@article {pmid32659023, year = {2020}, author = {Begum, R and Saran, S}, title = {Glimpses of Dictyostelid research in India.}, journal = {The International journal of developmental biology}, volume = {64}, number = {1-2-3}, pages = {99-107}, doi = {10.1387/ijdb.190208ss}, pmid = {32659023}, issn = {1696-3547}, abstract = {Simple organisms are preferred for understanding the molecular and cellular function(s) of complex processes. Dictyostelium discoideum is a lower eukaryote, a protist and a cellular slime mould, which has been in recent times used for various studies such as cell differentiation, development, cell death, stress responses etc. It is a soil amoeba (unicellular) that undertakes a remarkable, facultative shift to multicellularity when exposed to starvation and requires signal pathways that result in alteration of gene expression and finally show cell differentiation. The amoebae aggregate, differentiate and form fruiting bodies with two terminally differentiated cells: the dead stalk (non-viable) and dormant spores (viable). In India, starting from the isolation of Dictyostelium species to morphogenesis, cell signalling and social evolution has been studied with many more new research additions. Advances in molecular genetics make Dictyostelium an attractive model system to study cell biology, biochemistry, signal transduction and many more.}, }
@article {pmid32658971, year = {2020}, author = {Helsen, J and Voordeckers, K and Vanderwaeren, L and Santermans, T and Tsontaki, M and Verstrepen, KJ and Jelier, R}, title = {Gene loss predictably drives evolutionary adaptation.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaa172}, pmid = {32658971}, issn = {1537-1719}, abstract = {Loss of gene function is common throughout evolution, even though it often leads to reduced fitness. In this study, we systematically evaluated how an organism adapts after deleting genes that are important for growth under oxidative stress. By evolving, sequencing, and phenotyping over 200 yeast lineages, we found that gene loss can enhance an organism's capacity to evolve and adapt. Whereas gene loss often led to an immediate decrease in fitness, many mutants rapidly acquired suppressor mutations that restored fitness. Depending on the strain's genotype, some ultimately even attained higher fitness levels than similarly adapted wild-type cells. Further, cells with deletions in different modules of the genetic network followed distinct and predictable mutational trajectories. Finally, losing highly connected genes increased evolvability by facilitating the emergence of a more diverse array of phenotypes after adaptation. Together, our findings show that loss of specific parts of a genetic network can facilitate adaptation by opening alternative evolutionary paths.}, }
@article {pmid32653903, year = {2020}, author = {Plachetzki, D and Pankey, S and MacManes, MD and Lesser, MP and Walker, CW}, title = {The genome of the softshell clam Mya arenaria and the evolution of apoptosis.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evaa143}, pmid = {32653903}, issn = {1759-6653}, abstract = {Apoptosis is a fundamental feature of multicellular animals and is best understood in mammals, flies, and nematodes, with the invertebrate models being thought to represent a condition of ancestral simplicity. However, the existence of a leukemia-like cancer in the softshell clam Mya arenaria provides an opportunity to re-evaluate the evolution of the genetic machinery of apoptosis. Here we report the whole genome sequence for M. arenaria which we leverage with existing data to test evolutionary hypotheses on the origins of apoptosis in animals. We show that the ancestral bilaterian p53 locus, a master regulator of apoptosis, possessed a complex domain structure, in contrast to that of extant ecdysozoan p53s. Further, ecdysozoan taxa, but not chordates or lophotrochozoans like M. arenaria, show a widespread reduction in apoptosis gene copy number. Finally, phylogenetic exploration of apoptosis gene copy number reveals a striking linkage with p53 domain complexity across species. Our results challenge the current understanding of the evolution of apoptosis and highlight the ancestral complexity of the bilaterian apoptotic tool kit and its subsequent dismantlement during the ecdysozoan radiation.}, }
@article {pmid32651201, year = {2020}, author = {Klancher, CA and Newman, JD and Ball, AS and van Kessel, JC and Dalia, AB}, title = {Species-specific quorum sensing represses the chitobiose utilization locus in Vibrio cholerae.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1128/AEM.00915-20}, pmid = {32651201}, issn = {1098-5336}, abstract = {The marine facultative pathogen Vibrio cholerae forms complex multicellular communities on the chitinous shells of crustacean zooplankton in its aquatic reservoir. V. cholerae-chitin interactions are critical for the growth, evolution, and waterborne transmission of cholera. This is due, in part, to chitin-induced changes in gene expression in this pathogen. Here, we sought to identify factors that influence chitin-induced expression of one locus, the chitobiose utilization operon (chb), which is required for the uptake and catabolism of the chitin disaccharide. Through a series of genetic screens, we identified that the master regulator of quorum sensing, HapR, is a direct repressor of the chb operon. We also found that the levels of HapR in V. cholerae are regulated by the ClpAP protease. Furthermore, we show that the canonical quorum sensing cascade in V. cholerae regulates chb expression in a HapR-dependent manner. Through this analysis we found that signaling via the species-specific autoinducer CAI-1, but not the inter-species autoinducer AI-2, influences chb expression. This phenomenon of species-specific regulation may enhance the fitness of this pathogen in its environmental niche.Importance In nature, bacteria live in multicellular and multispecies communities. Microbial species can sense the density and composition of their community through chemical cues using a process called quorum sensing (QS). The marine pathogen Vibrio cholerae is found in communities on the chitinous shells of crustaceans in its aquatic reservoir. V. cholerae interactions with chitin are critical for the survival, evolution, and waterborne transmission of this pathogen. Here, we show that V. cholerae uses QS to regulate the expression of one locus required for V. cholerae-chitin interactions.}, }
@article {pmid32649861, year = {2020}, author = {Brunkard, JO}, title = {Exaptive Evolution of Target of Rapamycin Signaling in Multicellular Eukaryotes.}, journal = {Developmental cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.devcel.2020.06.022}, pmid = {32649861}, issn = {1878-1551}, abstract = {Target of rapamycin (TOR) is a protein kinase that coordinates metabolism with nutrient and energy availability in eukaryotes. TOR and its primary interactors, RAPTOR and LST8, have been remarkably evolutionarily static since they arose in the unicellular last common ancestor of plants, fungi, and animals, but the upstream regulatory mechanisms and downstream effectors of TOR signaling have evolved considerable diversity in these separate lineages. Here, I focus on the roles of exaptation and adaptation in the evolution of novel signaling axes in the TOR network in multicellular eukaryotes, concentrating especially on amino acid sensing, cell-cell signaling, and cell differentiation.}, }
@article {pmid32643307, year = {2020}, author = {Rose, CJ and Hammerschmidt, K and Pichugin, Y and Rainey, PB}, title = {Meta-population structure and the evolutionary transition to multicellularity.}, journal = {Ecology letters}, volume = {}, number = {}, pages = {}, doi = {10.1111/ele.13570}, pmid = {32643307}, issn = {1461-0248}, support = {//Marsden Fund Council from government funding administered by the Royal Society of New Zealand/ ; //Marsden Fund/ ; //Royal Society/ ; }, abstract = {The evolutionary transition to multicellularity has occurred on numerous occasions, but transitions to complex life forms are rare. Here, using experimental bacterial populations as proxies for nascent multicellular organisms, we manipulate ecological factors shaping the evolution of groups. Groups were propagated under regimes requiring reproduction via a life cycle replete with developmental and dispersal (propagule) phases, but in one treatment lineages never mixed, whereas in a second treatment, cells from different lineages experienced intense competition during the dispersal phase. The latter treatment favoured traits promoting cell growth at the expense of traits underlying group fitness - a finding that is supported by results from a mathematical model. Our results show that the transition to multicellularity benefits from ecological conditions that maintain discreteness not just of the group (soma) phase, but also of the dispersal (germline) phase.}, }
@article {pmid32642048, year = {2020}, author = {Hammarlund, EU}, title = {Harnessing hypoxia as an evolutionary driver of complex multicellularity.}, journal = {Interface focus}, volume = {10}, number = {4}, pages = {20190101}, doi = {10.1098/rsfs.2019.0101}, pmid = {32642048}, issn = {2042-8898}, abstract = {Animal tissue requires low-oxygen conditions for its maintenance. The need for low-oxygen conditions contrasts with the idea of an evolutionary leap in animal diversity as a result of expanding oxic conditions. To accommodate tissue renewal at oxic conditions, however, vertebrate animals and vascular plants demonstrate abilities to access hypoxia. Here, I argue that multicellular organisms sustain oxic conditions first after internalizing hypoxic conditions. The 'harnessing' of hypoxia has allowed multicellular evolution to leave niches that were stable in terms of oxygen concentrations for those where oxygen fluctuates. Since oxygen fluctuates in most settings on Earth's surface, the ancestral niche would have been a deep marine setting. The hypothesis that 'large life' depends on harnessing hypoxia is illustrated in the context of conditions that promote the immature cell phenotype (stemness) in animal physiology and tumour biology and offers one explanation for the general rarity of diverse multicellularity over most of Earth's history.}, }
@article {pmid31840773, year = {2019}, author = {Nanjundiah, V}, title = {Individual and collective behaviour in cellular slime mould development: contributions of John Bonner (1920-2019).}, journal = {The International journal of developmental biology}, volume = {63}, number = {8-9-10}, pages = {333-342}, doi = {10.1387/ijdb.190272vn}, pmid = {31840773}, issn = {1696-3547}, mesh = {Animals ; Biological Evolution ; Body Patterning ; Cell Biology/history ; Chemotaxis ; Developmental Biology/history ; Dictyostelium/*genetics/*physiology ; History, 20th Century ; History, 21st Century ; Humans ; Models, Biological ; Selection, Genetic ; }, abstract = {John Bonner used the cellular slime moulds to address issues that lie at the heart of evolutionary and developmental biology. He did so mostly by combining acute observation and a knack for asking the right questions with the methods of classical embryology. The present paper focusses on his contributions to understanding two phenomena that are characteristic of development in general: chemotaxis of single cells to an external attractant, and spatial patterning and proportioning of cell types in the multicellular aggregate. Brief mention is also made of other areas of slime mould biology where he made significant inputs. He saw cellular slime moulds as exemplars of development and worthy of study in their own right. His ideas continue to inspire researchers.}, }
@article {pmid32626570, year = {2020}, author = {Umen, JG}, title = {Volvox and volvocine green algae.}, journal = {EvoDevo}, volume = {11}, number = {}, pages = {13}, doi = {10.1186/s13227-020-00158-7}, pmid = {32626570}, issn = {2041-9139}, abstract = {The transition of life from single cells to more complex multicellular forms has occurred at least two dozen times among eukaryotes and is one of the major evolutionary transitions, but the early steps that enabled multicellular life to evolve and thrive remain poorly understood. Volvocine green algae are a taxonomic group that is uniquely suited to investigating the step-wise acquisition of multicellular organization. The multicellular volvocine species Volvox carteri exhibits many hallmarks of complex multicellularity including complete germ-soma division of labor, asymmetric cell divisions, coordinated tissue-level morphogenesis, and dimorphic sexes-none of which have obvious analogs in its closest unicellular relative, the model alga Chlamydomonas reinhardtii. Here, I summarize some of the key questions and areas of study that are being addressed with Volvox carteri and how increasing genomic information and methodologies for volvocine algae are opening up the entire group as an integrated experimental system for exploring the evolution of multicellularity and more.}, }
@article {pmid32617614, year = {2020}, author = {Seoighe, C and Kiniry, SJ and Peters, A and Baranov, PV and Yang, H}, title = {Selection Shapes Synonymous Stop Codon Use in Mammals.}, journal = {Journal of molecular evolution}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00239-020-09957-x}, pmid = {32617614}, issn = {1432-1432}, support = {210692/Z/18/Z//SFI-HRB-Wellcome Trust Biomedical Research Partnership/ ; 16/IA/4612/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {Phylogenetic models of the evolution of protein-coding sequences can provide insights into the selection pressures that have shaped them. In the application of these models synonymous nucleotide substitutions, which do not alter the encoded amino acid, are often assumed to have limited functional consequences and used as a proxy for the neutral rate of evolution. The ratio of nonsynonymous to synonymous substitution rates is then used to categorize the selective regime that applies to the protein (e.g., purifying selection, neutral evolution, diversifying selection). Here, we extend the Muse and Gaut model of codon evolution to explore the extent of purifying selection acting on substitutions between synonymous stop codons. Using a large collection of coding sequence alignments, we estimate that a high proportion (approximately 57%) of mammalian genes are affected by selection acting on stop codon preference. This proportion varies substantially by codon, with UGA stop codons far more likely to be conserved. Genes with evidence of selection acting on synonymous stop codons have distinctive characteristics, compared to unconserved genes with the same stop codon, including longer [Formula: see text] untranslated regions (UTRs) and shorter mRNA half-life. The coding regions of these genes are also much more likely to be under strong purifying selection pressure. Our results suggest that the preference for UGA stop codons found in many multicellular eukaryotes is selective rather than mutational in origin.}, }
@article {pmid32602227, year = {2020}, author = {Ryu, C and Walia, A and Ortiz, V and Perry, C and Woo, S and Reeves, BC and Sun, H and Winkler, J and Kanyo, JE and Wang, W and Vukmirovic, M and Ristic, N and Stratton, EA and Meena, SR and Minasyan, M and Kurbanov, D and Liu, X and Lam, TT and Farina, G and Gomez, JL and Gulati, M and Herzog, EL}, title = {Bioactive Plasma Mitochondrial DNA is Associated with Disease Progression in Scleroderma Associated Interstitial Lung Disease.}, journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/art.41418}, pmid = {32602227}, issn = {2326-5205}, abstract = {OBJECTIVE: SSc-ILD is characterized by variable clinical outcomes, activation of innate immune pattern recognition receptors (PRRs), and accumulation of αSMA expressing myofibroblasts. The association of these entities with mitochondrial DNA (mtDNA), an endogenous ligand for the intracellular DNA-sensing PRRs TLR9 and cGAS-STING, has yet to be determined.<br><br>METHODS: Human lung fibroblasts from normal donors (NHLFs) and SSc-ILD explants were treated with synthetic CpG DNA and assayed for αSMA expression and extracellular mtDNA using qPCR for the human MT-ATP6 gene. Plasma MT-ATP6 concentrations were evaluated in two independent SSc-ILD cohorts and demographically matched controls. The ability of control and SSc-ILD plasma to induce TLR9 and cGAS-STING activation was evaluated with commercially available HEK 293 reporter cells. Plasma concentrations of type I interferons, IL-6, and oxidized DNA were measured with using electrochemiluminescence and ELISA-based methods, respectively. Extracellular vesicles (EVs) precipitated from plasma were evaluated for MT-ATP6 concentrations and proteomics via liquid chromatography-mass spectrometry.<br><br>RESULTS: NHLFs and SSc-ILD fibroblasts develop increased αSMA expression and MT-ATP6 release following CpG stimulation. Plasma mtDNA concentrations are increased in two SSc-ILD cohorts, reflective of ventilatory decline, and positively associated with both TLR9 and cGAS-STING activation as well as Type I interferon and IL-6 expression. Plasma mtDNA is not oxidized and is conveyed by EVs displaying a proteomics profile consistent with a multicellular origin.<br><br>CONCLUSION: These findings demonstrate an unrecognized connection between EV-encapsulated mtDNA, clinical outcomes, and intracellular DNA-sensing PRR activation in SSc-ILD. Further study of these interactions could catalyze novel mechanistic and therapeutic insights into SSc-ILD and related disorders.}, }
@article {pmid32599749, year = {2020}, author = {Opalek, M and Wloch-Salamon, D}, title = {Aspects of Multicellularity in Saccharomyces cerevisiae Yeast: A Review of Evolutionary and Physiological Mechanisms.}, journal = {Genes}, volume = {11}, number = {6}, pages = {}, doi = {10.3390/genes11060690}, pmid = {32599749}, issn = {2073-4425}, support = {OPUS 2017/25/B/NZ8/01035//National Science Center of Poland/ ; DSC N18/MNS/000003//Faculty of Biology, Jagiellonian University/ ; N18/DBS/00003//Faculty of Biology, Jagiellonian University/ ; }, abstract = {The evolutionary transition from single-celled to multicellular growth is a classic and intriguing problem in biology. Saccharomyces cerevisiae is a useful model to study questions regarding cell aggregation, heterogeneity and cooperation. In this review, we discuss scenarios of group formation and how this promotes facultative multicellularity in S. cerevisiae. We first describe proximate mechanisms leading to aggregation. These mechanisms include staying together and coming together, and can lead to group heterogeneity. Heterogeneity is promoted by nutrient limitation, structured environments and aging. We then characterize the evolutionary benefits and costs of facultative multicellularity in yeast. We summarize current knowledge and focus on the newest state-of-the-art discoveries that will fuel future research programmes aiming to understand facultative microbial multicellularity.}, }
@article {pmid32592586, year = {2020}, author = {Lustofin, K and Świątek, P and Stolarczyk, P and Miranda, VFO and Płachno, BJ}, title = {Do food trichomes occur in Pinguicula (Lentibulariaceae) flowers?.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcaa123}, pmid = {32592586}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Floral food bodies (including edible trichomes) are a form of floral reward for pollinators. This type of nutritive reward has been recorded in several angiosperm families: Annonaceae, Araceae, Calycanthaceae, Eupomatiaceae, Himantandraceae, Nymphaeaceae, Orchidaceae, Pandanaceae and Winteraceae. Although these bodies are very diverse in their structure, their cells contain food material: starch grains, protein bodies or lipid droplets. In Pinguicula flowers, there are numerous multicellular clavate trichomes. Previous authors have proposed that these trichomes in the Pinguicula flower play the role of &quot;futterhaare&quot; (&quot;feeding hairs&quot;) and are eaten by pollinators. The main aim of this paper was to investigate whether the floral non-glandular trichomes of Pinguicula contain food reserves and thus are a reward for pollinators. The trichomes from the Pinguicula groups, which differ in their taxonomy (species from the subgenera: Temnoceras, Pinguicula, Isoloba) as well as the types of their pollinators (butterflies / flies and bees / hummingbirds), were examined. Thus, it was determined whether there are any connections between the occurrence of food trichomes and phylogeny position or pollination biology. Additionally, we determined the phylogenetic history of edible trichomes and pollinator evolution in the Pinguicula species.<br><br>METHODS: The species that were sampled were: Pinguicula moctezumae, P. esseriana, P. moranensis, P. emarginata, P. rectifolia, P. mesophytica, P. hemiepiphytica, P. agnata, P. albida, P. ibarrae, P. martinezii, P. filifolia, P. gigantea, P. lusitanica, P. alpina and P. vulgaris. Light microscopy, histochemistry, scanning and transmission electron microscopy were used to address our aims with a phylogenetic perspective based on matK/trnK DNA sequences.<br><br>KEY RESULTS: No accumulation of protein bodies or lipid droplets was recorded in the floral non-glandular trichomes of any of the analysed species. Starch grains occurred in the cells of the trichomes of the bee/fly-pollinated species: P. agnata, P. albida, P. ibarrae, P. martinezii, P. filifolia and P. gigantea but not in P. alpina or P. vulgaris. Moreover, starch grains were not recorded in the cells of the trichomes of the Pinguicula species that have long spurs, which are pollinated by Lepidoptera (P. moctezumae,P. esseriana, P. moranensis, P. emarginata, and P. rectifolia) or birds (P. mesophytica, P. hemiepihytica) or in species with a small and whitish corolla that self-pollinate (P. lusitanica). The results on the occurrence of edible trichomes and pollinator syndromes were mapped onto a phylogenetic reconstruction of the genus.<br><br>CONCLUSION: Floral non-glandular trichomes play the role of edible trichomes in some Pinguicula species (P. agnata, P. albida, P. ibarrae, P. martinezii, P. filifolia and P. gigantea), which are mainly classified as bee-pollinated species that had originated from Central and South America. It seems that in the Pinguicula that are pollinated by other pollinator groups (Lepidoptera, hummingbirds), the non-glandular trichomes in the flowers play a role other than that of a floral reward for their pollinators. Edible trichomes are symplesiomorphic for the Pinguicula species, and thus do not support a monophyletic group such as a synapomorphy. Nevertheless, edible trichomes are derived and are possibly a specialisation for fly and bee pollinators by acting as a food reward for these visitors.}, }
@article {pmid32582699, year = {2020}, author = {Dexheimer, PJ and Cochella, L}, title = {MicroRNAs: From Mechanism to Organism.}, journal = {Frontiers in cell and developmental biology}, volume = {8}, number = {}, pages = {409}, doi = {10.3389/fcell.2020.00409}, pmid = {32582699}, issn = {2296-634X}, abstract = {MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.}, }
@article {pmid32572049, year = {2020}, author = {Jacqueline, C and Parvy, JP and Rollin, ML and Faugère, D and Renaud, F and Missé, D and Thomas, F and Roche, B}, title = {The role of innate immunity in the protection conferred by a bacterial infection against cancer: study of an invertebrate model.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10106}, doi = {10.1038/s41598-020-66813-0}, pmid = {32572049}, issn = {2045-2322}, support = {INEE//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; A17196//Cancer Research UK (CRUK)/ ; STORY//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {All multicellular organisms are exposed to a diversity of infectious agents and to the emergence and proliferation of malignant cells. The protection conferred by some infections against cancer has been recently linked to the production of acquired immunity effectors such as antibodies. However, the evolution of innate immunity as a mechanism to prevent cancer and how it is jeopardized by infections remain poorly investigated. Here, we explored this question by performing experimental infections in two genetically modified invertebrate models (Drosophila melanogaster) that develop invasive or non-invasive neoplastic brain tumors. After quantifying tumor size and antimicrobial peptide gene expression, we found that Drosophila larvae infected with a naturally occurring bacterium had smaller tumors compared to controls and to fungus-infected larvae. This was associated with the upregulation of genes encoding two antimicrobial peptides-diptericin and drosomycin-that are known to be important mediators of tumor cell death. We further confirmed that tumor regression upon infection was associated with an increase in tumor cell death. Thus, our study suggests that infection could have a protective role through the production of antimicrobial peptides that increase tumor cell death. Finally, our study highlights the need to understand the role of innate immune effectors in the complex interactions between infections and cancer cell communities in order to develop innovative cancer treatment strategies.}, }
@article {pmid32571576, year = {2020}, author = {Li, XG and Zhang, WJ and Qi, XQ and Wu, LF}, title = {Genome analysis of Crassaminicella sp. SY095, an anaerobic mesophilic marine bacterium isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge.}, journal = {Marine genomics}, volume = {52}, number = {}, pages = {100733}, doi = {10.1016/j.margen.2019.100733}, pmid = {32571576}, issn = {1876-7478}, abstract = {Crassaminicella sp. strain SY095 is an anaerobic mesophilic marine bacterium that was recently isolated from a deep-sea hydrothermal vent on the Southwest Indian Ridge. Here, we present the complete genome sequence of strain SY095. The genome consists of a chromosome of 3,046,753 bp (G + C content of 30.81%) and a plasmid of 36,627 bp (G + C content of 31.29%), encodes 2966 protein, 135 tRNA genes, and 34 rRNA genes. Numerous genes are related to peptide transport, amino acid metabolism, motility, and sporulation. This agrees with the observation that strain SY095 is a spore-forming, motile, and chemoheterotrophic bacterium. Further, the genome harbors multiple prophages that carry all the genes necessary for viral particle synthesis. Some prophages carry additional genes that may be involved in the regulation of sporulation. This is the first reported genome of a bacterium from the genus Crassaminicella, providing insights into the microbial adaptation strategies to the deep-sea hydrothermal vent environment.}, }
@article {pmid32562277, year = {2020}, author = {Merle, N and Singh, P and Rahman, J and Kemper, C}, title = {Integrins meet complement: the evolutionary tip of an iceberg orchestrating metabolism and immunity.}, journal = {British journal of pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1111/bph.15168}, pmid = {32562277}, issn = {1476-5381}, abstract = {Immunologists have recently realized that there is more to the classic innate immune sensor systems than just mere protection against invading pathogens. It is becoming increasingly clear that such sensors, including the inflammasomes, toll-like receptors and the complement system, are heavily involved in the regulation of basic cell physiological processes and particularly those of metabolic nature. In fact, their 'non-canonical' activities make sense as no system directing immune cell activity can perform such task without the need for energy. Further, many of these ancient immune sensors appeared early and concurrently during evolution, particularly during the developmental leap from the single cell organisms to multicellularity, and therefore crosstalk heavily with each other. Here, we will review the current knowledge about the emerging cooperation between the major inter-cell communicators, integrins, and the cell-autonomous intracellularly and autocrine active complement, the complosome, during the regulation of single cell metabolism.}, }
@article {pmid32463355, year = {2020}, author = {Kuncha, SK and Venkadasamy, VL and Amudhan, G and Dahate, P and Kola, SR and Pottabathini, S and Kruparani, SP and Shekar, PC and Sankaranarayanan, R}, title = {Genomic innovation of ATD alleviates mistranslation associated with multicellularity in Animalia.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, doi = {10.7554/eLife.58118}, pmid = {32463355}, issn = {2050-084X}, support = {DST-INSPIRE//Department of Science and Technology, Ministry of Science and Technology/ ; J. C. Bose Fellowship//Science and Engineering Research Board/ ; Centre of Excellence//Department of Biotechnology , Ministry of Science and Technology/ ; Healthcare Theme project//Council of Scientific and Industrial Research/ ; Centre of Excellence//Department of Biotechnology, Ministry of Science and Technology/ ; }, abstract = {The emergence of multicellularity in Animalia is associated with increase in ROS and expansion of tRNA-isodecoders. tRNA expansion leads to misselection resulting in a critical error of L-Ala mischarged onto tRNAThr, which is proofread by Animalia-specific-tRNA Deacylase (ATD) in vitro. Here we show that in addition to ATD, threonyl-tRNA synthetase (ThrRS) can clear the error in cellular scenario. This two-tier functional redundancy for translation quality control breaks down during oxidative stress, wherein ThrRS is rendered inactive. Therefore, ATD knockout cells display pronounced sensitivity through increased mistranslation of threonine codons leading to cell death. Strikingly, we identify the emergence of ATD along with the error inducing tRNA species starting from Choanoflagellates thus uncovering an important genomic innovation required for multicellularity that occurred in unicellular ancestors of animals. The study further provides a plausible regulatory mechanism wherein the cellular fate of tRNAs can be switched from protein biosynthesis to non-canonical functions.}, }
@article {pmid32546936, year = {2020}, author = {Li, L and Liu, D and Liu, A and Li, J and Wang, H and Zhou, J}, title = {Genomic Survey of Tyrosine Kinases Repertoire in Electrophorus electricus With an Emphasis on Evolutionary Conservation and Diversification.}, journal = {Evolutionary bioinformatics online}, volume = {16}, number = {}, pages = {1176934320922519}, doi = {10.1177/1176934320922519}, pmid = {32546936}, issn = {1176-9343}, abstract = {Tyrosine kinases (TKs) play key roles in the regulation of multicellularity in organisms and involved primarily in cell growth, differentiation, and cell-to-cell communication. Genome-wide characterization of TKs has been conducted in many metazoans; however, systematic information regarding this superfamily in Electrophorus electricus (electric eel) is still lacking. In this study, we identified 114 TK genes in the E electricus genome and investigated their evolution, molecular features, and domain architecture using phylogenetic profiling to gain a better understanding of their similarities and specificity. Our results suggested that the electric eel TK (EeTK) repertoire was shaped by whole-genome duplications (WGDs) and tandem duplication events. Compared with other vertebrate TKs, gene members in Jak, Src, and EGFR subfamily duplicated specifically, but with members lost in Eph, Axl, and Ack subfamily in electric eel. We also conducted an exhaustive survey of TK genes in genomic databases, identifying 1674 TK proteins in 31 representative species covering all the main metazoan lineages. Extensive evolutionary analysis indicated that TK repertoire in vertebrates tended to be remarkably conserved, but the gene members in each subfamily were very variable. Comparative expression profile analysis showed that electric organ tissues and muscle shared a similar pattern with specific highly expressed TKs (ie, epha7, musk, jak1, and pdgfra), suggesting that regulation of TKs might play an important role in specifying an electric organ identity from its muscle precursor. We further identified TK genes exhibiting tissue-specific expression patterns, indicating that members in TKs participated in subfunctionalization representing an evolutionary divergence required for the performance of different tissues. This work generates valuable information for further gene function analysis and identifying candidate TK genes reflecting their unique tissue-function specializations in electric eel.}, }
@article {pmid32130216, year = {2020}, author = {Ronquist, F and Forshage, M and Häggqvist, S and Karlsson, D and Hovmöller, R and Bergsten, J and Holston, K and Britton, T and Abenius, J and Andersson, B and Buhl, PN and Coulianos, CC and Fjellberg, A and Gertsson, CA and Hellqvist, S and Jaschhof, M and Kjærandsen, J and Klopfstein, S and Kobro, S and Liston, A and Meier, R and Pollet, M and Riedel, M and Roháček, J and Schuppenhauer, M and Stigenberg, J and Struwe, I and Taeger, A and Ulefors, SO and Varga, O and Withers, P and Gärdenfors, U}, title = {Completing Linnaeus's inventory of the Swedish insect fauna: Only 5,000 species left?.}, journal = {PloS one}, volume = {15}, number = {3}, pages = {e0228561}, pmid = {32130216}, issn = {1932-6203}, mesh = {Animals ; *Biodiversity ; *Censuses ; Diptera/classification ; Ecosystem ; Europe ; *Extinction, Biological ; Insecta/*classification ; Phylogeny ; Records ; Sweden ; }, abstract = {Despite more than 250 years of taxonomic research, we still have only a vague idea about the true size and composition of the faunas and floras of the planet. Many biodiversity inventories provide limited insight because they focus on a small taxonomic subsample or a tiny geographic area. Here, we report on the size and composition of the Swedish insect fauna, thought to represent roughly half of the diversity of multicellular life in one of the largest European countries. Our results are based on more than a decade of data from the Swedish Taxonomy Initiative and its massive inventory of the country's insect fauna, the Swedish Malaise Trap Project The fauna is considered one of the best known in the world, but the initiative has nevertheless revealed a surprising amount of hidden diversity: more than 3,000 new species (301 new to science) have been documented so far. Here, we use three independent methods to analyze the true size and composition of the fauna at the family or subfamily level: (1) assessments by experts who have been working on the most poorly known groups in the fauna; (2) estimates based on the proportion of new species discovered in the Malaise trap inventory; and (3) extrapolations based on species abundance and incidence data from the inventory. For the last method, we develop a new estimator, the combined non-parametric estimator, which we show is less sensitive to poor coverage of the species pool than other popular estimators. The three methods converge on similar estimates of the size and composition of the fauna, suggesting that it comprises around 33,000 species. Of those, 8,600 (26%) were unknown at the start of the inventory and 5,000 (15%) still await discovery. We analyze the taxonomic and ecological composition of the estimated fauna, and show that most of the new species belong to Hymenoptera and Diptera groups that are decomposers or parasitoids. Thus, current knowledge of the Swedish insect fauna is strongly biased taxonomically and ecologically, and we show that similar but even stronger biases have distorted our understanding of the fauna in the past. We analyze latitudinal gradients in the size and composition of known European insect faunas and show that several of the patterns contradict the Swedish data, presumably due to similar knowledge biases. Addressing these biases is critical in understanding insect biomes and the ecosystem services they provide. Our results emphasize the need to broaden the taxonomic scope of current insect monitoring efforts, a task that is all the more urgent as recent studies indicate a possible worldwide decline in insect faunas.}, }
@article {pmid32535731, year = {2020}, author = {Hammarlund, EU and Amend, SR and Pienta, KJ}, title = {The issues with tissues: the wide range of cell fate separation enables the evolution of multicellularity and cancer.}, journal = {Medical oncology (Northwood, London, England)}, volume = {37}, number = {7}, pages = {62}, doi = {10.1007/s12032-020-01387-5}, pmid = {32535731}, issn = {1559-131X}, support = {2019-05254//Vetenskapsrådet/ ; 690817//H2020 Marie Skłodowska-Curie Actions/ ; U54CA143803//National Cancer Institute/ ; CA163124//National Cancer Institute/ ; CA093900//National Cancer Institute/ ; CA143055//National Cancer Institute/ ; }, abstract = {Our understanding of the rises of animal and cancer multicellularity face the same conceptual hurdles: what makes the clade originate and what makes it diversify. Between the events of origination and diversification lies complex tissue organization that gave rise to novel functionality for organisms and, unfortunately, for malignant transformation in cells. Tissue specialization with distinctly separated cell fates allowed novel functionality at organism level, such as for vertebrate animals, but also involved trade-offs at the cellular level that are potentially disruptive. These trade-offs are under-appreciated and here we discuss how the wide separation of cell phenotypes may contribute to cancer evolution by (a) how factors can reverse differentiated cells into a window of phenotypic plasticity, (b) the reversal to phenotypic plasticity coupled with asexual reproduction occurs in a way that the host cannot adapt, and (c) the power of the transformation factor correlates to the power needed to reverse tissue specialization. The role of reversed cell fate separation for cancer evolution is strengthened by how some tissues and organisms maintain high cell proliferation and plasticity without developing tumours at a corresponding rate. This demonstrates a potential proliferation paradox that requires further explanation. These insights from the cancer field, which observes tissue evolution in real time and closer than any other field, allow inferences to be made on evolutionary events in animal history. If a sweet spot of phenotypic and reproductive versatility is key to transformation, factors stimulating cell fate separation may have promoted also animal diversification on Earth.}, }
