicate that has a vasculature and circulating blood cells, and interesting stem-cell biology and immunity characteristics2-8. Self-recognition between genetically compatible B. schlosseri colonies leads to the formation of natural parabionts with shared circulation, whereas incompatible colonies reject each other3,4,7. Using flow cytometry, whole-transcriptome sequencing of defined cell populations and diverse functional assays, we identify HSCs, progenitors, immune effector cells and an HSC niche, and demonstrate that self-recognition inhibits allospecific cytotoxic reactions. Our results show that HSC and myeloid lineage immune cells emerged in a common ancestor of tunicates and vertebrates, and also suggest that haematopoietic bone marrow and the B. schlosseri endostyle niche evolved from a common origin.}, }
@article {pmid30510177, year = {2018}, author = {Kayser, J and Schreck, CF and Gralka, M and Fusco, D and Hallatschek, O}, title = {Collective motion conceals fitness differences in crowded cellular populations.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {1}, pages = {125-134}, doi = {10.1038/s41559-018-0734-9}, pmid = {30510177}, issn = {2397-334X}, support = {R01 GM115851/GM/NIGMS NIH HHS/United States ; }, mesh = {Biofilms/*growth &amp; development ; *Biological Evolution ; Biomechanical Phenomena ; Humans ; *Microbiota/genetics ; *Models, Biological ; Mutation ; Saccharomyces cerevisiae/genetics/*growth &amp; development ; }, abstract = {Many cellular populations are tightly packed, such as microbial colonies and biofilms, or tissues and tumours in multicellular organisms. The movement of one cell in these crowded assemblages requires motion of others, so that cell displacements are correlated over many cell diameters. Whenever movement is important for survival or growth, these correlated rearrangements could couple the evolutionary fate of different lineages. However, little is known about the interplay between mechanical forces and evolution in dense cellular populations. Here, by tracking slower-growing clones at the expanding edge of yeast colonies, we show that the collective motion of cells prevents costly mutations from being weeded out rapidly. Joint pushing by neighbouring cells generates correlated movements that suppress the differential displacements required for selection to act. This mechanical screening of fitness differences allows slower-growing mutants to leave more descendants than expected under non-mechanical models, thereby increasing their chance for evolutionary rescue. Our work suggests that, in crowded populations, cells cooperate with surrounding neighbours through inevitable mechanical interactions. This effect has to be considered when predicting evolutionary outcomes, such as the emergence of drug resistance or cancer evolution.}, }
@article {pmid30500812, year = {2018}, author = {Medina-Castellanos, E and Villalobos-Escobedo, JM and Riquelme, M and Read, ND and Abreu-Goodger, C and Herrera-Estrella, A}, title = {Danger signals activate a putative innate immune system during regeneration in a filamentous fungus.}, journal = {PLoS genetics}, volume = {14}, number = {11}, pages = {e1007390}, doi = {10.1371/journal.pgen.1007390}, pmid = {30500812}, issn = {1553-7404}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Biomarkers ; Calcium/metabolism ; Gene Expression Regulation, Fungal ; *Host-Pathogen Interactions ; Hyphae ; *Immunity, Innate ; Mycoses/immunology/*microbiology ; *Regeneration ; *Signal Transduction ; Trichoderma/*physiology ; }, abstract = {The ability to respond to injury is a biological process shared by organisms of different kingdoms that can even result in complete regeneration of a part or structure that was lost. Due to their immobility, multicellular fungi are prey to various predators and are therefore constantly exposed to mechanical damage. Nevertheless, our current knowledge of how fungi respond to injury is scarce. Here we show that activation of injury responses and hyphal regeneration in the filamentous fungus Trichoderma atroviride relies on the detection of two danger or alarm signals. As an early response to injury, we detected a transient increase in cytosolic free calcium ([Ca2+]c) that was promoted by extracellular ATP, and which is likely regulated by a mechanism of calcium-induced calcium-release. In addition, we demonstrate that the mitogen activated protein kinase Tmk1 plays a key role in hyphal regeneration. Calcium- and Tmk1-mediated signaling cascades activated major transcriptional changes early following injury, including induction of a set of regeneration associated genes related to cell signaling, stress responses, transcription regulation, ribosome biogenesis/translation, replication and DNA repair. Interestingly, we uncovered the activation of a putative fungal innate immune response, including the involvement of HET domain genes, known to participate in programmed cell death. Our work shows that fungi and animals share danger-signals, signaling cascades, and the activation of the expression of genes related to immunity after injury, which are likely the result of convergent evolution.}, }
@article {pmid30498215, year = {2018}, author = {Billerbeck, S and Brisbois, J and Agmon, N and Jimenez, M and Temple, J and Shen, M and Boeke, JD and Cornish, VW}, title = {A scalable peptide-GPCR language for engineering multicellular communication.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5057}, pmid = {30498215}, issn = {2041-1723}, support = {R01 AI110794/AI/NIAID NIH HHS/United States ; S10 RR027050/RR/NCRR NIH HHS/United States ; T32 GM007308/GM/NIGMS NIH HHS/United States ; T32 GM066704/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology/methods ; Peptides/genetics/*metabolism ; Protein Binding ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Signal Transduction ; Synthetic Biology/methods ; }, abstract = {Engineering multicellularity is one of the next breakthroughs for Synthetic Biology. A key bottleneck to building multicellular systems is the lack of a scalable signaling language with a large number of interfaces that can be used simultaneously. Here, we present a modular, scalable, intercellular signaling language in yeast based on fungal mating peptide/G-protein-coupled receptor (GPCR) pairs harnessed from nature. First, through genome-mining, we assemble 32 functional peptide-GPCR signaling interfaces with a range of dose-response characteristics. Next, we demonstrate that these interfaces can be combined into two-cell communication links, which serve as assembly units for higher-order communication topologies. Finally, we show 56 functional, two-cell links, which we use to assemble three- to six-member communication topologies and a three-member interdependent community. Importantly, our peptide-GPCR language is scalable and tunable by genetic encoding, requires minimal component engineering, and should be massively scalable by further application of our genome mining pipeline or directed evolution.}, }
@article {pmid30484227, year = {2018}, author = {Trosko, JE}, title = {The Role of the Mitochondria in the Evolution of Stem Cells, Including MUSE Stem Cells and Their Biology.}, journal = {Advances in experimental medicine and biology}, volume = {1103}, number = {}, pages = {131-152}, doi = {10.1007/978-4-431-56847-6_7}, pmid = {30484227}, issn = {0065-2598}, abstract = {From the transition of single-cell organisms to multicellularity of metazoans, evolutionary pressures selected new genes and phenotypes to cope with the oxygenation of the Earth's environment, especially via the symbiotic acquisition of the mitochondrial organelle. There were many new genes and phenotypes that appeared, namely, stem cells, low-oxygen-micro-environments to house these genes (&quot;niches&quot;), new epigenetic mechanisms to regulate , selectively, the gene repertoire to control proliferation, differentiation, apoptosis, senescence and DNA protection mechanisms, including antioxidant genes and DNA repair. This transition required a critical regulation of the metabolism of glucose to produce energy for both the stem cell quiescent state and the energy-requiring differentiated state. While the totipotent-, embryonic-, pluripotent-, and a few adult organ-specific stem cells were recognized, only relatively recently, because of the isolation of somatic cell nuclear transfer (SCNT) stem cells and &quot;induced pluripotent stem&quot; cells, challenges to the origin of these &quot;iPS&quot; cells have been made. The isolation and characterization of human MUSE stem cells and more adult organ-specific adult stem cells have indicated that these MUSE cells have many shared characteristics of the &quot;iPS&quot; cells, yet they do not form teratomas but can give rise to the trigeminal cell layers. While the MUSE cells are a subset of human fibroblastic cells, they have not been characterized, yet, for the mitochondrial metabolic genes, either in the stem cell state or during their differentiation processes. A description of other human adult stem cells will be made to set future studies of how the MUSE stem cells compare to all other stem cells.}, }
@article {pmid30478288, year = {2019}, author = {Pollier, J and Vancaester, E and Kuzhiumparambil, U and Vickers, CE and Vandepoele, K and Goossens, A and Fabris, M}, title = {A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis.}, journal = {Nature microbiology}, volume = {4}, number = {2}, pages = {226-233}, doi = {10.1038/s41564-018-0305-5}, pmid = {30478288}, issn = {2058-5276}, mesh = {Biosynthetic Pathways ; Coenzymes ; Diatoms/enzymology/genetics/metabolism ; Eukaryota/classification/*enzymology/genetics/metabolism ; Gene Expression ; Genetic Complementation Test ; Membrane Proteins/chemistry/genetics/metabolism ; Mixed Function Oxygenases/chemistry/*genetics/*metabolism ; Phylogeny ; Protein Conformation ; Saccharomyces cerevisiae/drug effects/enzymology/genetics/metabolism ; Squalene/analogs &amp; derivatives/metabolism ; Squalene Monooxygenase/chemistry/genetics/metabolism ; Steroids/*biosynthesis ; Terbinafine/pharmacology ; }, abstract = {Steroids are essential triterpenoid molecules that are present in all eukaryotes and modulate the fluidity and flexibility of cell membranes. Steroids also serve as signalling molecules that are crucial for growth, development and differentiation of multicellular organisms1-3. The steroid biosynthetic pathway is highly conserved and is key in eukaryote evolution4-7. The flavoprotein squalene epoxidase (SQE) catalyses the first oxygenation reaction in this pathway and is rate limiting. However, despite its conservation in animals, plants and fungi, several phylogenetically widely distributed eukaryote genomes lack an SQE-encoding gene7,8. Here, we discovered and characterized an alternative SQE (AltSQE) belonging to the fatty acid hydroxylase superfamily. AltSQE was identified through screening of a gene library of the diatom Phaeodactylum tricornutum in a SQE-deficient yeast. In accordance with its divergent protein structure and need for cofactors, we found that AltSQE is insensitive to the conventional SQE inhibitor terbinafine. AltSQE is present in many eukaryotic lineages but is mutually exclusive with SQE and shows a patchy distribution within monophyletic clades. Our discovery provides an alternative element for the conserved steroid biosynthesis pathway, raises questions about eukaryote metabolic evolution and opens routes to develop selective SQE inhibitors to control hazardous organisms.}, }