@article {pmid32523039, year = {2020}, author = {Duraivelan, K and Samanta, D}, title = {Tracing the evolution of nectin and nectin-like cell adhesion molecules.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9434}, doi = {10.1038/s41598-020-66461-4}, pmid = {32523039}, issn = {2045-2322}, abstract = {Nectin and nectin-like cell adhesion molecules (collectively referred as nectin family henceforth) are known to mediate cell-cell adhesion and related functions. While current literature suggests that nectins are prevalent in vertebrates, there are no in-depth analyses regarding the evolution of nectin family as a whole. In this work, we examine the evolutionary origin of the nectin family, using selected multicellular metazoans representing diverse clades whose whole genome sequencing data is available. Our results show that this family may have appeared earlier during metazoan evolution than previously believed. Systematic analyses indicate the order in which various members of nectin family seem to have evolved, with some nectin-like molecules appearing first, followed by the evolution of other members. Furthermore, we also found a few possible ancient homologues of nectins. While our study confirms the previous grouping of the nectin family into nectins and nectin-like molecules, it also shows poliovirus receptor (PVR/nectin-like-5) to possess characteristics that are intermediate between these two groups. Interestingly, except for PVR, the other nectins show surprising sequence conservations across species, suggesting evolutionary constraints due to critical roles played by these proteins.}, }
@article {pmid32521019, year = {2020}, author = {Phansopa, C and Dunning, LT and Reid, JD and Christin, PA}, title = {Lateral gene transfer acts as an evolutionary shortcut to efficient C4 biochemistry.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaa143}, pmid = {32521019}, issn = {1537-1719}, abstract = {The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase (PEPC), an enzyme that catalyses one of the key reactions in the C4 pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C4 trait much earlier. By comparing the enzyme kinetics we show that native isoforms with few amino acid replacements have substrate KM values similar to the non-C4 ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C4 isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.}, }
@article {pmid32517626, year = {2020}, author = {Laundon, D and Chrismas, N and Wheeler, G and Cunliffe, M}, title = {Chytrid rhizoid morphogenesis resembles hyphal development in multicellular fungi and is adaptive to resource availability.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1928}, pages = {20200433}, doi = {10.1098/rspb.2020.0433}, pmid = {32517626}, issn = {1471-2954}, abstract = {Key to the ecological prominence of fungi is their distinctive cell biology, our understanding of which has been principally based on dikaryan hyphal and yeast forms. The early-diverging Chytridiomycota (chytrids) are ecologically important and a significant component of fungal diversity, yet their cell biology remains poorly understood. Unlike dikaryan hyphae, chytrids typically attach to substrates and feed osmotrophically via anucleate rhizoids. The evolution of fungal hyphae appears to have occurred from rhizoid-bearing lineages and it has been hypothesized that a rhizoid-like structure was the precursor to multicellular hyphae. Here, we show in a unicellular chytrid, Rhizoclosmatium globosum, that rhizoid development exhibits striking similarities with dikaryan hyphae and is adaptive to resource availability. Rhizoid morphogenesis exhibits analogous patterns to hyphal growth and is controlled by β-glucan-dependent cell wall synthesis and actin polymerization. Chytrid rhizoids growing from individual cells also demonstrate adaptive morphological plasticity in response to resource availability, developing a searching phenotype when carbon starved and spatial differentiation when interacting with particulate organic matter. We demonstrate that the adaptive cell biology and associated developmental plasticity considered characteristic of hyphal fungi are shared more widely across the Kingdom Fungi and therefore could be conserved from their most recent common ancestor.}, }
@article {pmid32514997, year = {2020}, author = {Villagra, C and Frías-Lasserre, D}, title = {Epigenetic Molecular Mechanisms in Insects.}, journal = {Neotropical entomology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s13744-020-00777-8}, pmid = {32514997}, issn = {1678-8052}, abstract = {Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.}, }
@article {pmid32505051, year = {2020}, author = {Oates, AC}, title = {Waiting on the Fringe: cell autonomy and signaling delays in segmentation clocks.}, journal = {Current opinion in genetics &amp; development}, volume = {63}, number = {}, pages = {61-70}, doi = {10.1016/j.gde.2020.04.008}, pmid = {32505051}, issn = {1879-0380}, abstract = {The rhythmic and sequential segmentation of the vertebrate body axis into somites during embryogenesis is governed by a multicellular, oscillatory patterning system called the segmentation clock. Despite many overt similarities between vertebrates, differences in genetic and dynamic regulation have been reported, raising intriguing questions about the evolution and conservation of this fundamental patterning process. Recent studies have brought insights into two important and related issues: (1) whether individual cells of segmentation clocks are autonomous oscillators or require cell-cell communication for their rhythm; and (2) the role of delays in the cell-cell communication that synchronizes the population of genetic oscillators. Although molecular details differ between species, conservation may exist at the level of the dynamics, hinting at rules for evolutionary trajectories in the system.}, }
@article {pmid32496191, year = {2020}, author = {Booth, DS and King, N}, title = {Genome editing enables reverse genetics of multicellular development in the choanoflagellate Salpingoeca rosetta.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, doi = {10.7554/eLife.56193}, pmid = {32496191}, issn = {2050-084X}, abstract = {In a previous study, we established a forward genetic screen to identify genes required for multicellular development in the choanoflagellate, Salpingoeca rosetta (Levin et al., 2014). Yet, the paucity of reverse genetic tools for choanoflagellates has hampered direct tests of gene function and impeded the establishment of choanoflagellates as a model for reconstructing the origin of their closest living relatives, the animals. Here we establish CRISPR/Cas9-mediated genome editing in S. rosetta by engineering a selectable marker to enrich for edited cells. We then use genome editing to disrupt the coding sequence of a S. rosetta C-type lectin gene, rosetteless, and thereby demonstrate its necessity for multicellular rosette development. This work advances S. rosetta as a model system in which to investigate how genes identified from genetic screens and genomic surveys function in choanoflagellates and evolved as critical regulators of animal biology.}, }
@article {pmid30912270, year = {2019}, author = {Hamant, O and Bhat, R and Nanjundiah, V and Newman, SA}, title = {Does resource availability help determine the evolutionary route to multicellularity?.}, journal = {Evolution &amp; development}, volume = {21}, number = {3}, pages = {115-119}, pmid = {30912270}, issn = {1525-142X}, support = {ICTS/Prog-LivingMatter2018/04//International Centre for Theoretical Sciences (ICTS)/International ; ERC-2013-CoG-615739 &quot;MechanoDevo&quot;/ERC_/European Research Council/International ; 0412//CSIR/International ; 1586//SERB DST Early Career Grant/International ; }, mesh = {Animals ; *Biological Evolution ; *Gene Expression Regulation, Developmental ; *Genetic Variation ; }, abstract = {Genetic heterogeneity and homogeneity are associated with distinct sets of adaptive advantages and bottlenecks, both in developmental biology and population genetics. Whereas populations of individuals are usually genetically heterogeneous, most multicellular metazoans are genetically homogeneous. Observing that resource scarcity fuels genetic heterogeneity in populations, we propose that monoclonal development is compatible with the resource-rich and stable internal environments that complex multicellular bodies offer. In turn, polyclonal development persists in tumors and in certain metazoans, both exhibiting a closer dependence on external resources. This eco-evo-devo approach also suggests that multicellularity may originally have emerged through polyclonal development in early metazoans, because of their reduced shielding from environmental fluctuations.}, }
@article {pmid32472019, year = {2020}, author = {Lawal, HM and Schilde, C and Kin, K and Brown, MW and James, J and Prescott, AR and Schaap, P}, title = {Cold climate adaptation is a plausible cause for evolution of multicellular sporulation in Dictyostelia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8797}, doi = {10.1038/s41598-020-65709-3}, pmid = {32472019}, issn = {2045-2322}, abstract = {Unicellular protozoa that encyst individually upon starvation evolved at least eight times into organisms that instead form multicellular fruiting bodies with spores. The Dictyostelia are the largest and most complex group of such organisms. They can be subdivided into 4 major groups, with many species in groups 1-3 having additionally retained encystment. To understand fitness differences between spores and cysts, we measured long-term survival of spores and cysts under climate-mimicking conditions, investigated spore and cyst ultrastructure, and related fitness characteristics to species ecology. We found that spores and cysts survived 22 °C equally well, but that spores survived wet and dry frost better than cysts, with group 4 spores being most resilient. Spore walls consist of three layers and those of cysts of maximally two, while spores were also more compacted than cysts, with group 4 spores being the most compacted. Group 4 species were frequently isolated from arctic and alpine zones, which was rarely the case for group 1-3 species. We inferred a fossil-calibrated phylogeny of Dictyostelia, which showed that its two major branches diverged 0.52 billion years ago, following several global glaciations. Our results suggest that Dictyostelium multicellular sporulation was a likely adaptation to a cold climate.}, }
@article {pmid32471172, year = {2020}, author = {Demin, SI and Bogolyubov, DS and Granovitch, AI and Mikhailova, NA}, title = {New data on spermatogenic cyst formation and cellular composition of the testis in a marine gastropod, Littorina saxatilis.}, journal = {International journal of molecular sciences}, volume = {21}, number = {11}, pages = {}, doi = {10.3390/ijms21113792}, pmid = {32471172}, issn = {1422-0067}, support = {АААА-А17-117122790092-9//Russian Academy of Sciences/ ; 19-14-00321//Russian Science Support Foundation/ ; 0.40.491.2017//St. Petersburg State University/ ; }, abstract = {Knowledge of the testis structure is important for gastropod taxonomy and phylogeny, particularly for the comparative analysis of sympatric Littorina species. Observing fresh tissue and squashing fixed tissue with gradually increasing pressure, we have recently described a peculiar type of cystic spermatogenesis, rare in mollusks. It has not been documented in most mollusks until now. The testis of adult males consists of numerous lobules filled with multicellular cysts containing germline cells at different stages of differentiation. Each cyst is formed by one cyst cell of somatic origin. Here, we provide evidence for the existence of two ways of cyst formation in Littorina saxatilis. One of them begins with a goniablast cyst formation; it somewhat resembles cyst formation in Drosophila testes. The second way begins with capture of a free spermatogonium by the polyploid cyst cell which is capable to move along the gonad tissues. This way of cyst formation has not been described previously. Our data expand the understanding of the diversity of spermatogenesis types in invertebrates.}, }
@article {pmid32471018, year = {2020}, author = {Kuroiwa, A}, title = {Enhancers, development, and evolution.}, journal = {Development, growth &amp; differentiation}, volume = {}, number = {}, pages = {}, doi = {10.1111/dgd.12683}, pmid = {32471018}, issn = {1440-169X}, abstract = {A single-celled fertilized egg develops into a complex, multicellular animal through a series of selection processes of developmental pathways. During these processes, regulatory genes exhibit spatiotemporally restricted expression under the control of the species-specific genetic program, and dictate developmental processes from germ layer formation to cellular differentiation. Elucidation of molecular mechanisms underlying developmental processes and also of mechanistic bases for morphological diversification during evolution is one of the central issues in contemporary developmental biology. Progress has been made due to recent technological innovations, such as high-throughput nucleotide sequencing, live-cell imaging, efficient genetic manipulation, and establishment of the organoid system, opening new avenues to the above issues.}, }
@article {pmid32462426, year = {2020}, author = {Casanova, JL and Abel, L}, title = {The human genetic determinism of life-threatening infectious diseases: genetic heterogeneity and physiological homogeneity?.}, journal = {Human genetics}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00439-020-02184-w}, pmid = {32462426}, issn = {1432-1203}, abstract = {Multicellular eukaryotes emerged late in evolution from an ocean of viruses, bacteria, archaea, and unicellular eukaryotes. These macroorganisms are exposed to and infected by a tremendous diversity of microorganisms. Those that are large enough can even be infected by multicellular fungi and parasites. Each interaction is unique, if only because it operates between two unique living organisms, in an infinite diversity of circumstances. This is neatly illustrated by the extraordinarily high level of interindividual clinical variability in human infections, even for a given pathogen, ranging from a total absence of clinical manifestations to death. We discuss here the idea that the determinism of human life-threatening infectious diseases can be governed by single-gene inborn errors of immunity, which are rarely Mendelian and frequently display incomplete penetrance. We briefly review the evidence in support of this notion obtained over the last two decades, referring to a number of focused and thorough reviews published by eminent colleagues in this issue of Human Genetics. It seems that almost any life-threatening infectious disease can be driven by at least one, and, perhaps, a great many diverse monogenic inborn errors, which may nonetheless be immunologically related. While the proportions of monogenic cases remain unknown, a picture in which genetic heterogeneity is combined with physiological homogeneity is emerging from these studies. A preliminary sketch of the human genetic architecture of severe infectious diseases is perhaps in sight.}, }
@article {pmid32253342, year = {2020}, author = {Urrejola, C and von Dassow, P and van den Engh, G and Salas, L and Mullineaux, CW and Vicuña, R and Sánchez-Baracaldo, P}, title = {Loss of Filamentous Multicellularity in Cyanobacteria: the Extremophile Gloeocapsopsis sp. Strain UTEX B3054 Retained Multicellular Features at the Genomic and Behavioral Levels.}, journal = {Journal of bacteriology}, volume = {202}, number = {12}, pages = {}, doi = {10.1128/JB.00514-19}, pmid = {32253342}, issn = {1098-5530}, abstract = {Multicellularity in Cyanobacteria played a key role in their habitat expansion, contributing to the Great Oxidation Event around 2.45 billion to 2.32 billion years ago. Evolutionary studies have indicated that some unicellular cyanobacteria emerged from multicellular ancestors, yet little is known about how the emergence of new unicellular morphotypes from multicellular ancestors occurred. Our results give new insights into the evolutionary reversion from which the Gloeocapsopsis lineage emerged. Flow cytometry and microscopy results revealed morphological plasticity involving the patterned formation of multicellular morphotypes sensitive to environmental stimuli. Genomic analyses unveiled the presence of multicellularity-associated genes in its genome. Calcein-fluorescence recovery after photobleaching (FRAP) experiments confirmed that Gloeocapsopsis sp. strain UTEX B3054 carries out cell-to-cell communication in multicellular morphotypes but at slower time scales than filamentous cyanobacteria. Although traditionally classified as unicellular, our results suggest that Gloeocapsopsis displays facultative multicellularity, a condition that may have conferred ecological advantages for thriving as an extremophile for more than 1.6 billion years.IMPORTANCECyanobacteria are among the few prokaryotes that evolved multicellularity. The early emergence of multicellularity in Cyanobacteria (2.5 billion years ago) entails that some unicellular cyanobacteria reverted from multicellular ancestors. We tested this evolutionary hypothesis by studying the unicellular strain Gloeocapsopsis sp. UTEX B3054 using flow cytometry, genomics, and cell-to-cell communication experiments. We demonstrate the existence of a well-defined patterned organization of cells in clusters during growth, which might change triggered by environmental stimuli. Moreover, we found genomic signatures of multicellularity in the Gloeocapsopsis genome, giving new insights into the evolutionary history of a cyanobacterial lineage that has thrived in extreme environments since the early Earth. The potential benefits in terms of resource acquisition and the ecological relevance of this transient behavior are discussed.}, }
@article {pmid32455681, year = {2020}, author = {Kim, SK and Jang, SD and Kim, H and Chung, S and Park, JK and Kuh, HJ}, title = {Phenotypic Heterogeneity and Plasticity of Cancer Cell Migration in a Pancreatic Tumor Three-Dimensional Culture Model.}, journal = {Cancers}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/cancers12051305}, pmid = {32455681}, issn = {2072-6694}, support = {2019R1A5A2027588//National Research Foundation of Korea/ ; 2019R1A2B5B02070524//National Research Foundation of Korea/ ; }, abstract = {Invasive cancer cell migration is a key feature of metastatic human pancreatic ductal adenocarcinoma (PDAC), yet the underlying mechanisms remain poorly understood. Here, we investigated modes of cancer cell invasion using two pancreatic cancer cell lines with differential epithelial-mesenchymal status, PANC-1 and BxPC-3, under 3D culture conditions. Multicellular tumor spheroids (TSs) were grown in a collagen matrix co-cultured with pancreatic stellate cells (PSCs) using microchannel chips. PANC-1 cells showed individual migration from TSs via invadopodium formation. BxPC-3 cells showed plasticity between collective and individual migration in either mesenchymal mode, with filopodium-like protrusions, or blebby amoeboid mode. These two cell lines showed significantly different patterns of extracellular matrix (ECM) remodeling, with MMP-dependent degradation in a limited area of ECM around invadopodia for PANC-1 cells, or MMP-independent extensive deformation of ECM for BxPC-3 cells. Cancer cell migration out of the collagen channel significantly increased by PSCs and directional cancer cell migration was mediated by fibronectin deposited by PSCs. Our results highlight the phenotypic heterogeneity and plasticity of PDAC cell migration and ECM remodeling under 3D culture conditions. This 3D co-culture model of pancreatic cancer cells and PSCs offers a useful tool for studying cancer cell migration and ECM remodeling to identify and develop potential molecular targets and anti-cancer agents against human PDAC.}, }
@article {pmid32455487, year = {2020}, author = {Kumler, WE and Jorge, J and Kim, PM and Iftekhar, N and Koehl, MAR}, title = {Does Formation of Multicellular Colonies by Choanoflagellates Affect Their Susceptibility to Capture by Passive Protozoan Predators?.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12808}, pmid = {32455487}, issn = {1550-7408}, abstract = {Microbial eukaryotes, critical links in aquatic food webs, are unicellular, but some, such as choanoflagellates, form multicellular colonies. Are there consequences to predator avoidance of being unicellular versus forming larger colonies? Choanoflagellates share a common ancestor with animals and are used as model organisms to study the evolution of multicellularity. Escape in size from protozoan predators is suggested as a selective factor favoring evolution of multicellularity. Heterotrophic protozoans are categorized as suspension feeders, motile raptors, or passive predators that eat swimming prey which bump into them. We focused on passive predation and measured the mechanisms responsible for the susceptibility of unicellular versus multicellular choanoflagellates, Salpingoeca helianthica, to capture by passive heliozoan predators, Actinosphaerium nucleofilum, which trap prey on axopodia radiating from the cell body. Microvideography showed that unicellular and colonial choanoflagellates entered the predator's capture zone at similar frequencies, but a greater proportion of colonies contacted axopodia. However, more colonies than single cells were lost during transport by axopodia to the cell body. Thus, feeding efficiency (proportion of prey entering the capture zone that were engulfed in phagosomes) was the same for unicellular and multicellular prey, suggesting that colony formation is not an effective defense against such passive predators.}, }
@article {pmid32450967, year = {2020}, author = {McQueen, E and Rebeiz, M}, title = {On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution?.}, journal = {Current topics in developmental biology}, volume = {139}, number = {}, pages = {375-405}, doi = {10.1016/bs.ctdb.2020.03.002}, pmid = {32450967}, issn = {1557-8933}, abstract = {The process of multicellular organismal development hinges upon the specificity of developmental programs: for different parts of the organism to form unique features, processes must exist to specify each part. This specificity is thought to be hardwired into gene regulatory networks, which activate cohorts of genes in particular tissues at particular times during development. However, the evolution of gene regulatory networks sometimes occurs by mechanisms that sacrifice specificity. One such mechanism is network co-option, in which existing gene networks are redeployed in new developmental contexts. While network co-option may offer an efficient mechanism for generating novel phenotypes, losses of tissue specificity at redeployed network genes could restrict the ability of the affected traits to evolve independently. At present, there has not been a detailed discussion regarding how tissue specificity of network genes might be altered due to gene network co-option at its initiation, as well as how trait independence can be retained or restored after network co-option. A lack of clarity about network co-option makes it more difficult to speculate on the long-term evolutionary implications of this mechanism. In this review, we will discuss the possible initial outcomes of network co-option, outline the mechanisms by which networks may retain or subsequently regain specificity after network co-option, and comment on some of the possible evolutionary consequences of network co-option. We place special emphasis on the need to consider selectively-neutral outcomes of network co-option to improve our understanding of the role of this mechanism in trait evolution.}, }
@article {pmid32444651, year = {2020}, author = {Heaton, LLM and Jones, NS and Fricker, MD}, title = {A mechanistic explanation of the transition to simple multicellularity in fungi.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2594}, doi = {10.1038/s41467-020-16072-4}, pmid = {32444651}, issn = {2041-1723}, abstract = {Development of multicellularity was one of the major transitions in evolution and occurred independently multiple times in algae, plants, animals, and fungi. However recent comparative genome analyses suggest that fungi followed a different route to other eukaryotic lineages. To understand the driving forces behind the transition from unicellular fungi to hyphal forms of growth, we develop a comparative model of osmotrophic resource acquisition. This predicts that whenever the local resource is immobile, hard-to-digest, and nutrient poor, hyphal osmotrophs outcompete motile or autolytic unicellular osmotrophs. This hyphal advantage arises because transporting nutrients via a contiguous cytoplasm enables continued exploitation of remaining resources after local depletion of essential nutrients, and more efficient use of costly exoenzymes. The model provides a mechanistic explanation for the origins of multicellular hyphal organisms, and explains why fungi, rather than unicellular bacteria, evolved to dominate decay of recalcitrant, nutrient poor substrates such as leaf litter or wood.}, }
@article {pmid32438974, year = {2020}, author = {Yang, S and Qu, G and Fu, B and Yang, F and Zeng, W and Cai, Y and Ye, T and Yang, Y and Deng, X and Xiang, W and Peng, D and Zhou, B}, title = {The function of KptA/Tpt1 gene - a minor review.}, journal = {Functional plant biology : FPB}, volume = {}, number = {}, pages = {}, doi = {10.1071/FP19159}, pmid = {32438974}, issn = {1445-4416}, abstract = {Rapid response of uni- and multicellular organisms to environmental changes and their own growth is achieved through a series of molecular mechanisms, often involving modification of macromolecules, including nucleic acids, proteins and lipids. The ADP-ribosylation process has ability to modify these different macromolecules in cells, and is closely related to the biological processes, such as DNA replication, transcription, signal transduction, cell division, stress, microbial aging and pathogenesis. In addition, tRNA plays an essential role in the regulation of gene expression, as effector molecules, no-load tRNA affects the overall gene expression level of cells under some nutritional stress. KptA/Tpt1 is an essential phosphotransferase in the process of pre-tRNA splicing, releasing mature tRNA and participating in ADP-ribose. The objective of this review is concluding the gene structure, the evolution history and the function of KptA/Tpt1 from prokaryote to eukaryote organisms. At the same time, the results of promoter elements analysis were also shown in the present study. Moreover, the problems in the function of KptA/Tpt1 that have not been clarified at the present time are summarised, and some suggestions to solve those problems are given. This review presents no only a summary of clear function of KptA/Tpt1 in the process of tRNA splicing and ADP-ribosylation of organisms, but also gives some proposals to clarify unclear problems of it in the future.}, }
@article {pmid32431731, year = {2020}, author = {Krueger-Hadfield, SA}, title = {What's ploidy got to do with it? Understanding the evolutionary ecology of macroalgal invasions necessitates incorporating life cycle complexity.}, journal = {Evolutionary applications}, volume = {13}, number = {3}, pages = {486-499}, doi = {10.1111/eva.12843}, pmid = {32431731}, issn = {1752-4571}, abstract = {Biological invasions represent grave threats to terrestrial, aquatic, and marine ecosystems, but our understanding of the role of evolution during invasions remains rudimentary. In marine environments, macroalgae account for a large percentage of invaders, but their complicated life cycles render it difficult to move methodologies and predictions wholesale from species with a single, free-living ploidy stage, such as plants or animals. In haplodiplontic macroalgae, meiosis and fertilization are spatiotemporally separated by long-lived, multicellular haploid and diploid stages, and gametes are produced by mitosis, not meiosis. As a consequence, there are unique eco-evolutionary constraints that are not typically considered in invasions. First, selfing can occur in both monoicious (i.e., hermaphroditic) and dioicious (i.e., separate sexes) haplodiplontic macroalgae. In the former, fertilization between gametes produced by the same haploid thallus results in instantaneous, genome-wide homozygosity. In the latter, cross-fertilization between separate male and female haploids that share the same diploid parent is analogous to selfing in plants or animals. Separate sexes, therefore, cannot be used as a proxy for outcrossing. Second, selfing likely facilitates invasions (i.e., Baker's law) and the long-lived haploid stage may enable purging of deleterious mutations, further contributing to invasion success. Third, asexual reproduction will result in the dominance of one ploidy and/or sex and the loss of the other(s). Whether or not sexual reproduction can be recovered depends on which stage is maintained. Finally, fourth, haplodiplontic life cycles are predicted to be maintained through niche differentiation in the haploid and diploid stages. Empirical tests are rare, but fundamental to our understanding of macroalgal invasion dynamics. By highlighting these four phenomena, we can build a framework with which to empirically and theoretically address important gaps in the literature on marine evolutionary ecology, of which biological invasions can serve as unnatural laboratories.}, }
@article {pmid32428501, year = {2020}, author = {Arendt, D}, title = {The Evolutionary Assembly of Neuronal Machinery.}, journal = {Current biology : CB}, volume = {30}, number = {10}, pages = {R603-R616}, doi = {10.1016/j.cub.2020.04.008}, pmid = {32428501}, issn = {1879-0445}, abstract = {Neurons are highly specialized cells equipped with a sophisticated molecular machinery for the reception, integration, conduction and distribution of information. The evolutionary origin of neurons remains unsolved. How did novel and pre-existing proteins assemble into the complex machinery of the synapse and of the apparatus conducting current along the neuron? In this review, the step-wise assembly of functional modules in neuron evolution serves as a paradigm for the emergence and modification of molecular machinery in the evolution of cell types in multicellular organisms. The pre-synaptic machinery emerged through modification of calcium-regulated large vesicle release, while the postsynaptic machinery has different origins: the glutamatergic postsynapse originated through the fusion of a sensory signaling module and a module for filopodial outgrowth, while the GABAergic postsynapse incorporated an ancient actin regulatory module. The synaptic junction, in turn, is built around two adhesion modules controlled by phosphorylation, which resemble septate and adherens junctions. Finally, neuronal action potentials emerged via a series of duplications and modifications of voltage-gated ion channels. Based on these origins, key molecular innovations are identified that led to the birth of the first neuron in animal evolution.}, }
@article {pmid32421773, year = {2020}, author = {Tollis, M and Schneider-Utaka, AK and Maley, CC}, title = {The Evolution of Human Cancer Gene Duplications across Mammals.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaa125}, pmid = {32421773}, issn = {1537-1719}, abstract = {Cancer is caused by genetic alterations that affect cellular fitness, and multicellular organisms have evolved mechanisms to suppress cancer such as cell cycle checkpoints and apoptosis. These pathways may be enhanced by the addition of tumor suppressor gene paralogs or deletion of oncogenes. To provide insights to the evolution of cancer suppression across the mammalian radiation, we estimated copy numbers for 548 human tumor suppressor gene and oncogene homologs in 63 mammalian genome assemblies. The naked mole rat contained the most cancer gene copies, consistent with the extremely low rates of cancer found in this species. We found a positive correlation between a species' cancer gene copy number and it's longevity, but not body size, contrary to predictions from Peto's Paradox. Extremely long-lived mammals also contained more copies of caretaker genes in their genomes, suggesting that the maintenance of genome integrity is an essential form of cancer prevention in long-lived species. We found the strongest association between longevity and copy numbers of genes that are both germline and somatic tumor suppressor genes, suggesting selection has acted to suppress both hereditary and sporadic cancers. We also found a strong relationship between the number of tumor suppressor genes and the number of oncogenes in mammalian genomes, suggesting complex regulatory networks mediate the balance between cell proliferation and checks on tumor progression. This study is the first to investigate cancer gene expansions across the mammalian radiation and provides a springboard for potential human therapies based on evolutionary medicine.}, }
@article {pmid32419346, year = {2020}, author = {Guzmán-Herrera, A and Arias Del Angel, JA and Rivera-Yoshida, N and Benítez, M and Franci, A}, title = {Dynamical patterning modules and network motifs as joint determinants of development: Lessons from an aggregative bacterium.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22946}, pmid = {32419346}, issn = {1552-5015}, support = {471963//Consejo Nacional de Ciencia y Tecnología/ ; 580236//Consejo Nacional de Ciencia y Tecnología/ ; A1-S-10610//Consejo Nacional de Ciencia y Tecnología/ ; PAPIIT IA105518//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México: Programa de Becas Posdoctorales/ ; }, abstract = {Development and evolution are dynamical processes under the continuous control of organismic and environmental factors. Generic physical processes, associated with biological materials and certain genes or molecules, provide a morphological template for the evolution and development of organism forms. Generic dynamical behaviors, associated with recurring network motifs, provide a temporal template for the regulation and coordination of biological processes. The role of generic physical processes and their associated molecules in development is the topic of the dynamical patterning module (DPM) framework. The role of generic dynamical behaviors in biological regulation is studied via the identification of the associated network motifs (NMs). We propose a joint DPM-NM perspective on the emergence and regulation of multicellularity focusing on a multicellular aggregative bacterium, Myxococcus xanthus. Understanding M. xanthus development as a dynamical process embedded in a physical substrate provides novel insights into the interaction between developmental regulatory networks and generic physical processes in the evolutionary transition to multicellularity.}, }
@article {pmid32415185, year = {2020}, author = {Hörandl, E and Hadacek, F}, title = {Oxygen, life forms, and the evolution of sexes in multicellular eukaryotes.}, journal = {Heredity}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41437-020-0317-9}, pmid = {32415185}, issn = {1365-2540}, abstract = {The evolutionary advantage of different sexual systems in multicellular eukaryotes is still not well understood, because the differentiation into male and female individuals halves offspring production compared with asexuality. Here we propose that various physiological adaptations to oxidative stress could have forged sessility versus motility, and consequently the evolution of sexual systems in multicellular animals, plants, and fungi. Photosynthesis causes substantial amounts of oxidative stress in photoautotrophic plants and, likewise, oxidative chemistry of polymer breakdown, cellulose and lignin, for saprotrophic fungi. In both cases, its extent precludes motility, an additional source of oxidative stress. Sessile life form and the lack of neuronal systems, however, limit options for mate recognition and adult sexual selection, resulting in inefficient mate-searching systems. Hence, sessility requires that all individuals can produce offspring, which is achieved by hermaphroditism in plants and/or by multiple mating types in fungi. In animals, motility requires neuronal systems, and muscle activity, both of which are highly sensitive to oxidative damage. As a consequence, motility has evolved in animals as heterotrophic organisms that (1) are not photosynthetically active, and (2) are not primary decomposers. Adaptations to motility provide prerequisites for an active mating behavior and efficient mate-searching systems. These benefits compensate for the &quot;cost of males&quot;, and may explain the early evolution of sex chromosomes in metazoans. We conclude that different sexual systems evolved under the indirect physiological constraints of lifestyles.}, }
@article {pmid32412616, year = {2018}, author = {Xiao, S and Tang, Q}, title = {After the boring billion and before the freezing millions: evolutionary patterns and innovations in the Tonian Period.}, journal = {Emerging topics in life sciences}, volume = {2}, number = {2}, pages = {161-171}, doi = {10.1042/ETLS20170165}, pmid = {32412616}, issn = {2397-8554}, abstract = {The Tonian Period (ca. 1000-720 Ma) follows the 'boring billion' in the Mesoproterozoic Era and precedes 'snowball Earth' glaciations in the Cryogenian Period. It represents a critical transition in Earth history. Geochemical data indicate that the Tonian Period may have witnessed a significant increase in atmospheric pO2 levels and a major transition from predominantly sulfidic to ferruginous mid-depth seawaters. Molecular clock estimates suggest that early animals may have diverged in the Tonian Period, raising the intriguing possibility of coupled environmental changes and evolutionary innovations. The co-evolution of life and its environment during the Tonian Period can be tested against the fossil record by examining diversity trends in the Proterozoic and evolutionary innovations in the Tonian. Compilations of Proterozoic microfossils and macrofossils apparently support a Tonian increase in global taxonomic diversity and morphological range relative to the Mesoproterozoic Era, although this is not reflected in assemblage-level diversity patterns. The fossil record suggests that major eukaryote groups (including Opisthokonta, Amoebozoa, Plantae, and SAR) may have diverged and important evolutionary innovations (e.g. multicellularity and cell differentiation in several groups, eukaryovory, eukaryote biomineralization, and heterocystous cyanobacteria) may have arisen by the Tonian Period, but thus far no convincing animal fossils have been found in the Tonian. Tonian paleontology is still in its nascent stage, and it offers many opportunities to explore Earth-life evolution in this critical geological period.}, }
@article {pmid32412615, year = {2018}, author = {Mills, DB and Francis, WR and Canfield, DE}, title = {Animal origins and the Tonian Earth system.}, journal = {Emerging topics in life sciences}, volume = {2}, number = {2}, pages = {289-298}, doi = {10.1042/ETLS20170160}, pmid = {32412615}, issn = {2397-8554}, abstract = {The Neoproterozoic Era (1000-541 million years ago, Ma) was characterized by dramatic environmental and evolutionary change, including at least two episodes of extensive, low-latitude glaciation, potential changes in the redox structure of the global ocean, and the origin and diversification of animal life. How these different events related to one another remains an active area of research, particularly how these environmental changes influenced, and were influenced by, the earliest evolution of animals. Animal multicellularity is estimated to have evolved in the Tonian Period (1000-720 Ma) and represents one of at least six independent acquisitions of complex multicellularity, characterized by cellular differentiation, three-dimensional body plans, and active nutrient transport. Compared with the other instances of complex multicellularity, animals represent the only clade to have evolved from wall-less, phagotrophic flagellates, which likely placed unique cytological and trophic constraints on the evolution of animal multicellularity. Here, we compare recent molecular clock estimates with compilations of the chromium isotope, micropaleontological, and organic biomarker records, suggesting that, as of now, the origin of animals was not obviously correlated to any environmental-ecological change in the Tonian Period. This lack of correlation is consistent with the idea that the evolution of animal multicellularity was primarily dictated by internal, developmental constraints and occurred independently of the known environmental-ecological changes that characterized the Neoproterozoic Era.}, }
@article {pmid32413288, year = {2020}, author = {Okamoto, K and Ferreira, RJ and Larsson, DSD and Maia, FRNC and Isawa, H and Sawabe, K and Murata, K and Hajdu, J and Iwasaki, K and Kasson, PM and Miyazaki, N}, title = {Acquired Functional Capsid Structures in Metazoan Totivirus-like dsRNA Virus.}, journal = {Structure (London, England : 1993)}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.str.2020.04.016}, pmid = {32413288}, issn = {1878-4186}, abstract = {Non-enveloped icosahedral double-stranded RNA (dsRNA) viruses possess multifunctional capsids required for their proliferation. Whereas protozoan/fungal dsRNA viruses have a relatively simple capsid structure, which suffices for the intracellular phase in their life cycle, metazoan dsRNA viruses have acquired additional structural features as an adaptation for extracellular cell-to-cell transmission in multicellular hosts. Here, we present the first atomic model of a metazoan dsRNA totivirus-like virus and the structure reveals three unique structural traits: a C-terminal interlocking arm, surface projecting loops, and an obstruction at the pore on the 5-fold symmetry axis. These traits are keys to understanding the capsid functions of metazoan dsRNA viruses, such as particle stability and formation, cell entry, and endogenous intraparticle transcription of mRNA. On the basis of molecular dynamics simulations of the obstructed pore, we propose a possible mechanism of intraparticle transcription in totivirus-like viruses, which dynamically switches between open and closed states of the pore(s).}, }
@article {pmid32411685, year = {2020}, author = {Yuan, F and Pan, X and Zeng, T and Zhang, YH and Chen, L and Gan, Z and Huang, T and Cai, YD}, title = {Identifying Cell-Type Specific Genes and Expression Rules Based on Single-Cell Transcriptomic Atlas Data.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {350}, doi = {10.3389/fbioe.2020.00350}, pmid = {32411685}, issn = {2296-4185}, abstract = {Single-cell sequencing technologies have emerged to address new and longstanding biological and biomedical questions. Previous studies focused on the analysis of bulk tissue samples composed of millions of cells. However, the genomes within the cells of an individual multicellular organism are not always the same. In this study, we aimed to identify the crucial and characteristically expressed genes that may play functional roles in tissue development and organogenesis, by analyzing a single-cell transcriptomic atlas of mice. We identified the most relevant gene features and decision rules classifying 18 cell categories, providing a list of genes that may perform important functions in the process of tissue development because of their tissue-specific expression patterns. These genes may serve as biomarkers to identify the origin of unknown cell subgroups so as to recognize specific cell stages/states during the dynamic process, and also be applied as potential therapy targets for developmental disorders.}, }
@article {pmid32399193, year = {2020}, author = {Zardoya, R}, title = {Recent advances in understanding mitochondrial genome diversity.}, journal = {F1000Research}, volume = {9}, number = {}, pages = {}, doi = {10.12688/f1000research.21490.1}, pmid = {32399193}, issn = {2046-1402}, abstract = {Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.}, }
@article {pmid32393866, year = {2020}, author = {Yu, L and Boström, C and Franzenburg, S and Bayer, T and Dagan, T and Reusch, TBH}, title = {Somatic genetic drift and multilevel selection in a clonal seagrass.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41559-020-1196-4}, pmid = {32393866}, issn = {2397-334X}, abstract = {All multicellular organisms are genetic mosaics owing to somatic mutations. The accumulation of somatic genetic variation in clonal species undergoing asexual (or clonal) reproduction may lead to phenotypic heterogeneity among autonomous modules (termed ramets). However, the abundance and dynamics of somatic genetic variation under clonal reproduction remain poorly understood. Here we show that branching events in a seagrass (Zostera marina) clone or genet lead to population bottlenecks of tissue that result in the evolution of genetically differentiated ramets in a process of somatic genetic drift. By studying inter-ramet somatic genetic variation, we uncovered thousands of single nucleotide polymorphisms that segregated among ramets. Ultra-deep resequencing of single ramets revealed that the strength of purifying selection on mosaic genetic variation was greater within than among ramets. Our study provides evidence for multiple levels of selection during the evolution of seagrass genets. Somatic genetic drift during clonal propagation leads to the emergence of genetically unique modules that constitute an elementary level of selection and individuality in long-lived clonal species.}, }
@article {pmid32383482, year = {2020}, author = {Kimata, Y and Leturcq, M and Aradhya, R}, title = {Emerging roles of metazoan CCRs as coordinators of the cell cycle and differentiation.}, journal = {FEBS letters}, volume = {}, number = {}, pages = {}, doi = {10.1002/1873-3468.13805}, pmid = {32383482}, issn = {1873-3468}, abstract = {In multicellular organisms, cell proliferation must be tightly coordinated with other developmental processes to form functional tissues and organs. Despite significant advances in our understanding of how the cell cycle is controlled by conserved cell cycle regulators (CCRs), how the cell cycle is coordinated with cell differentiation in metazoan organisms and how CCRs contribute to this process remain poorly understood. Here we review the emerging roles of metazoan CCRs as intracellular proliferation-differentiation coordinators in multicellular organisms. We illustrate how major CCRs regulate cellular events that are required for cell-fate acquisition and subsequent differentiation. To this end, CCRs employ diverse mechanisms, some of which are separable from those underpinning the conventional cell cycle-regulatory functions of CCRs. By controlling cell type-specific specification/differentiation processes alongside the progression of the cell cycle, CCRs enable spatiotemporal coupling between differentiation and cell proliferation in various developmental contexts in vivo. We discuss the significance and implications of this underappreciated role of metazoan CCRs for development, disease and evolution.}, }
@article {pmid32084159, year = {2020}, author = {Finoshin, AD and Adameyko, KI and Mikhailov, KV and Kravchuk, OI and Georgiev, AA and Gornostaev, NG and Kosevich, IA and Mikhailov, VS and Gazizova, GR and Shagimardanova, EI and Gusev, OA and Lyupina, YV}, title = {Iron metabolic pathways in the processes of sponge plasticity.}, journal = {PloS one}, volume = {15}, number = {2}, pages = {e0228722}, pmid = {32084159}, issn = {1932-6203}, mesh = {Animals ; Computational Biology ; Gene Expression Profiling ; Iron/*metabolism ; Iron-Regulatory Proteins/genetics/metabolism ; Molecular Sequence Annotation ; Phylogeny ; Porifera/genetics/*metabolism ; RNA-Seq ; }, abstract = {The ability to regulate oxygen consumption evolved in ancestral animals and is intrinsically linked to iron metabolism. The iron pathways have been intensively studied in mammals, whereas data on distant invertebrates are limited. Sea sponges represent the oldest animal phylum and have unique structural plasticity and capacity to reaggregate after complete dissociation. We studied iron metabolic factors and their expression during reaggregation in the White Sea cold-water sponges Halichondria panicea and Halisarca dujardini. De novo transcriptomes were assembled using RNA-Seq data, and evolutionary trends were analyzed with bioinformatic tools. Differential expression during reaggregation was studied for H. dujardini. Enzymes of the heme biosynthesis pathway and transport globins, neuroglobin (NGB) and androglobin (ADGB), were identified in sponges. The globins mutate at higher evolutionary rates than the heme synthesis enzymes. Highly conserved iron-regulatory protein 1 (IRP1) presumably interacts with the iron-responsive elements (IREs) found in mRNAs of ferritin (FTH1) and a putative transferrin receptor NAALAD2. The reaggregation process is accompanied by increased expression of IRP1, the antiapoptotic factor BCL2, the inflammation factor NFκB (p65), FTH1 and NGB, as well as by an increase in mitochondrial density. Our data indicate a complex mechanism of iron regulation in sponge structural plasticity and help to better understand general mechanisms of morphogenetic processes in multicellular species.}, }
@article {pmid31615963, year = {2019}, author = {Blank-Landeshammer, B and Teichert, I and Märker, R and Nowrousian, M and Kück, U and Sickmann, A}, title = {Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31615963}, issn = {2150-7511}, mesh = {Alternative Splicing/*genetics ; Genome, Fungal/*genetics ; Molecular Sequence Annotation ; Peptides/*metabolism ; Phylogeny ; Proteogenomics/*methods ; }, abstract = {Proteogenomics combines proteomics, genomics, and transcriptomics and has considerably improved genome annotation in poorly investigated phylogenetic groups for which homology information is lacking. Furthermore, it can be advantageous when reinvestigating well-annotated genomes. Here, we applied an advanced proteogenomics approach, combining standard proteogenomics with peptide de novo sequencing, to refine annotation of the well-studied model fungus Sordaria macrospora We investigated samples from different developmental and physiological conditions, resulting in the detection of 104 so-far hidden proteins and annotation changes in 575 genes, including 389 splice site refinements. Significantly, our approach provides peptide-level evidence for 113 single-amino-acid variations and 15 C-terminal protein elongations originating from A-to-I RNA editing, a phenomenon recently detected in fungi. Coexpression and phylostratigraphic analysis of the refined proteome suggest that new functions in evolutionarily young genes correlate with distinct developmental stages. In conclusion, our advanced proteogenomics approach supports and promotes functional studies of fungal model systems.IMPORTANCE Next-generation sequencing techniques have considerably increased the number of completely sequenced eukaryotic genomes. These genomes are mostly automatically annotated, and ab initio gene prediction is commonly combined with homology-based search approaches and often supported by transcriptomic data. The latter in particular improve the prediction of intron splice sites and untranslated regions. However, correct prediction of translation initiation sites (TIS), alternative splice junctions, and protein-coding potential remains challenging. Here, we present an advanced proteogenomics approach, namely, the combination of proteogenomics and de novo peptide sequencing analysis, in conjunction with Blast2GO and phylostratigraphy. Using the model fungus Sordaria macrospora as an example, we provide a comprehensive view of the proteome that not only increases the functional understanding of this multicellular organism at different developmental stages but also immensely enhances the genome annotation quality.}, }
@article {pmid30810962, year = {2019}, author = {Bai, SN}, title = {Plant Morphogenesis 123: a renaissance in modern botany?.}, journal = {Science China. Life sciences}, volume = {62}, number = {4}, pages = {453-466}, doi = {10.1007/s11427-018-9457-1}, pmid = {30810962}, issn = {1869-1889}, mesh = {Biological Evolution ; Botany/*trends ; Life Cycle Stages ; Meristem/cytology/growth &amp; development ; Models, Biological ; Morphogenesis ; *Plant Development ; Plant Structures/growth &amp; development ; Reproduction ; }, abstract = {Plants are a group of multicellular organisms crucial for the biosphere on the Earth. In the 17th century, the founding fathers of modern botany viewed the bud as the basic unit undergoing the plant life cycle. However, for many understandable reasons, the dominant conceptual framework evolved away from the &quot;bud-centered&quot; viewpoint to a &quot;plant-centered&quot; viewpoint that treated the whole plant, consisting of numerous buds, as a unit and considered the entire plant to be the functional equivalent of an animal individual. While this &quot;plant-centered&quot; viewpoint is convenient and great progress has been made using this conceptual framework, some fundamental problems remain logically unsolvable. Previously, I have proposed a new conceptual framework for interpretation of plant morphogenesis, called Plant Morphogenesis 123, which revives a &quot;bud-centered&quot; viewpoint. The perspective of Plant Morphogenesis 123 allows us to address new questions regarding to the mechanisms of plant morphogenesis that are important, and technically accessible, but previously neglected under the &quot;plant-centered&quot; conceptual framework. In addition to describing these questions, I address a more fundamental question for further discussion: why do people study plants?}, }
@article {pmid30989827, year = {2019}, author = {Hehmeyer, J}, title = {Two potential evolutionary origins of the fruiting bodies of the dictyostelid slime moulds.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {94}, number = {5}, pages = {1591-1604}, doi = {10.1111/brv.12516}, pmid = {30989827}, issn = {1469-185X}, mesh = {*Biological Evolution ; Dictyostelium/classification/genetics/*physiology ; Fruiting Bodies, Fungal/genetics/*physiology ; Phylogeny ; Spores, Fungal/genetics/physiology ; }, abstract = {Dictyostelium discoideum and the other dictyostelid slime moulds ('social amoebae') are popular model organisms best known for their demonstration of sorocarpic development. In this process, many cells aggregate to form a multicellular unit that ultimately becomes a fruiting body bearing asexual spores. Several other unrelated microorganisms undergo comparable processes, and in some it is evident that their multicellular development evolved from the differentiation process of encystation. While it has been argued that the dictyostelid fruiting body had similar origins, it has also been proposed that dictyostelid sorocarpy evolved from the unicellular fruiting process found in other amoebozoan slime moulds. This paper reviews the developmental biology of the dictyostelids and other relevant organisms and reassesses the two hypotheses on the evolutionary origins of dictyostelid development. Recent advances in phylogeny, genetics, and genomics and transcriptomics indicate that further research is necessary to determine whether or not the fruiting bodies of the dictyostelids and their closest relatives, the myxomycetes and protosporangids, are homologous.}, }
@article {pmid32355003, year = {2020}, author = {Lazzaro, BP and Zasloff, M and Rolff, J}, title = {Antimicrobial peptides: Application informed by evolution.}, journal = {Science (New York, N.Y.)}, volume = {368}, number = {6490}, pages = {}, doi = {10.1126/science.aau5480}, pmid = {32355003}, issn = {1095-9203}, abstract = {Antimicrobial peptides (AMPs) are essential components of immune defenses of multicellular organisms and are currently in development as anti-infective drugs. AMPs have been classically assumed to have broad-spectrum activity and simple kinetics, but recent evidence suggests an unexpected degree of specificity and a high capacity for synergies. Deeper evaluation of the molecular evolution and population genetics of AMP genes reveals more evidence for adaptive maintenance of polymorphism in AMP genes than has previously been appreciated, as well as adaptive loss of AMP activity. AMPs exhibit pharmacodynamic properties that reduce the evolution of resistance in target microbes, and AMPs may synergize with one another and with conventional antibiotics. Both of these properties make AMPs attractive for translational applications. However, if AMPs are to be used clinically, it is crucial to understand their natural biology in order to lessen the risk of collateral harm and avoid the crisis of resistance now facing conventional antibiotics.}, }
@article {pmid32353148, year = {2020}, author = {Hoffman, SK and Seitz, KW and Havird, JC and Weese, DA and Santos, SR}, title = {Phenotypic Comparability from Genotypic Variability among Physically Structured Microbial Consortia.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaa022}, pmid = {32353148}, issn = {1557-7023}, abstract = {Microbiomes represent the collective bacteria, archaea, protist, fungi, and virus communities living in or on individual organisms that are typically multicellular eukaryotes. Such consortia have become recognized as having significant impacts on the development, health, and disease status of their hosts. Since understanding the mechanistic connections between an individual's genetic makeup and their complete set of traits (i.e., genome to phenome) requires consideration at different levels of biological organization, this should include interactions with, and the organization of, microbial consortia. To understand microbial consortia organization, we elucidated the genetic constituents amongst phenotypically similar (and hypothesized functionally-analogous) layers (i.e., top orange, second orange, pink, and green layers) in the unique laminated orange cyanobacterial-bacterial crusts endemic to Hawaii's anchialine ecosystem. High-throughput amplicon sequencing of ribosomal RNA hypervariable regions (i.e., Bacteria-specific V6 and Eukarya-biased V9) revealed microbial richness increasing by crust layer depth, with samples of a given layer more similar to different layers from the same geographic site than to their phenotypically-analogous layer from different sites. Furthermore, samples from sites on the same island were more similar to each other, regardless of which layer they originated from, than to analogous layers from another island. However, cyanobacterial and algal taxa were abundant in all surface and bottom layers, with anaerobic and chemoautotrophic taxa concentrated in the middle two layers, suggesting crust oxygenation from both above and below. Thus, the arrangement of oxygenated vs. anoxygenated niches in these orange crusts are functionally distinct relative to other laminated cyanobacterial-bacterial communities examined to date, with convergent evolution due to similar environmental conditions a likely driver for these phenotypically comparable but genetically distinct microbial consortia.}, }
@article {pmid32315081, year = {2020}, author = {Rainey, L and Deevi, RK and McClements, J and Khawaja, H and Watson, CJ and Roudier, M and Van Schaeybroeck, S and Campbell, FC}, title = {Fundamental control of grade-specific colorectal cancer morphology by Src regulation of ezrin-centrosome engagement.}, journal = {The Journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/path.5452}, pmid = {32315081}, issn = {1096-9896}, abstract = {The phenotypic spectrum of colorectal cancer (CRC) is remarkably diverse with seemingly endless variations of cell shape, mitotic figures, and multicellular configurations. Despite this morphological complexity, histological grading of collective phenotype patterns provides robust prognostic stratification in CRC. While mechanistic understanding is incomplete, previous studies show that the cortical protein ezrin controls diversification of cell shape, mitotic figure geometry and multicellular architecture, in three-dimensional (3D) organotypic CRC cultures. Because ezrin is a substrate of Src tyrosine kinase that is frequently overexpressed in CRC, we investigated Src regulation of ezrin and morphogenic growth in 3D CRC cultures. Here we show that Src perturbations disrupt CRC epithelial spatial organization. Aberrant Src activity suppresses formation of the cortical ezrin cap that anchors interphase centrosomes. In CRC cells with normal centrosome number, these events lead to mitotic spindle misorientation, perturbation of cell cleavage, abnormal epithelial stratification, apical membrane misalignment, multi-lumen formation and evolution of cribriform multicellular morphology, a feature of low-grade cancer. In isogenic CRC cells with centrosome amplification, aberrant Src signalling promotes multipolar mitotic spindle (MMS) formation, pleomorphism and morphological features of high-grade cancer. Translational studies in archival human CRC revealed associations between Src intensity, MMS frequency and high-grade cancer morphology. Collectively, our study reveals Src regulation of CRC morphogenic growth via ezrin-centrosome engagement and uncovers combined perturbations underlying transition to high-grade CRC morphology. This article is protected by copyright. All rights reserved.}, }
@article {pmid32305342, year = {2020}, author = {Friedman, DA and Johnson, BR and Linksvayer, TA}, title = {Distributed physiology and the molecular basis of social life in eusocial insects.}, journal = {Hormones and behavior}, volume = {}, number = {}, pages = {104757}, doi = {10.1016/j.yhbeh.2020.104757}, pmid = {32305342}, issn = {1095-6867}, abstract = {The traditional focus of physiological and functional genomic research is on molecular processes that play out within a single multicellular organism. In the colonial (eusocial) insects such as ants, bees, and termites, molecular and behavioral responses of interacting nestmates are tightly linked, and key physiological processes are regulated at the scale of the colony. Such colony-level physiological processes regulate nestmate physiology in a distributed fashion, through various social communication mechanisms. As a result of physiological decentralization over evolutionary time, organismal mechanisms, for example related to pheromone detection, hormone signaling, and neural signaling pathways, are deployed in novel contexts to influence nestmate and colony traits. Here we explore how functional genomic, physiological, and behavioral studies can benefit from considering the traits of eusocial insects in this light. We highlight functional genomic work exploring how nestmate-level and colony-level traits arise and are influenced by interactions among physiologically-specialized nestmates of various developmental stages. We also consider similarities and differences between nestmate-level (organismal) and colony-level (superorganismal) physiological processes, and make specific hypotheses regarding the physiology of eusocial taxa. Integrating theoretical models of distributed systems with empirical functional genomics approaches will be useful in addressing fundamental questions related to the evolution of eusociality and collective behavior in natural systems.}, }
@article {pmid32301582, year = {2020}, author = {Naranjo-Ortiz, MA and Gabaldón, T}, title = {Fungal evolution: cellular, genomic and metabolic complexity.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.12605}, pmid = {32301582}, issn = {1469-185X}, support = {PT17/0009/0023 - ISCIII-SGEFI/ERDF//INB Grant/ ; H2020-MSCA-IF-2017-793699//Marie Sklodowska-Curie/ ; ERC-2016-724173//European Union's Horizon 2020/ ; SGR423//Catalan Research Agency (AGAUR)/ ; //CERCA Programme/Generalitat de Catalunya/ ; //European Regional Development Fund/ ; //Spanish Ministry of Science and Innovation/ ; }, abstract = {The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.}, }
@article {pmid32286494, year = {2020}, author = {Masuda, T and Inomura, K and Takahata, N and Shiozaki, T and Sano, Y and Deutsch, C and Prášil, O and Furuya, K}, title = {Heterogeneous nitrogen fixation rates confer energetic advantage and expanded ecological niche of unicellular diazotroph populations.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {172}, doi = {10.1038/s42003-020-0894-4}, pmid = {32286494}, issn = {2399-3642}, support = {544338//Simons Foundation/ ; 3775//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, abstract = {Nitrogen fixing plankton provide nitrogen to fuel marine ecosystems and biogeochemical cycles but the factors that constrain their growth and habitat remain poorly understood. Here we investigate the importance of metabolic specialization in unicellular diazotroph populations, using laboratory experiments and model simulations. In clonal cultures of Crocosphaera watsonii and Cyanothece sp. spiked with 15N2, cellular 15N enrichment developed a bimodal distribution within colonies, indicating that N2 fixation was confined to a subpopulation. In a model of population metabolism, heterogeneous nitrogen (N2) fixation rates substantially reduce the respiration rate required to protect nitrogenase from O2. The energy savings from metabolic specialization is highest at slow growth rates, allowing populations to survive in deeper waters where light is low but nutrients are high. Our results suggest that heterogeneous N2 fixation in colonies of unicellular diazotrophs confers an energetic advantage that expands the ecological niche and may have facilitated the evolution of multicellular diazotrophs.}, }
@article {pmid32283732, year = {2020}, author = {Annenkova, NV and Giner, CR and Logares, R}, title = {Tracing the Origin of Planktonic Protists in an Ancient Lake.}, journal = {Microorganisms}, volume = {8}, number = {4}, pages = {}, doi = {10.3390/microorganisms8040543}, pmid = {32283732}, issn = {2076-2607}, support = {18-74-00054//Russian Science Foundation/ ; 0345-2016-0009//Russian state assignment/ ; RYC-2013-12554//Ministerio de Economía y Competitividad/ ; }, abstract = {Ancient lakes are among the most interesting models for evolution studies because their biodiversity is the result of a complex combination of migration and speciation. Here, we investigate the origin of single celled planktonic eukaryotes from the oldest lake in the world-Lake Baikal (Russia). By using 18S rDNA metabarcoding, we recovered 1414 Operational Taxonomic Units (OTUs) belonging to protists populating surface waters (1-50 m) and representing pico/nano-sized cells. The recovered communities resembled other lacustrine freshwater assemblages found elsewhere, especially the taxonomically unclassified protists. However, our results suggest that a fraction of Baikal protists could belong to glacial relicts and have close relationships with marine/brackish species. Moreover, our results suggest that rapid radiation may have occurred among some protist taxa, partially mirroring what was already shown for multicellular organisms in Lake Baikal. We found 16% of the OTUs belonging to potential species flocks in Stramenopiles, Alveolata, Opisthokonta, Archaeplastida, Rhizaria, and Hacrobia. Putative flocks predominated in Chrysophytes, which are highly diverse in Lake Baikal. Also, the 18S rDNA of a number of species (7% of the total) differed >10% from other known sequences. These taxa as well as those belonging to the flocks may be endemic to Lake Baikal. Overall, our study points to novel diversity of planktonic protists in Lake Baikal, some of which may have emerged in situ after evolutionary diversification.}, }
@article {pmid32282832, year = {2020}, author = {Brun-Usan, M and Thies, C and Watson, RA}, title = {How to fit in: The learning principles of cell differentiation.}, journal = {PLoS computational biology}, volume = {16}, number = {4}, pages = {e1006811}, doi = {10.1371/journal.pcbi.1006811}, pmid = {32282832}, issn = {1553-7358}, abstract = {Cell differentiation in multicellular organisms requires cells to respond to complex combinations of extracellular cues, such as morphogen concentrations. Some models of phenotypic plasticity conceptualise the response as a relatively simple function of a single environmental cues (e.g. a linear function of one cue), which facilitates rigorous analysis. Conversely, more mechanistic models such those implementing GRNs allows for a more general class of response functions but makes analysis more difficult. Therefore, a general theory describing how cells integrate multi-dimensional signals is lacking. In this work, we propose a theoretical framework for understanding the relationships between environmental cues (inputs) and phenotypic responses (outputs) underlying cell plasticity. We describe the relationship between environment and cell phenotype using logical functions, making the evolution of cell plasticity equivalent to a simple categorisation learning task. This abstraction allows us to apply principles derived from learning theory to understand the evolution of multi-dimensional plasticity. Our results show that natural selection is capable of discovering adaptive forms of cell plasticity associated with complex logical functions. However, developmental dynamics cause simpler functions to evolve more readily than complex ones. By using conceptual tools derived from learning theory we show that this developmental bias can be interpreted as a learning bias in the acquisition of plasticity functions. Because of that bias, the evolution of plasticity enables cells, under some circumstances, to display appropriate plastic responses to environmental conditions that they have not experienced in their evolutionary past. This is possible when the selective environment mirrors the bias of the developmental dynamics favouring the acquisition of simple plasticity functions-an example of the necessary conditions for generalisation in learning systems. These results illustrate the functional parallelisms between learning in neural networks and the action of natural selection on environmentally sensitive gene regulatory networks. This offers a theoretical framework for the evolution of plastic responses that integrate information from multiple cues, a phenomenon that underpins the evolution of multicellularity and developmental robustness.}, }
@article {pmid32278076, year = {2020}, author = {Hehenberger, E and Eitel, M and Fortunato, SAV and Miller, DJ and Keeling, PJ and Cahill, MA}, title = {Early eukaryotic origins and metazoan elaboration of MAPR family proteins.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {106814}, doi = {10.1016/j.ympev.2020.106814}, pmid = {32278076}, issn = {1095-9513}, abstract = {The membrane-associated progesterone receptor (MAPR) family consists of heme-binding proteins containing a cytochrome b5 (cytb5) domain characterized by the presence of a MAPR-specific interhelical insert region (MIHIR) between helices 3 and 4 of the canonical cytb5-domain fold. Animals possess three MAPR genes (PGRMC-like, Neuferricin and Neudesin). Here we show that all three animal MAPR genes were already present in the common ancestor of the opisthokonts (comprising animals and fungi as well as related single-celled taxa). All three MAPR genes acquired extensions C-terminal to the cytb5 domain, either before or with the evolution of animals. The archetypical MAPR protein, progesterone receptor membrane component 1 (PGRMC1), contains phosphorylated tyrosines Y139 and Y180. The combination of Y139/Y180 appeared in the common ancestor of cnidarians and bilaterians, along with an early embryological organizer and synapsed neurons, and is strongly conserved in all bilaterian animals. A predicted protein interaction motif in the PGRMC1 MIHIR is potentially regulated by Y139 phosphorylation. A multilayered model of animal MAPR function acquisition includes some pre-metazoan functions (e.g., heme binding and cytochrome P450 interactions) and some acquired animal-specific functions that involve regulation of strongly conserved protein interaction motifs acquired by animals (Metazoa). This study provides a conceptual framework for future studies, against which especially PGRMC1's multiple functions can perhaps be stratified and functionally dissected.}, }
@article {pmid32272915, year = {2020}, author = {Tikhonenkov, DV and Hehenberger, E and Esaulov, AS and Belyakova, OI and Mazei, YA and Mylnikov, AP and Keeling, PJ}, title = {Insights into the origin of metazoan multicellularity from predatory unicellular relatives of animals.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {39}, doi = {10.1186/s12915-020-0762-1}, pmid = {32272915}, issn = {1741-7007}, support = {18-14-00239//Russian Science Foundation/ ; 227301//Natural Sciences and Engineering Research Council of Canada (CA)/ ; }, abstract = {BACKGROUND: The origin of animals from their unicellular ancestor was one of the most important events in evolutionary history, but the nature and the order of events leading up to the emergence of multicellular animals are still highly uncertain. The diversity and biology of unicellular relatives of animals have strongly informed our understanding of the transition from single-celled organisms to the multicellular Metazoa. Here, we analyze the cellular structures and complex life cycles of the novel unicellular holozoans Pigoraptor and Syssomonas (Opisthokonta), and their implications for the origin of animals.<br><br>RESULTS: Syssomonas and Pigoraptor are characterized by complex life cycles with a variety of cell types including flagellates, amoeboflagellates, amoeboid non-flagellar cells, and spherical cysts. The life cycles also include the formation of multicellular aggregations and syncytium-like structures, and an unusual diet for single-celled opisthokonts (partial cell fusion and joint sucking of a large eukaryotic prey), all of which provide new insights into the origin of multicellularity in Metazoa. Several existing models explaining the origin of multicellular animals have been put forward, but these data are interestingly consistent with one, the &quot;synzoospore hypothesis.&quot;<br><br>CONCLUSIONS: The feeding modes of the ancestral metazoan may have been more complex than previously thought, including not only bacterial prey, but also larger eukaryotic cells and organic structures. The ability to feed on large eukaryotic prey could have been a powerful trigger in the formation and development of both aggregative (e.g., joint feeding, which also implies signaling) and clonal (e.g., hypertrophic growth followed by palintomy) multicellular stages that played important roles in the emergence of multicellular animals.}, }
@article {pmid32262456, year = {2015}, author = {Rocha, PRF and Schlett, P and Schneider, L and Dröge, M and Mailänder, V and Gomes, HL and Blom, PWM and de Leeuw, DM}, title = {Low frequency electric current noise in glioma cell populations.}, journal = {Journal of materials chemistry. B}, volume = {3}, number = {25}, pages = {5035-5039}, doi = {10.1039/c5tb00144g}, pmid = {32262456}, issn = {2050-7518}, abstract = {Measuring the electrical activity of large and defined populations of cells is currently a major technical challenge to electrophysiology, especially in the picoampere-range. For this purpose, we developed and applied a bidirectional transducer based on a chip with interdigitated gold electrodes to record the electrical response of cultured glioma cells. Recent research determined that also non-neural brain glia cells are electrically active and excitable. Their transformed counterparts, e.g. glioma cells, were suggested to partially retain these electric features. Such electrophysiological studies however are usually performed on individual cells and are limited in their predictive power for the overall electrical activity of the multicellular tumour bulk. Our extremely low-noise measuring system allowed us to detect not only prominent electrical bursts of neuronal cells but also minute, yet constantly occurring and functional, membrane capacitive current oscillations across large populations of C6 glioma cells, which we termed electric current noise. At the same time, tumour cells of non-brain origin (HeLa) proved to be electrically quiescent in comparison. Finally, we determined that the glioma cell activity is primarily caused by the opening of voltage-gated Na+ and K+ ion channels and can be efficiently abolished using specific pharmacological inhibitors. Thus, we offer here a unique approach for studying electrophysiological properties of large cancer cell populations as an in vitro reference for tumour bulks in vivo.}, }
@article {pmid32260425, year = {2020}, author = {Simeone, P and Bologna, G and Lanuti, P and Pierdomenico, L and Guagnano, MT and Pieragostino, D and Del Boccio, P and Vergara, D and Marchisio, M and Miscia, S and Mariani-Costantini, R}, title = {Extracellular Vesicles as Signaling Mediators and Disease Biomarkers across Biological Barriers.}, journal = {International journal of molecular sciences}, volume = {21}, number = {7}, pages = {}, doi = {10.3390/ijms21072514}, pmid = {32260425}, issn = {1422-0067}, abstract = {Extracellular vesicles act as shuttle vectors or signal transducers that can deliver specific biological information and have progressively emerged as key regulators of organized communities of cells within multicellular organisms in health and disease. Here, we survey the evolutionary origin, general characteristics, and biological significance of extracellular vesicles as mediators of intercellular signaling, discuss the various subtypes of extracellular vesicles thus far described and the principal methodological approaches to their study, and review the role of extracellular vesicles in tumorigenesis, immunity, non-synaptic neural communication, vascular-neural communication through the blood-brain barrier, renal pathophysiology, and embryo-fetal/maternal communication through the placenta.}, }