@article {pmid30473004, year = {2018}, author = {Gruenheit, N and Parkinson, K and Brimson, CA and Kuwana, S and Johnson, EJ and Nagayama, K and Llewellyn, J and Salvidge, WM and Stewart, B and Keller, T and van Zon, W and Cotter, SL and Thompson, CRL}, title = {Cell Cycle Heterogeneity Can Generate Robust Cell Type Proportioning.}, journal = {Developmental cell}, volume = {47}, number = {4}, pages = {494-508.e4}, pmid = {30473004}, issn = {1878-1551}, support = {//Wellcome Trust/United Kingdom ; 095643/A/11/Z//Wellcome Trust/United Kingdom ; 101582/Z/13/Z//Wellcome Trust/United Kingdom ; 105610/Z/14/Z//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Cycle/*physiology ; Cell Differentiation/*physiology ; Cell Division/*physiology ; Cell Lineage/physiology ; Dictyostelium/*metabolism ; Spores, Fungal/metabolism ; }, abstract = {Cell-cell heterogeneity can facilitate lineage choice during embryonic development because it primes cells to respond to differentiation cues. However, remarkably little is known about the origin of heterogeneity or whether intrinsic and extrinsic variation can be controlled to generate reproducible cell type proportioning seen in vivo. Here, we use experimentation and modeling in D. discoideum to demonstrate that population-level cell cycle heterogeneity can be optimized to generate robust cell fate proportioning. First, cell cycle position is quantitatively linked to responsiveness to differentiation-inducing signals. Second, intrinsic variation in cell cycle length ensures cells are randomly distributed throughout the cell cycle at the onset of multicellular development. Finally, extrinsic perturbation of optimal cell cycle heterogeneity is buffered by compensatory changes in global signal responsiveness. These studies thus illustrate key regulatory principles underlying cell-cell heterogeneity optimization and the generation of robust and reproducible fate choice in development.}, }
@article {pmid30465731, year = {2018}, author = {Beji, O and Adouani, N and Poncin, S and Hamdi, M and Li, HZ}, title = {Mineral pollutants removal through immobilized microalgae-bacterial flocs in a multitrophic microreactor.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-31}, doi = {10.1080/09593330.2018.1551939}, pmid = {30465731}, issn = {1479-487X}, abstract = {Microalgae-bacterial flocs (MaB-flocs) immobilization technique using polyvinyl alcohol (PVA) crosslinked with sodium alginate represent a novel approach for sustainable pollutants removal. The present work was performed to evaluate the performance of a multitrophic batch reactor at microscale for treating two synthetic wastewater solutions prepared with two different initial Chemical Oxygen Demand (COD): 200 mg.L-1 and 450 mg.L-1, respectively. Three MaB-flocs concentrations were entrapped into PVA-alginate beads: C1 (2%, v/v), C2 (5%, v/v) and C3 (10%, v/v), without O2 supply, during three periods 2, 4 and 6 days of batch incubation. PVA-alginate beads containing the highest concentration C3 of MaB-flocs improved the performance of the microreactor to remove significantly NH4+ and PO43- of about 61% and 82%, respectively, from wastewater more than two other concentrations used. This result confirms that C3 of MaB-flocs displays not only a good potential for nutrients removals but also the highest MaB-flocs morphological progression after 6 days of treatment with the highest COD of 450 mg.L-1. The feasibility of the PVA-alginate for cells immobilization, investigated through microscopy analysis, reveals that the evolution of multicellularity in MaB-flocs, for all experiments.}, }
@article {pmid30458131, year = {2018}, author = {Titus, MA and Goodson, HV}, title = {Developing Evolutionary Cell Biology.}, journal = {Developmental cell}, volume = {47}, number = {4}, pages = {395-396}, doi = {10.1016/j.devcel.2018.11.006}, pmid = {30458131}, issn = {1878-1551}, mesh = {Animals ; Biological Evolution ; *Choanoflagellata ; *Phylogeny ; Septins ; Transfection ; }, abstract = {Recent advances in both phylogenetic comparisons and the development of experimentally tractable organisms, in the growing field of evolutionary cell biology, pave the way for gaining a molecular understanding of the development of multicellularity in the animal lineage.}, }
@article {pmid30445510, year = {2019}, author = {Saxena, AS 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 = {36}, number = {2}, pages = {239-251}, doi = {10.1093/molbev/msy213}, pmid = {30445510}, issn = {1537-1719}, support = {R01 GM072639/GM/NIGMS NIH HHS/United States ; R01 GM107227/GM/NIGMS NIH HHS/United States ; }, 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 an 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. &quot;First-order MA&quot; (O1MA) lines maintained under minimal selection for ∼250 generations were divided into high-fitness and low-fitness groups and sets of &quot;second-order MA&quot; (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. Approximately 90% of the variance in standing nucleotide variation is explained by mutability. Total mutation rate increased in the O2MA lines, as predicted by the &quot;drift barrier&quot; 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 = {2019}, 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 = {Epstein-Barr Virus Infection of Cell Lines Derived from Diffuse Large B-Cell Lymphomas Alters MicroRNA Loading of the Ago2 Complex.}, journal = {Journal of virology}, volume = {93}, number = {3}, 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 DLBCL (ABC-DLBCL) and germinal center B-cell DLBCL (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 microRNAs (miRNAs) in EBV-negative ABC-DLBCL and GCB-DLBCL cell lines and their EBV-infected counterparts. In parallel, total miRNA profiles of these cells were determined to capture the cellular miRNA profile for comparison with the functionally active profile. Selected miRNAs with differential abundances were validated using real-time quantitative PCR (RT-qPCR) and Northern blotting. We found 6 miRNAs with differential abundances (2 upregulated and 4 downregulated miRNAs) between EBV-negative and -positive ABC-DLBCL cells and 12 miRNAs with differential abundances (3 upregulated and 9 downregulated miRNAs) between EBV-negative and -positive GCB-DLBCL cells. Eight and twelve miRNAs were confirmed using RT-qPCR in ABC-DLBCL and GCB-DLBCL cells, respectively. Selected miRNAs were analyzed in additional type I/II versus type III EBV latency DLBCL cell lines. Furthermore, upregulation of miR-221-3p and downregulation of let7c-5p in ABC-DLBCL cells and upregulation of miR-363-3p and downregulation of miR-423-5p in GCB-DLBCL cells were verified using RIP-Northern blotting. Our comprehensive sequence analysis of the DLBCL miRNA profiles identified sets of deregulated miRNAs by Ago2-RIP-seq. Our Ago2-IP-seq miRNA profile could be considered an important data set for the detection of deregulated functionally active miRNAs in DLBCLs and could possibly lead to the identification of miRNAs as biomarkers for the classification of DLBCLs 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 mRNA. MicroRNAs are tethered to their target mRNAs by &quot;Argonaute&quot; proteins. Here we compared the overall miRNA content of the Ago2 complex by differential loading 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 not only changes the overall content of miRNAs but also influences the expression of proteins by affecting the Ago complexes.}, }
@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}, support = {NE/K006029/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 202769/Z/16/Z//Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Biological/physiology ; Adaptation, Physiological/*physiology ; Animals ; Biological Evolution ; Computer Simulation ; Erythrocytes/parasitology ; Host-Parasite Interactions ; Malaria/*parasitology ; Models, Theoretical ; Parasites ; Plasmodium/*physiology ; Plasmodium chabaudi/physiology ; Reproduction/physiology ; Reproduction, Asexual/physiology ; }, 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 {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}, 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 {pmid30415103, year = {2018}, author = {Schuler, GA and Tice, AK and Pearce, RA and Foreman, E and Stone, J and Gammill, S and Willson, JD and Reading, C and Silberman, JD and Brown, MW}, title = {Phylogeny and Classification of Novel Diversity in Sainouroidea (Cercozoa, Rhizaria) Sheds Light on a Highly Diverse and Divergent Clade.}, journal = {Protist}, volume = {169}, number = {6}, pages = {853-874}, doi = {10.1016/j.protis.2018.08.002}, pmid = {30415103}, issn = {1618-0941}, mesh = {Cercozoa/*classification/cytology/genetics/*isolation &amp; purification ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Environmental Microbiology ; Microscopy ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Sainouroidea is a molecularly diverse clade of cercozoan flagellates and amoebae in the eukaryotic supergroup Rhizaria. Previous 18S rDNA environmental sequencing of globally collected fecal and soil samples revealed great diversity and high sequence divergence in the Sainouroidea. However, a very limited amount of this diversity has been observed or described. The two described genera of amoebae in this clade are Guttulinopsis, which displays aggregative multicellularity, and Rosculus, which does not. Although the identity of Guttulinopsis is straightforward due to the multicellular fruiting bodies they form, the same is not true for Rosculus, and the actual identity of the original isolate is unclear. Here we isolated amoebae with morphologies like that of Guttulinopsis and Rosculus from many environments and analyzed them using 18S rDNA sequencing, light microscopy, and transmission electron microscopy. We define a molecular species concept for Sainouroidea that resulted in the description of 4 novel genera and 12 novel species of naked amoebae. Aggregative fruiting is restricted to the genus Guttulinopsis, but other than this there is little morphological variation amongst these taxa. Taken together, simple identification of these amoebae is problematic and potentially unresolvable without the 18S rDNA sequence.}, }