@article {pmid32253306, year = {2020}, author = {Shao, S and Koh, M and Schultz, PG}, title = {Expanding the genetic code of the human hematopoietic system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1914408117}, pmid = {32253306}, issn = {1091-6490}, abstract = {The genetic incorporation of noncanonical amino acids (ncAAs) into proteins has been realized in bacteria, yeast, and mammalian cells, and recently, in multicellular organisms including plants and animals. However, the addition of new building blocks to the genetic code of tissues from human origin has not yet been achieved. To this end, we report a self-replicating Epstein-Barr virus-based episomal vector for the long-term encoding of ncAAs in human hematopoietic stem cells and reconstitution of this genetically engineered hematopoietic system in mice.}, }
@article {pmid32251406, year = {2020}, author = {Kazer, SW and Aicher, TP and Muema, DM and Carroll, SL and Ordovas-Montanes, J and Miao, VN and Tu, AA and Ziegler, CGK and Nyquist, SK and Wong, EB and Ismail, N and Dong, M and Moodley, A and Berger, B and Love, JC and Dong, KL and Leslie, A and Ndhlovu, ZM and Ndung'u, T and Walker, BD and Shalek, AK}, title = {Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41591-020-0799-2}, pmid = {32251406}, issn = {1546-170X}, support = {Beckman Young Investigator Program//Arnold and Mabel Beckman Foundation/ ; Pew-Stewart Scholars for Cancer Research//Pew Charitable Trusts/ ; Sloan Fellowship in Chemistry//Alfred P. Sloan Foundation/ ; 2U19AI089992//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2P01AI039671//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 5U24AI118672//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1R01AI138546//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; K08AI118538//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1R01AI145305//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1R37AI067073//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01HL095791//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1R01HL134539//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1U54CA217377//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; 2RM1HG006193//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; 1R01DA046277//U.S. Department of Health &amp; Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; Graduate Student Fellowship Award//National Science Foundation (NSF)/ ; HHMI Fellow DRG-2274-16//Damon Runyon Cancer Research Foundation (Cancer Research Fund of the Damon Runyon-Walter Winchell Foundation)/ ; 107752/Z/15/Z//Wellcome Trust (Wellcome)/ ; 210662/Z/18/Z//Wellcome Trust (Wellcome)/ ; UKZNRSA1001//International AIDS Vaccine Initiative (International AIDS Vaccine Initiative, Inc.)/ ; 00406//Gilead Sciences (Gilead)/ ; OPP1066973//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; OPP1146433//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; P30AI060354//Harvard University Center for AIDS Research (HU CFAR)/ ; }, abstract = {Cellular immunity is critical for controlling intracellular pathogens, but individual cellular dynamics and cell-cell cooperativity in evolving human immune responses remain poorly understood. Single-cell RNA-sequencing (scRNA-seq) represents a powerful tool for dissecting complex multicellular behaviors in health and disease1,2 and nominating testable therapeutic targets3. Its application to longitudinal samples could afford an opportunity to uncover cellular factors associated with the evolution of disease progression without potentially confounding inter-individual variability4. Here, we present an experimental and computational methodology that uses scRNA-seq to characterize dynamic cellular programs and their molecular drivers, and apply it to HIV infection. By performing scRNA-seq on peripheral blood mononuclear cells from four untreated individuals before and longitudinally during acute infection5, we were powered within each to discover gene response modules that vary by time and cell subset. Beyond previously unappreciated individual- and cell-type-specific interferon-stimulated gene upregulation, we describe temporally aligned gene expression responses obscured in bulk analyses, including those involved in proinflammatory T cell differentiation, prolonged monocyte major histocompatibility complex II upregulation and persistent natural killer (NK) cell cytolytic killing. We further identify response features arising in the first weeks of infection, for example proliferating natural killer cells, which potentially may associate with future viral control. Overall, our approach provides a unified framework for characterizing multiple dynamic cellular responses and their coordination.}, }
@article {pmid32246828, year = {2020}, author = {Zheng, W and Chen, J and Doak, TG and Song, W and Yan, Y}, title = {ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaa226}, pmid = {32246828}, issn = {1367-4811}, abstract = {MOTIVATION: Programmed DNA elimination plays a crucial role in the transitions between germline and somatic genomes in diverse organisms ranging from unicellular ciliates to multicellular nematodes. However, software specific to the detection of DNA splicing events is scarce. In this paper, we describe ADFinder, an efficient detector of programmed DNA eliminations using NGS high-throughput sequencing data. ADFinder can predict programmed DNA eliminations with relatively low sequencing coverage, detect multiple alternative splicing forms in the same genomic location, and calculate the frequency for each splicing event. This software will facilitate research of programmed DNA eliminations and all down-stream analyses.<br><br>RESULTS: By analyzing genome-wide DNA splicing events in two micronuclear genomes of Oxytricha trifallax and Tetrahymena thermophila we prove that ADFinder is effective in predicting large scale programmed DNA eliminations.<br><br>AVAILABILITY: The source codes and manual of ADFinder are available in our GitHub website: https://github.com/weibozheng/ADFinder.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid32244231, year = {2020}, author = {Copley, SD}, title = {The physical basis and practical consequences of biological promiscuity.}, journal = {Physical biology}, volume = {}, number = {}, pages = {}, doi = {10.1088/1478-3975/ab8697}, pmid = {32244231}, issn = {1478-3975}, abstract = {Proteins interact with metabolites, nucleic acids, and other proteins to orchestrate the myriad catalytic, structural and regulatory functions that support life from the simplest microbes to the most complex multicellular organisms. These molecular interactions are often exquisitely specific, but never perfectly so. Adventitious &quot;promiscuous&quot; interactions are ubiquitous due to the thousands of macromolecules and small molecules crowded together in cells. Such interactions may perturb protein function at the molecular level, but as long as they do not compromise organismal fitness, they will not be removed by natural selection. Although promiscuous interactions are physiologically irrelevant, they are important because they can provide a vast reservoir of potential functions that can provide the starting point for evolution of new functions, both in nature and in the laboratory.}, }
@article {pmid32234827, year = {2020}, author = {Pienta, KJ and Hammarlund, EU and Axelrod, R and Amend, SR and Brown, JS}, title = {Convergent evolution, evolving evolvability, and the origins of lethal cancer.}, journal = {Molecular cancer research : MCR}, volume = {}, number = {}, pages = {}, doi = {10.1158/1541-7786.MCR-19-1158}, pmid = {32234827}, issn = {1557-3125}, abstract = {Advances in curative treatment to remove the primary tumor have increased survival of localized cancers for most solid tumor types, yet cancers that have spread are typically incurable and account for >90% of cancer-related deaths. Metastatic disease remains incurable because, somehow, tumors evolve resistance to all known compounds, including therapies. In all of these incurable patients, de novo lethal cancer evolves capacities for both metastasis and resistance. Therefore, cancers in different patients appear to follow the same eco-evolutionary path that independently manifests in affected patients. This convergent outcome that always includes the ability to metastasize and exhibit resistance demands an explanation beyond the slow and steady accrual of stochastic mutations. The common denominator may be that cancer starts as a speciation event when a unicellular protist breaks away from its multicellular host and initiates a cancer clade within the patient. As the cancer cells speciate and diversify further, some evolve the capacity to evolve: evolvability. Evolvability becomes a heritable trait that influences the available variation of other phenotypes that can then be acted upon by natural selection. Evolving evolvability may be an adaptation for cancer cells. By generating and maintaining considerable heritable variation, the cancer clade can with high certainty serendipitously produce cells resistant to therapy and cells capable of metastasizing. Understanding that cancer cells can swiftly evolve responses to novel and varied stressors create opportunities for adaptive therapy, double-bind therapies, and extinction therapies; all involving strategic decision making that steers and anticipates the convergent co-evolutionary responses of the cancers.}, }
@article {pmid32234519, year = {2020}, author = {Nelson, WJ}, title = {The Glue that Binds Us: The Hunt for the Molecular Basis for Multicellularity.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2020.03.017}, pmid = {32234519}, issn = {1097-4172}, abstract = {This year's Canada Gairdner International Prize is shared by Rolf Kemler and Masatoshi Takeichi for the discovery of the cadherin family of Ca2+-dependent cell-cell adhesion proteins, which play essential roles in animal evolution, tissue development, and homeostasis, and are disrupted in human cancers.}, }
@article {pmid31212208, year = {2019}, author = {Masuyama, N and Mori, H and Yachie, N}, title = {DNA barcodes evolve for high-resolution cell lineage tracing.}, journal = {Current opinion in chemical biology}, volume = {52}, number = {}, pages = {63-71}, doi = {10.1016/j.cbpa.2019.05.014}, pmid = {31212208}, issn = {1879-0402}, mesh = {Animals ; Biomarkers ; *Cell Lineage ; Clustered Regularly Interspaced Short Palindromic Repeats ; *DNA Barcoding, Taxonomic ; Evolution, Molecular ; Humans ; Mutation ; Single-Cell Analysis ; }, abstract = {Mammalian development involves continuous dynamic processes in which cells propagate, differentiate, orchestrate, and decease to produce high-order functions. Although accurate cell lineage information can provide a strong foundation to understand such complex processes, the cell lineages involved in development of the whole mammalian body remain largely unclear, except for in early embryogenesis, which is observable under a microscope. With CRISPR genome editing, the concept of 'evolving DNA barcodes' has rapidly emerged for large-scale, high-resolution cell lineage tracing, where cell-embedded DNA barcodes continuously accumulate random mutations that are inherited from mother to daughter cells. Similar to evolutionary tree reconstruction using species' DNA sequences, cell lineages can be reconstructed using shared mutation patterns in the DNA barcodes identified using massively parallel sequencing. The dramatic developments of single-cell and imaging technologies have enabled analyses of the molecular and spatial architecture of heterogeneous cells. The evolving DNA barcodes can also consolidate this information on a reconstructed cell lineage tree and accelerate our understanding of multicellular organisms.}, }
@article {pmid31744876, year = {2019}, author = {Vassallo, CN and Wall, D}, title = {Self-identity barcodes encoded by six expansive polymorphic toxin families discriminate kin in myxobacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {49}, pages = {24808-24818}, pmid = {31744876}, issn = {1091-6490}, mesh = {Alleles ; Bacterial Outer Membrane Proteins/genetics/metabolism ; Bacterial Toxins/classification/*genetics/immunology/*isolation &amp; purification ; Cation Transport Proteins/genetics/metabolism ; Lipoproteins ; Myxococcales/*genetics/*metabolism ; Myxococcus xanthus/genetics/metabolism ; Phylogeny ; Receptors, Cell Surface/*metabolism ; Sequence Analysis ; }, abstract = {Myxobacteria are an example of how single-cell individuals can transition into multicellular life by an aggregation strategy. For these and all organisms that consist of social groups of cells, discrimination against, and exclusion of, nonself is critical. In myxobacteria, TraA is a polymorphic cell surface receptor that identifies kin by homotypic binding, and in so doing exchanges outer membrane (OM) proteins and lipids between cells with compatible receptors. However, TraA variability alone is not sufficient to discriminate against all cells, as traA allele diversity is not necessarily high among local strains. To increase discrimination ability, myxobacteria include polymorphic OM lipoprotein toxins called SitA in their delivered cargo, which poison recipient cells that lack the cognate, allele-specific SitI immunity protein. We previously characterized 3 SitAI toxin/immunity pairs that belong to 2 families. Here, we discover 4 additional SitA families. Each family is unique in sequence, but share the characteristic features of SitA: OM-associated toxins delivered by TraA. We demonstrate that, within a SitA family, C-terminal nuclease domains are polymorphic and often modular. Remarkably, sitA loci are strikingly numerous and diverse, with most genomes possessing >30 and up to 83 distinct sitAI loci. Interestingly, all SitA protein families are serially transferred between cells, allowing a SitA inhibitor cell to poison multiple targets, including cells that never made direct contact. The expansive suites of sitAI loci thus serve as identify barcodes to exquisitely discriminate against nonself to ensure populations are genetically homogenous to conduct cooperative behaviors.}, }
@article {pmid32226593, year = {2020}, author = {Xu, H and Zhang, S and Yi, X and Plewczynski, D and Li, MJ}, title = {Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction.}, journal = {Computational and structural biotechnology journal}, volume = {18}, number = {}, pages = {558-570}, doi = {10.1016/j.csbj.2020.02.013}, pmid = {32226593}, issn = {2001-0370}, abstract = {Mechanisms underlying gene regulation are key to understand how multicellular organisms with various cell types develop from the same genetic blueprint. Dynamic interactions between enhancers and genes are revealed to play central roles in controlling gene transcription, but the determinants to link functional enhancer-promoter pairs remain elusive. A major challenge is the lack of reliable approach to detect and verify functional enhancer-promoter interactions (EPIs). In this review, we summarized the current methods for detecting EPIs and described how developing techniques facilitate the identification of EPI through assessing the merits and drawbacks of these methods. We also reviewed recent state-of-art EPI prediction methods in terms of their rationale, data usage and characterization. Furthermore, we briefly discussed the evolved strategies for validating functional EPIs.}, }
@article {pmid32224105, year = {2020}, author = {Mikhailovsky, G and Gordon, R}, title = {Shuffling type of biological evolution based on horizontal gene transfer and the biosphere gene pool hypothesis.}, journal = {Bio Systems}, volume = {}, number = {}, pages = {104131}, doi = {10.1016/j.biosystems.2020.104131}, pmid = {32224105}, issn = {1872-8324}, abstract = {Widespread horizontal gene transfer (HGT) may appear a significant factor that accelerates biological evolution. Here we look at HGT primarily from the point of view of prokaryote clones, which we take as the descendants of a single cell, all of whom have exactly the same nucleotide sequence. Any novelty that emerges as a random mutation, creating a new clone, could either disappear before its first HGT, or survive for a period and be transferred to another clone. Due to the chain character of HGT, each gene with an adaptive mutation is thus spread among numerous existing clones, creating further new clones in the process. This makes propagation far faster than elimination, and such genes become practically immortal and form a kind of &quot;biosphere gene pool&quot; (BGP). Not all of these genes exist in every clone, and moreover not all of them are expressed. A significant fraction of the BGP includes of genes repressed by regulatory genes. However, these genes express often enough to be subject to natural selection. In a changing environment, both repressed and expressed genes, after transferring to another clone, may prove useful in an alternative environment, and this will give rise to new clones. This mechanism for testing repressed genes for adaptability can be thought as a &quot;shuffle of a deck of genes&quot; by analogy with shuffling a deck of cards. In the Archean and Proterozoic eons, both BGP and the operational part of each genome were rather poor, and the probability of incorporation of randomly expressed genes into the operational part of each genome was very small. Accordingly, biological evolution during these eons was slow due to rare adaptive mutations. This explains why the realm of prokaryotes as the sole organisms on Earth lasted so long. However, over about 3.5 billion years before the Phanerozoic eon, the BGP gradually accumulated a huge number of genes. Each of them was useful in a certain environment of past eras. We suggest that multicellular eukaryotes that appeared at the end of the Proterozoic eon could shuffle these genes accumulated in BGP via HGT from prokaryotes that live in these multicellular organisms. Perhaps this was the cause of the &quot;Cambrian explosion&quot; and the high (and increasing) rate of evolution in the Phanerozoic eon compared with the Archean and Proterozoic.}, }
@article {pmid31633482, year = {2019}, author = {Murphy, DP and Hughes, AE and Lawrence, KA and Myers, CA and Corbo, JC}, title = {Cis-regulatory basis of sister cell type divergence in the vertebrate retina.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31633482}, issn = {2050-084X}, support = {T32 EY013360/EY/NEI NIH HHS/United States ; T32EY013360/EY/NEI NIH HHS/United States ; R01EY024958/EY/NEI NIH HHS/United States ; R01EY025196/EY/NEI NIH HHS/United States ; R01EY026672/EY/NEI NIH HHS/United States ; F32EY029571/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; Binding Sites ; Chromatin/metabolism ; *Evolution, Molecular ; Gene Expression Profiling ; *Gene Regulatory Networks ; Mice ; Photoreceptor Cells/*physiology ; Regulatory Sequences, Nucleic Acid/*genetics ; Retinal Bipolar Cells/*physiology ; }, abstract = {Multicellular organisms evolved via repeated functional divergence of transcriptionally related sister cell types, but the mechanisms underlying sister cell type divergence are not well understood. Here, we study a canonical pair of sister cell types, retinal photoreceptors and bipolar cells, to identify the key cis-regulatory features that distinguish them. By comparing open chromatin maps and transcriptomic profiles, we found that while photoreceptor and bipolar cells have divergent transcriptomes, they share remarkably similar cis-regulatory grammars, marked by enrichment of K50 homeodomain binding sites. However, cell class-specific enhancers are distinguished by enrichment of E-box motifs in bipolar cells, and Q50 homeodomain motifs in photoreceptors. We show that converting K50 motifs to Q50 motifs represses reporter expression in bipolar cells, while photoreceptor expression is maintained. These findings suggest that partitioning of Q50 motifs within cell type-specific cis-regulatory elements was a critical step in the evolutionary divergence of the bipolar transcriptome from that of photoreceptors.}, }
@article {pmid32220299, year = {2020}, author = {Aich, M and Chakraborty, D}, title = {Role of lncRNAs in stem cell maintenance and differentiation.}, journal = {Current topics in developmental biology}, volume = {138}, number = {}, pages = {73-112}, doi = {10.1016/bs.ctdb.2019.11.003}, pmid = {32220299}, issn = {1557-8933}, abstract = {Embryonic Stem cells are widely studied to elucidate the disease and developmental processes because of their capability to differentiate into cells of any lineage, Pervasive transcription is a distinct feature of all multicellular organisms and genomic elements such as enhancers and bidirectional or unidirectional promoters regulate these processes. Thousands of loci in each species produce a class of transcripts called noncoding RNAs (ncRNAs), that are well known for their influential regulatory roles in multiple biological processes including stem cell pluripotency and differentiation. The number of lncRNA species increases in more complex organisms highlighting the importance of RNA-based control in the evolution of multicellular organisms. Over the past decade, numerous studies have shed light on lncRNA biogenesis and functional significance in the cell and the organism. In this review, we focus primarily on lncRNAs affecting the stem cell state and developmental pathways.}, }
@article {pmid32206719, year = {2020}, author = {Guo, Z and Richardson, JJ and Kong, B and Liang, K}, title = {Nanobiohybrids: Materials approaches for bioaugmentation.}, journal = {Science advances}, volume = {6}, number = {12}, pages = {eaaz0330}, doi = {10.1126/sciadv.aaz0330}, pmid = {32206719}, issn = {2375-2548}, abstract = {Nanobiohybrids, synthesized by integrating functional nanomaterials with living systems, have emerged as an exciting branch of research at the interface of materials engineering and biological science. Nanobiohybrids use synthetic nanomaterials to impart organisms with emergent properties outside their scope of evolution. Consequently, they endow new or augmented properties that are either innate or exogenous, such as enhanced tolerance against stress, programmed metabolism and proliferation, artificial photosynthesis, or conductivity. Advances in new materials design and processing technologies made it possible to tailor the physicochemical properties of the nanomaterials coupled with the biological systems. To date, many different types of nanomaterials have been integrated with various biological systems from simple biomolecules to complex multicellular organisms. Here, we provide a critical overview of recent developments of nanobiohybrids that enable new or augmented biological functions that show promise in high-tech applications across many disciplines, including energy harvesting, biocatalysis, biosensing, medicine, and robotics.}, }
@article {pmid32118436, year = {2020}, author = {Xu, L and Wang, J}, title = {Curl Flux as a Dynamical Origin of the Bifurcations/Phase Transitions of Nonequilibrium Systems: Cell Fate Decision Making.}, journal = {The journal of physical chemistry. B}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jpcb.9b11998}, pmid = {32118436}, issn = {1520-5207}, abstract = {The underlying interactions in physical and biological systems often lead to a variety of behaviors and emergent states or phases. Under certain conditions, these phases can be transformed from one to another. The phase transition behaviors can be described by the bifurcation or catastrophe where different stable/unstable states can branch out or meet together with the birth of the new and death of the old states. Despite significant efforts, how the bifurcation and catastrophe actually occur dynamically and the associated mechanisms for nonequilibrium systems are still not very clear. As an example, we study the underlying mechanism of cell differentiation through bifurcations. Cell differentiation is one of the key fate decision-making processes that a cell faces. It is crucial for the development of multicellular organisms. Under induction, gene regulation changes, or stochastic fluctuations, the cell fate decision-making processes can exhibit different types of bifurcations or phase transitions. In order to understand the underlying mechanism, it is crucial to find out where and how the bifurcation occurs. However, this is still largely unknown. In this study, we found that the average of the curl flux as a major component of the driving force for the dynamics in addition to the landscape gradient and the associated entropy production rate both reach maximum near the bifurcation. This indicates that the curl flux and entropy production rate may provide the dynamical and thermodynamic origins of the bifurcation/catastrophe or phase transitions for cell differentiation and this possibly applies to many other nonequilibrium active systems.}, }
@article {pmid32198827, year = {2020}, author = {Koehl, MAR}, title = {Selective factors in the evolution of multicellularity in choanoflagellates.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22941}, pmid = {32198827}, issn = {1552-5015}, support = {IOS-1147215//National Science Foundation/ ; IOS-1655318//National Science Foundation/ ; }, abstract = {Choanoflagellates, unicellular eukaryotes that can form multicellular colonies by cell division and that share a common ancestor with animals, are used as a model system to study functional consequences of being unicellular versus colonial. This review examines performance differences between unicellular and multicellular choanoflagellates in swimming, feeding, and avoiding predation, to provide insights about possible selective advantages of being multicellular for the protozoan ancestors of animals. Each choanoflagellate cell propels water by beating a single flagellum and captures bacterial prey on a collar of microvilli around the flagellum. Formation of multicellular colonies does not improve the swimming performance, but the flux of prey-bearing water to the collars of some of the cells in colonies of certain configurations can be greater than for single cells. Colony geometry appears to affect whether cells in colonies catch more prey per cell per time than do unicellular choanoflagellates. Although multicellular choanoflagellates show chemokinetic behavior in response to oxygen, only the unicellular dispersal stage (fast swimmers without collars) use pH signals to aggregate in locations where bacterial prey might be abundant. Colonies produce larger hydrodynamic signals than do single cells, and raptorial protozoan predators capture colonies while ignoring single cells. In contrast, ciliate predators entrain both single cells and colonies in their feeding currents, but reject larger colonies, whereas passive heliozoan predators show no preference. Thus, the ability of choanoflagellate cells to differentiate into different morphotypes, including multicellular forms, in response to variable aquatic environments might have provided a selective advantage to the ancestors of animals.}, }
@article {pmid32191325, year = {2020}, author = {Merényi, Z and Prasanna, AN and Wang, Z and Kovács, K and Hegedüs, B and Bálint, B and Papp, B and Townsend, JP and Nagy, LG}, title = {Unmatched level of molecular convergence among deeply divergent complex multicellular fungi.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaa077}, pmid = {32191325}, issn = {1537-1719}, abstract = {Convergent evolution is pervasive in nature, but it is poorly understood how various constraints and natural selection limit the diversity of evolvable phenotypes. Here, we analyze the transcriptome across fruiting body development to understand the independent evolution of complex multicellularity in the two largest clades of fungi-the Agarico- and Pezizomycotina. Despite >650 million years of divergence between these clades, we find that very similar sets of genes have convergently been co-opted for complex multicellularity, followed by expansions of their gene families by duplications. Over 82% of shared multicellularity-related gene families were expanding in both clades, indicating a high prevalence of convergence also at the gene-family level. This convergence is coupled with a rich inferred repertoire of multicellularity-related genes in the most recent common ancestor of the Agarico- and Pezizomycotina, consistent with the hypothesis that the coding capacity of ancestral fungal genomes might have promoted the repeated evolution of complex multicellularity. We interpret this repertoire as an indication of evolutionary predisposition of fungal ancestors for evolving complex multicellular fruiting bodies. Our work suggests that evolutionary convergence may happen not only when organisms are closely related or are under similar selection pressures, but also when ancestral genomic repertoires render certain evolutionary trajectories more likely than others, even across large phylogenetic distances.}, }
@article {pmid32188162, year = {2020}, author = {Zhang, WJ and Wu, LF}, title = {Flagella and Swimming Behavior of Marine Magnetotactic Bacteria.}, journal = {Biomolecules}, volume = {10}, number = {3}, pages = {}, doi = {10.3390/biom10030460}, pmid = {32188162}, issn = {2218-273X}, support = {A-M-AAP-EI-17-07-170301-07.50-WU-ENV//Fondation Aix-Marseille Universite/ ; LIA-MagMC//Centre National de la Recherche Scientifique/ ; 91751202//National Natural Science Foundation of China/ ; 91751108//National Natural Science Foundation of China/ ; }, abstract = {Marine environments are generally characterized by low bulk concentrations of nutrients that are susceptible to steady or intermittent motion driven by currents and local turbulence. Marine bacteria have therefore developed strategies, such as very fast-swimming and the exploitation of multiple directional sensing-response systems in order to efficiently migrate towards favorable places in nutrient gradients. The magnetotactic bacteria (MTB) even utilize Earth's magnetic field to facilitate downward swimming into the oxic-anoxic interface, which is the most favorable place for their persistence and proliferation, in chemically stratified sediments or water columns. To ensure the desired flagella-propelled motility, marine MTBs have evolved an exquisite flagellar apparatus, and an extremely high number (tens of thousands) of flagella can be found on a single entity, displaying a complex polar, axial, bounce, and photosensitive magnetotactic behavior. In this review, we describe gene clusters, the flagellar apparatus architecture, and the swimming behavior of marine unicellular and multicellular magnetotactic bacteria. The physiological significance and mechanisms that govern these motions are discussed.}, }
@article {pmid32188032, year = {2020}, author = {Goyeneche, A and Lisio, MA and Fu, L and Srinivasan, R and Valdez Capuccino, J and Gao, ZH and Telleria, C}, title = {The Capacity of High-Grade Serous Ovarian Cancer Cells to Form Multicellular Structures Spontaneously along Disease Progression Correlates with Their Orthotopic Tumorigenicity in Immunosuppressed Mice.}, journal = {Cancers}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/cancers12030699}, pmid = {32188032}, issn = {2072-6694}, support = {35635//Canada Foundation for Innovation/ ; 164222/CA/NCI NIH HHS/United States ; }, abstract = {Many studies have examined the biology, genetics, and chemotherapeutic response of ovarian cancer's solid component; its liquid facet, however, remains critically underinvestigated. Floating within peritoneal effusions known as ascites, ovarian cancer cells form multicellular structures, creating a cancer niche in suspension. This study explores the pathobiology of spontaneously formed, multicellular, ovarian cancer structures derived from serous ovarian cancer cells isolated along disease evolution. It also tests their capacity to cause peritoneal disease in immunosuppressed mice. Results stem from an analysis of cell lines representing the most frequently diagnosed ovarian cancer histotype (high-grade serous ovarian cancer), derived from ascites of the same patient at distinct stages of disease progression. When cultured under adherent conditions, in addition to forming cellular monolayers, the cultures developed areas in which the cells grew upwards, forming densely packed multilayers that ultimately detached from the bottom of the plates and lived as free-floating, multicellular structures. The capacity to form foci and to develop multicellular structures was proportional to disease progression at the time of ascites extraction. Self-assembled in culture, these structures varied in size, were either compact or hollow, irregular, or spheroidal, and exhibited replicative capacity and an epithelial nature. Furthermore, they fully recreated ovarian cancer disease in immunosuppressed mice: accumulation of malignant ascites and pleural effusions; formation of discrete, solid, macroscopic, peritoneal tumors; and microscopic growths in abdominal organs. They also reproduced the histopathological features characteristic of high-grade serous ovarian cancer when diagnosed in patients. The following results encourage the development of therapeutic interventions to interrupt the formation and/or survival of multicellular structures that constitute a floating niche in the peritoneal fluid, which in turn halts disease progression and prevents recurrence.}, }
@article {pmid32129607, year = {2020}, author = {Han, X and Tomaszewski, EJ and Sorwat, J and Pan, Y and Kappler, A and Byrne, JM}, title = {Effect of Microbial Biomass and Humic Acids on Abiotic and Biotic Magnetite Formation.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.9b07095}, pmid = {32129607}, issn = {1520-5851}, abstract = {Magnetite (Fe3O4) is an environmentally ubiquitous mixed-valent iron (Fe) mineral, which can form via biotic or abiotic transformation of Fe(III) (oxyhydr)oxides such as ferrihydrite (Fh). It is currently unclear whether environmentally relevant biogenic Fh from Fe(II)-oxidizing bacteria, containing cell-derived organic matter, can transform to magnetite. We compared abiotic and biotic transformation: (1) abiogenic Fh (aFh); (2) abiogenic Fh coprecipitated with humic acids (aFh-HA); (3) biogenic Fh produced by phototrophic Fe(II)-oxidizer Rhodobacter ferrooxidans SW2 (bFh); and (4) biogenic Fh treated with bleach to remove biogenic organic matter (bFh-bleach). Abiotic or biotic transformation of Fh was promoted by Feaq2+ or Fe(III)-reducing bacteria. Feaq2+-catalyzed abiotic reaction with aFh and bFh-bleach led to complete transformation to magnetite. In contrast, aFh-HA only partially (68%) transformed to magnetite, and bFh (17%) transformed to goethite. We hypothesize that microbial biomass stabilized bFh against reaction with Feaq2+. All four Fh substrates were transformed into magnetite during biotic reduction, suggesting that Fh remains bioavailable even when associated with microbial biomass. Additionally, there were poorly ordered magnetic components detected in the biogenic end products for aFh and aFh-HA. Nevertheless, abiotic transformation was much faster than biotic transformation, implying that initial Feaq2+ concentration, passivation of Fh, and/or sequestration of Fe(II) by bacterial cells and associated biomass play major roles in the rate of magnetite formation from Fh. These results improve our understanding of factors influencing secondary mineralization of Fh in the environment.}, }
@article {pmid31818732, year = {2020}, author = {Shuryak, I}, title = {Review of resistance to chronic ionizing radiation exposure under environmental conditions in multicellular organisms.}, journal = {Journal of environmental radioactivity}, volume = {212}, number = {}, pages = {106128}, doi = {10.1016/j.jenvrad.2019.106128}, pmid = {31818732}, issn = {1879-1700}, mesh = {Animals ; Humans ; Phylogeny ; *Radiation Exposure ; *Radiation Monitoring ; Radiation, Ionizing ; Radioisotopes ; }, abstract = {Ionizing radiation resistance occurs among many phylogenetic groups and its mechanisms remain incompletely understood. Tolerances to acute and chronic irradiation do not always correlate because different mechanisms may be involved. The radioresistance phenomenon becomes even more complex in the field than in the laboratory because the effects of radioactive contamination on natural populations are intertwined with those of other factors, such as bioaccumulation of radionuclides, interspecific competition, seasonal variations in environmental conditions, and land use changes due to evacuation of humans from contaminated areas. Previous reviews of studies performed in radioactive sites like the Kyshtym, Chernobyl, and Fukushima accident regions, and of protracted irradiation experiments, often focused on detecting radiation effects at low doses in radiosensitive organisms. Here we review the literature with a different purpose: to identify organisms with high tolerance to chronic irradiation under environmental conditions, which maintained abundant populations and/or outcompeted more radiosensitive species at high dose rates. Taxa for which consistent evidence for radioresistance came from multiple studies conducted in different locations and at different times were found among plants (e.g. willow and birch trees, sedges), invertebrate and vertebrate animals (e.g. rotifers, some insects, crustaceans and freshwater fish). These organisms are not specialized &quot;extremophiles&quot;, but tend to tolerate broad ranges of environmental conditions and stresses, have small genomes, reproduce quickly and/or disperse effectively over long distances. Based on these findings, resistance to radioactive contamination can be examined in a more broad context of chronic stress responses.}, }