@article {pmid30410727, year = {2018}, author = {Morris, JJ}, title = {What is the hologenome concept of evolution?.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {}, pmid = {30410727}, issn = {2046-1402}, mesh = {Animals ; *Biological Evolution ; Biota ; Genome ; Humans ; Microbiota/*genetics ; Phenotype ; Selection, Genetic ; }, 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}, pmid = {30410109}, issn = {2045-2322}, support = {SC2 AI116566/AI/NIAID NIH HHS/United States ; }, 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 = {115}, number = {47}, pages = {E11053-E11060}, pmid = {30404915}, issn = {1091-6490}, support = {P01 CA042063/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; *Cell Physiological Phenomena ; *Computer Simulation ; Humans ; *Models, Biological ; Protein Domains/physiology ; Proteins/metabolism ; }, 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 = {2019}, 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 = {93}, number = {3}, 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, in which 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. In this study, we used a recently isolated DNA virus of Drosophila melanogaster, Kallithea virus (KV; family Nudiviridae), to probe known antiviral immune responses and virus evasion tactics in the context of DNA virus infection. We found that fly mutants for RNA interference and immune deficiency (Imd), but not Toll, pathways are more susceptible to Kallithea virus infection. We identified 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 found that Kallithea virus gp83 inhibits Toll signalling through the regulation of NF-κB transcription factors. Furthermore, we found that gp83 of the closely related Drosophila innubila nudivirus (DiNV) suppresses D. melanogaster Toll signalling, suggesting an evolutionarily 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 Coevolution 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 immunosuppression 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 RNA interference (RNAi) and Imd pathways. We found that KV suppresses the Toll pathway and identified gp83 as a KV-encoded protein that underlies this suppression. This immunosuppressive ability is conserved in another nudivirus, suggesting that 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 they 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}, pmid = {30396330}, issn = {1741-7007}, mesh = {Animals ; Computational Biology ; *Dimerization ; *Evolution, Molecular ; *Genes, Homeobox ; Phylogeny ; Plants/*genetics ; Transcription Factors/chemistry/*genetics ; }, 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 = {2019}, 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 = {9}, number = {1}, pages = {61-71}, doi = {10.1534/g3.118.200797}, pmid = {30389796}, issn = {2160-1836}, mesh = {Animals ; Copper/toxicity ; Daphnia/drug effects/*genetics ; Genetic Fitness/drug effects/*genetics ; Genome/*drug effects ; Mutation/drug effects ; Mutation Accumulation ; Mutation Rate ; Nickel/toxicity ; Reproduction/*drug effects/genetics ; Sequence Deletion/drug effects ; }, 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}, pmid = {30386324}, issn = {1664-3224}, support = {R01 AI131634/AI/NIAID NIH HHS/United States ; R01 AI134040/AI/NIAID NIH HHS/United States ; R01 DK113790/DK/NIDDK NIH HHS/United States ; R56 AI124691/AI/NIAID NIH HHS/United States ; }, 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 = {2019}, 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, BG}, title = {Unicellular ancestry and mechanisms of diversification of Goodpasture antigen-binding protein.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {3}, pages = {759-769}, doi = {10.1074/jbc.RA118.006225}, pmid = {30377252}, issn = {1083-351X}, support = {R01 DK018381/DK/NIDDK NIH HHS/United States ; R25 DK096999/DK/NIDDK NIH HHS/United States ; }, mesh = {Basement Membrane/metabolism ; *Evolution, Molecular ; Humans ; Isoenzymes/genetics/metabolism ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; }, abstract = {The emergence of the basement membrane (BM), a specialized form of extracellular matrix, was essential in the unicellular transition to multicellularity. However, the mechanism is unknown. Goodpasture antigen-binding protein (GPBP), a BM 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 that is further enhanced by membrane-bound GPBP-3 in mammalians, whereas GPBP-2 retained intracellular function. Moreover, GPBP-2 possesses a dual intracellular/extracellular function in cnidarians, an early nonbilaterian 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 {pmid30368592, year = {2019}, 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 = {256}, number = {3}, pages = {585-599}, 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 = {}, pmid = {30362942}, issn = {2050-084X}, support = {Discovery grant//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; Epistasis, Genetic ; Light ; Rhodopsin/genetics ; Selection, Genetic ; *Vertebrates ; Vision, Ocular/*physiology ; }, 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}, 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/ ; }, mesh = {Dictyostelium/*cytology/*genetics/metabolism ; Gene Expression Regulation ; Gene Ontology ; Metabolic Networks and Pathways/genetics ; RNA, Protozoan/*genetics ; *Sequence Analysis, RNA ; Transcription Factors/genetics ; }, 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 {pmid30339672, year = {2018}, author = {Crombie, TA and Saber, S and Saxena, AS and Egan, R and Baer, CF}, title = {Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0201507}, pmid = {30339672}, issn = {1932-6203}, support = {R01 GM107227/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Automation ; Biological Evolution ; Caenorhabditis elegans/*genetics/*physiology ; *Genetic Fitness ; Genotype ; Green Fluorescent Proteins/metabolism ; Models, Biological ; Models, Statistical ; Reproducibility of Results ; Software ; }, abstract = {Organismal fitness is relevant in many contexts in biology. The most meaningful experimental measure of fitness is competitive fitness, when two or more entities (e.g., genotypes) are allowed to compete directly. In theory, competitive fitness is simple to measure: an experimental population is initiated with the different types in known proportions and allowed to evolve under experimental conditions to a predefined endpoint. In practice, there are several obstacles to obtaining robust estimates of competitive fitness in multicellular organisms, the most pervasive of which is simply the time it takes to count many individuals of different types from many replicate populations. Methods by which counting can be automated in high throughput are desirable, but for automated methods to be useful, the bias and technical variance associated with the method must be (a) known, and (b) sufficiently small relative to other sources of bias and variance to make the effort worthwhile. The nematode Caenorhabditis elegans is an important model organism, and the fitness effects of genotype and environmental conditions are often of interest. We report a comparison of three experimental methods of quantifying competitive fitness, in which wild-type strains are competed against GFP-marked competitors under standard laboratory conditions. Population samples were split into three replicates and counted (1) &quot;by eye&quot; from a saved image, (2) from the same image using CellProfiler image analysis software, and (3) with a large particle flow cytometer (a &quot;worm sorter&quot;). From 720 replicate samples, neither the frequency of wild-type worms nor the among-sample variance differed significantly between the three methods. CellProfiler and the worm sorter provide at least a tenfold increase in sample handling speed with little (if any) bias or increase in variance.}, }
@article {pmid30336184, year = {2019}, author = {Miller, WB and Torday, JS and Baluška, F}, title = {Biological evolution as defense of 'self'.}, journal = {Progress in biophysics and molecular biology}, volume = {142}, number = {}, pages = {54-74}, 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 of 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 = {35}, number = {12}, pages = {2851-2861}, 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 {pmid30323207, year = {2018}, author = {Zumberge, JA and Love, GD and Cárdenas, P and Sperling, EA and Gunasekera, S and Rohrssen, M and Grosjean, E and Grotzinger, JP and Summons, RE}, title = {Demosponge steroid biomarker 26-methylstigmastane provides evidence for Neoproterozoic animals.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {11}, pages = {1709-1714}, doi = {10.1038/s41559-018-0676-2}, pmid = {30323207}, issn = {2397-334X}, mesh = {Animals ; *Biological Evolution ; Biomarkers/*analysis ; *Fossils ; Phylogeny ; Porifera/*chemistry ; Steroids/*analysis ; }, abstract = {Sterane biomarkers preserved in ancient sedimentary rocks hold promise for tracking the diversification and ecological expansion of eukaryotes. The earliest proposed animal biomarkers from demosponges (Demospongiae) are recorded in a sequence around 100 Myr long of Neoproterozoic-Cambrian marine sedimentary strata from the Huqf Supergroup, South Oman Salt Basin. This C30 sterane biomarker, informally known as 24-isopropylcholestane (24-ipc), possesses the same carbon skeleton as sterols found in some modern-day demosponges. However, this evidence is controversial because 24-ipc is not exclusive to demosponges since 24-ipc sterols are found in trace amounts in some pelagophyte algae. Here, we report a new fossil sterane biomarker that co-occurs with 24-ipc in a suite of late Neoproterozoic-Cambrian sedimentary rocks and oils, which possesses a rare hydrocarbon skeleton that is uniquely found within extant demosponge taxa. This sterane is informally designated as 26-methylstigmastane (26-mes), reflecting the very unusual methylation at the terminus of the steroid side chain. It is the first animal-specific sterane marker detected in the geological record that can be unambiguously linked to precursor sterols only reported from extant demosponges. These new findings strongly suggest that demosponges, and hence multicellular animals, were prominent in some late Neoproterozoic marine environments at least extending back to the Cryogenian period.}, }