@article {pmid31581262, year = {2019}, author = {Garud, A and Carrillo, AJ and Collier, LA and Ghosh, A and Kim, JD and Lopez-Lopez, B and Ouyang, S and Borkovich, KA}, title = {Genetic relationships between the RACK1 homolog cpc-2 and heterotrimeric G protein subunit genes in Neurospora crassa.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0223334}, pmid = {31581262}, issn = {1932-6203}, support = {T34 GM062756/GM/NIGMS NIH HHS/United States ; }, mesh = {Genes, Fungal ; Heterotrimeric GTP-Binding Proteins/chemistry/*genetics/metabolism ; Models, Biological ; Mutation ; Neurospora crassa/classification/*genetics/immunology ; Phenotype ; Phylogeny ; Protein Binding ; Recombinant Proteins ; rho-Associated Kinases/chemistry/*genetics/metabolism ; }, abstract = {Receptor for Activated C Kinase-1 (RACK1) is a multifunctional eukaryotic scaffolding protein with a seven WD repeat structure. Among their many cellular roles, RACK1 homologs have been shown to serve as alternative Gβ subunits during heterotrimeric G protein signaling in many systems. We investigated genetic interactions between the RACK1 homolog cpc-2, the previously characterized Gβ subunit gnb-1 and other G protein signaling components in the multicellular filamentous fungus Neurospora crassa. Results from cell fractionation studies and from fluorescent microscopy of a strain expressing a CPC-2-GFP fusion protein revealed that CPC-2 is a cytoplasmic protein. Genetic epistasis experiments between cpc-2, the three Gα genes (gna-1, gna-2 and gna-3) and gnb-1 demonstrated that cpc-2 is epistatic to gna-2 with regards to basal hyphae growth rate and aerial hyphae height, while deletion of cpc-2 mitigates the increased macroconidiation on solid medium observed in Δgnb-1 mutants. Δcpc-2 mutants inappropriately produce conidiophores during growth in submerged culture and mutational activation of gna-3 alleviates this defect. Δcpc-2 mutants are female-sterile and fertility could not be restored by mutational activation of any of the three Gα genes. With the exception of macroconidiation on solid medium, double mutants lacking cpc-2 and gnb-1 exhibited more severe defects for all phenotypic traits, supporting a largely synergistic relationship between GNB-1 and CPC-2 in N. crassa.}, }
@article {pmid32168596, year = {2020}, author = {de Maleprade, H and Moisy, F and Ishikawa, T and Goldstein, RE}, title = {Motility and phototaxis of Gonium, the simplest differentiated colonial alga.}, journal = {Physical review. E}, volume = {101}, number = {2-1}, pages = {022416}, doi = {10.1103/PhysRevE.101.022416}, pmid = {32168596}, issn = {2470-0053}, abstract = {Green algae of the Volvocine lineage, spanning from unicellular Chlamydomonas to vastly larger Volvox, are models for the study of the evolution of multicellularity, flagellar dynamics, and developmental processes. Phototactic steering in these organisms occurs without a central nervous system, driven solely by the response of individual cells. All such algae spin about a body-fixed axis as they swim; directional photosensors on each cell thus receive periodic signals when that axis is not aligned with the light. The flagella of Chlamydomonas and Volvox both exhibit an adaptive response to such signals in a manner that allows for accurate phototaxis, but in the former the two flagella have distinct responses, while the thousands of flagella on the surface of spherical Volvox colonies have essentially identical behavior. The planar 16-cell species Gonium pectorale thus presents a conundrum, for its central 4 cells have a Chlamydomonas-like beat that provide propulsion normal to the plane, while its 12 peripheral cells generate rotation around the normal through a Volvox-like beat. Here we combine experiment, theory, and computations to reveal how Gonium, perhaps the simplest differentiated colonial organism, achieves phototaxis. High-resolution cell tracking, particle image velocimetry of flagellar driven flows, and high-speed imaging of flagella on micropipette-held colonies show how, in the context of a recently introduced model for Chlamydomonas phototaxis, an adaptive response of the peripheral cells alone leads to photoreorientation of the entire colony. The analysis also highlights the importance of local variations in flagellar beat dynamics within a given colony, which can lead to enhanced reorientation dynamics.}, }
@article {pmid31943343, year = {2020}, author = {Wang, Y and Wang, F and Hong, DK and Gao, SJ and Wang, R and Wang, JD}, title = {Molecular characterization of DNA methyltransferase 1 and its role in temperature change of armyworm Mythimna separata Walker.}, journal = {Archives of insect biochemistry and physiology}, volume = {103}, number = {4}, pages = {e21651}, doi = {10.1002/arch.21651}, pmid = {31943343}, issn = {1520-6327}, support = {2017J01422//National Key R&amp;D Program of China/ ; CARS-17//Sugar Crop Research System/ ; 31601363//National Natural Science Foundation of China/ ; 2017J01422//Nature Science Foundation of Fujian/ ; }, mesh = {Amino Acid Sequence ; Animals ; Body Temperature ; DNA (Cytosine-5-)-Methyltransferase 1/chemistry/*genetics/metabolism ; Insect Proteins/chemistry/*genetics/metabolism ; Larva/genetics/growth &amp; development/physiology ; Moths/genetics/growth &amp; development/*physiology ; Ovum/growth &amp; development/physiology ; Phylogeny ; Pupa/genetics/growth &amp; development/physiology ; Sequence Alignment ; }, abstract = {DNA methylation refers to the addition of cytosine residues in a CpG context (5'-cytosine-phosphate-guanine-3'). As one of the most common mechanisms of epigenetic modification, it plays a crucial role in regulating gene expression and in a diverse range of biological processes across all multicellular organisms. The relationship between temperature and DNA methylation and how it acts on the adaptability of migratory insects remain unknown. In the present work, a 5,496 bp full-length complementary DNA encoding 1,436 amino acids (named MsDnmt1) was cloned from the devastating migratory pest oriental armyworm, Mythimna separata Walker. The protein shares 36.8-84.4% identity with other insect Dnmt1 isoforms. Spatial and temporal expression analysis revealed that MsDnmt1 was highly expressed in adult stages and head tissue. The changing temperature decreased the expression of MsDnmt1 in both high and low temperature condition. Besides, we found that M. separata exhibited the shortest duration time from the last instar to pupae under 36°C environment when injected with DNA methylation inhibitor. Therefore, our data highlight a potential role for DNA methylation in thermal resistance, which help us to understand the biological role adaptability and colonization of migratory pest in various environments.}, }
@article {pmid32163611, year = {2020}, author = {Nedelcu, AM and Michod, RE}, title = {Stress Responses Co-Opted for Specialized Cell Types During the Early Evolution of Multicellularity: The Role of Stress in the Evolution of Cell Types Can Be Traced Back to the Early Evolution of Multicellularity.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2000029}, doi = {10.1002/bies.202000029}, pmid = {32163611}, issn = {1521-1878}, support = {//Natural Sciences and Engineering Research Council (NSERC) of Canada and Harrison McCain Foundation/ ; NNX13AH41G/NASA/NASA/United States ; MCB-1412395//National Science Foundation/ ; //Natural Sciences and Engineering Research Council of Canada/ ; }, }
@article {pmid32163413, year = {2020}, author = {Rodríguez-Rojas, A and Kim, JJ and Johnston, P and Makarova, O and Eravci, M and Weise, C and Hengge, R and Rolff, J}, title = {Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress.}, journal = {PLoS genetics}, volume = {16}, number = {3}, pages = {e1008649}, doi = {10.1371/journal.pgen.1008649}, pmid = {32163413}, issn = {1553-7404}, abstract = {Unicellular organisms have the prevalent challenge to survive under oxidative stress of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). ROS are present as by-products of photosynthesis and aerobic respiration. These reactive species are even employed by multicellular organisms as potent weapons against microbes. Although bacterial defences against lethal and sub-lethal oxidative stress have been studied in model bacteria, the role of fluctuating H2O2 concentrations remains unexplored. It is known that sub-lethal exposure of Escherichia coli to H2O2 results in enhanced survival upon subsequent exposure. Here we investigate the priming response to H2O2 at physiological concentrations. The basis and the duration of the response (memory) were also determined by time-lapse quantitative proteomics. We found that a low level of H2O2 induced several scavenging enzymes showing a long half-life, subsequently protecting cells from future exposure. We then asked if the phenotypic resistance against H2O2 alters the evolution of resistance against oxygen stress. Experimental evolution of H2O2 resistance revealed faster evolution and higher levels of resistance in primed cells. Several mutations were found to be associated with resistance in evolved populations affecting different loci but, counterintuitively, none of them was directly associated with scavenging systems. Our results have important implications for host colonisation and infections where microbes often encounter reactive oxygen species in gradients.}, }
@article {pmid32146616, year = {2020}, author = {Fuchs, M and Lohmann, JU}, title = {Aiming for the top: non-cell autonomous control of shoot stem cells in Arabidopsis.}, journal = {Journal of plant research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10265-020-01174-3}, pmid = {32146616}, issn = {1618-0860}, support = {SFB873//Deutsche Forschungsgemeinschaft/ ; }, abstract = {In multicellular organisms, not all cells are created equal. Instead, organismal complexity is achieved by specialisation and division of labour between distinct cell types. Therefore, the organism depends on the presence, correct proportion and function of all cell types. It follows that early development is geared towards setting up the basic body plan and to specify cell lineages. Since plants employ a post-embryonic mode of development, the continuous growth and addition of new organs require a source of new cells, as well as a strict regulation of cellular composition throughout the entire life-cycle. To meet these demands, evolution has brought about complex regulatory systems to maintain and control continuously active stem cell systems. Here, we review recent work on the mechanisms of non cell-autonomous control of shoot stem cells in the model plant Arabidopsis thaliana with a strong focus on the cell-to-cell mobility and function of the WUSCHEL homeodomain transcription factor.}, }
@article {pmid32143753, year = {2020}, author = {Klesen, S and Hill, K and Timmermans, MCP}, title = {Small RNAs as plant morphogens.}, journal = {Current topics in developmental biology}, volume = {137}, number = {}, pages = {455-480}, doi = {10.1016/bs.ctdb.2019.11.001}, pmid = {32143753}, issn = {1557-8933}, abstract = {The coordination of cell fate decisions within complex multicellular structures rests on intercellular communication. To generate ordered patterns, cells need to know their relative positions within the growing structure. This is commonly achieved via the production and perception of mobile signaling molecules. In animal systems, such positional signals often act as morphogens and subdivide a field of cells into domains of discrete cell identities using a threshold-based readout of their mobility gradient. Reflecting the independent origin of multicellularity, plants evolved distinct signaling mechanisms to drive cell fate decisions. Many of the basic principles underlying developmental patterning are, however, shared between animals and plants, including the use of signaling gradients to provide positional information. In plant development, small RNAs can act as mobile instructive signals, and similar to classical morphogens in animals, employ a threshold-based readout of their mobility gradient to generate precisely defined cell fate boundaries. Given the distinctive nature of peptide morphogens and small RNAs, how might mechanisms underlying the function of traditionally morphogens be adapted to create morphogen-like behavior using small RNAs? In this review, we highlight the contributions of mobile small RNAs to pattern formation in plants and summarize recent studies that have advanced our understanding regarding the formation, stability, and interpretation of small RNA gradients.}, }
@article {pmid32133683, year = {2020}, author = {Horton, MB and Hawkins, ED and Heinzel, S and Hodgkin, PD}, title = {Speculations on the evolution of humoral adaptive immunity.}, journal = {Immunology and cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imcb.12323}, pmid = {32133683}, issn = {1440-1711}, abstract = {The protection of a multicellular organism from infection, at both a cell and humoral level has been a tremendous driver of gene selection and cellular response strategies. Here we focus on a critical event in the development of humoral immunity: The transition from principally innate responses, to a system of adaptive cell selection, with all the attendant mechanical problems that must be solved in order for it to work effectively. Here we review recent advances, but our major goal is to highlight that the development of adaptive immunity resulted from the adoption, reuse and repurposing of an ancient, autonomous cellular programme, that combines and exploits three titratable cellular fate timers. We illustrate how this common cell machinery recurs and appears throughout biology, and has been essential for the evolution of complex organisms, at many levels of scale.}, }
@article {pmid31451789, year = {2019}, author = {Bruno, L and Ramlall, V and Studer, RA and Sauer, S and Bradley, D and Dharmalingam, G and Carroll, T and Ghoneim, M and Chopin, M and Nutt, SL and Elderkin, S and Rueda, DS and Fisher, AG and Siggers, T and Beltrao, P and Merkenschlager, M}, title = {Selective deployment of transcription factor paralogs with submaximal strength facilitates gene regulation in the immune system.}, journal = {Nature immunology}, volume = {20}, number = {10}, pages = {1372-1380}, doi = {10.1038/s41590-019-0471-5}, pmid = {31451789}, issn = {1529-2916}, support = {099276/WT_/Wellcome Trust/United Kingdom ; MC_U120027516/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R01 AI116829/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cell Differentiation ; Cell Lineage ; Conserved Sequence ; Core Binding Factor alpha Subunits/*genetics ; Evolution, Molecular ; Gene Duplication ; Humans ; Immune System/*physiology ; Langerhans Cells/*physiology ; Mammals ; Organ Specificity/*genetics ; Signal Transduction ; T-Lymphocytes, Regulatory/*physiology ; Transcriptome ; }, abstract = {In multicellular organisms, duplicated genes can diverge through tissue-specific gene expression patterns, as exemplified by highly regulated expression of RUNX transcription factor paralogs with apparent functional redundancy. Here we asked what cell-type-specific biologies might be supported by the selective expression of RUNX paralogs during Langerhans cell and inducible regulatory T cell differentiation. We uncovered functional nonequivalence between RUNX paralogs. Selective expression of native paralogs allowed integration of transcription factor activity with extrinsic signals, while non-native paralogs enforced differentiation even in the absence of exogenous inducers. DNA binding affinity was controlled by divergent amino acids within the otherwise highly conserved RUNT domain and evolutionary reconstruction suggested convergence of RUNT domain residues toward submaximal strength. Hence, the selective expression of gene duplicates in specialized cell types can synergize with the acquisition of functional differences to enable appropriate gene expression, lineage choice and differentiation in the mammalian immune system.}, }
@article {pmid30967090, year = {2019}, author = {Cotter, SC and Pincheira-Donoso, D and Thorogood, R}, title = {Defences against brood parasites from a social immunity perspective.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1769}, pages = {20180207}, doi = {10.1098/rstb.2018.0207}, pmid = {30967090}, issn = {1471-2970}, mesh = {Animals ; Biological Evolution ; *Birds/parasitology/physiology ; *Cues ; *Host-Parasite Interactions ; *Insecta/parasitology/physiology ; *Recognition, Psychology ; *Social Behavior ; }, abstract = {Parasitic interactions are so ubiquitous that all multicellular organisms have evolved a system of defences to reduce their costs, whether the parasites they encounter are the classic parasites which feed on the individual, or brood parasites which usurp parental care. Many parallels have been drawn between defences deployed against both types of parasite, but typically, while defences against classic parasites have been selected to protect survival, those against brood parasites have been selected to protect the parent's inclusive fitness, suggesting that the selection pressures they impose are fundamentally different. However, there is another class of defences against classic parasites that have specifically been selected to protect an individual's inclusive fitness, known as social immunity. Social immune responses include the anti-parasite defences typically provided for others in kin-structured groups, such as the antifungal secretions produced by termite workers to protect the brood. Defences against brood parasites, therefore, are more closely aligned with social immune responses. Much like social immunity, host defences against brood parasitism are employed by a donor (a parent) for the benefit of one or more recipients (typically kin), and as with social defences against classic parasites, defences have therefore evolved to protect the donor's inclusive fitness, not the survival or ultimately the fitness of individual recipients This can lead to severe conflicts between the different parties, whose interests are not always aligned. Here, we consider defences against brood parasitism in the light of social immunity, at different stages of parasite encounter, addressing where conflicts occur and how they might be resolved. We finish with considering how this approach could help us to address longstanding questions in our understanding of brood parasitism. This article is part of the theme issue 'The coevolutionary biology of brood parasitism: from mechanism to pattern'.}, }
@article {pmid32130880, year = {2020}, author = {González, A and Hall, MN and Lin, SC and Hardie, DG}, title = {AMPK and TOR: The Yin and Yang of Cellular Nutrient Sensing and Growth Control.}, journal = {Cell metabolism}, volume = {31}, number = {3}, pages = {472-492}, doi = {10.1016/j.cmet.2020.01.015}, pmid = {32130880}, issn = {1932-7420}, abstract = {The AMPK (AMP-activated protein kinase) and TOR (target-of-rapamycin) pathways are interlinked, opposing signaling pathways involved in sensing availability of nutrients and energy and regulation of cell growth. AMPK (Yin, or the &quot;dark side&quot;) is switched on by lack of energy or nutrients and inhibits cell growth, while TOR (Yang, or the &quot;bright side&quot;) is switched on by nutrient availability and promotes cell growth. Genes encoding the AMPK and TOR complexes are found in almost all eukaryotes, suggesting that these pathways arose very early during eukaryotic evolution. During the development of multicellularity, an additional tier of cell-extrinsic growth control arose that is mediated by growth factors, but these often act by modulating nutrient uptake so that AMPK and TOR remain the underlying regulators of cellular growth control. In this review, we discuss the evolution, structure, and regulation of the AMPK and TOR pathways and the complex mechanisms by which they interact.}, }
@article {pmid32122349, year = {2020}, author = {Gray, MW and Burger, G and Derelle, R and Klimeš, V and Leger, MM and Sarrasin, M and Vlček, Č and Roger, AJ and Eliáš, M and Lang, BF}, title = {The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {22}, doi = {10.1186/s12915-020-0741-6}, pmid = {32122349}, issn = {1741-7007}, support = {RGPIN-2014-05286//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN- 2017-05411//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN-2016-06792//Natural Sciences and Engineering Research Council of Canada/ ; AFR grant PHD-08-001//Fonds National de la Recherche Luxembourg/ ; 18-13458S//Czech Science Foundation/ ; OPVVV 16_019/0000759//ERD Funds/ ; }, abstract = {BACKGROUND: Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date.<br><br>RESULTS: In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids.<br><br>CONCLUSIONS: As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.}, }
@article {pmid32109395, year = {2020}, author = {Tan, Y and Barnbrook, M and Wilson, Y and Molnár, A and Bukys, A and Hudson, A}, title = {Shared Mutations in a Novel Glutaredoxin Repressor of Multicellular Trichome Fate Underlie Parallel Evolution of Antirrhinum Species.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2020.01.060}, pmid = {32109395}, issn = {1879-0445}, abstract = {Most angiosperms produce trichomes-epidermal hairs that have protective or more specialized roles. Trichomes are multicellular in almost all species and, in the majority, secretory. Despite the importance of multicellular trichomes for plant protection and as a source of high-value products, the mechanisms that control their development are only poorly understood. Here, we investigate the control of multicellular trichome patterns using natural variation within the genus Antirrhinum (snapdragons), which has evolved hairy alpine-adapted species or lowland species with a restricted trichome pattern multiple times in parallel. We find that a single gene, Hairy (H), which is needed to repress trichome fate, underlies variation in trichome patterns between all Antirrhinum species except one. We show that H encodes a novel epidermis-specific glutaredoxin and that the pattern of trichome distribution within individuals reflects the location of H expression. Phylogenetic and functional tests suggest that H gained its trichome-repressing role late in the history of eudicots and that the ancestral Antirrhinum had an active H gene and restricted trichome distribution. Loss of H function was involved in an early divergence of alpine and lowland Antirrhinum lineages, and the alleles underlying this split were later reused in parallel evolution of alpines from lowland ancestors, and vice versa. We also find evidence for an evolutionary reversal from a widespread to restricted trichome distribution involving a suppressor mutation and for a pleiotropic effect of H on plant growth that might constrain the evolution of trichome pattern.}, }
@article {pmid32102937, year = {2020}, author = {Elliott, L and Moore, I and Kirchhelle, C}, title = {Spatio-temporal control of post-Golgi exocytic trafficking in plants.}, journal = {Journal of cell science}, volume = {133}, number = {4}, pages = {}, doi = {10.1242/jcs.237065}, pmid = {32102937}, issn = {1477-9137}, abstract = {A complex and dynamic endomembrane system is a hallmark of eukaryotic cells and underpins the evolution of specialised cell types in multicellular organisms. Endomembrane system function critically depends on the ability of the cell to (1) define compartment and pathway identity, and (2) organise compartments and pathways dynamically in space and time. Eukaryotes possess a complex molecular machinery to control these processes, including small GTPases and their regulators, SNAREs, tethering factors, motor proteins, and cytoskeletal elements. Whereas many of the core components of the eukaryotic endomembrane system are broadly conserved, there have been substantial diversifications within different lineages, possibly reflecting lineage-specific requirements of endomembrane trafficking. This Review focusses on the spatio-temporal regulation of post-Golgi exocytic transport in plants. It highlights recent advances in our understanding of the elaborate network of pathways transporting different cargoes to different domains of the cell surface, and the molecular machinery underpinning them (with a focus on Rab GTPases, their interactors and the cytoskeleton). We primarily focus on transport in the context of growth, but also highlight how these pathways are co-opted during plant immunity responses and at the plant-pathogen interface.}, }
@article {pmid31512055, year = {2019}, author = {Alcorta, J and Vergara-Barros, P and Antonaru, LA and Alcamán-Arias, ME and Nürnberg, DJ and Díez, B}, title = {Fischerella thermalis: a model organism to study thermophilic diazotrophy, photosynthesis and multicellularity in cyanobacteria.}, journal = {Extremophiles : life under extreme conditions}, volume = {23}, number = {6}, pages = {635-647}, pmid = {31512055}, issn = {1433-4909}, support = {1150171//Fondo de Fomento al Desarrollo Científico y Tecnológico/ ; 1190998//Fondo de Fomento al Desarrollo Científico y Tecnológico/ ; }, mesh = {Acclimatization/*physiology ; *Biological Evolution ; Cyanobacteria/*physiology ; Hot Springs/*microbiology ; *Hot Temperature ; *Models, Biological ; Trichomes/physiology ; }, abstract = {The true-branching cyanobacterium Fischerella thermalis (also known as Mastigocladus laminosus) is widely distributed in hot springs around the world. Morphologically, it has been described as early as 1837. However, its taxonomic placement remains controversial. F. thermalis belongs to the same genus as mesophilic Fischerella species but forms a monophyletic clade of thermophilic Fischerella strains and sequences from hot springs. Their recent divergence from freshwater or soil true-branching species and the ongoing process of specialization inside the thermal gradient make them an interesting evolutionary model to study. F. thermalis is one of the most complex prokaryotes. It forms a cellular network in which the main trichome and branches exchange metabolites and regulators via septal junctions. This species can adapt to a variety of environmental conditions, with its photosynthetic apparatus remaining active in a temperature range from 15 to 58 °C. Together with its nitrogen-fixing ability, this allows it to dominate in hot spring microbial mats and contribute significantly to the de novo carbon and nitrogen input. Here, we review the current knowledge on the taxonomy and distribution of F. thermalis, its morphological complexity, and its physiological adaptations to an extreme environment.}, }
@article {pmid31152521, year = {2019}, author = {Odendall, C and Kagan, JC}, title = {Host-Encoded Sensors of Bacteria: Our Windows into the Microbial World.}, journal = {Microbiology spectrum}, volume = {7}, number = {3}, pages = {}, doi = {10.1128/microbiolspec.BAI-0011-2019}, pmid = {31152521}, issn = {2165-0497}, support = {R01 AI093589/AI/NIAID NIH HHS/United States ; R01 AI116550/AI/NIAID NIH HHS/United States ; U19 AI133524/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*immunology/pathogenicity ; Bacterial Infections/*immunology/microbiology ; Evolution, Molecular ; Germ-Free Life ; Host-Pathogen Interactions/*immunology/*physiology ; Humans ; Neutrophil Infiltration ; Receptors, Pattern Recognition/immunology/*physiology ; Virulence Factors ; }, abstract = {Bacterial pathogens can be very efficient at causing disease and are the cause of some of the worst epidemics that have affected humanity. However, most infections are prevented by the actions of our immune system. Immune activation depends on the rapid detection of bacteria by a diverse family of sensory proteins known as pattern recognition receptors. These receptors detect conserved features of bacteria that are not found in humans but are often necessary for survival within the host or environment. In this review, we discuss the strategies used by pattern recognition receptors to detect bacteria and their products. We also discuss emerging evidence that some pattern recognition receptors can be activated by bacterial pathogens specifically, through the surveillance of host activities that are commonly targeted by virulence factors. This collection of surveillance mechanisms provides an interconnected network of defense, which is important to maintain the germ-free environment of the inner organs of humans and other multicellular organisms.}, }
@article {pmid32097591, year = {2020}, author = {Greyson-Gaito, CJ and Bartley, TJ and Cottenie, K and Jarvis, WMC and Newman, AEM and Stothart, MR}, title = {Into the wild: microbiome transplant studies need broader ecological reality.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1921}, pages = {20192834}, doi = {10.1098/rspb.2019.2834}, pmid = {32097591}, issn = {1471-2954}, abstract = {Gut microbial communities (microbiomes) profoundly shape the ecology and evolution of multicellular life. Interactions between host and microbiome appear to be reciprocal, and ecological theory is now being applied to better understand how hosts and their microbiome influence each other. However, some ecological processes that underlie reciprocal host-microbiome interactions may be obscured by the current convention of highly controlled transplantation experiments. Although these approaches have yielded invaluable insights, there is a need for a broader array of approaches to fully understand host-microbiome reciprocity. Using a directed review, we surveyed the breadth of ecological reality in the current literature on gut microbiome transplants with non-human recipients. For 55 studies, we categorized nine key experimental conditions that impact the ecological reality (EcoReality) of the transplant, including host taxon match and donor environment. Using these categories, we rated the EcoReality of each transplant. Encouragingly, the breadth of EcoReality has increased over time, but some components of EcoReality are still relatively unexplored, including recipient host environment and microbiome state. The conceptual framework we develop here maps the landscape of possible EcoReality to highlight where fundamental ecological processes can be considered in future transplant experiments.}, }
@article {pmid32095969, year = {2020}, author = {Moody, LA}, title = {Three-dimensional growth: a developmental innovation that facilitated plant terrestrialization.}, journal = {Journal of plant research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10265-020-01173-4}, pmid = {32095969}, issn = {1618-0860}, support = {BB/M020517/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; University Research Fellowship//Royal Society/ ; }, abstract = {One of the most transformative events in the history of life on earth was the transition of plants from water to land approximately 470 million years ago. Within the Charophyte green algae, the closest living relatives of land plants, body plans have evolved from those that comprise simple unicells to those that are morphologically complex, large and multicellular. The Charophytes developed these broad ranging body plans by exploiting a range of one-dimensional and two-dimensional growth strategies to produce filaments, mats and branches. When plants were confronted with harsh conditions on land, they were required to make significant changes to the way they shaped their body plans. One of the fundamental developmental transitions that occurred was the evolution of three-dimensional growth and the acquisition of apical cells with three or more cutting faces. Plants subsequently developed a range of morphological adaptations (e.g. vasculature, roots, flowers, seeds) that enabled them to colonise progressively drier environments. 3D apical growth also evolved convergently in the brown algae, completely independently of the green lineage. This review summarises the evolving developmental complexities observed in the early divergent Charophytes all the way through to the earliest conquerors of land, and investigates 3D apical growth in the brown algae.}, }
@article {pmid32094536, year = {2020}, author = {Tang, Q and Pang, K and Yuan, X and Xiao, S}, title = {A one-billion-year-old multicellular chlorophyte.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41559-020-1122-9}, pmid = {32094536}, issn = {2397-334X}, support = {41602007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41602007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 80NSSC18K1086/NASA/NASA/United States ; }, abstract = {Chlorophytes (representing a clade within the Viridiplantae and a sister group of the Streptophyta) probably dominated marine export bioproductivity and played a key role in facilitating ecosystem complexity before the Mesozoic diversification of phototrophic eukaryotes such as diatoms, coccolithophorans and dinoflagellates. Molecular clock and biomarker data indicate that chlorophytes diverged in the Mesoproterozoic or early Neoproterozoic, followed by their subsequent phylogenetic diversification, multicellular evolution and ecological expansion in the late Neoproterozoic and Palaeozoic. This model, however, has not been rigorously tested with palaeontological data because of the scarcity of Proterozoic chlorophyte fossils. Here we report abundant millimetre-sized, multicellular and morphologically differentiated macrofossils from rocks approximately 1,000 million years ago. These fossils are described as Proterocladus antiquus new species and are interpreted as benthic siphonocladalean chlorophytes, suggesting that chlorophytes acquired macroscopic size, multicellularity and cellular differentiation nearly a billion years ago, much earlier than previously thought.}, }
@article {pmid32094163, year = {2020}, author = {Yahalomi, D and Atkinson, SD and Neuhof, M and Chang, ES and Philippe, H and Cartwright, P and Bartholomew, JL and Huchon, D}, title = {A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1909907117}, pmid = {32094163}, issn = {1091-6490}, abstract = {Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria-related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no mitochondrial genome, and thus has lost the ability to perform aerobic cellular respiration. This indicates that these core eukaryotic features are not ubiquitous among animals. Our analyses suggest that H. salminicola lost not only its mitochondrial genome but also nearly all nuclear genes involved in transcription and replication of the mitochondrial genome. In contrast, we identified many genes that encode proteins involved in other mitochondrial pathways and determined that genes involved in aerobic respiration or mitochondrial DNA replication were either absent or present only as pseudogenes. As a control, we used the same sequencing and annotation methods to show that a closely related myxozoan, Myxobolus squamalis, has a mitochondrial genome. The molecular results are supported by fluorescence micrographs, which show the presence of mitochondrial DNA in M. squamalis, but not in H. salminicola. Our discovery confirms that adaptation to an anaerobic environment is not unique to single-celled eukaryotes, but has also evolved in a multicellular, parasitic animal. Hence, H. salminicola provides an opportunity for understanding the evolutionary transition from an aerobic to an exclusive anaerobic metabolism.}, }
@article {pmid32032743, year = {2020}, author = {Dokanehiifard, S and Soltani, BM and Ghiasi, P and Baharvand, H and Reza Ganjali, M and Hosseinkhani, S}, title = {hsa-miR-766-5p as a new regulator of mitochondrial apoptosis pathway for discriminating of cell death from cardiac differentiation.}, journal = {Gene}, volume = {736}, number = {}, pages = {144448}, doi = {10.1016/j.gene.2020.144448}, pmid = {32032743}, issn = {1879-0038}, abstract = {Dispose of unnecessary cells in multicellular organism take place through apoptosis as a mode of programmed cell death (PCD). This process is triggered through two main pathway including extrinsic pathway or death receptor pathway and intrinsic or mitochondrial pathway. An alternative role for mitochondrial pathway of cell death is its involvement in cell differentiation. Biochemistry of cell differentiation indicates a common origin for differentiation and apoptosis. miRNAs are a group of small non coding mediator RNAs in regulation of many routes such as apoptosis and differentiation. By using bioinformatics tools hsa-miR-766-5p was predicted to target the BAX, BAK and BOK genes involved in mitochondrial apoptosis pathway. RT-qPCR and dual luciferase assay showed targeting of BAX, BAK and BOK 3'UTRs via hsa-miR-766, detected in SW480 and HEK293T cell lines. Caspases 3/7 and 9 activity assay revealed the involvement of hsa-miR-766-5p in mitochondrial apoptosis pathway regulation detected following overexpression and downregulation of this miRNA, detected in SW480 cells treated with 1 μM doxorubicin. Flow cytometry and MTT assay indicated cell death reduction and viability elevation effect of hsa-miR-766 in SW480 cells after its overexpression. Endogenous expression of hsa-miR-766 during the course of human embryonic stem cells (hESCs) differentiation into cardiomyocytes revealed an inverse expression status of this miRNA with BOK. However, the expression of this miRNA was inversely related to BAX and BAK for some time points of differentiation. Overall this results show the involvement of hsa-miR-766 in regulation of mitochondrial apoptosis pathway.}, }
@article {pmid31722397, year = {2020}, author = {López, EH and Palumbi, SR}, title = {Somatic Mutations and Genome Stability Maintenance in Clonal Coral Colonies.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {828-838}, doi = {10.1093/molbev/msz270}, pmid = {31722397}, issn = {1537-1719}, abstract = {One challenge for multicellular organisms is maintaining genome stability in the face of mutagens across long life spans. Imperfect genome maintenance leads to mutation accumulation in somatic cells, which is associated with tumors and senescence in vertebrates. Colonial reef-building corals are often large, can live for hundreds of years, rarely develop recognizable tumors, and are thought to convert somatic cells into gamete producers, so they are a pivotal group in which to understand long-term genome maintenance. To measure rates and patterns of somatic mutations, we analyzed transcriptomes from 17 to 22 branches from each of four Acropora hyacinthus colonies, determined putative single nucleotide variants, and verified them with Sanger resequencing. Unlike for human skin carcinomas, there is no signature of mutations caused by UV damage, indicating either higher efficiency of repair than in vertebrates, or strong sunscreen protection in these shallow water tropical animals. The somatic mutation frequency per nucleotide in A. hyacinthus is on the same order of magnitude (10-7) as noncancerous human somatic cells, and accumulation of mutations with age is similar. Loss of heterozygosity variants outnumber gain of heterozygosity mutations ∼2:1. Although the mutation frequency is similar in mammals and corals, the preponderance of loss of heterozygosity changes and potential selection may reduce the frequency of deleterious mutations in colonial animals like corals. This may limit the deleterious effects of somatic mutations on the coral organism as well as potential offspring.}, }
@article {pmid32079678, year = {2020}, author = {Erwin, DH}, title = {The origin of animal body plans: a view from fossil evidence and the regulatory genome.}, journal = {Development (Cambridge, England)}, volume = {147}, number = {4}, pages = {}, doi = {10.1242/dev.182899}, pmid = {32079678}, issn = {1477-9129}, abstract = {The origins and the early evolution of multicellular animals required the exploitation of holozoan genomic regulatory elements and the acquisition of new regulatory tools. Comparative studies of metazoans and their relatives now allow reconstruction of the evolution of the metazoan regulatory genome, but the deep conservation of many genes has led to varied hypotheses about the morphology of early animals and the extent of developmental co-option. In this Review, I assess the emerging view that the early diversification of animals involved small organisms with diverse cell types, but largely lacking complex developmental patterning, which evolved independently in different bilaterian clades during the Cambrian Explosion.}, }
@article {pmid32078984, year = {2020}, author = {Moreau, CS}, title = {Symbioses among ants and microbes.}, journal = {Current opinion in insect science}, volume = {39}, number = {}, pages = {1-5}, doi = {10.1016/j.cois.2020.01.002}, pmid = {32078984}, issn = {2214-5753}, abstract = {Ants have been shown to engage in symbiosis across the tree of life, although our knowledge is far from complete. These interactions range from mutualistic to parasitic with several instances of manipulation of host behavior. Nutrient contributions in these symbioses include both farming for food and nitrogen recycling by gut-associated microbes. Interestingly, the ants that are mostly likely to host diverse and likely functional gut microbial communities are those that feed on extreme diets. Although we do see many instances of symbiosis between ants and microbes, there are also examples of species without a functional gut microbiome. Symbiosis among microbes and eukaryotic hosts is common and often considered a hallmark of multicellular evolution [1]. This is true among many of the over 13000 species of ants, although symbiosis between ants and microbes are not ubiquitous. These microbial-ant symbiotic interactions span the tree of life and include microbial eukaryotes, fungi, viruses, and bacteria. These interactions range from pathogenic to mutualistic, with many relationships still not well understood. Although our knowledge of the diversity of these microbes in ants is growing rapidly, and in some cases we know the function and interaction with the host, we still have much to learn about - the little things that run the little things that run the world!}, }
@article {pmid32076502, year = {2020}, author = {Noh, S and Christopher, L and Strassmann, JE and Queller, DC}, title = {Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development.}, journal = {Ecology and evolution}, volume = {10}, number = {3}, pages = {1119-1134}, doi = {10.1002/ece3.5924}, pmid = {32076502}, issn = {2045-7758}, abstract = {When multiple strains of microbes form social groups, such as the multicellular fruiting bodies of Dictyostelium discoideum, conflict can arise regarding cell fate. Both fixed and plastic differences among strains can contribute to cell fate, and plastic responses may be particularly important if social environments frequently change. We used RNA-sequencing and photographic time series analysis to detect possible conflict-induced plastic differences between wild D. discoideum aggregates formed by single strains compared with mixed pairs of strains (chimeras). We found one hundred and two differentially expressed genes that were enriched for biological processes including cytoskeleton organization and cyclic AMP response (up-regulated in chimeras), and DNA replication and cell cycle (down-regulated in chimeras). In addition, our data indicate that in reference to a time series of multicellular development in the laboratory strain AX4, chimeras may be slightly behind clonal aggregates in their development. Finally, phenotypic analysis supported slower splitting of aggregates and a nonsignificant trend for larger group sizes in chimeras. The transcriptomic comparison and phenotypic analyses support discoordination among aggregate group members due to social conflict. These results are consistent with previously observed factors that affect cell fate decision in D. discoideum and provide evidence for plasticity in cAMP signaling and phenotypic coordination during development in response to social conflict in D. discoideum and similar microbial social groups.}, }
@article {pmid32075388, year = {2020}, author = {Raudenská, M and Svobodová, M and Gumulec, J and Falk, M and Masařík, M}, title = {The Importance of Cancer-Associated Fibroblasts in the Pathogenesis of Head and Neck Cancers.}, journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti}, volume = {33}, number = {1}, pages = {39-48}, doi = {10.14735/amko202039}, pmid = {32075388}, issn = {1802-5307}, abstract = {BACKGROUND: Despite progress in anticancer therapies, head and neck squamous cell carcinoma (HNSCC) has still a low survival rate. Recent studies have shown that tumour stroma may play an important role in the pathogenesis of this malignant disease. Fibroblasts are a major component of the tumour microenvironment and may significantly influence HNSCC progression as indicated by the contribution they make to important hallmarks of cancer, such as inflammation, non-restricted growth, angiogenesis, invasion, metastasis, and therapy resistance. It is well known that tumour cells can confer a cancer-associated fibroblast (CAF) phenotype that supports the growth and dissemination of cancer cells. CAFs can stimulate cancer progression through cell-cell contacts and communication, remodelling of extracellular matrix, and production of many signal molecules and matrix metalloproteinases. Consequently, genetic changes in epithelial cells are probably not the only factor that drives HNSCC carcinogenesis. Non-genetic changes in the tumour stroma can also be significantly involved. Stress-induced signals can induce a multicellular program, creating a field of tissue that is predisposed to malignant transformation. The &#8220;field cancerization&#8221; concept represents a process of active evolution of intercellular interactions and feedback loops between tumour and stromal cells. This model paves the way to study cancer from a new perspective and identify new therapeutic targets.<br><br>PURPOSE: In this review, we discuss current knowledge about CAFs, such as their cellular origin, phenotypical plasticity and functional heterogeneity, and stress their contribution to HNSCC progression. This article was supported by the project AZV 16-29835A. The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 18. 6. 2019 Accepted: 9. 9. 2019.}, }
@article {pmid32072723, year = {2020}, author = {Kulanthaivelu, K and Bhat, MD and Prasad, C and Srinivas, D and Mhatre, R and Nandeesh, BN}, title = {Brain MRI Findings in Coenurosis: A Helminth Infection.}, journal = {Journal of neuroimaging : official journal of the American Society of Neuroimaging}, volume = {}, number = {}, pages = {}, doi = {10.1111/jon.12696}, pmid = {32072723}, issn = {1552-6569}, abstract = {BACKGROUND AND PURPOSE: Parasitic neuroinfections in humans have etiological agents spanning a broad spectrum from unicellular (protozoan) to multicellular helminthic (metazoan) organisms. Cerebral coenurosis is a rare cestodal helminthic infection caused by Taenia multiceps. The neuroimaging features of this entity were reviewed to discern an imaging phenotype.<br><br>METHODS: Retrospective analysis was performed on 6 cases of cerebral coenurosis, whose diagnoses were confirmed by histopathology. The clinical, imaging, and histopathological features were recorded for analysis.<br><br>RESULTS: Clinical expressions included focal neurological deficit due to mass effect (n = 4), intraventricular obstruction with features of raised intracranial tension (n = 1), headache (n = 3), seizures (n = 3), and incidental lesions (n = 1). One patient presented with recurrence 1 year after surgical excision. Neuroimaging revealed cystic thin-walled lesions with clustered eccentric internal nodules corresponding to the plenitude of protoscolices of the tapeworm. Three of the lesions showed a multilocular cystic morphology. Spectroscopic metabolite signature of alanine and succinate commensurate with the parasitic etiology was remarkable in the lesions. Enhancement and edema inversely correlated with the signal suppression on fluid-attenuated inversion recovery (FLAIR) imaging. The lesions had a predominantly juxtacortical distribution.<br><br>CONCLUSIONS: In an appropriate clinical setting, a cystic lesion with clustered eccentric internal nodular foci ought to raise the suspicion of this rare infection. Magnetic resonance spectroscopic signature of succinate and alanine, if present, further strengthens the likelihood of coenurosis. Signal characteristics, wall enhancement, and perilesional edema may vary, possibly determined by the stage in the evolution of the parasite.}, }
@article {pmid32067938, year = {2020}, author = {Agosti, A and Marchesi, S and Scita, G and Ciarletta, P}, title = {Modelling cancer cell budding in-vitro as a self-organised, non-equilibrium growth process.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {110203}, doi = {10.1016/j.jtbi.2020.110203}, pmid = {32067938}, issn = {1095-8541}, abstract = {Tissue self-organization into defined and well-controlled three-dimensional structures is essential during development for the generation of organs. A similar, but highly deranged process might also occur during the aberrant growth of cancers, which frequently display a loss of the orderly structures of the tissue of origin, but retain a multicellular organization in the form of spheroids, strands, and buds. The latter structures are often seen when tumors masses switch to an invasive behavior into surrounding tissues. However, the general physical principles governing the self-organized architectures of tumor cell populations remain by and large unclear. In this work, we perform in-vitro experiments to characterize the growth properties of glioblastoma budding emerging from monolayers. We further propose a theoretical model and its finite element implementation to characterize such a topological transition, that is modelled as a self-organised, non-equilibrium phenomenon driven by the trade-off of mechanical forces and physical interactions exerted at cell-cell and cell-substrate adhesions. Notably, the unstable disorder states of uncontrolled cellular proliferation macroscopically emerge as complex spatio-temporal patterns that evolve statistically correlated by a universal law.}, }
@article {pmid32061337, year = {2020}, author = {Ishibashi, K and Tanaka, Y and Morishita, Y}, title = {Perspectives on the evolution of aquaporin superfamily.}, journal = {Vitamins and hormones}, volume = {112}, number = {}, pages = {1-27}, doi = {10.1016/bs.vh.2019.08.001}, pmid = {32061337}, issn = {0083-6729}, abstract = {Aquaporins (AQPs) belong to a transmembrane protein superfamily composed of an internal repeat of a three membrane-spanning domain and each has a highly conserved NPA box. Based on the more variable carboxyl-terminal NPA box, AQPs can be divided into three subfamilies: (1) glycerol-channel aquaglyceroporin (gAQP) (2) water-selective AQP (wAQP), and (3) deviated superaquaporin (sAQP) in the order of passible evolution. This classification has functional and localization relevance: most wAQPs transports water selectively whereas gAQPs and sAQPs also transport small molecules with sAQPs mostly localized inside the cell. As this classification is not based on the function, some wAQPs functioning as glycerol channels will not be included in gAQPs. AQP ancestors may have first originated in eubacteria as gAQPs to transport small molecules such as glycerol. Later some of them may have acquired a water-selective filter to become wAQPs. Although AQPs are absent in many bacteria, especially in archaea, both gAQPs and wAQPs may have been carried over to eukaryotes or horizontally transferred. Finally, multicellular organisms have obtained new sAQPs, which are curiously absent in fungi and plants. Interestingly, both plants and higher insects independently have lost gAQPs, whose functions, however, have been taken over by functionally modified wAQPs partly obtained by horizontal gene transfers from bacteria. This evolutionary viewpoints on AQPs will facilitate further functional analysis of AQP-like sequences and expand our viewpoints on AQP superfamily.}, }
@article {pmid32045589, year = {2020}, author = {Duan, H and Ni, S and Yang, S and Zhou, Y and Zhang, Y and Zhang, S}, title = {Conservation of eATP perception throughout multicellular animal evolution: Identification and functional characterization of coral and amphioxus P2X7-like receptors and flounder P2X7 receptor.}, journal = {Developmental and comparative immunology}, volume = {}, number = {}, pages = {103641}, doi = {10.1016/j.dci.2020.103641}, pmid = {32045589}, issn = {1879-0089}, abstract = {Perception of extracellular ATP (eATP), a common endogenous damage-associated molecular pattern, is through its receptor P2X7R. If eATP/P2X7R signaling is conserved throughout animal evolution is unknown. Moreover, little information is currently available regarding P2X7R in invertebrates. Here we demonstrated that the coral P2X7-like receptor, AdP2X7RL, the amphioxus P2X7-like receptor, BjP2X7RL and the flounder P2X7 receptor, PoP2X7R, shared common features characteristic of mammalian P2X7R, and their 3D structures displayed high resemblance to that of human P2X7R. Expression of Adp2x7rl, Bjp2x7rl and Pop2x7r was all subjected to the regulation by LPS and ATP. We also showed that AdP2X7RL, BjP2X7RL and PoP2X7R were distributed on the plasma membrane in AdP2X7RL-, BjP2X7RL- and PoP2X7R-expressing HEK cells, and had strong affinity to eATP. Importantly, the binding of AdP2X7RL, BjP2X7RL and PoP2X7R to eATP all induced similar downstream responses, including induction of cytokines (IL-1β, IL-6, IL-8 and CCL-2), enhancement of phagocytosis and activation of AKT/ERK-associated signaling pathway observed for mammalian P2X7R. Collectively, our results indicate for the first time that both coral and amphioxus P2X7RL as well as flounder P2X7R can interact with eATP, and induce events that trigger mammalian mechanisms, suggesting the high conservation of eATP perception throughout multicellular animal evolution.}, }
@article {pmid32044287, year = {2020}, author = {Kuwabara, T and Igarashi, K}, title = {Thermotogales origin scenario of eukaryogenesis.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {110192}, doi = {10.1016/j.jtbi.2020.110192}, pmid = {32044287}, issn = {1095-8541}, abstract = {How eukaryotes were generated is an enigma of evolutionary biology. Widely accepted archaeal-origin eukaryogenesis scenarios, based on similarities of genes and related characteristics between archaea and eukaryotes, cannot explain several eukaryote-specific features of the last eukaryotic common ancestor, such as glycerol-3-phosphate-type membrane lipids, large cells and genomes, and endomembrane formation. Thermotogales spheroids, having multicopy-integrated large nucleoids and producing progeny in periplasm, may explain all of these features as well as endoplasmic reticulum-type signal cleavage sites, although they cannot divide. We hypothesize that the progeny chromosome is formed by random joining small DNAs in immature progeny, followed by reorganization by mechanisms including homologous recombination enabled with multicopy-integrated large genome (MILG). We propose that Thermotogales ancestor spheroids came to divide owing to the archaeal cell division genes horizontally transferred via virus-related particles, forming the first eukaryotic common ancestor (FECA). Referring to the hypothesis, the archaeal information-processing system would have been established in FECA by random joining DNAs excised from the MILG, which contained horizontally transferred archaeal and bacterial DNAs, followed by reorganization by the MILG-enabled homologous recombination. Thus, the large genome may have been a prerequisite, but not a consequence, of eukaryogenesis. The random joining of DNAs likely provided the basic mechanisms for eukaryotic evolution: producing the diversity by the formations of supergroups, novel genes, and introns, which are involved in exon shuffling.}, }
@article {pmid32042121, year = {2020}, author = {Black, AJ and Bourrat, P and Rainey, PB}, title = {Ecological scaffolding and the evolution of individuality.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41559-019-1086-9}, pmid = {32042121}, issn = {2397-334X}, abstract = {Evolutionary transitions in individuality are central to the emergence of biological complexity. Recent experiments provide glimpses of processes underpinning the transition from single cells to multicellular life and draw attention to the critical role of ecology. Here, we emphasize this ecological dimension and argue that its current absence from theoretical frameworks hampers development of general explanatory solutions. Using mechanistic mathematical models, we show how a minimal ecological structure comprising patchily distributed resources and between-patch dispersal can scaffold Darwinian-like properties on collectives of cells. This scaffolding causes cells to participate directly in the process of evolution by natural selection as if they were members of multicellular collectives, with collectives participating in a death-birth process arising from the interplay between the timing of dispersal events and the rate of resource use by cells. When this timescale is sufficiently long and new collectives are founded by single cells, collectives experience conditions that favour evolution of a reproductive division of labour. Together our simple model makes explicit key events in the major evolutionary transition to multicellularity. It also makes predictions concerning the life history of certain pathogens and serves as an ecological recipe for experimental realization of evolutionary transitions.}, }
@article {pmid32039188, year = {2020}, author = {Li, R and Hornberger, K and Dutton, JR and Hubel, A}, title = {Cryopreservation of Human iPS Cell Aggregates in a DMSO-Free Solution-An Optimization and Comparative Study.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {1}, doi = {10.3389/fbioe.2020.00001}, pmid = {32039188}, issn = {2296-4185}, abstract = {Human induced pluripotent stem cells (hiPSCs) are an important cell source for regenerative medicine products. Effective methods of preservation are critical to their clinical and commercial applications. The use of a dimethyl sulfoxide (DMSO)-free solution containing all non-toxic molecules offers an effective alternative to the conventional DMSO and alleviates pain points associated with the use of DMSO in the cryopreservation of hiPSCs. Both hiPSCs and cells differentiated from them are commonly multicellular systems, which are more sensitive to stresses of freezing and thawing than single cells. In this investigation, low-temperature Raman spectroscopy visualized freezing behaviors of hiPSC aggregates in different solutions. These aggregates exhibited sensitivity to undercooling in DMSO-containing solutions. We demonstrated the ability to replace DMSO with non-toxic molecules, improve post-thaw cell survival, and reduce sensitivity to undercooling. An accelerated optimization process capitalized on the positive synergy among multiple DMSO-free molecules, which acted in concert to influence ice formation and protect cells during freezing and thawing. A differential evolution algorithm was used to optimize the multi-variable, DMSO-free preservation protocol in 8 experiments. hiPSC aggregates frozen in the optimized solution did not exhibit the same sensitivity to undercooling as those frozen in non-optimized solutions or DMSO, indicating superior adaptability of the optimized solution to different freezing modalities and unplanned deviations. This investigation shows the importance of optimization, explains the mechanisms and advantages of a DMSO-free solution, and enables not only improved cryopreservation of hiPSCs but potentially other cell types for translational regenerative medicine.}, }
@article {pmid32027371, year = {2020}, author = {Posada, D}, title = {CellCoal: coalescent simulation of single-cell sequencing samples.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msaa025}, pmid = {32027371}, issn = {1537-1719}, abstract = {Our capacity to study individual cells has enabled a new level of resolution for understanding complex biological systems like multicellular organisms or microbial communities. Not surprisingly, several methods have been developed in recent years with a formidable potential to investigate the somatic evolution of single cells in both healthy and pathological tissues. However, single-cell genomic data can be quite noisy due to different technical biases, so inferences resulting from these new methods need to be carefully contrasted. Here I introduce CellCoal, a software tool for the coalescent simulation of single-cell genotypes. CellCoal simulates the history of single-cell samples obtained from somatic cell populations with different demographic histories and produces single-nucleotide variants under a variety of mutation models, sequencing read counts and genotype likelihoods, considering allelic imbalance, allelic dropout, amplification and sequencing errors, typical of this type of data. CellCoal is a flexible tool that can be used to understand the implications of different somatic evolutionary processes at the single-cell level, and to benchmark dedicated bioinformatic tools for the analysis of single-cell genotypes.}, }
@article {pmid32024776, year = {2020}, author = {Munke, A and Kimura, K and Tomaru, Y and Okamoto, K}, title = {Capsid structure of a marine algae virus of the order Picornavirales.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {}, doi = {10.1128/JVI.01855-19}, pmid = {32024776}, issn = {1098-5514}, abstract = {The order Picornavirales includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as algae, presumably possess certain characteristics that have changed little over the course of evolution, and thus these viruses may resemble the Picornavirales ancestor in some respects. Herein, we present the capsid structure of Chaetoceros tenuissimus RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first of an algae virus belonging to the family Marnaviridae of the order Picornavirales A structural comparison to related invertebrate and vertebrate viruses revealed a unique surface loop of the major CP VP1 that had not been observed previously, and further, that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian Picornavirales viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of Picornavirales viruses. Based on the above-mentioned and other critical structural features, the acquired traits among Picornavirales viruses were categorized for profound discussions. The observations afford new insights on three long-standing theories among Picornavirales: the canyon hypothesis, the primordial VP2 domain swap, and the hypothesis that algae picorna-like viruses could share characteristics with the Picornavirales ancestor.ImportanceIdentifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The Picornavirales viruses infect a broad spectrum of hosts, ranging from unicellular algae to insects and mammals, and include many human pathogens. Those viruses that infect unicellular protists, such as algae, are likely to have undergone fewer structural changes during the course of evolution compared to those viruses that infect multicellular eukaryotes, and thus still share some characteristics with the Picornavirales ancestor. This manuscript describes the first atomic capsid structure of an alga Marnavirus, CtenRNAV-II. A comparison to capsid structures of the related invertebrate and vertebrate viruses identified a number of structural traits that have been functionally acquired or lost during the course of evolution. These observations provide new insights on past theories on the viability and evolution of Picornavirales viruses.}, }
@article {pmid32020592, year = {2020}, author = {Nishino, J and Watanabe, S and Miya, F and Kamatani, T and Sugawara, T and Boroevich, KA and Tsunoda, T}, title = {Quantification of multicellular colonization in tumor metastasis using exome sequencing data.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.32910}, pmid = {32020592}, issn = {1097-0215}, abstract = {Metastasis is a major cause of cancer-related mortality, and it is essential to understand how metastasis occurs in order to overcome it. One relevant question is the origin of a metastatic tumor cell population. Although the hypothesis of a single-cell origin for metastasis from a primary tumor has long been prevalent, several recent studies using mouse models have supported a multi-cellular origin of metastasis. Human bulk whole-exome sequencing (WES) studies also have demonstrated a multiple 'clonal' origin of metastasis, with different mutational compositions. Specifically, there has not yet been strong research to determine how many founder cells colonize a metastatic tumor. To address this question, under the metastatic model of 'single bottleneck followed by rapid growth', we developed a method to quantify the 'founder cell population size' in a metastasis using paired WES data from primary and metachronous metastatic tumors. Simulation studies demonstrated the proposed method gives unbiased results with sufficient accuracy in the range of realistic settings. Applying the proposed method to real WES data from four colorectal cancer patients, all samples supported a multi-cellular origin of metastasis and the founder size was quantified, ranging from 3 to 17 cells. Such a wide-range of founder sizes estimated by the proposed method suggests that there are large variations in genetic similarity between primary and metastatic tumors in the same subjects, which may explain the observed (dis)similarity of drug responses between tumors. This article is protected by copyright. All rights reserved.}, }
@article {pmid32016363, year = {2020}, author = {Alsufyani, T and Califano, G and Deicke, M and Grueneberg, J and Weiss, A and Engelen, AH and Kwantes, M and Mohr, JF and Ulrich, JF and Wichard, T}, title = {Macroalgal-bacterial interactions: Identification and role of thallusin in morphogenesis of the seaweed Ulva (Chlorophyta).}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/eraa066}, pmid = {32016363}, issn = {1460-2431}, abstract = {Macroalgal microbiomes have core functions related to biofilm formation, growth, and morphogenesis of seaweeds. In particular, the growth and development of the sea lettuce Ulva spp. (Chlorophyta) depends on bacteria releasing morphogenetic compounds. Under axenic conditions, the macroalga Ulva mutabilis develops a callus-like phenotype with cell wall protrusions. However, coculturing with Roseovarius sp. (MS2) and Maribacter sp. (MS6), which produce various stimulatory chemical mediators, completely recovers morphogenesis. This ecological reconstruction forms a tripartite community which can be further studied for its role in cross-kingdom interactions. Hence, our study sought to identify algal growth- and morphogenesis-promoting factors (AGMPFs) capable of phenocopying the activity of Maribacter spp. We performed bioassay-guided solid-phase extraction in water samples collected from U. mutabilis aquaculture systems. We uncovered novel ecophysiological functions of thallusin, a sesquiterpenoid morphogen, identified for the first time in algal aquaculture. Thallusin, released by Maribacter sp., induced rhizoid and cell wall formation at a concentration of 11 pmol L-1. We further demonstrated that gametes acquired the iron complex of thallusin, thereby linking morphogenetic processes with intracellular iron homeostasis. Understanding macroalgae-bacteria interactions permits further elucidation of the evolution of multicellularity and cellular differentiation and development of new applications in microbiome-mediated aquaculture systems.}, }
@article {pmid32003151, year = {2020}, author = {Rimskaya-Korsakova, N and Dyachuk, V and Temereva, E}, title = {Parapodial glandular organs in Owenia borealis (Annelida: Oweniidae) and their possible relationship with nephridia.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22928}, pmid = {32003151}, issn = {1552-5015}, support = {18-14-00082//Russian Science Foundation/ ; }, abstract = {Oweniidae is a basal group of recent annelids and nowadays it attracts the attention of researchers of many biological fields. Surprisingly, details of their anatomy, like the adult excretory system, remain obscure. Researchers recently suggested that the paired organs of tubeworms in the family Oweniidae are related to nephridia. In the current study of Owenia borealis adults, we determined that these structures are parapodial glandular organs (PGOs) and are located in the first two segments of adults. The PGOs are complex subepidermal multicellular glands that contain secretory cells, that is, goblet cells, which are differentiated by the type of the producing tube matter. The goblet cells are surrounded by muscles that are used to extrude material stored in the PGO's lumen into the external environment. The anterior pair of PGOs have very well-developed rough endoplasmatic reticulum in the proximal cells, spacious Golgi complexes, numerous nail-shaped microvilli, and apocrine secretory processes in the goblet cells of the distal parts. The posterior pair of PGOs only consists of cells, which probably produce proteinaceous fibrils. We discuss the homology of goblet cells with specific nail-shaped microvilli that produce β-chitin within annelids. We also discuss the possibility that PGOs and nephridia have a common origin. This study provides new information on the ultrastructure of cells that secrete the organic material used to form the tubes inhabited by tube-dwelling annelids.}, }
@article {pmid31983537, year = {2020}, author = {Yao, M and Ventura, PB and Jiang, Y and Rodriguez, FJ and Wang, L and Perry, JSA and Yang, Y and Wahl, K and Crittenden, RB and Bennett, ML and Qi, L and Gong, CC and Li, XN and Barres, BA and Bender, TP and Ravichandran, KS and Janes, KA and Eberhart, CG and Zong, H}, title = {Astrocytic trans-Differentiation Completes a Multicellular Paracrine Feedback Loop Required for Medulloblastoma Tumor Growth.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2019.12.024}, pmid = {31983537}, issn = {1097-4172}, abstract = {The tumor microenvironment (TME) is critical for tumor progression. However, the establishment and function of the TME remain obscure because of its complex cellular composition. Using a mouse genetic system called mosaic analysis with double markers (MADMs), we delineated TME evolution at single-cell resolution in sonic hedgehog (SHH)-activated medulloblastomas that originate from unipotent granule neuron progenitors in the brain. First, we found that astrocytes within the TME (TuAstrocytes) were trans-differentiated from tumor granule neuron precursors (GNPs), which normally never differentiate into astrocytes. Second, we identified that TME-derived IGF1 promotes tumor progression. Third, we uncovered that insulin-like growth factor 1 (IGF1) is produced by tumor-associated microglia in response to interleukin-4 (IL-4) stimulation. Finally, we found that IL-4 is secreted by TuAstrocytes. Collectively, our studies reveal an evolutionary process that produces a multi-lateral network within the TME of medulloblastoma: a fraction of tumor cells trans-differentiate into TuAstrocytes, which, in turn, produce IL-4 that stimulates microglia to produce IGF1 to promote tumor progression.}, }
@article {pmid31975241, year = {2020}, author = {Puzakov, MV and Puzakova, LV and Cheresiz, SV}, title = {The Tc1-like elements with the spliceosomal introns in mollusk genomes.}, journal = {Molecular genetics and genomics : MGG}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00438-020-01645-1}, pmid = {31975241}, issn = {1617-4623}, abstract = {Transposable elements (TEs) are DNA sequences capable of transpositions within the genome and thus exerting a considerable influence on the genome functioning and structure and serving as a source of new genes. TE biodiversity studies in previously unexplored species are important for the fundamental understanding of the TE influence on eukaryotic genomes. TEs are classified into retrotransposons and DNA transposons. IS630/Tc1/mariner (ITm) superfamily of DNA transposons is one of the most diverse groups broadly represented among the eukaryotes. The study of 19 mollusk genomes revealed a new group of ITm superfamily elements, which we henceforth refer to as TLEWI. These TEs are characterized by the low copy number, the lack of terminal inverted repeats, the catalytic domain with DD36E signature and the presence of spliceosomal introns in transposase coding sequence. Their prevalence among the mollusks is limited to the class Bivalvia. Since TLEWI possess the features of domesticated TE and structures similar to the eukaryotic genes which are not typical for the DNA transposons, we consider the hypothesis of co-optation of TLEWI gene by the bivalves. The results of our study will fill the gap of knowledge about the prevalence, activity, and evolution of the ITm DNA transposons in multicellular genomes and will facilitate our understanding of the mechanisms of TE domestication by the host genome.}, }
@article {pmid31973071, year = {2020}, author = {Auboeuf, D}, title = {Physicochemical Foundations of Life that Direct Evolution: Chance and Natural Selection are not Evolutionary Driving Forces.}, journal = {Life (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/life10020007}, pmid = {31973071}, issn = {2075-1729}, support = {Salary//Institut National de la Santé et de la Recherche Médicale/ ; }, abstract = {The current framework of evolutionary theory postulates that evolution relies on random mutations generating a diversity of phenotypes on which natural selection acts. This framework was established using a top-down approach as it originated from Darwinism, which is based on observations made of complex multicellular organisms and, then, modified to fit a DNA-centric view. In this article, it is argued that based on a bottom-up approach starting from the physicochemical properties of nucleic and amino acid polymers, we should reject the facts that (i) natural selection plays a dominant role in evolution and (ii) the probability of mutations is independent of the generated phenotype. It is shown that the adaptation of a phenotype to an environment does not correspond to organism fitness, but rather corresponds to maintaining the genome stability and integrity. In a stable environment, the phenotype maintains the stability of its originating genome and both (genome and phenotype) are reproduced identically. In an unstable environment (i.e., corresponding to variations in physicochemical parameters above a physiological range), the phenotype no longer maintains the stability of its originating genome, but instead influences its variations. Indeed, environment- and cellular-dependent physicochemical parameters define the probability of mutations in terms of frequency, nature, and location in a genome. Evolution is non-deterministic because it relies on probabilistic physicochemical rules, and evolution is driven by a bidirectional interplay between genome and phenotype in which the phenotype ensures the stability of its originating genome in a cellular and environmental physicochemical parameter-depending manner.}, }
@article {pmid31971511, year = {2020}, author = {Narasimhan, M and Johnson, A and Prizak, R and Kaufmann, WA and Tan, S and Casillas-Pérez, B and Friml, J}, title = {Evolutionarily unique mechanistic framework of clathrin-mediated endocytosis in plants.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, doi = {10.7554/eLife.52067}, pmid = {31971511}, issn = {2050-084X}, support = {742985//H2020 European Research Council/ ; I3630B25//Austrian Science Fund/ ; ALTF 723-2015//European Molecular Biology Organization/ ; }, abstract = {In plants, clathrin mediated endocytosis (CME) represents the major route for cargo internalisation from the cell surface. It has been assumed to operate in an evolutionary conserved manner as in yeast and animals. Here we report characterisation of ultrastructure, dynamics and mechanisms of plant CME as allowed by our advancement in electron microscopy and quantitative live imaging techniques. Arabidopsis CME appears to follow the constant curvature model and the bona fide CME population generates vesicles of a predominantly hexagonal-basket type; larger and with faster kinetics than in other models. Contrary to the existing paradigm, actin is dispensable for CME events at the surface but plays a unique role in collecting endocytic vesicles, sorting of internalised cargos and directional endosome movement that itself actively promote CME events. Internalized vesicles display a strongly delayed and sequential uncoating. These unique features highlight the independent evolution of the plant CME mechanism during the autonomous rise of multicellularity in eukaryotes.}, }
@article {pmid31965986, year = {2020}, author = {Reddy, PC and Pradhan, SJ and Karmodiya, K and Galande, S}, title = {Origin of RNA Polymerase II pause in eumetazoans: Insights from Hydra.}, journal = {Journal of biosciences}, volume = {45}, number = {}, pages = {}, pmid = {31965986}, issn = {0973-7138}, abstract = {Multicellular organisms have evolved sophisticated mechanisms for responding to various developmental, environmental and physical stimuli by regulating transcription. The correlation of distribution of RNA Polymerase II (RNA Pol II) with transcription is well established in higher metazoans, however genome-wide information about its distribution in early metazoans, such as Hydra, is virtually absent. To gain insights into RNA Pol II-mediated transcription and chromatin organization in Hydra, we performed chromatin immunoprecipitation (ChIP)-coupled high-throughput sequencing (ChIP-seq) for RNA Pol II and Histone H3. Strikingly, we found that Hydra RNA Pol II is uniformly distributed across the entire gene body, as opposed to its counterparts in bilaterians such as human and mouse. Furthermore, correlation with transcriptome data revealed that the levels of RNA Pol II correlate with the magnitude of gene expression. Strikingly, the characteristic peak of RNA Pol II pause typically observed in bilaterians at the transcription start sites (TSSs) was not observed in Hydra. The RNA Pol II traversing ratio in Hydra was found to be intermediate to yeast and bilaterians. The search for factors involved in RNA Pol II pause revealed that RNA Pol II pausing machinery was most likely acquired first in Cnidaria. However, only a small subset of genes exhibited the promoter proximal RNP Pol II pause. Interestingly, the nucleosome occupancy is highest over the subset of paused genes as compared to total Hydra genes, which is another indication of paused RNA Pol II at these genes. Thus, this study provides evidence for the molecular basis of RNA Pol II pause early during the evolution of multicellular organisms.}, }