@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}, 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 = {115}, number = {44}, pages = {E10333-E10341}, pmid = {30309963}, issn = {1091-6490}, mesh = {Actins/metabolism ; Animals ; Aquatic Organisms/metabolism/*physiology ; Cells, Cultured ; Epithelial Cells/metabolism/*physiology ; Epithelium/metabolism/*physiology ; Myosins/metabolism ; Placozoa/metabolism/*physiology ; }, 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}, mesh = {Animals ; *Biological Evolution ; Fossils/*anatomy &amp; histology ; Invertebrates/*anatomy &amp; histology/classification ; Phylogeny ; }, 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 = {54}, number = {6}, pages = {879-887}, 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}, 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 = {2019}, author = {Zhou, W and Gao, B and Zhu, S}, title = {Did cis- and trans-defensins derive from a common ancestor?.}, journal = {Immunogenetics}, volume = {71}, number = {1}, pages = {61-69}, 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}, 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 = {72}, number = {12}, pages = {2595-2607}, 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}, 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}, pmid = {30231028}, issn = {1932-6203}, mesh = {Base Sequence ; Coprinus/*genetics ; Fruiting Bodies, Fungal/*genetics ; Fungal Proteins/genetics ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Genomics ; High-Throughput Nucleotide Sequencing ; MicroRNAs/*genetics ; Phylogeny ; RNA, Fungal/*genetics ; Transcriptome ; }, 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}, 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 = {18}, number = {21-22}, 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}, 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 = {52}, number = {}, pages = {397-419}, doi = {10.1146/annurev-genet-120417-031501}, pmid = {30212236}, issn = {1545-2948}, 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 ; }, 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.}, }
@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}, 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}, 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}, 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}, support = {BB/M021610/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Catalysis ; Cations, Monovalent/metabolism ; Cell Membrane/*metabolism ; Coenzymes/*metabolism ; Diphosphates/metabolism ; Enzyme Assays/instrumentation/*methods ; Hydrolysis ; Models, Molecular ; Mutagenesis, Site-Directed ; Potassium/*metabolism ; Pyrophosphatases/chemistry/genetics/isolation &amp; purification/*metabolism ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Saccharomyces cerevisiae ; }, 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 = {173}, number = {}, pages = {73-82}, doi = {10.1016/j.biosystems.2018.08.005}, pmid = {30134151}, issn = {1872-8324}, mesh = {Algorithms ; Animals ; Biological Evolution ; *Cybernetics ; Developmental Biology/history ; Ecosystem ; *Embryonic Development ; Entropy ; History, 19th Century ; History, 20th Century ; Humans ; *Models, Biological ; Phenotype ; Thermodynamics ; }, 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}, 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 = {}, 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}, pmid = {30102347}, issn = {1759-6653}, mesh = {Chlorophyta/genetics ; DNA, Algal/*genetics ; Evolution, Molecular ; *Genome, Plastid ; Plastids/genetics ; Sequence Analysis, DNA ; Volvox/*genetics ; }, 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}, pmid = {30089142}, issn = {1932-6203}, mesh = {Biological Evolution ; Cell Communication/*physiology ; Cell Differentiation/*physiology ; Cell Survival/physiology ; Chlorophyta/cytology/*physiology ; Fertility/*physiology ; Germ Cells, Plant/physiology ; *Models, Biological ; }, 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}, mesh = {Arabidopsis/genetics ; Arabidopsis Proteins/*genetics ; Chromatin/genetics ; Epigenesis, Genetic/genetics ; Flowers/genetics ; Gene Expression Regulation, Plant/genetics ; Gene Silencing/*physiology ; Genes, Plant/*genetics ; Histones/genetics ; Polycomb Repressive Complex 1/genetics ; Polycomb Repressive Complex 2/genetics ; Polycomb-Group Proteins/*genetics ; }, 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}, 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}, 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 = {}, pmid = {30068565}, issn = {2046-2441}, mesh = {Animals ; Biological Evolution ; Cell Movement ; Cell Polarity ; Centrosome/*metabolism ; Cilia/*metabolism ; Planarians/*physiology ; }, 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 = {137}, number = {2}, pages = {197-206}, 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/ ; }, mesh = {*Adaptation, Biological ; Adaptation, Physiological/genetics ; Animals ; *Genetic Speciation ; Host-Parasite Interactions/genetics ; Microbiota ; Philosophy ; Plants ; Species Specificity ; *Symbiosis ; }, 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}, 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}, 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}, support = {1R01HD057974-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Body Size ; Drosophila melanogaster/*anatomy &amp; histology ; Female ; Male ; *Sex Characteristics ; }, 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}, pmid = {30059538}, issn = {1553-7404}, support = {WT095831//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Annelida/genetics/immunology/microbiology ; Argonaute Proteins/genetics ; Cnidaria/genetics/immunology/microbiology ; DNA Transposable Elements/genetics ; Echinodermata/genetics/immunology/microbiology ; Host Microbial Interactions/*genetics/immunology ; *Metagenomics ; Mollusca/genetics/immunology/microbiology ; Phaeophyta/genetics/immunology/microbiology ; Phylogeny ; Porifera/genetics/immunology/microbiology ; RNA Interference/*immunology ; RNA Viruses/genetics/*immunology ; RNA, Small Interfering/genetics/metabolism ; RNA, Viral/*genetics/immunology ; Ribonuclease III/genetics ; Sequence Analysis, RNA ; }, 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 {pmid30033369, year = {2018}, author = {Glass, DS and Riedel-Kruse, IH}, title = {A Synthetic Bacterial Cell-Cell Adhesion Toolbox for Programming Multicellular Morphologies and Patterns.}, journal = {Cell}, volume = {174}, number = {3}, pages = {649-658.e16}, doi = {10.1016/j.cell.2018.06.041}, pmid = {30033369}, issn = {1097-4172}, mesh = {Bacterial Physiological Phenomena ; Biological Evolution ; Cell Adhesion/genetics/*physiology ; Cell Differentiation/genetics/physiology ; Escherichia coli/genetics ; Gene Library ; Metabolic Engineering/*methods ; Metabolic Networks and Pathways ; Single-Domain Antibodies/genetics/immunology/physiology ; Synthetic Biology/*methods ; }, abstract = {Synthetic multicellular systems hold promise as models for understanding natural development of biofilms and higher organisms and as tools for engineering complex multi-component metabolic pathways and materials. However, such efforts require tools to adhere cells into defined morphologies and patterns, and these tools are currently lacking. Here, we report a 100% genetically encoded synthetic platform for modular cell-cell adhesion in Escherichia coli, which provides control over multicellular self-assembly. Adhesive selectivity is provided by a library of outer membrane-displayed nanobodies and antigens with orthogonal intra-library specificities, while affinity is controlled by intrinsic adhesin affinity, competitive inhibition, and inducible expression. We demonstrate the resulting capabilities for quantitative rational design of well-defined morphologies and patterns through homophilic and heterophilic interactions, lattice-like self-assembly, phase separation, differential adhesion, and sequential layering. Compatible with synthetic biology standards, this adhesion toolbox will enable construction of high-level multicellular designs and shed light on the evolutionary transition to multicellularity.}, }
@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}, 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 = {35}, number = {5-6}, pages = {361-367}, pmid = {29992410}, issn = {1573-7276}, mesh = {Carcinogenesis/*genetics ; Cell Proliferation/*genetics ; Disease Progression ; Humans ; Melanoma/*genetics/pathology ; Neoplasm Metastasis ; Tumor Microenvironment/*genetics ; }, 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}, pmid = {29966484}, issn = {1555-8584}, mesh = {Adaptation, Biological ; Biological Evolution ; Dictyostelium/genetics/*metabolism ; Gene Knockout Techniques ; Genome, Protozoan/genetics ; High-Throughput Nucleotide Sequencing ; MicroRNAs/analysis/*biosynthesis/genetics ; Oligonucleotide Probes/analysis/genetics/metabolism ; Promoter Regions, Genetic/genetics ; Protozoan Proteins/genetics/*metabolism ; RNA, Protozoan/analysis/*biosynthesis/genetics ; Ribonuclease III/genetics/*metabolism ; Transcription, Genetic ; }, 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}, pmid = {29942020}, issn = {2397-334X}, support = {309706//European Research Council/International ; }, mesh = {Animals ; *Biological Evolution ; Ctenophora/*cytology/genetics ; Placozoa/*cytology/genetics ; Porifera/*cytology/genetics ; Sequence Analysis, RNA ; Transcription, Genetic/*physiology ; }, 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}, mesh = {Animals ; Cell Differentiation/genetics/physiology ; Cell Plasticity/genetics/physiology ; Cell Transdifferentiation/genetics/physiology ; Gene Expression Profiling ; Homeostasis/genetics/*physiology ; Porifera/cytology/genetics/*physiology ; Regeneration/genetics/*physiology ; Reproduction/genetics/physiology ; Stem Cells/cytology/metabolism/*physiology ; }, 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}, 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}, 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/ ; }, mesh = {Animals ; Bacteria/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Humans ; Phylogeny ; Prokaryotic Cells/*metabolism ; }, 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 {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}, 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 {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}, 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}, mesh = {Animals ; *Biological Evolution ; Ctenophora/*physiology ; *Ecosystem ; *Life History Traits ; Porifera/*physiology ; }, 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 {pmid29885639, year = {2018}, author = {Rivera-Yoshida, N and Arias Del Angel, JA and Benítez, M}, title = {Microbial multicellular development: mechanical forces in action.}, journal = {Current opinion in genetics &amp; development}, volume = {51}, number = {}, pages = {37-45}, doi = {10.1016/j.gde.2018.05.006}, pmid = {29885639}, issn = {1879-0380}, mesh = {Bacteria/genetics/*growth &amp; development ; *Biological Evolution ; Cell Lineage/*genetics ; *Mechanical Phenomena ; Models, Biological ; }, abstract = {Multicellular development occurs in diverse microbial lineages and involves the complex interaction among biochemical, physical and ecological factors. We focus on the mechanical forces that appear to be relevant for the scale and material qualities of individual cells and small cellular conglomerates. We review the effects of such forces on the development of some paradigmatic microorganisms, as well as their overall consequences in multicellular structures. Microbes exhibiting multicellular development have been considered models for the evolutionary transition to multicellularity. Therefore, we discuss how comparative, integrative and dynamic approaches to the mechanical effects involved in microbial development can provide valuable insights into some of the principles behind the evolutionary transition to multicellularity.}, }