@article {pmid31959809, year = {2020}, author = {Oña, L and Lachmann, M}, title = {Signalling architectures can prevent cancer evolution.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {674}, doi = {10.1038/s41598-020-57494-w}, pmid = {31959809}, issn = {2045-2322}, abstract = {Cooperation between cells in multicellular organisms is preserved by an active regulation of growth through the control of cell division. Molecular signals used by cells for tissue growth are usually present during developmental stages, angiogenesis, wound healing and other processes. In this context, the use of molecular signals triggering cell division is a puzzle, because any molecule inducing and aiding growth can be exploited by a cancer cell, disrupting cellular cooperation. A significant difference is that normal cells in a multicellular organism have evolved in competition between high-level organisms to be altruistic, being able to send signals even if it is to their detriment. Conversely, cancer cells evolve their abuse over the cancer's lifespan by out-competing their neighbours. A successful mutation leading to cancer must evolve to be adaptive, enabling a cancer cell to send a signal that results in higher chances to be selected. Using a mathematical model of such molecular signalling mechanism, this paper argues that a signal mechanism would be effective against abuse by cancer if it affects the cell that generates the signal as well as neighbouring cells that would receive a benefit without any cost, resulting in a selective disadvantage for a cancer signalling cell. We find that such molecular signalling mechanisms normally operate in cells as exemplified by growth factors. In scenarios of global and local competition between cells, we calculate how this process affects the fixation probability of a mutant cell generating such a signal, and find that this process can play a key role in limiting the emergence of cancer.}, }
@article {pmid31956023, year = {2019}, author = {Bowles, AMC and Bechtold, U and Paps, J}, title = {The Origin of Land Plants Is Rooted in Two Bursts of Genomic Novelty.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2019.11.090}, pmid = {31956023}, issn = {1879-0445}, abstract = {Over the last 470 Ma, plant evolution has seen major evolutionary transitions, such as the move from water to land and the origins of vascular tissues, seeds, and flowers [1]. These have resulted in the evolution of terrestrial flora that has shaped modern ecosystems and the diversification of the Plant Kingdom, Viridiplantae, into over 374,000 described species [2]. Each of these transitions was accompanied by the gain and loss of genes in plant genomes. For example, whole-genome duplications are known to be fundamental to the origins of both seed and flowering plants [3, 4]. With the ever-increasing quality and quantity of whole-genome data, evolutionary insight into origins of distinct plant groups using comparative genomic techniques is now feasible. Here, using an evolutionary genomics pipeline to compare 208 complete genomes, we analyze the gene content of the ancestral genomes of the last common ancestor of land plants and all other major groups of plant. This approach reveals an unprecedented level of fundamental genomic novelties in two nodes related to the origin of land plants: the first in the origin of streptophytes during the Ediacaran and another in the ancestor of land plants in the Ordovician. Our findings highlight the biological processes that evolved with the origin of land plants and emphasize the importance of conserved gene novelties in plant diversification. Comparisons to other eukaryotic studies suggest a separation of the genomic origins of multicellularity and terrestrialization in plants.}, }
@article {pmid31942240, year = {2019}, author = {Green, KJ and Jaiganesh, A and Broussard, JA}, title = {Desmosomes: Essential contributors to an integrated intercellular junction network.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {}, doi = {10.12688/f1000research.20942.1}, pmid = {31942240}, issn = {2046-1402}, abstract = {The development of adhesive connections between cells was critical for the evolution of multicellularity and for organizing cells into complex organs with discrete compartments. Four types of intercellular junction are present in vertebrates: desmosomes, adherens junctions, tight junctions, and gap junctions. All are essential for the development of the embryonic layers and organs as well as adult tissue homeostasis. While each junction type is defined as a distinct entity, it is now clear that they cooperate physically and functionally to create a robust and functionally diverse system. During evolution, desmosomes first appeared in vertebrates as highly specialized regions at the plasma membrane that couple the intermediate filament cytoskeleton at points of strong cell-cell adhesion. Here, we review how desmosomes conferred new mechanical and signaling properties to vertebrate cells and tissues through their interactions with the existing junctional and cytoskeletal network.}, }
@article {pmid31932592, year = {2020}, author = {Li, Q and Li, S and Zhang, X and Xu, W and Han, X}, title = {Programmed magnetic manipulation of vesicles into spatially coded prototissue architectures arrays.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {232}, doi = {10.1038/s41467-019-14141-x}, pmid = {31932592}, issn = {2041-1723}, support = {21773050//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {In nature, cells self-assemble into spatially coded tissular configurations to execute higher-order biological functions as a collective. This mechanism has stimulated the recent trend in synthetic biology to construct tissue-like assemblies from protocell entities, with the aim to understand the evolution mechanism of multicellular mechanisms, create smart materials or devices, and engineer tissue-like biomedical implant. However, the formation of spatially coded and communicating micro-architectures from large quantity of protocell entities, especially for lipid vesicle-based systems that mostly resemble cells, is still challenging. Herein, we magnetically assemble giant unilamellar vesicles (GUVs) or cells into various microstructures with spatially coded configurations and spatialized cascade biochemical reactions using a stainless steel mesh. GUVs in these tissue-like aggregates exhibit uncustomary osmotic stability that cannot be achieved by individual GUVs suspensions. This work provides a versatile and cost-effective strategy to form robust tissue-mimics and indicates a possible superiority of protocell colonies to individual protocells.}, }
@article {pmid31928871, year = {2019}, author = {Miller, SR and Longley, R and Hutchins, PR and Bauersachs, T}, title = {Cellular Innovation of the Cyanobacterial Heterocyst by the Adaptive Loss of Plasticity.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2019.11.056}, pmid = {31928871}, issn = {1879-0445}, abstract = {Cellular innovation is central to biological diversification, yet its underlying mechanisms remain poorly understood [1]. One potential source of new cellular traits is environmentally induced phenotypic variation, or phenotypic plasticity. The plasticity-first hypothesis [2-4] proposes that natural selection can improve upon an ancestrally plastic phenotype to produce a locally adaptive trait, but the role of plasticity for adaptive evolution is still unclear [5-10]. Here, we show that a structurally novel form of the heterocyst, the specialized nitrogen-fixing cell of the multicellular cyanobacterium Fischerella thermalis, has evolved multiple times from ancestrally plastic developmental variation during adaptation to high temperature. Heterocyst glycolipids (HGs) provide an extracellular gas diffusion barrier that protects oxygen-sensitive nitrogenase [11, 12], and cyanobacteria typically exhibit temperature-induced plasticity in HG composition that modulates heterocyst permeability [13, 14]. By contrast, high-temperature specialists of F. thermalis constitutively overproduce glycolipid isomers associated with high temperature to levels unattained by plastic strains. This results in a less-permeable heterocyst, which is advantageous at high temperature but deleterious at low temperature for both nitrogen fixation activity and fitness. Our study illustrates how the origin of a novel cellular phenotype by the genetic assimilation and adaptive refinement of a plastic trait can be a source of biological diversity and contribute to ecological specialization.}, }
@article {pmid31925005, 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 = {1}, pages = {160}, doi = {10.1038/s42003-019-0417-3}, pmid = {31925005}, 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 {pmid31921561, year = {2020}, author = {Liang, Z and Geng, Y and Ji, C and Du, H and Wong, CE and Zhang, Q and Zhang, Y and Zhang, P and Riaz, A and Chachar, S and Ding, Y and Wen, J and Wu, Y and Wang, M and Zheng, H and Wu, Y and Demko, V and Shen, L and Han, X and Zhang, P and Gu, X and Yu, H}, title = {Mesostigma viride Genome and Transcriptome Provide Insights into the Origin and Evolution of Streptophyta.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {7}, number = {1}, pages = {1901850}, doi = {10.1002/advs.201901850}, pmid = {31921561}, issn = {2198-3844}, abstract = {The Streptophyta include unicellular and multicellular charophyte green algae and land plants. Colonization of the terrestrial habitat by land plants is a major evolutionary event that has transformed the planet. So far, lack of genome information on unicellular charophyte algae hinders the understanding of the origin and the evolution from unicellular to multicellular life in Streptophyta. This work reports the high-quality reference genome and transcriptome of Mesostigma viride, a single-celled charophyte alga with a position at the base of Streptophyta. There are abundant segmental duplications and transposable elements in M. viride, which contribute to a relatively large genome with high gene content compared to other algae and early diverging land plants. This work identifies the origin of genetic tools that multicellular Streptophyta have inherited and key genetic innovations required for the evolution of land plants from unicellular aquatic ancestors. The findings shed light on the age-old questions of the evolution of multicellularity and the origin of land plants.}, }
@article {pmid31920779, year = {2019}, author = {Levin, M}, title = {The Computational Boundary of a &quot;Self&quot;: Developmental Bioelectricity Drives Multicellularity and Scale-Free Cognition.}, journal = {Frontiers in psychology}, volume = {10}, number = {}, pages = {2688}, doi = {10.3389/fpsyg.2019.02688}, pmid = {31920779}, issn = {1664-1078}, abstract = {All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, and molecular networks) that are themselves complex and competent in their own native contexts. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan creatures' bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent larger organism. In this article, I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: &quot;Scale-Free Cognition.&quot; I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface - the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive &quot;light cone&quot; which defines the scale and limits of its cognition. I hypothesize that higher level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress - the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggest a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the basic drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology.}, }
@article {pmid31911467, year = {2020}, author = {Del Cortona, A and Jackson, CJ and Bucchini, F and Van Bel, M and D'hondt, S and Škaloud, P and Delwiche, CF and Knoll, AH and Raven, JA and Verbruggen, H and Vandepoele, K and De Clerck, O and Leliaert, F}, title = {Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1910060117}, pmid = {31911467}, issn = {1091-6490}, abstract = {The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.}, }
@article {pmid30794780, year = {2019}, author = {Tucci, V and Isles, AR and Kelsey, G and Ferguson-Smith, AC and , }, title = {Genomic Imprinting and Physiological Processes in Mammals.}, journal = {Cell}, volume = {176}, number = {5}, pages = {952-965}, doi = {10.1016/j.cell.2019.01.043}, pmid = {30794780}, issn = {1097-4172}, support = {MR/K011332/1/MRC_/Medical Research Council/United Kingdom ; MR/L010305/1/MRC_/Medical Research Council/United Kingdom ; 210757/Z/18/WT_/Wellcome Trust/United Kingdom ; MR/R009791/1/MRC_/Medical Research Council/United Kingdom ; MR/S000437/1/MRC_/Medical Research Council/United Kingdom ; BBS/E/B/000C0426/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P008623/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P002307/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alleles ; Animals ; Biological Evolution ; Chromosomes ; DNA Methylation ; Epigenesis, Genetic/genetics/physiology ; Genomic Imprinting/*genetics/*physiology ; Mammals/*genetics/metabolism ; Physiological Phenomena ; }, abstract = {Complex multicellular organisms, such as mammals, express two complete sets of chromosomes per nucleus, combining the genetic material of both parents. However, epigenetic studies have demonstrated violations to this rule that are necessary for mammalian physiology; the most notable parental allele expression phenomenon is genomic imprinting. With the identification of endogenous imprinted genes, genomic imprinting became well-established as an epigenetic mechanism in which the expression pattern of a parental allele influences phenotypic expression. The expanding study of genomic imprinting is revealing a significant impact on brain functions and associated diseases. Here, we review key milestones in the field of imprinting and discuss mechanisms and systems in which imprinted genes exert a significant role.}, }
@article {pmid30350947, year = {2019}, author = {Budin, I and Keasling, JD}, title = {Synthetic Biology for Fundamental Biochemical Discovery.}, journal = {Biochemistry}, volume = {58}, number = {11}, pages = {1464-1469}, doi = {10.1021/acs.biochem.8b00915}, pmid = {30350947}, issn = {1520-4995}, mesh = {Biological Evolution ; Gene Regulatory Networks ; Protein Engineering/methods/*trends ; Research/trends ; Research Design/trends ; Synthetic Biology/*methods/*trends ; }, abstract = {Synthetic biologists have developed sophisticated molecular and genetic tools to engineer new biochemical functions in cells. Applications for these tools have focused on important problems in energy and medicine, but they can also be applied to address basic science topics that cannot be easily accessed by classical approaches. We focus on recent work that has utilized synthetic biology approaches, ranging from promoter engineering to the de novo synthesis of cellular parts, to investigate a wide range of biochemical and cellular questions. Insights obtained by these efforts include how fatty acid composition mediates cellular metabolism, how transcriptional circuits act to stabilize multicellular networks, and fitness trade-offs involved in the selection of genetic regulatory elements. We also highlight common themes about how &quot;discovery by synthesis&quot; approaches can aid fundamental research. For example, rewiring of native metabolism through metabolic engineering is a powerful tool for investigating biological molecules whose exact composition and abundance are key for function. Meanwhile, endeavors to synthesize cells and their components allow scientists to address evolutionary questions that are otherwise constrained by extant laboratory models.}, }
@article {pmid31883344, year = {2019}, author = {Milocco, L and Salazar-Ciudad, I}, title = {Is evolution predictable? Quantitative genetics under complex genotype-phenotype maps.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1111/evo.13907}, pmid = {31883344}, issn = {1558-5646}, abstract = {A fundamental aim of post-genomic 21st century biology is to understand the genotype-phenotype map (GPM) or how specific genetic variation relates to specific phenotypic variation. Quantitative genetics approximates such maps using linear models, and has developed methods to predict the response to selection in a population. The other major field of research concerned with the GPM, developmental evolutionary biology or evo-devo, has found the GPM to be highly nonlinear and complex. Here we quantify how the predictions of quantitative genetics are affected by a complex, nonlinear map based on the development of a multicellular organ. We compared the predicted change in mean phenotype for a single generation using the multivariate breeder's equation, with the change observed from the model of development. We found that there are frequent disagreements between predicted and observed responses to selection due to the nonlinear nature of the genotype-phenotype map. Our results are a step towards integrating the fields studying the GPM. This article is protected by copyright. All rights reserved.}, }
@article {pmid31880593, year = {2019}, author = {Wang, DG and Huang, FR and Chen, W and Zhou, Y and Wang, CY and Zhu, F and Shao, BJ and Luo, D}, title = {Clinicopathological Analysis of Acquired Melanocytic Nevi and a Preliminary Study on the Possible Origin of Nevus Cells.}, journal = {The American Journal of dermatopathology}, volume = {}, number = {}, pages = {}, doi = {10.1097/DAD.0000000000001599}, pmid = {31880593}, issn = {1533-0311}, abstract = {BACKGROUND: The pathogenesis of acquired melanocytic nevi (AMN) is still unclear, and the origin of nevus cells has not been clarified.<br><br>OBJECTIVE: To analyze the clinical features and pathological types of AMN and identify the possible origin of nevus cells.<br><br>METHODS: A retrospective study of 2929 cases of AMN was conducted, and 96 specimens of intradermal and junctional nevi were selected. Immunohistochemical assays were performed to detect the expression of basement membrane component receptor DDR-1 and the molecular markers on epidermal melanocytes, dermal stem cells (DSCs), and hair follicle stem cells.<br><br>RESULTS: Junctional nevi and compound nevi were prone to occur on glabrous skin, such as the palms, soles, and vulva, and on the extremities in children, whereas intradermal nevi tended to develop on the trunk, head, and face of adults. The immunohistochemical data revealed that both junctional nevi and intradermal nevi expressed the epidermal melanocyte surface markers E-cadherin, DDR-1, and integrin α6 and the DSC molecular markers NGFRp-75 and nestin. CD34 was expressed only in junctional nevi, whereas K19 was not expressed in any type of melanocytic nevi. There was no significant difference in molecular expression at different sites or in different ages of onset. Nestin expression was markedly stronger in the intradermal nevi than in the junctional nevi, but there was no difference between the superficial and deep nevus cell nests of intradermal nevi.<br><br>CONCLUSION: AMN may have a multicellular origin that commonly follows the mode of Abtropfung. Furthermore, DSCs may partly or independently participate in the formation of nevus cells.}, }
@article {pmid31879283, year = {2019}, author = {Erives, A and Fritzsch, B}, title = {A Screen for Gene Paralogies Delineating Evolutionary Branching Order of Early Metazoa.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1534/g3.119.400951}, pmid = {31879283}, issn = {2160-1836}, abstract = {The evolutionary diversification of animals is one of Earth's greatest marvels, yet its earliest steps are shrouded in mystery. Animals, the monophyletic clade known as Metazoa, evolved wildly divergent multicellular life strategies featuring ciliated sensory epithelia. In many lineages epithelial sensoria became coupled to increasingly complex nervous systems. Currently, different phylogenetic analyses of single-copy genes support mutually-exclusive possibilities that either Porifera or Ctenophora is sister to all other animals. Resolving this dilemma would advance the ecological and evolutionary understanding of the first animals and the evolution of nervous systems. Here we describe a comparative phylogenetic approach based on gene duplications. We computationally identify and analyze gene families with early metazoan duplications using an approach that mitigates apparent gene loss resulting from the miscalling of paralogs. In the transmembrane channel-like (TMC) family of mechano-transducing channels, we find ancient duplications that define separate clades for Eumetazoa (Placozoa + Cnidaria + Bilateria) versus Ctenophora, and one duplication that is shared only by Eumetazoa and Porifera. In the Max-like protein X (MLX and MLXIP) family of bHLH-ZIP regulators of metabolism, we find that all major lineages from Eumetazoa and Porifera (sponges) share a duplicated gene pair that is sister to the single-copy gene maintained in Ctenophora. These results suggest a new avenue for deducing deep phylogeny by choosing rather than avoiding ancient gene paralogies.}, }
@article {pmid31866780, year = {2019}, author = {Durand, PM and Barreto Filho, MM and Michod, RE}, title = {Cell Death in Evolutionary Transitions in Individuality.}, journal = {The Yale journal of biology and medicine}, volume = {92}, number = {4}, pages = {651-662}, pmid = {31866780}, issn = {1551-4056}, abstract = {Programmed cell death (PCD) in cell groups and microbial communities affects population structures, nutrient recycling, and sociobiological interactions. A less explored area is the role played by PCD in the emergence of higher-level individuals. Here, we examine how cell death impacted evolutionary transitions in individuality (ETIs). The focus is on three specific ETIs - the emergence of the eukaryote cell, multicellularity, and social insects - and we review the theoretical and empirical evidence for the role of PCD in these three transitions. We find that PCD likely contributed to many of the processes involved in eukaryogenesis and the transition to multicellularity. PCD is important for the formation of cooperative groups and is a mechanism by which mutual dependencies between individuals evolve. PCD is also a conflict mediator and involved in division of labor in social groups and in the origin of new cell types. In multicellularity, PCD facilitates the transfer of fitness to the higher-level individual. In eusocial insects, PCD of the gonadal cells in workers is the basis for conflict mediation and the division of labor in the colony. In the three ETIs discussed here, PCD likely played an essential role, without which alternate mechanisms would have been necessary for these increases in complexity to occur.}, }
@article {pmid31855240, year = {2019}, author = {Pan, H and Dong, Y and Teng, Z and Li, J and Zhang, W and Xiao, T and Wu, LF}, title = {A species of magnetotactic deltaproteobacterium was detected at the highest abundance during an algal bloom.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnz253}, pmid = {31855240}, issn = {1574-6968}, abstract = {Magnetotactic bacteria (MTB) are a group of microorganisms that have the ability to synthesize intracellular magnetic crystals (magnetosomes). They prefer microaerobic or anaerobic aquatic sediments. Thus, there is growing interest in their ecological roles in various habitats. In this study we found co-occurrence of a large rod-shaped deltaproteobacterial magnetotactic bacterium (tentatively named LR-1) in the sediment of a brackish lagoon with algal bloom. Electron microscopy observations showed that they were ovoid to slightly curved rods having a mean length of 6.3 ± 1.1 μm and a mean width of 4.1 ± 0.4 μm. Each cell had a single polar flagellum. They contained hundreds of bullet-shaped intracellular magnetite magnetosomes. Phylogenetic analysis revealed that they were most closely related to Desulfamplus magnetovallimortis strain BW-1, and belonged to the Deltaproteobacteria. Our findings indicate that LR-1 may be a new species of magnetotactic bacteria. We propose that deltaproteobacterial magnetotactic bacteria may play an important role in iron cycling and so may represent a reservoir of iron, and be an indicator species for monitoring algal blooms in such eutrophic ecosystems. These observations provide new clues to the cultivation of magnetotactic Deltaproteobacteria and the control of algal blooms, although further studies are needed.}, }
@article {pmid31854473, year = {2019}, author = {Costa, ML and de Andrade Rosa, I and Andrade, L and Mermelstein, C and C Coutinho, C}, title = {Distinct interactions between epithelial and mesenchymal cells control cell morphology and collective migration during sponge epithelial to mesenchymal transition.}, journal = {Journal of morphology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jmor.21090}, pmid = {31854473}, issn = {1097-4687}, support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {Epithelial and mesenchymal cell types are basic for animal multicellularity and they have complementary functions coordinated by cellular interactions. Sponges are especially important model organisms to address the evolutionary basis of morphogenetic programs for epithelial and mesenchymal organization in animals. Evolutionary studies in sponges can contribute to the understanding of the mechanisms that control tissue maintenance and tumor progression in humans. In the present study, sponge mesenchymal and epithelial cells were isolated from the demosponge Hymeniacidon heliophila, and aggregate formation was observed by video microscopy. Epithelial-mesenchymal interaction, epithelial transition, and cell migration led to sponge cell aggregation after drastic stress. Based on their different morphologies, adhesion specificities, and motilities, we suggest a role for different sponge cell types as well as complementary functions in cell aggregation. Micromanipulation under the microscope and cell tracking were also used to promote specific grafting-host interaction, to further test the effects of cell type interaction. The loss of cell polarity and flattened shape during the epithelial to mesenchymal cell transition generated small immobile aggregates of round/amoeboid cells. The motility of these transited epithelial-cell aggregates was observed by cell tracking using fluorescent dye, but only after interaction with streams of migratory mesenchymal cells. Cell motility occurred independently of morphological changes, indicating a progressive step in the transition toward a migratory mesenchymal state. Our data suggest a two-step signaling process: (a) the lack of interaction between mesenchymal and epithelial cells triggers morphological changes; and (b) migratory mesenchymal cells instruct epithelial cells for directional cell motility. These results could have an impact on the understanding of evolutionary aspects of metastatic cancer cells. HIGHLIGHTS: Morphogenetic movements observed in modern sponges could have a common evolutionary origin with collective cell migration of human metastatic cells. A sponge regenerative model was used here to characterize epithelial and mesenchymal cells, and for the promotion of grafting/host interactions with subsequent cell tracking. The transition from epithelial to mesenchymal cell type can be observed in sponges in two steps: (a) withdrawal of epithelial/mesenchymal cell interactions to trigger morphological changes; (b) migratory mesenchymal cells to induce epithelial cells to a collective migratory state.}, }
@article {pmid31847093, year = {2019}, author = {Nakamura, T and Fahmi, M and Tanaka, J and Seki, K and Kubota, Y and Ito, M}, title = {Genome-Wide Analysis of Whole Human Glycoside Hydrolases by Data-Driven Analysis in Silico.}, journal = {International journal of molecular sciences}, volume = {20}, number = {24}, pages = {}, doi = {10.3390/ijms20246290}, pmid = {31847093}, issn = {1422-0067}, support = {NA//MEXT-Supported Program for the Strategic Research Foundation at Private Universities (2015-2019)/ ; NA//Takeda Science Foundation/ ; }, abstract = {Glycans are involved in various metabolic processes via the functions of glycosyltransferases and glycoside hydrolases. Analysing the evolution of these enzymes is essential for improving the understanding of glycan metabolism and function. Based on our previous study of glycosyltransferases, we performed a genome-wide analysis of whole human glycoside hydrolases using the UniProt, BRENDA, CAZy and KEGG databases. Using cluster analysis, 319 human glycoside hydrolases were classified into four clusters based on their similarity to enzymes conserved in chordates or metazoans (Class 1), metazoans (Class 2), metazoans and plants (Class 3) and eukaryotes (Class 4). The eukaryote and metazoan clusters included N- and O-glycoside hydrolases, respectively. The significant abundance of disordered regions within the most conserved cluster indicated a role for disordered regions in the evolution of glycoside hydrolases. These results suggest that the biological diversity of multicellular organisms is related to the acquisition of N- and O-linked glycans.}, }
@article {pmid31845961, year = {2019}, author = {Majic, P and Payne, JL}, title = {Enhancers facilitate the birth of de novo genes and gene integration into regulatory networks.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msz300}, pmid = {31845961}, issn = {1537-1719}, abstract = {Regulatory networks control the spatiotemporal gene expression patterns that give rise to and define the individual cell types of multicellular organisms. In eumetazoa, distal regulatory elements called enhancers play a key role in determining the structure of such networks, particularly the wiring diagram of &quot;who regulates whom.&quot; Mutations that affect enhancer activity can therefore rewire regulatory networks, potentially causing adaptive changes in gene expression. Here, we use whole-tissue and single-cell transcriptomic and chromatin accessibility data from mouse to show that enhancers play an additional role in the evolution of regulatory networks: They facilitate network growth by creating transcriptionally active regions of open chromatin that are conducive to de novo gene evolution. Specifically, our comparative transcriptomic analysis with three other mammalian species shows that young, mouse-specific intergenic open reading frames are preferentially located near enhancers, whereas older open reading frames are not. Mouse-specific intergenic open reading frames that are proximal to enhancers are more highly and stably transcribed than those that are not proximal to enhancers or promoters, and they are transcribed in a limited diversity of cellular contexts. Furthermore, we report several instances of mouse-specific intergenic open reading frames proximal to promoters showing evidence of being repurposed enhancers. We also show that open reading frames gradually acquire interactions with enhancers over macro-evolutionary timescales, helping integrate genes - those that have arisen de novo or by other means - into existing regulatory networks. Taken together, our results highlight a dual role of enhancers in expanding and rewiring gene regulatory networks.}, }
@article {pmid30919490, year = {2019}, author = {Marshall, RC and Whitworth, DE}, title = {Is &quot;Wolf-Pack&quot; Predation by Antimicrobial Bacteria Cooperative? Cell Behaviour and Predatory Mechanisms Indicate Profound Selfishness, Even when Working Alongside Kin.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {4}, pages = {e1800247}, doi = {10.1002/bies.201800247}, pmid = {30919490}, issn = {1521-1878}, mesh = {Anti-Bacterial Agents/*metabolism ; Biological Evolution ; Models, Biological ; Myxococcales/*cytology ; Time Factors ; }, abstract = {For decades, myxobacteria have been spotlighted as exemplars of social &quot;wolf-pack&quot; predation, communally secreting antimicrobial substances into the shared public milieu. This behavior has been described as cooperative, becoming more efficient if performed by more cells. However, laboratory evidence for cooperativity is limited and of little relevance to predation in a natural setting. In contrast, there is accumulating evidence for predatory mechanisms promoting &quot;selfish&quot; behavior during predation, which together with conflicting definitions of cooperativity, casts doubt on whether microbial &quot;wolf-pack&quot; predation really is cooperative. Here, it is hypothesized that public-goods-mediated predation is not cooperative, and it is argued that a holistic model of microbial predation is needed, accounting for predator and prey relatedness, social phenotypes, spatial organization, activity/specificity/transport of secreted toxins, and prey resistance mechanisms. Filling such gaps in our knowledge is vital if the evolutionary benefits of potentially costly microbial behaviors mediated by public goods are to be properly understood.}, }
@article {pmid31841515, year = {2019}, author = {Lamelza, P and Young, JM and Noble, LM and Caro, L and Isakharov, A and Palanisamy, M and Rockman, MV and Malik, HS and Ailion, M}, title = {Hybridization promotes asexual reproduction in Caenorhabditis nematodes.}, journal = {PLoS genetics}, volume = {15}, number = {12}, pages = {e1008520}, doi = {10.1371/journal.pgen.1008520}, pmid = {31841515}, issn = {1553-7404}, abstract = {Although most unicellular organisms reproduce asexually, most multicellular eukaryotes are obligately sexual. This implies that there are strong barriers that prevent the origin or maintenance of asexuality arising from an obligately sexual ancestor. By studying rare asexual animal species we can gain a better understanding of the circumstances that facilitate their evolution from a sexual ancestor. Of the known asexual animal species, many originated by hybridization between two ancestral sexual species. The balance hypothesis predicts that genetic incompatibilities between the divergent genomes in hybrids can modify meiosis and facilitate asexual reproduction, but there are few instances where this has been shown. Here we report that hybridizing two sexual Caenorhabditis nematode species (C. nouraguensis females and C. becei males) alters the normal inheritance of the maternal and paternal genomes during the formation of hybrid zygotes. Most offspring of this interspecies cross die during embryogenesis, exhibiting inheritance of a diploid C. nouraguensis maternal genome and incomplete inheritance of C. becei paternal DNA. However, a small fraction of offspring develop into viable adults that can be either fertile or sterile. Fertile offspring are produced asexually by sperm-dependent parthenogenesis (also called gynogenesis or pseudogamy); these progeny inherit a diploid maternal genome but fail to inherit a paternal genome. Sterile offspring are hybrids that inherit both a diploid maternal genome and a haploid paternal genome. Whole-genome sequencing of individual viable worms shows that diploid maternal inheritance in both fertile and sterile offspring results from an altered meiosis in C. nouraguensis oocytes and the inheritance of two randomly selected homologous chromatids. We hypothesize that hybrid incompatibility between C. nouraguensis and C. becei modifies maternal and paternal genome inheritance and indirectly induces gynogenetic reproduction. This system can be used to dissect the molecular mechanisms by which hybrid incompatibilities can facilitate the emergence of asexual reproduction.}, }
@article {pmid31841362, year = {2019}, author = {Damer, B and Deamer, D}, title = {The Hot Spring Hypothesis for an Origin of Life.}, journal = {Astrobiology}, volume = {}, number = {}, pages = {}, doi = {10.1089/ast.2019.2045}, pmid = {31841362}, issn = {1557-8070}, abstract = {We present a testable hypothesis related to an origin of life on land in which fluctuating volcanic hot spring pools play a central role. The hypothesis is based on experimental evidence that lipid-encapsulated polymers can be synthesized by cycles of hydration and dehydration to form protocells. Drawing on metaphors from the bootstrapping of a simple computer operating system, we show how protocells cycling through wet, dry, and moist phases will subject polymers to combinatorial selection and draw structural and catalytic functions out of initially random sequences, including structural stabilization, pore formation, and primitive metabolic activity. We propose that protocells aggregating into a hydrogel in the intermediate moist phase of wet-dry cycles represent a primitive progenote system. Progenote populations can undergo selection and distribution, construct niches in new environments, and enable a sharing network effect that can collectively evolve them into the first microbial communities. Laboratory and field experiments testing the first steps of the scenario are summarized. The scenario is then placed in a geological setting on the early Earth to suggest a plausible pathway from life's origin in chemically optimal freshwater hot spring pools to the emergence of microbial communities tolerant to more extreme conditions in dilute lakes and salty conditions in marine environments. A continuity is observed for biogenesis beginning with simple protocell aggregates, through the transitional form of the progenote, to robust microbial mats that leave the fossil imprints of stromatolites so representative in the rock record. A roadmap to future testing of the hypothesis is presented. We compare the oceanic vent with land-based pool scenarios for an origin of life and explore their implications for subsequent evolution to multicellular life such as plants. We conclude by utilizing the hypothesis to posit where life might also have emerged in habitats such as Mars or Saturn's icy moon Enceladus. &quot;To postulate one fortuitously catalyzed reaction, perhaps catalyzed by a metal ion, might be reasonable, but to postulate a suite of them is to appeal to magic.&quot; -Leslie Orgel.}, }