@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}, 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 ; }, mesh = {Actins/analysis/metabolism ; Animals ; Cell Adhesion ; Focal Adhesions/metabolism ; Models, Molecular ; Porifera/*cytology/metabolism/ultrastructure ; Protein Binding ; Protein Conformation ; Pseudopodia/metabolism/ultrastructure ; Talin/analysis/metabolism ; Vinculin/analysis/*metabolism ; }, 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}, 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 = {}, pmid = {29866913}, issn = {1471-2970}, mesh = {Aggression ; Animals ; *Biological Evolution ; *Host-Parasite Interactions ; Insecta/*parasitology/*physiology ; Reproduction ; Social Behavior ; }, 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}, mesh = {Actins/chemistry ; Amino Acid Motifs ; Animals ; Chromatin/metabolism ; Cluster Analysis ; Gene Expression Profiling ; *Gene Expression Regulation, Developmental ; Genome ; Genomics ; Neurons/*physiology ; Phylogeny ; *RNA ; Sea Anemones/genetics/*physiology ; Sequence Analysis, RNA ; Transcriptome ; Tubulin/chemistry ; }, 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 ; /HHMI/Howard Hughes Medical Institute/United States ; P50 GM081879/GM/NIGMS NIH HHS/United States ; R00 EB021030/EB/NIBIB NIH HHS/United States ; T32 GM008412/GM/NIGMS NIH HHS/United States ; //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 {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}, 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 {pmid29849168, year = {2018}, author = {Woo, C and An, C and Xu, S and Yi, SM and Yamamoto, N}, title = {Taxonomic diversity of fungi deposited from the atmosphere.}, journal = {The ISME journal}, volume = {12}, number = {8}, pages = {2051-2060}, pmid = {29849168}, issn = {1751-7370}, mesh = {*Air Microbiology ; Atmosphere ; Environmental Monitoring ; Fungi/*classification/genetics/*isolation &amp; purification ; Phylogeny ; Spores, Fungal/classification/genetics/isolation &amp; purification ; }, abstract = {Fungi release spores into the global atmosphere. The emitted spores are deposited to the surface of the Earth by sedimentation (dry deposition) and precipitation (wet deposition), and therefore contribute to the global cycling of substances. However, knowledge is scarce regarding the diversities of fungi deposited from the atmosphere. Here, an automatic dry and wet deposition sampler and high-throughput sequencing plus quantitative PCR were used to observe taxonomic diversities and flux densities of atmospheric fungal deposition. Taxon-specific fungal deposition velocities and aerodynamic diameters (da) were determined using a collocated cascade impactor for volumetric, particle-size-resolved air sampling. Large multicellular spore-producing dothideomycetes (da ≥ 10.0 μm) were predominant in dry deposition, with a mean velocity of 0.80 cm s-1 for all fungal taxa combined. Higher taxonomic richness was observed in fungal assemblages in wet deposition than in dry deposition, suggesting the presence of fungal taxa that are deposited only in wet form. In wet deposition, agaricomycetes, including mushroom-forming fungi, and sordariomycetes, including plant pathogenic species, were enriched, indicating that such fungal spores serve as nuclei in clouds, and/or are discharged preferentially during precipitation. Moreover, this study confirmed that fungal assemblage memberships and structures were significantly different between dry and wet deposition (P-test, p < 0.001). Overall, these findings suggest taxon-specific involvement of fungi in precipitation, and provide important insights into potential links between environmental changes that can disturb regional microbial communities (e.g., deforestation) and changes in precipitation patterns that might be mediated by changes in microbial communities in the atmosphere.}, }
@article {pmid29848439, year = {2018}, author = {Hamada, M and Schröder, K and Bathia, J and Kürn, U and Fraune, S and Khalturina, M and Khalturin, K and Shinzato, C and Satoh, N and Bosch, TC}, title = {Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29848439}, issn = {2050-084X}, mesh = {Animals ; *Biological Evolution ; Chlorella/drug effects/genetics/*metabolism ; Conserved Sequence ; Darkness ; Epithelial Cells/drug effects/metabolism ; Gene Expression Regulation ; Genome ; Hydra/drug effects/genetics/growth &amp; development/*metabolism ; Molecular Sequence Annotation ; Nitrates/metabolism ; Nitrogen/metabolism ; Photosynthesis/genetics ; RNA, Ribosomal, 18S/genetics/metabolism ; Species Specificity ; Sugars/pharmacology ; *Symbiosis/drug effects/genetics ; }, abstract = {Many multicellular organisms rely on symbiotic associations for support of metabolic activity, protection, or energy. Understanding the mechanisms involved in controlling such interactions remains a major challenge. In an unbiased approach we identified key players that control the symbiosis between Hydra viridissima and its photosynthetic symbiont Chlorella sp. A99. We discovered significant up-regulation of Hydra genes encoding a phosphate transporter and glutamine synthetase suggesting regulated nutrition supply between host and symbionts. Interestingly, supplementing the medium with glutamine temporarily supports in vitro growth of the otherwise obligate symbiotic Chlorella, indicating loss of autonomy and dependence on the host. Genome sequencing of Chlorella sp. A99 revealed a large number of amino acid transporters and a degenerated nitrate assimilation pathway, presumably as consequence of the adaptation to the host environment. Our observations portray ancient symbiotic interactions as a codependent partnership in which exchange of nutrients appears to be the primary driving force.}, }
@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}, mesh = {Animals ; *Biological Evolution ; Evolution, Molecular ; Genome ; Genomics/*methods ; Invertebrates/classification/*genetics ; Molecular Biology/*methods ; *Phylogeny ; Vertebrates/classification/genetics ; }, 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}, 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}, mesh = {Animals ; *Biological Evolution ; *Cooperative Behavior ; Models, Biological ; *Selection, Genetic ; Social Behavior ; }, 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}, support = {F31 CA206459/CA/NCI NIH HHS/United States ; R01 CA184510/CA/NCI NIH HHS/United States ; R35 CA210018/CA/NCI NIH HHS/United States ; U01 CA176287/CA/NCI NIH HHS/United States ; }, mesh = {9,10-Dimethyl-1,2-benzanthracene ; Animals ; Carcinoma, Squamous Cell/chemically induced/*genetics/metabolism/secondary ; *Cell Lineage ; Cell Movement/*genetics ; Cell Proliferation/genetics ; Cell Transformation, Neoplastic/chemically induced/*genetics/metabolism/pathology ; *Clonal Evolution ; Epithelial Cells/metabolism/*pathology ; Female ; Gene Expression Regulation, Neoplastic ; Genes, ras ; Genetic Predisposition to Disease ; Male ; Mice, Transgenic ; Mutation ; Neoplasms, Experimental/chemically induced/*genetics/metabolism/pathology ; Phenotype ; Skin Neoplasms/chemically induced/*genetics/metabolism/pathology ; Tetradecanoylphorbol Acetate ; Time Factors ; Tumor Burden/genetics ; }, 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}, 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}, pmid = {29789717}, issn = {1476-5594}, mesh = {Abdomen/*pathology ; Anoikis/physiology ; Ascites/pathology ; Carcinoma, Ovarian Epithelial/*pathology ; Cell Line, Tumor ; Drug Resistance, Neoplasm/physiology ; Female ; Humans ; Neoplasm Recurrence, Local/pathology ; Ovarian Neoplasms/*pathology ; Spheroids, Cellular/*pathology ; }, 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}, pmid = {29788279}, issn = {1759-6653}, mesh = {Animals ; Conserved Sequence/genetics ; Evolution, Molecular ; MicroRNAs/*genetics ; Molecular Sequence Annotation/methods ; Phenotype ; Phylogeny ; }, 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}, 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}, 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 = {}, 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}, mesh = {Animals ; Biological Evolution ; Humans ; Neurons/classification/*metabolism ; *Neurosciences ; Single-Cell Analysis/methods ; Transcriptome/*physiology ; }, 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 {pmid29728614, year = {2018}, author = {Pehr, K and Love, GD and Kuznetsov, A and Podkovyrov, V and Junium, CK and Shumlyanskyy, L and Sokur, T and Bekker, A}, title = {Ediacara biota flourished in oligotrophic and bacterially dominated marine environments across Baltica.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1807}, pmid = {29728614}, issn = {2041-1723}, mesh = {Asia ; Bacteria/growth &amp; development ; Biological Evolution ; Biomarkers/analysis ; *Biota ; Ecosystem ; Europe ; *Fossils ; Geography ; Geologic Sediments/*chemistry/*microbiology ; Hydrocarbons/analysis ; Lipids/analysis ; Prochlorococcus/growth &amp; development ; Synechococcus/growth &amp; development ; }, abstract = {Middle-to-late Ediacaran (575-541 Ma) marine sedimentary rocks record the first appearance of macroscopic, multicellular body fossils, yet little is known about the environments and food sources that sustained this enigmatic fauna. Here, we perform a lipid biomarker and stable isotope (δ15Ntotal and δ13CTOC) investigation of exceptionally immature late Ediacaran strata (<560 Ma) from multiple locations across Baltica. Our results show that the biomarker assemblages encompass an exceptionally wide range of hopane/sterane ratios (1.6-119), which is a broad measure of bacterial/eukaryotic source organism inputs. These include some unusually high hopane/sterane ratios (22-119), particularly during the peak in diversity and abundance of the Ediacara biota. A high contribution of bacteria to the overall low productivity may have bolstered a microbial loop, locally sustaining dissolved organic matter as an important organic nutrient. These oligotrophic, shallow-marine conditions extended over hundreds of kilometers across Baltica and persisted for more than 10 million years.}, }
@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}, mesh = {Animals ; *Biological Evolution ; Biota ; Fossils/*anatomy &amp; histology ; Invertebrates/*anatomy &amp; histology/*physiology ; }, 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}, mesh = {Ammonium Compounds/chemistry ; China ; Deltaproteobacteria/classification/cytology/genetics/*physiology ; Ferrosoferric Oxide ; Geologic Sediments/chemistry/*microbiology ; Lakes/chemistry/*microbiology ; Locomotion ; Magnetosomes/physiology ; Oxidation-Reduction ; *Seasons ; Silicates/chemistry ; }, 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}, 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 = {}, 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 = {140}, number = {}, pages = {49-73}, doi = {10.1016/j.pbiomolbio.2018.04.006}, pmid = {29685747}, issn = {1873-1732}, mesh = {Animals ; *Biological Evolution ; Cells/*cytology ; *Cognition ; Humans ; Signal Transduction ; }, 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/International ; ERC_HU Grant #118722//NRDI Office/International ; }, mesh = {*Biological Evolution ; Ecosystem ; Fungi/*cytology/*genetics ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Genomics ; }, 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}, pmid = {29663630}, issn = {1469-185X}, support = {//Wellcome Trust/United Kingdom ; 104978/Z/14/Z//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Genetic Predisposition to Disease ; Humans ; *Hydra ; *Neoplasms ; Species Specificity ; }, 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}, pmid = {29662839}, issn = {2235-2988}, mesh = {Animals ; Anti-Infective Agents/metabolism/pharmacology ; Bacillus megaterium/drug effects ; Bacterial Infections/*immunology ; Dictyostelium/genetics/*immunology/metabolism/*microbiology ; Gastropoda/immunology/metabolism/microbiology ; Gene Expression Profiling ; Host-Pathogen Interactions/*immunology ; *Immunity, Innate ; Ion Channels/metabolism/pharmacology ; Klebsiella pneumoniae/drug effects/pathogenicity ; Liposomes/metabolism ; Peptides/genetics/metabolism/pharmacology ; Protozoan Proteins/metabolism/pharmacology ; Recombinant Proteins ; Saposins/genetics/immunology/*metabolism/*pharmacology ; }, 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}, 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 = {}, 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 {pmid29632261, year = {2018}, author = {Halatek, J and Brauns, F and Frey, E}, title = {Self-organization principles of intracellular pattern formation.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {373}, number = {1747}, pages = {}, pmid = {29632261}, issn = {1471-2970}, mesh = {Animals ; Caenorhabditis elegans/*genetics ; Caenorhabditis elegans Proteins/genetics ; Escherichia coli/*genetics ; Escherichia coli Proteins/genetics ; *Evolution, Molecular ; Models, Genetic ; Saccharomyces cerevisiae/*genetics ; cdc42 GTP-Binding Protein, Saccharomyces cerevisiae/genetics ; }, abstract = {Dynamic patterning of specific proteins is essential for the spatio-temporal regulation of many important intracellular processes in prokaryotes, eukaryotes and multicellular organisms. The emergence of patterns generated by interactions of diffusing proteins is a paradigmatic example for self-organization. In this article, we review quantitative models for intracellular Min protein patterns in Escherichia coli, Cdc42 polarization in Saccharomyces cerevisiae and the bipolar PAR protein patterns found in Caenorhabditis elegans By analysing the molecular processes driving these systems we derive a theoretical perspective on general principles underlying self-organized pattern formation. We argue that intracellular pattern formation is not captured by concepts such as 'activators', 'inhibitors' or 'substrate depletion'. Instead, intracellular pattern formation is based on the redistribution of proteins by cytosolic diffusion, and the cycling of proteins between distinct conformational states. Therefore, mass-conserving reaction-diffusion equations provide the most appropriate framework to study intracellular pattern formation. We conclude that directed transport, e.g. cytosolic diffusion along an actively maintained cytosolic gradient, is the key process underlying pattern formation. Thus the basic principle of self-organization is the establishment and maintenance of directed transport by intracellular protein dynamics.This article is part of the theme issue 'Self-organization in cell biology'.}, }
@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 = {}, pmid = {29632050}, issn = {1477-9137}, support = {R01 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}, 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}, pmid = {29616867}, issn = {1555-8584}, mesh = {Animals ; *Evolution, Molecular ; *Genome ; Porifera/cytology/genetics/*metabolism ; RNA, Long Noncoding/genetics/*metabolism ; }, 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 = {}, 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}, mesh = {Animals ; Biological Evolution ; Endocrine System/physiology ; Imaginal Discs/growth &amp; development ; Insecta/anatomy &amp; histology/*growth &amp; development/physiology ; Morphogenesis/*physiology ; Phenotype ; Signal Transduction ; }, 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 {pmid29597064, year = {2018}, author = {Presting, GG}, title = {Centromeric retrotransposons and centromere function.}, journal = {Current opinion in genetics &amp; development}, volume = {49}, number = {}, pages = {79-84}, doi = {10.1016/j.gde.2018.03.004}, pmid = {29597064}, issn = {1879-0380}, mesh = {Centromere/*genetics ; DNA Breaks, Double-Stranded ; Eukaryota/genetics ; *Evolution, Molecular ; Retroelements/*genetics ; Tandem Repeat Sequences/*genetics ; }, abstract = {The centromeric DNA of most multicellular eukaryotes consists of tandem repeats (TR) that bind centromere-specific proteins and act as a substrate for the efficient repair of frequent double-stranded DNA breaks. Some retrotransposons target active centromeres during integration with such specificity that they can be used to deduce current and historic centromere positions. The roles of transposons in centromere function remain incompletely understood but appear to include maintaining centromere size and increasing the repeat content of neocentromeres that lack TR. Retrotransposons are known to give rise to TR. Centromere-targeting elements thus have the potential to replace centromeric TR essentially in situ, providing a mechanism to explain the centromere paradox, that is, the presence of unrelated centromeric TRs in closely related species.}, }
@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 = {}, pmid = {29593113}, issn = {1471-2954}, mesh = {*Adaptation, Physiological ; *Biological Evolution ; Confidence Intervals ; Drug Resistance, Bacterial/genetics/physiology ; Gene Deletion ; Genetic Fitness/genetics/*physiology ; Genotype ; Myxococcus xanthus/genetics/*physiology ; Rifampin/metabolism ; Spores, Bacterial ; }, 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}, 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}, pmid = {29587819}, issn = {1756-3305}, support = {MC_UU_12014/8//Medical Research Council/United Kingdom ; ANR-10-LABX-62-IBEID//Investissement d'Avenir program Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases/International ; MC_UU_12014/1//Medical Research Council/United Kingdom ; ANR-16-CE35-0004-01//Agence Nationale de la Recherche/International ; ANR-17-ERC2-0016-01//Agence Nationale de la Recherche/International ; 734584//European Union's Horizon 2020 research and innovation programme under ZikaPLAN/International ; MC_UU_12014//Medical Research Council/United Kingdom ; ANR10-INBS-09-08//France Génomique consortium/International ; 2015-FED-192//Programme Opérationnel FEDER-Guadeloupe-Conseil Régional/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}, pmid = {29581530}, issn = {1751-7370}, mesh = {Bacteria/*genetics ; Ferrosoferric Oxide/*metabolism ; Genome, Bacterial ; Iron ; Likelihood Functions ; Magnetics ; Magnetosomes/*chemistry ; Metagenome ; *Metagenomics ; Multigene Family ; *Phylogeny ; Proteobacteria/genetics ; Sulfides ; }, 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}, pmid = {29579574}, issn = {1879-0380}, support = {F32 GM126736/GM/NIGMS NIH HHS/United States ; R01 GM119125/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence/*genetics ; Chromosome Segregation/genetics ; DNA, Satellite/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Genome/genetics ; Reproductive Isolation ; }, 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}, mesh = {Animals ; *Biological Evolution ; Eukaryota ; Genetic Variation ; *Individuality ; *Models, Biological ; }, 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}, mesh = {Animals ; *Biological Evolution ; Cnidaria/classification ; Ctenophora/classification ; Evolution, Molecular ; Germany ; Phylogeny ; Placozoa/classification ; Porifera/classification ; }, 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 = {}, 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 = {}, pmid = {29563281}, issn = {1744-957X}, mesh = {Antimicrobial Cationic Peptides/administration &amp; dosage/*pharmacology ; Escherichia coli/drug effects/*genetics ; *Recombination, Genetic/drug effects ; }, 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}, pmid = {29559848}, issn = {1449-2288}, mesh = {Acanthamoeba castellanii/*genetics/*physiology ; Actins/genetics ; *Adaptation, Physiological ; *Comparative Genomic Hybridization ; Entamoeba histolytica/*genetics/*physiology ; Gene Expression ; Genes, Protozoan ; Sequence Analysis, RNA ; Transcriptome ; }, 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 = {}, 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}, 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}, 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}, support = {F32 NS055492/NS/NINDS NIH HHS/United States ; }, mesh = {*Genes, src ; Mitogen-Activated Protein Kinases/genetics ; Peptides, Cyclic/genetics ; Phosphorylation ; Phosphotyrosine/*metabolism ; Protein-Tyrosine Kinases/genetics ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Signal Transduction ; Tyrosine/metabolism ; }, 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 {pmid29545531, year = {2018}, author = {Moroni, M and Servin-Vences, MR and Fleischer, R and Sánchez-Carranza, O and Lewin, GR}, title = {Voltage gating of mechanosensitive PIEZO channels.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {1096}, pmid = {29545531}, issn = {2041-1723}, mesh = {Animals ; Cell Line ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster ; Evolution, Molecular ; Humans ; Ion Channels/genetics/*metabolism ; *Mechanotransduction, Cellular ; Mice ; Mutation, Missense ; Patch-Clamp Techniques ; Zebrafish ; Zebrafish Proteins/genetics/*metabolism ; }, abstract = {Mechanosensitive PIEZO ion channels are evolutionarily conserved proteins whose presence is critical for normal physiology in multicellular organisms. Here we show that, in addition to mechanical stimuli, PIEZO channels are also powerfully modulated by voltage and can even switch to a purely voltage-gated mode. Mutations that cause human diseases, such as xerocytosis, profoundly shift voltage sensitivity of PIEZO1 channels toward the resting membrane potential and strongly promote voltage gating. Voltage modulation may be explained by the presence of an inactivation gate in the pore, the opening of which is promoted by outward permeation. Older invertebrate (fly) and vertebrate (fish) PIEZO proteins are also voltage sensitive, but voltage gating is a much more prominent feature of these older channels. We propose that the voltage sensitivity of PIEZO channels is a deep property co-opted to add a regulatory mechanism for PIEZO activation in widely different cellular contexts.}, }
@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 = {}, pmid = {29540517}, issn = {1471-2954}, support = {260986//European Research Council/International ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Antimicrobial Cationic Peptides/*pharmacology ; Computer Simulation ; Drug Resistance, Microbial/*genetics ; *Evolution, Molecular ; Microbial Sensitivity Tests ; Models, Genetic ; }, 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}, 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}, 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}, 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}, 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}, mesh = {Embryoid Bodies/*drug effects ; Embryonic Stem Cells/drug effects ; Humans ; Pluripotent Stem Cells/drug effects ; Teratology/*methods ; Toxicity Tests/methods ; }, 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}, 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}, support = {U01 CA187956/CA/NCI NIH HHS/United States ; }, 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}, 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 {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 &amp; 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 &amp; 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 {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}, mesh = {Biomass ; Cell Adhesion ; Cell Division ; Eutrophication/physiology ; Microcystis/*physiology ; }, 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 = {}, 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 = {}, 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 = {}, 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 = {}, 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 = {}, pmid = {29436502}, issn = {1471-2954}, mesh = {*Biological Evolution ; Eukaryota/*physiology ; Oxygen/*metabolism ; Reactive Oxygen Species/metabolism ; *Sex ; Symbiosis/physiology ; }, 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}, 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}, 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 {pmid29427837, year = {2018}, author = {Baldauf, SL and Romeralo, M and Fiz-Palacios, O and Heidari, N}, title = {A Deep Hidden Diversity of Dictyostelia.}, journal = {Protist}, volume = {169}, number = {1}, pages = {64-78}, doi = {10.1016/j.protis.2017.12.005}, pmid = {29427837}, issn = {1618-0941}, mesh = {*Biodiversity ; DNA Primers/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dictyostelium/classification/*genetics/isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Dictyostelia is a monophyletic group of transiently multicellular (sorocarpic) amoebae, whose study is currently limited to laboratory culture. This tends to favour faster growing species with robust sorocarps, while species with smaller more delicate sorocarps constitute most of the group's taxonomic breadth. The number of known species is also small (∼150) given Dictyostelia's molecular depth and apparent antiquity (>600 myr). Nonetheless, dictyostelid sequences are rarely recovered in culture independent sampling (ciPCR) surveys. We developed ciPCR primers to specifically target dictyostelid small subunit (SSU or 18S) rDNA and tested them on total DNAs extracted from a wide range of soils from five continents. The resulting clone libraries show mostly dictyostelid sequences (∼90%), and phylogenetic analyses of these sequences indicate novel lineages in all four dictyostelid families and most genera. This is especially true for the species-rich Heterostelium and Dictyosteliaceae but also the less species-rich Raperosteliaceae. However, the most novel deep branches are found in two very species-poor taxa, including the deepest branch yet seen in the highly divergent Cavenderiaceae. These results confirm a deep hidden diversity of Dictyostelia, potentially including novel morphologies and developmental schemes. The primers and protocols presented here should also enable more comprehensive studies of dictyostelid ecology.}, }
@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}, mesh = {Animals ; Behavior Rating Scale ; Electrophysiology/methods ; Humans ; Ion Channel Gating/drug effects ; Ion Channels/chemistry/metabolism/pharmacology ; Models, Animal ; Neurons/*drug effects/physiology ; Neuropharmacology/*methods ; Neurotoxins/*pharmacology/*therapeutic use ; Sensory Receptor Cells/chemistry/*metabolism ; }, 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}, mesh = {Animals ; Biocompatible Materials/*chemistry ; *Bioprinting ; Brain Diseases/therapy ; Extracellular Matrix/chemistry ; Humans ; Hydrogels/chemistry ; Models, Animal ; Neuroglia/chemistry ; Neurons/chemistry ; *Printing, Three-Dimensional ; *Tissue Engineering ; }, 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 = {}, 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}, mesh = {Animals ; Atmosphere/analysis ; Bacteria/chemistry/metabolism ; *Biological Evolution ; Earth (Planet) ; Electron Transport ; Energy Metabolism ; *Origin of Life ; Oxidation-Reduction ; Oxygen/chemistry/*metabolism ; Photosynthesis/*physiology ; Plants/chemistry/*metabolism ; Reactive Oxygen Species/chemistry/*metabolism ; Time Factors ; }, 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}, support = {K12 GM093857/GM/NIGMS NIH HHS/United States ; }, 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}, pmid = {29400699}, issn = {1530-0307}, mesh = {Amino Acid Sequence ; Cell Migration Assays ; *Cell Movement ; Eukaryota/*enzymology/genetics ; Evolution, Molecular ; HeLa Cells ; Humans ; NM23 Nucleoside Diphosphate Kinases/chemistry/genetics/*metabolism ; }, 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}, 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}, 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}, mesh = {Amino Acid Sequence ; Brachypodium/classification/*genetics/metabolism ; Centromere/*genetics/metabolism ; Chromosomes, Plant/genetics/metabolism ; DNA, Plant/*genetics/metabolism ; Evolution, Molecular ; Genome, Plant/*genetics ; Histones/genetics/metabolism ; In Situ Hybridization, Fluorescence ; Nucleosomes/genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/metabolism ; Polyploidy ; Protein Binding ; Sequence Homology, Amino Acid ; }, 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}, 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}, 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 {pmid29373067, year = {2017}, author = {Lindström, JB and Pierce, NT and Latz, MI}, title = {Role of TRP Channels in Dinoflagellate Mechanotransduction.}, journal = {The Biological bulletin}, volume = {233}, number = {2}, pages = {151-167}, doi = {10.1086/695421}, pmid = {29373067}, issn = {1939-8697}, mesh = {Biological Evolution ; Dinoflagellida/classification/genetics/*physiology ; Signal Transduction/genetics ; Transient Receptor Potential Channels/genetics/*metabolism ; }, abstract = {Transient receptor potential (TRP) ion channels are common components of mechanosensing pathways, mainly described in mammals and other multicellular organisms. To gain insight into the evolutionary origins of eukaryotic mechanosensory proteins, we investigated the involvement of TRP channels in mechanosensing in a unicellular eukaryotic protist, the dinoflagellate Lingulodinium polyedra. BLASTP analysis of the protein sequences predicted from the L. polyedra transcriptome revealed six sequences with high similarity to human TRPM2, TRPM8, TRPML2, TRPP1, and TRPP2; and characteristic TRP domains were identified in all sequences. In a phylogenetic tree including all mammalian TRP subfamilies and TRP channel sequences from unicellular and multicellular organisms, the L. polyedra sequences grouped with the TRPM, TPPML, and TRPP clades. In pharmacological experiments, we used the intrinsic bioluminescence of L. polyedra as a reporter of mechanoresponsivity. Capsaicin and RN1734, agonists of mammalian TRPV, and arachidonic acid, an agonist of mammalian TRPV, TRPA, TRPM, and Drosophila TRP, all stimulated bioluminescence in L. polyedra. Mechanical stimulation of bioluminescence, but not capsaicin-stimulated bioluminescence, was inhibited by gadolinium (Gd3+), a general inhibitor of mechanosensitive ion channels, and the phospholipase C (PLC) inhibitor U73122. These pharmacological results are consistent with the involvement of TRP-like channels in mechanosensing by L. polyedra. The TRP channels do not appear to be mechanoreceptors but rather are components of the mechanotransduction signaling pathway and may be activated via a PLC-dependent mechanism. The presence and function of TRP channels in a dinoflagellate emphasize the evolutionary conservation of both the channel structures and their functions.}, }
@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 = {}, 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}, mesh = {Anaerobiosis ; Animals ; *Biological Evolution ; Cell Hypoxia/*physiology ; Oxygen/*physiology ; Stem Cells/*physiology ; }, 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}, 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}, 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 ; }, mesh = {Breast Neoplasms/metabolism/pathology ; Carcinoma/metabolism/*pathology ; Cell Line, Tumor ; Cell Movement/physiology ; Collagen/metabolism ; Extracellular Matrix/metabolism/pathology ; Female ; Humans ; Imaging, Three-Dimensional ; Microscopy, Fluorescence, Multiphoton ; Models, Biological ; Neoplasm Invasiveness/*pathology/physiopathology ; Systems Biology ; }, 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}, pmid = {29337961}, issn = {1532-1827}, mesh = {Animals ; Biological Evolution ; Gene Regulatory Networks ; Humans ; Neoplasms/*genetics/*pathology ; }, 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}, 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}, mesh = {Acanthamoeba castellanii/*genetics/*physiology ; Amino Acid Sequence ; Carbonic Anhydrases/chemistry/genetics ; Computational Biology ; *Evolution, Molecular ; Homeostasis/*genetics ; Humans ; Hydrogen-Ion Concentration ; Membrane Transport Proteins/chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Protozoan Proteins/chemistry/*genetics ; Sequence Homology, Amino Acid ; Water ; }, 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 = {}, 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}, 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}, mesh = {*Biological Evolution ; Chlorophyta/*genetics ; Cyclins/genetics ; Genes, Retinoblastoma ; *Genes, cdc ; *Genome Components ; Multigene Family ; Proteasome Endopeptidase Complex/genetics ; Selection, Genetic ; Transcriptome ; Ubiquitin/genetics ; }, 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}, 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}, mesh = {Animals ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome ; Sequence Analysis/methods ; }, 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}, 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 ; }, mesh = {Animals ; Antigens/*genetics ; Astrocytes/pathology ; Axons/*pathology ; Cell Proliferation/drug effects ; Cicatrix/*genetics/pathology ; Fibrosis/pathology ; Glial Fibrillary Acidic Protein/biosynthesis/genetics ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Neovascularization, Pathologic/*genetics/pathology ; Neuroglia/metabolism/pathology ; Pericytes/metabolism/pathology ; Proteoglycans/*genetics ; Recovery of Function/genetics ; Spinal Cord Injuries/*genetics/*pathology ; }, 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 = {}, 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}, 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}, 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}, 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 = {}, 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}, pmid = {29225309}, issn = {1349-2896}, mesh = {Cell Count/methods ; Cell Culture Techniques/methods ; Cell Division ; Cell Size ; Chlorophyta/*cytology ; Electrophoresis, Polyacrylamide Gel/methods ; }, 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}, 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}, 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}, pmid = {29191225}, issn = {1474-760X}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; P30-CA008748//National Cancer Institute/ ; R01 NS083833/NS/NINDS NIH HHS/United States ; R01-GM083300//National Institute of General Medical Sciences/ ; R01-NS083833//National Institute of Neurological Disorders and Stroke/ ; 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}, 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}, mesh = {Animals ; *Biological Evolution ; Cells/cytology/metabolism ; Cognition ; Humans ; }, 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}, mesh = {Allomyces/*physiology ; *Chemotaxis ; *Phototaxis ; Sensation ; Spores, Fungal/*physiology ; }, 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}, 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}, 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}, 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}, 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}, 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}, 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 = {}, 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 {pmid29128405, year = {2018}, author = {Soni, B and Saha, B and Singh, S}, title = {Systems cues governing IL6 signaling in leishmaniasis.}, journal = {Cytokine}, volume = {106}, number = {}, pages = {169-175}, doi = {10.1016/j.cyto.2017.11.001}, pmid = {29128405}, issn = {1096-0023}, mesh = {Animals ; Computer Simulation ; Interleukin-6/*metabolism ; Leishmaniasis/*metabolism ; Mice ; Models, Biological ; Phylogeny ; Principal Component Analysis ; *Signal Transduction ; *Systems Biology ; Toll-Like Receptors/metabolism ; }, abstract = {IL-6 has been proposed to favor the development of Th2 responses and play an important role in the communication between cells of multicellular organisms. They are involved in the regulation of complex cellular processes such as proliferation, differentiation and act as key player during inflammation and immune response. Th2 cytokines play an immunoregulatory role in early infection. Literature says in mice infected with L. major, IL-6 may promote the development of both Th1 and Th2 responses. IL-4 is also considered to be the signature cytokine of Th-2 response. IL-10 was initially characterized as a Th2 cytokine but later on it was proved to be a pleiotropic cytokine, secreted from different cell types including the macrophages. A major challenge is to understand how these complex non-linear processes are connected and regulated. Systems biology approaches may be used to tackle this challenge in an iterative process of quantitative mathematical analysis. In this study, we created an in silico model of IL6 mediated macrophage activation which suffers from an excessive impact of the negative feedback loop involving SOCS3. The strategy adopted in this framework may help to reduce the complexity of the leishmanial IL6 model analysis and also laydown various physiological or pathological conditions of IL6 signaling in future.}, }
@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}, 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 = {}, 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}, 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 = {}, 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 = {}, 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 = {}, 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 = {}, 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}, 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}, 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 = {}, 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}, pmid = {29069493}, issn = {1537-1719}, mesh = {Animals ; Arachis/*genetics ; Arthropods/*genetics ; Base Sequence ; *Gene Transfer, Horizontal ; Genome, Plant ; Phylogeny ; *Retroelements ; Sequence Homology, Nucleic Acid ; }, 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}, 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 = {}, 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 = {}, 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 = {}, 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}, 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 DK097948/DK/NIDDK 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 = {}, pmid = {29021161}, issn = {1742-5662}, support = {BB/M01116X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L010232/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N009754/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, 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}, 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 ; 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 = {Arabidopsis/genetics/growth &amp; development/*physiology ; Cytokinins/metabolism ; Evolution, Molecular ; Flowers/genetics/growth &amp; development/*physiology ; Indoleacetic Acids/metabolism ; Plant Growth Regulators/*metabolism ; Plant Leaves/genetics/growth &amp; development/physiology ; }, 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}, 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}, 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}, 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}, 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}, mesh = {*Biomechanical Phenomena ; Humans ; Models, Biological ; }, 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 = {2018}, 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 = {10}, number = {11}, 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}, 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}, 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}, 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}, 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}, 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}, 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}, 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}, 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 = {}, 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}, 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}, 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}, 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}, 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}, 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 = {}, 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}, 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}, mesh = {Adaptive Immunity/*genetics ; Animals ; *Biological Evolution ; Genetic Fitness ; Vertebrates/*genetics/*immunology ; }, 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}, 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}, 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 = {}, 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}, mesh = {*Biological Evolution ; *Cell Biology ; Eukaryotic Cells/*metabolism ; *Genetic Variation ; Phylogeny ; Plastids/genetics ; }, 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}, 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}, 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}, 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}, 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}, 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 = {}, 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}, 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}, 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 = {}, 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}, 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}, 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 = {2019}, 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 = {28}, number = {4}, pages = {503-508}, 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}, pmid = {28592899}, issn = {2045-2322}, mesh = {*Biological Evolution ; Evolution, Molecular ; *Fresh Water ; Genes, Plant ; Genetic Variation ; Genome, Chloroplast ; Genome, Mitochondrial ; Genomics/methods ; Phylogeny ; Rhodophyta/*classification/*genetics ; }, 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}, pmid = {28588313}, issn = {2045-2322}, mesh = {Alginates/*metabolism ; Cell Wall/*chemistry/*metabolism ; Chromatography, High Pressure Liquid ; Fluorescent Antibody Technique ; Glucans/*chemistry/*metabolism ; Immunohistochemistry ; Organ Specificity ; Phaeophyta/classification/genetics/*metabolism ; Solubility ; }, 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}, 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}, pmid = {28580966}, issn = {2041-1723}, mesh = {Biological Evolution ; Cluster Analysis ; *Ecology ; Flocculation ; Genotype ; Green Fluorescent Proteins/metabolism ; Kluyveromyces/genetics/*physiology ; Microscopy, Confocal ; Phenotype ; Saccharomyces cerevisiae/genetics/*physiology ; Species Specificity ; Video Recording ; }, 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}, 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}, 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}, 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}, mesh = {Animals ; *Behavior, Animal ; *Biological Evolution ; Insecta/*genetics/*physiology ; Selection, Genetic ; *Social Behavior ; }, 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}, 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 = {}, 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 = {}, 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 {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}, 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 {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}, 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}, 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}, 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}, 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}, 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}, 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 ;