@article {pmid31840777, year = {2019}, author = {Kundert, P and Shaulsky, G}, title = {Cellular allorecognition and its roles in Dictyostelium development and social evolution.}, journal = {The International journal of developmental biology}, volume = {63}, number = {8-9-10}, pages = {383-393}, doi = {10.1387/ijdb.190239gs}, pmid = {31840777}, issn = {1696-3547}, abstract = {The social amoeba Dictyostelium discoideum is a tractable model organism to study cellular allorecognition, which is the ability of a cell to distinguish itself and its genetically similar relatives from more distantly related organisms. Cellular allorecognition is ubiquitous across the tree of life and affects many biological processes. Depending on the biological context, these versatile systems operate both within and between individual organisms, and both promote and constrain functional heterogeneity. Some of the most notable allorecognition systems mediate neural self-avoidance in flies and adaptive immunity in vertebrates. D. discoideum's allorecognition system shares several structures and functions with other allorecognition systems. Structurally, its key regulators reside at a single genomic locus that encodes two highly polymorphic proteins, a transmembrane ligand called TgrC1 and its receptor TgrB1. These proteins exhibit isoform-specific, heterophilic binding across cells. Functionally, this interaction determines the extent to which co-developing D. discoideum strains co-aggregate or segregate during the aggregation phase of multicellular development. The allorecognition system thus affects both development and social evolution, as available evidence suggests that the threat of developmental cheating represents a primary selective force acting on it. Other significant characteristics that may inform the study of allorecognition in general include that D. discoideum's allorecognition system is a continuous and inclusive trait, it is pleiotropic, and it is temporally regulated.}, }
@article {pmid31840776, year = {2019}, author = {Medina, JM and Shreenidhi, PM and Larsen, TJ and Queller, DC and Strassmann, JE}, title = {Cooperation and conflict in the social amoeba Dictyostelium discoideum.}, journal = {The International journal of developmental biology}, volume = {63}, number = {8-9-10}, pages = {371-382}, doi = {10.1387/ijdb.190158jm}, pmid = {31840776}, issn = {1696-3547}, abstract = {The social amoeba Dictyostelium discoideum has provided considerable insight into the evolution of cooperation and conflict. Under starvation, D. discoideum amoebas cooperate to form a fruiting body comprised of hardy spores atop a stalk. The stalk development is altruistic because stalk cells die to aid spore dispersal. The high relatedness of cells in fruiting bodies in nature implies that this altruism often benefits relatives. However, since the fruiting body forms through aggregation there is potential for non-relatives to join the aggregate and create conflict over spore and stalk fates. Cheating is common in chimeras of social amoebas, where one genotype often takes advantage of the other and makes more spores. This social conflict is a significant force in nature as indicated by rapid rates of adaptive evolution in genes involved in cheating and its resistance. However, cheating can be prevented by high relatedness, allorecognition via tgr genes, pleiotropy and evolved resistance. Future avenues for the study of cooperation and conflict in D. discoideum include the sexual cycle as well as the relationship between D. discoideum and its bacterial symbionts. D. discoideum's tractability in the laboratory as well as its uncommon mode of aggregative multicellularity have established it as a promising model for future studies of cooperation and conflict.}, }
@article {pmid31840775, year = {2019}, author = {Kawabe, Y and Du, Q and Schilde, C and Schaap, P}, title = {Evolution of multicellularity in Dictyostelia.}, journal = {The International journal of developmental biology}, volume = {63}, number = {8-9-10}, pages = {359-369}, doi = {10.1387/ijdb.190108ps}, pmid = {31840775}, issn = {1696-3547}, abstract = {The well-orchestrated multicellular life cycle of Dictyostelium discoideum has fascinated biologists for over a century. Self-organisation of its amoebas into aggregates, migrating slugs and fruiting structures by pulsatile cAMP signalling and their ability to follow separate differentiation pathways in well-regulated proportions continue to be topics under investigation. A striking aspect of D. discoideum development is the recurrent use of cAMP as chemoattractant, differentiation inducing signal and second messenger for other signals that control the developmental programme. D. discoideum is one of >150 species of Dictyostelia and aggregative life styles similar to those of Dictyostelia evolved many times in eukaryotes. Here we review experimental studies investigating how phenotypic complexity and cAMP signalling co-evolved in Dictyostelia. In addition, we summarize comparative genomic studies of multicellular Dictyostelia and unicellular Amoebozoa aimed to identify evolutionary conservation and change in all genes known to be essential for D. discoideum development.}, }
@article {pmid31830880, year = {2019}, author = {Heredia-Soto, V and Redondo, A and Kreilinger, JJP and Martínez-Marín, V and Berjón, A and Mendiola, M}, title = {3D culture modelling: An emerging approach for Translational Cancer Research in Sarcomas.}, journal = {Current medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0929867326666191212162102}, pmid = {31830880}, issn = {1875-533X}, abstract = {Sarcomas are tumours of mesenchymal origin, which can arise in bone or soft tissues. They are rare but frequently quite aggressive and with a poor outcome. New approaches are needed to characterise these tumours and their resistance mechanisms to current therapies, responsible for tumour recurrence and treatment failure. This review is focused on the potential of three-dimensional (3D) in vitro models, including multicellular tumour spheroids (MCTS) and organoids, and the latest data about their utility for the study of important properties for tumour development. We also discuss the use of spheroids as a particularly valuable alternative for compound high throughput screening (HTS) in different areas of cancer biology, which enable the identification of new therapeutic opportunities in commonly resistant tumours.}, }
@article {pmid31829529, year = {2020}, author = {Rivera-Yoshida, N and Hernández-Terán, A and Escalante, AE and Benítez, M}, title = {Laboratory biases hinder Eco-Evo-Devo integration: Hints from the microbial world.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {334}, number = {1}, pages = {14-24}, doi = {10.1002/jez.b.22917}, pmid = {31829529}, issn = {1552-5015}, abstract = {How specific environmental contexts contribute to the robustness and variation of developmental trajectories and evolutionary transitions is a central point in Ecological Evolutionary Developmental Biology (&quot;Eco-Evo-Devo&quot;). However, the articulation of ecological, evolutionary and developmental processes into integrative frameworks has been elusive, partly because standard experimental designs neglect or oversimplify ecologically meaningful contexts. Microbial models are useful to expose and discuss two possible sources of bias associated with conventional gene-centered experimental designs: the use of laboratory strains and standard laboratory environmental conditions. We illustrate our point by showing how contrasting developmental phenotypes in Myxococcus xanthus depend on the joint variation of temperature and substrate stiffness. Microorganismal development can provide key information for better understanding the role of environmental conditions in the evolution of developmental variation, and to overcome some of the limitations associated with current experimental approaches.}, }
@article {pmid31589468, year = {2019}, author = {Blutt, SE and Klein, OD and Donowitz, M and Shroyer, N and Guha, C and Estes, MK}, title = {Use of organoids to study regenerative responses to intestinal damage.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {317}, number = {6}, pages = {G845-G852}, doi = {10.1152/ajpgi.00346.2018}, pmid = {31589468}, issn = {1522-1547}, abstract = {Intestinal organoid cultures provide an in vitro model system for studying pathways and mechanisms involved in epithelial damage and repair. Derived from either embryonic or induced pluripotent stem cells or adult intestinal stem cells or tissues, these self-organizing, multicellular structures contain polarized mature cells that recapitulate both the physiology and heterogeneity of the intestinal epithelium. These cultures provide a cutting-edge technology for defining regenerative pathways that are induced following radiation or chemical damage, which directly target the cycling intestinal stem cell, or damage resulting from viral, bacterial, or parasitic infection of the epithelium. Novel signaling pathways or biological mechanisms identified from organoid studies that mediate regeneration of the epithelium following damage are likely to be important targets of preventive or therapeutic modalities to mitigate intestinal injury. The evolution of these cultures to include more components of the intestinal wall and the ability to genetically modify them are key components for defining the mechanisms that modulate epithelial regeneration.}, }
@article {pmid31819969, year = {2019}, author = {Niklas, KJ and Newman, SA}, title = {The Many Roads To (and From) Multicellularity.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erz547}, pmid = {31819969}, issn = {1460-2431}, abstract = {The multiple origins of multicellularity had far-reaching consequences ranging from the appearance of phenotypically complex life-forms to their effects on Earth's aquatic and terrestrial ecosystems. Yet, many important but as yet unanswered questions remain. For example, do all lineages and clades share an ancestral developmental predisposition for multicellularity emerging from genomic and biophysical motifs shared from a last common ancestor, or are the multiple origins of multicellularity truly independent evolutionary events? In this review, we highlight recent developments and pitfalls in understanding the evolution of multicellularity with an emphasis on plants (here, defined broadly as &quot;plants&quot; to include the polyphyletic algae), but also draw upon insights from animals and their holozoan relatives, fungi and amoebozoans. Based on our review, we conclude that the evolution of multicellular organisms requires three phases (origination by disparate cell-cell attachment modalities, followed by integration by lineage-specific physiological mechanisms, and autonomization by natural selection) that they have been achieved differently in different lineages.}, }
@article {pmid31818848, year = {2019}, author = {Lee, MF and Trotman, LC}, title = {PTEN: Bridging Endocytosis and Signaling.}, journal = {Cold Spring Harbor perspectives in medicine}, volume = {}, number = {}, pages = {}, doi = {10.1101/cshperspect.a036103}, pmid = {31818848}, issn = {2157-1422}, abstract = {The transduction of signals in the PTEN/PI3-kinase (PI3K) pathway is built around a phosphoinositide (PIP) lipid messenger, phosphatidylinositol trisphosphate, PI(3,4,5)P3 or PIP3 Another, more ancient role of this family of messengers is the control of endocytosis, where a handful of separate PIPs act like postal codes. Prominent among them is PI(3)P, which helps to ensure that endocytic vesicles, their cargo, and membranes themselves reach their correct destinations. Traditionally, the cancer and the endocytic functions of the PI3K signaling pathway have been studied by cancer and membrane biologists, respectively, with some notable but overall minimal overlap. Modern microscopy has enabled monitoring of the PTEN/PI3K pathway in action. Here, we explore the flurry of groundbreaking concepts emerging from those efforts. The discovery that PTEN contains an autonomous PI(3)P reader domain, fused to the catalytic PIP3 eraser domain has prompted us to explore the relationship between PI3K signaling and endocytosis. This revealed how PTEN can achieve signal termination in a precisely controlled fashion, because endocytosis can package the PIP3 signal into discrete units that PTEN will erase. We explore how PTEN can bridge the worlds of endocytosis and PI3K signaling and discuss progress on how PI3K/AKT signaling can be acting from internal membranes. We discuss how the PTEN/PI3K system for growth control may have emerged from principles of endocytosis, and how this development could have affected the evolution of multicellular organisms.}, }
@article {pmid31814500, year = {2019}, author = {Nguyen, H and Das, U and Xie, J}, title = {Genome-Wide Evolution of Wobble Base-Pairing Nucleotides of Branchpoint Motifs with Increasing Organismal Complexity.}, journal = {RNA biology}, volume = {}, number = {}, pages = {}, doi = {10.1080/15476286.2019.1697548}, pmid = {31814500}, issn = {1555-8584}, abstract = {How have the branchpoints evolved in organisms of different complexity? Here we identified and examined the consensus motifs (R1C2T3R4A5Y6, R: A or G, Y: C or T) of 898 fungal genomes. In Ascomycota unicellular yeasts, the G4/A4 ratio is mostly (98%) below 0.125 but increases sharply in multicellular species by about 40 times on average, and in the more complex Basidiomycota it increases further by about 7 times. The global G4 increase is consistent with A4 to G4 transitions in evolution. Of the G4/A4-interacting amino acids of the branchpoint binding protein MSL5 (SF1) and the HSH155 (SF3B1), as well as the 5' splice sites (SS) and U2 snRNA genes, the 5' splice site G3/A3 co-vary with the G4. However, corresponding increase of the G4-complementary GCAGTA-U2 gene is rare, suggesting wobble-base pairing between the branchpoint motif and U2 in most species. Interestingly, the G4/A4 ratio correlates well with the abundance of alternative splicing in the two phyla, and G4 enriched significantly in the alternative splice sites of genes in RNA metabolism, kinases and membrane proteins. Similar wobble nucleotides also enriched in the splice sites of multicellular fungi with only thousands of protein-coding genes. Thus, branchpoint motifs have evolved U2-complementarity in unicellular Ascomycota yeasts, but have gradually gained more wobble base-pairing nucleotides in fungi of higher complexity, likely to destabilize branchpoint-U2 interaction and/or branchpoint A protrusion for alternative splicing. This implies an important role of the relaxation of branchpoint signals in the multicellularity and further complexity of fungi.}, }
@article {pmid31805037, year = {2019}, author = {Thomas, F and Giraudeau, M and Renaud, F and Ujvari, B and Roche, B and Pujol, P and Raymond, M and Lemaitre, JF and Alvergne, A}, title = {Can postfertile life stages evolve as an anticancer mechanism?.}, journal = {PLoS biology}, volume = {17}, number = {12}, pages = {e3000565}, doi = {10.1371/journal.pbio.3000565}, pmid = {31805037}, issn = {1545-7885}, abstract = {Why a postfertile stage has evolved in females of some species has puzzled evolutionary biologists for over 50 years. We propose that existing adaptive explanations have underestimated in their formulation an important parameter operating both at the specific and the individual levels: the balance between cancer risks and cancer defenses. During their life, most multicellular organisms naturally accumulate oncogenic processes in their body. In parallel, reproduction, notably the pregnancy process in mammals, exacerbates the progression of existing tumors in females. When, for various ecological or evolutionary reasons, anticancer defenses are too weak, given cancer risk, older females could not pursue their reproduction without triggering fatal metastatic cancers nor even maintain a normal reproductive physiology if the latter also promotes the growth of existing oncogenic processes, e.g., hormone-dependent malignancies. At least until stronger anticancer defenses are selected for in these species, females could achieve higher inclusive fitness by ceasing their reproduction and/or going through menopause (assuming that these traits are easier to select than anticancer defenses), thereby limiting the risk of premature death due to metastatic cancers. Because relatively few species experience such an evolutionary mismatch between anticancer defenses and cancer risks, the evolution of prolonged life after reproduction could also be a rare, potentially transient, anticancer adaptation in the animal kingdom.}, }
@article {pmid31802185, year = {2019}, author = {Walker, DM and Hill, AJ and Albecker, MA and McCoy, MW and Grisnik, M and Romer, A and Grajal-Puche, A and Camp, C and Kelehear, C and Wooten, J and Rheubert, J and Graham, SP}, title = {Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01456-x}, pmid = {31802185}, issn = {1432-184X}, abstract = {A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.}, }
@article {pmid31799909, year = {2020}, author = {Fields, C and Bischof, J and Levin, M}, title = {Morphological Coordination: A Common Ancestral Function Unifying Neural and Non-Neural Signaling.}, journal = {Physiology (Bethesda, Md.)}, volume = {35}, number = {1}, pages = {16-30}, doi = {10.1152/physiol.00027.2019}, pmid = {31799909}, issn = {1548-9221}, abstract = {Nervous systems are traditionally thought of as providing sensing and behavioral coordination functions at the level of the whole organism. What is the evolutionary origin of the mechanisms enabling the nervous systems' information processing ability? Here, we review evidence from evolutionary, developmental, and regenerative biology suggesting a deeper, ancestral function of both pre-neural and neural cell-cell communication systems: the long-distance coordination of cell division and differentiation required to create and maintain body-axis symmetries. This conceptualization of the function of nervous system activity sheds new light on the evolutionary transition from the morphologically rudimentary, non-neural Porifera and Placazoa to the complex morphologies of Ctenophores, Cnidarians, and Bilaterians. It further allows a sharp formulation of the distinction between long-distance axis-symmetry coordination based on external coordinates, e.g., by whole-organism scale trophisms as employed by plants and sessile animals, and coordination based on body-centered coordinates as employed by motile animals. Thus we suggest that the systems that control animal behavior evolved from ancient mechanisms adapting preexisting ionic and neurotransmitter mechanisms to regulate individual cell behaviors during morphogenesis. An appreciation of the ancient, non-neural origins of bioelectrically mediated computation suggests new approaches to the study of embryological development, including embryological dysregulation, cancer, regenerative medicine, and synthetic bioengineering.}, }
@article {pmid31798628, year = {2019}, author = {Baumgartner, M and Drake, K and Kanadia, RN}, title = {An Integrated Model of Minor Intron Emergence and Conservation.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1113}, doi = {10.3389/fgene.2019.01113}, pmid = {31798628}, issn = {1664-8021}, abstract = {Minor introns constitute <0.5% of the introns in the human genome and have remained an enigma since their discovery. These introns are removed by a distinct splicing complex, the minor spliceosome. Both are ancient, tracing back to the last eukaryotic common ancestor (LECA), which is reflected by minor intron enrichment in specific gene families, such as the mitogen activated-protein kinase kinases, voltage-gated sodium and calcium ion channels, and E2F transcription factors. Most minor introns occur as single introns in genes with predominantly major introns. Due to this organization, minor intron-containing gene (MIG) expression requires the coordinated action of two spliceosomes, which increases the probability of missplicing. Thus, one would expect loss of minor introns via purifying selection. This has resulted in complete minor intron loss in at least nine eukaryotic lineages. However, minor introns are highly conserved in land plants and metazoans, where their importance is underscored by embryonic lethality when the minor spliceosome is inactivated. Conditional inactivation of the minor spliceosome has shown that rapidly dividing progenitor cells are highly sensitive to minor spliceosome loss. Indeed, we found that MIGs were significantly enriched in a screen for genes essential for survival in 341 cycling cell lines. Here, we propose that minor introns inserted randomly into genes in LECA or earlier and were subsequently conserved in genes crucial for cycling cell survival. We hypothesize that the essentiality of MIGs allowed minor introns to endure through the unicellularity of early eukaryotic evolution. Moreover, we identified 59 MIGs that emerged after LECA, and that many of these are essential for cycling cell survival, reinforcing our essentiality model for MIG conservation. This suggests that minor intron emergence is dynamic across eukaryotic evolution, and that minor introns should not be viewed as molecular fossils. We also posit that minor intron splicing was co-opted in multicellular evolution as a regulatory switch for en masse control of MIG expression and the biological processes they regulate. Specifically, this mode of regulation could control cell proliferation and thus body size, an idea supported by domestication syndrome, wherein MIGs are enriched in common candidate animal domestication genes.}, }
@article {pmid31794757, year = {2019}, author = {Jékely, G}, title = {Evolution: How Not to Become an Animal.}, journal = {Current biology : CB}, volume = {29}, number = {23}, pages = {R1240-R1242}, doi = {10.1016/j.cub.2019.10.014}, pmid = {31794757}, issn = {1879-0445}, abstract = {The origin of animals has always fascinated biologists. Studies on choanoflagellates, the closest living relatives of animals, have contributed major insights. The discovery of a multicellular choanoflagellate with light-regulated collective behaviour now provides a new perspective.}, }
@article {pmid31788034, year = {2019}, author = {Southworth, J and Grace, CA and Marron, AO and Fatima, N and Carr, M}, title = {A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage.}, journal = {Mobile DNA}, volume = {10}, number = {}, pages = {44}, doi = {10.1186/s13100-019-0189-9}, pmid = {31788034}, issn = {1759-8753}, abstract = {Background: Unicellular species make up the majority of eukaryotic diversity, however most studies on transposable elements (TEs) have centred on multicellular host species. Such studies may have therefore provided a limited picture of how transposable elements evolve across eukaryotes. The choanoflagellates, as the sister group to Metazoa, are an important study group for investigating unicellular to multicellular transitions. A previous survey of the choanoflagellate Monosiga brevicollis revealed the presence of only three families of LTR retrotransposons, all of which appeared to be active. Salpingoeca rosetta is the second choanoflagellate to have its whole genome sequenced and provides further insight into the evolution and population biology of transposable elements in the closest relative of metazoans.<br><br>Results: Screening the genome revealed the presence of a minimum of 20 TE families. Seven of the annotated families are DNA transposons and the remaining 13 families are LTR retrotransposons. Evidence for two putative non-LTR retrotransposons was also uncovered, but full-length sequences could not be determined. Superfamily phylogenetic trees indicate that vertical inheritance and, in the case of one family, horizontal transfer have been involved in the evolution of the choanoflagellates TEs. Phylogenetic analyses of individual families highlight recent element activity in the genome, however six families did not show evidence of current transposition. The majority of families possess young insertions and the expression levels of TE genes vary by four orders of magnitude across families. In contrast to previous studies on TEs, the families present in S. rosetta show the signature of selection on codon usage, with families favouring codons that are adapted to the host translational machinery. Selection is stronger in LTR retrotransposons than DNA transposons, with highly expressed families showing stronger codon usage bias. Mutation pressure towards guanosine and cytosine also appears to contribute to TE codon usage.<br><br>Conclusions: S. rosetta increases the known diversity of choanoflagellate TEs and the complement further highlights the role of horizontal gene transfer from prey species in choanoflagellate genome evolution. Unlike previously studied TEs, the S. rosetta families show evidence for selection on their codon usage, which is shown to act via translational efficiency and translational accuracy.}, }
@article {pmid30633408, year = {2019}, author = {Škaloud, P and Škaloudová, M and Doskočilová, P and Kim, JI and Shin, W and Dvořák, P}, title = {Speciation in protists: Spatial and ecological divergence processes cause rapid species diversification in a freshwater chrysophyte.}, journal = {Molecular ecology}, volume = {28}, number = {5}, pages = {1084-1095}, doi = {10.1111/mec.15011}, pmid = {30633408}, issn = {1365-294X}, support = {17-13254S//Czech Science Foundation/International ; NRF-2015R1A2A2A01003192//National Research Foundation of Korea/International ; }, mesh = {Biodiversity ; *Biological Evolution ; Chrysophyta/*genetics/growth &amp; development ; DNA, Mitochondrial/genetics ; *Ecosystem ; Fresh Water ; *Genetic Speciation ; Haplotypes/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Although eukaryotic microorganisms are extremely numerous, diverse and essential to global ecosystem functioning, they are largely understudied by evolutionary biologists compared to multicellular macroscopic organisms. In particular, very little is known about the speciation mechanisms which may give rise to the diversity of microscopic eukaryotes. It was postulated that the enormous population sizes and ubiquitous distribution of these organisms could lead to a lack of population differentiation and therefore very low speciation rates. However, such assumptions have traditionally been based on morphospecies, which may not accurately reflect the true diversity, missing cryptic taxa. In this study, we aim to articulate the major diversification mechanisms leading to the contemporary molecular diversity by using a colonial freshwater flagellate, Synura sphagnicola, as an example. Phylogenetic analysis of five sequenced loci showed that S. sphagnicola differentiated into two morphologically distinct lineages approximately 15.4 million years ago, which further diverged into several evolutionarily recent haplotypes during the late Pleistocene. The most recent haplotypes are ecologically and biogeographically much more differentiated than the old lineages, presumably because of their persistent differentiation after the allopatric speciation events. Our study shows that in microbial eukaryotes, species diversification via the colonization of new geographical regions or ecological resources occurs much more readily than was previously thought. Consequently, divergence times of microorganisms in some lineages may be equivalent to the estimated times of speciation in plants and animals.}, }
@article {pmid30846531, year = {2019}, author = {Sequeira-Mendes, J and Vergara, Z and Peiró, R and Morata, J and Aragüez, I and Costas, C and Mendez-Giraldez, R and Casacuberta, JM and Bastolla, U and Gutierrez, C}, title = {Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins.}, journal = {Genome research}, volume = {29}, number = {5}, pages = {784-797}, doi = {10.1101/gr.240986.118}, pmid = {30846531}, issn = {1549-5469}, mesh = {Arabidopsis/*genetics/growth &amp; development ; Base Composition/genetics ; Cells, Cultured ; Chromatin/metabolism ; *DNA Replication ; Heterochromatin/*genetics ; Replication Origin/*genetics ; Retroelements/genetics ; Transcription Initiation Site ; Transcription, Genetic ; }, abstract = {Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have identified a set of ORIs of Arabidopsis thaliana and their chromatin landscape at two stages of post-embryonic development. ORIs associate with multiple chromatin signatures including transcription start sites (TSS) but also proximal and distal regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin, but at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the set of ORIs active in an organism at the post-embryo stage that should allow us to study ORI biology in response to development, environment, and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.}, }
@article {pmid31766724, year = {2019}, author = {Kar, R and Jha, NK and Jha, SK and Sharma, A and Dholpuria, S and Asthana, N and Chaurasiya, K and Singh, VK and Burgee, S and Nand, P}, title = {A &quot;NOTCH&quot; Deeper into the Epithelial-To-Mesenchymal Transition (EMT) Program in Breast Cancer.}, journal = {Genes}, volume = {10}, number = {12}, pages = {}, doi = {10.3390/genes10120961}, pmid = {31766724}, issn = {2073-4425}, abstract = {Notch signaling is a primitive signaling pathway having various roles in the normal origin and development of each multicellular organisms. Therefore, any aberration in the pathway will inevitably lead to deadly outcomes such as cancer. It has now been more than two decades since Notch was acknowledged as an oncogene in mouse mammary tumor virus-infected mice. Since that discovery, activated Notch signaling and consequent up-regulation of tumor-promoting Notch target genes have been observed in human breast cancer. Moreover, consistent over-expression of Notch ligands and receptors has been shown to correlate with poor prognosis in human breast cancer. Notch regulates a number of key processes during breast carcinogenesis, of which, one key phenomenon is epithelial-mesenchymal transition (EMT). EMT is a key process for large-scale cell movement during morphogenesis at the time of embryonic development. Cancer cells aided by transcription factors usurp this developmental program to execute the multi-step process of tumorigenesis and metastasis. In this review, we recapitulate recent progress in breast cancer research that has provided new perceptions into the molecular mechanisms behind Notch-mediated EMT regulation during breast tumorigenesis.}, }
@article {pmid30860988, year = {2019}, author = {Riahi, H and Brekelmans, C and Foriel, S and Merkling, SH and Lyons, TA and Itskov, PM and Kleefstra, T and Ribeiro, C and van Rij, RP and Kramer, JM and Schenck, A}, title = {The histone methyltransferase G9a regulates tolerance to oxidative stress-induced energy consumption.}, journal = {PLoS biology}, volume = {17}, number = {3}, pages = {e2006146}, doi = {10.1371/journal.pbio.2006146}, pmid = {30860988}, issn = {1545-7885}, mesh = {Animals ; Antioxidants/metabolism ; Energy Metabolism/genetics/physiology ; Epigenesis, Genetic/genetics ; Glycogen Phosphorylase/genetics/metabolism ; Histone Methyltransferases/genetics/*metabolism ; Histone-Lysine N-Methyltransferase/genetics/metabolism ; Humans ; Male ; Oxidative Stress/genetics/physiology ; Phylogeny ; Sequence Analysis, RNA ; }, abstract = {Stress responses are crucial processes that require activation of genetic programs that protect from the stressor. Stress responses are also energy consuming and can thus be deleterious to the organism. The mechanisms coordinating energy consumption during stress response in multicellular organisms are not well understood. Here, we show that loss of the epigenetic regulator G9a in Drosophila causes a shift in the transcriptional and metabolic responses to oxidative stress (OS) that leads to decreased survival time upon feeding the xenobiotic paraquat. During OS exposure, G9a mutants show overactivation of stress response genes, rapid depletion of glycogen, and inability to access lipid energy stores. The OS survival deficiency of G9a mutants can be rescued by a high-sugar diet. Control flies also show improved OS survival when fed a high-sugar diet, suggesting that energy availability is generally a limiting factor for OS tolerance. Directly limiting access to glycogen stores by knocking down glycogen phosphorylase recapitulates the OS-induced survival defects of G9a mutants. We propose that G9a mutants are sensitive to stress because they experience a net reduction in available energy due to (1) rapid glycogen use, (2) an inability to access lipid energy stores, and (3) an overinduced transcriptional response to stress that further exacerbates energy demands. This suggests that G9a acts as a critical regulatory hub between the transcriptional and metabolic responses to OS. Our findings, together with recent studies that established a role for G9a in hypoxia resistance in cancer cell lines, suggest that G9a is of wide importance in controlling the cellular and organismal response to multiple types of stress.}, }
@article {pmid31752673, year = {2019}, author = {Forbes, G and Chen, ZH and Kin, K and Lawal, HM and Schilde, C and Yamada, Y and Schaap, P}, title = {Phylogeny-wide conservation and change in developmental expression, cell-type specificity and functional domains of the transcriptional regulators of social amoebas.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {890}, doi = {10.1186/s12864-019-6239-3}, pmid = {31752673}, issn = {1471-2164}, support = {100293/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; 742288//H2020 European Research Council/ ; RPG-2016-220//Leverhulme Trust/ ; ALTF 295-2015//European Molecular Biology Organization/ ; H28-1002//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: Dictyostelid social amoebas self-organize into fruiting bodies, consisting of spores and up to four supporting cell types in the phenotypically most complex taxon group 4. High quality genomes and stage- and cell-type specific transcriptomes are available for representative species of each of the four taxon groups. To understand how evolution of gene regulation in Dictyostelia contributed to evolution of phenotypic complexity, we analysed conservation and change in abundance, functional domain architecture and developmental regulation of their transcription factors (TFs).<br><br>RESULTS: We detected 440 sequence-specific TFs across 33 families, of which 68% were upregulated in multicellular development and about half conserved throughout Dictyostelia. Prespore cells expressed two times more TFs than prestalk cells, but stalk cells expressed more TFs than spores, suggesting that gene expression events that define spores occur earlier than those that define stalk cells. Changes in TF developmental expression, but not in TF abundance or functional domains occurred more frequently between group 4 and groups 1-3, than between the more distant branches formed by groups 1 + 2 and 3 + 4.<br><br>CONCLUSIONS: Phenotypic innovation is correlated with changes in TF regulation, rather than functional domain- or TF acquisition. The function of only 34 TFs is known. Of 12 TFs essential for cell differentiation, 9 are expressed in the cell type for which they are required. The information acquired here on conserved cell type specifity of 120 additional TFs can effectively guide further functional analysis, while observed evolutionary change in TF developmental expression may highlight how genotypic change caused phenotypic innovation.}, }
@article {pmid31751628, year = {2019}, author = {Williams, LM and Inge, MM and Mansfield, KM and Rasmussen, A and Afghani, J and Agrba, M and Albert, C and Andersson, C and Babaei, M and Babaei, M and Bagdasaryants, A and Bonilla, A and Browne, A and Carpenter, S and Chen, T and Christie, B and Cyr, A and Dam, K and Dulock, N and Erdene, G and Esau, L and Esonwune, S and Hanchate, A and Huang, X and Jennings, T and Kasabwala, A and Kehoe, L and Kobayashi, R and Lee, M and LeVan, A and Liu, Y and Murphy, E and Nambiar, A and Olive, M and Patel, D and Pavesi, F and Petty, CA and Samofalova, Y and Sanchez, S and Stejskal, C and Tang, Y and Yapo, A and Cleary, JP and Yunes, SA and Siggers, T and Gilmore, TD}, title = {Transcription factor NF-κB in a basal metazoan, the sponge, has conserved and unique sequences, activities, and regulation.}, journal = {Developmental and comparative immunology}, volume = {}, number = {}, pages = {103559}, doi = {10.1016/j.dci.2019.103559}, pmid = {31751628}, issn = {1879-0089}, abstract = {Herein, we characterize transcription factor NF-κB from the demosponge Amphimedon queenslandica (Aq). Aq-NF-κB is most similar to NF-κB p100/p105 among vertebrate proteins, with an N-terminal DNA-binding domain, a C-terminal Ankyrin (ANK) repeat domain, and a DNA binding-site profile akin to human NF-κB proteins. Like mammalian NF-κB p100, C-terminal truncation allows nuclear translocation of Aq-NF-κB and increases its transcriptional activation activity. Expression of IκB kinases (IKKs) induces proteasome-dependent C-terminal processing of Aq-NF-κB in human cells, and processing requires C-terminal serines in Aq-NF-κB. Unlike NF-κB p100, C-terminal sequences of Aq-NF-κB do not inhibit its DNA-binding activity. Tissue of a black encrusting demosponge contains NF-κB site DNA-binding activity, as well as nuclear and processed NF-κB. Treatment of sponge tissue with LPS increases both DNA-binding activity and processing of NF-κB. A. queenslandica transcriptomes contain homologs to upstream NF-κB pathway components. This is first functional characterization of NF-κB in sponge, the most basal multicellular animal.}, }
@article {pmid30113099, year = {2018}, author = {Stelbrink, B and Jovanovska, E and Levkov, Z and Ognjanova-Rumenova, N and Wilke, T and Albrecht, C}, title = {Diatoms do radiate: evidence for a freshwater species flock.}, journal = {Journal of evolutionary biology}, volume = {31}, number = {12}, pages = {1969-1975}, doi = {10.1111/jeb.13368}, pmid = {30113099}, issn = {1420-9101}, mesh = {Diatoms/*genetics/*physiology ; *Evolution, Molecular ; Fossils ; *Fresh Water ; *Genetic Variation ; *Phylogeny ; Time Factors ; }, abstract = {Due to the ubiquity and high dispersal capacity of unicellular eukaryotes, their often extraordinary diversity found in isolated and long-lived ecosystems such as ancient lakes is typically attributed to multiple colonization events rather than to in situ speciation. However, respective evolutionary studies are very scarce and the often high number of species flocks in ancient lakes across multicellular taxa raises the question whether unicellular species, such as diatoms, may radiate as well. Here, we use an integrative approach that includes molecular data from benthic diatom species of the genus Aneumastus endemic to ancient Lake Ohrid, fossil data obtained from the sediment record of a recent deep-drilling project and biogeographical information to test if this group, indeed, constitutes a species flock. Molecular-clock and phylogenetic analyses indicate a young monophyletic group of several endemic species. Molecular, fossil and biogeographical data strongly suggest a rapid intralacustrine diversification, which was possibly triggered by the emergence of novel habitats. This finding is the first evidence for a species flock in diatoms and suggests that in situ speciation is also a relevant evolutionary process for unicellular eukaryotes in isolated ecosystems.}, }
@article {pmid31743442, year = {2019}, author = {Brenneis, G and Beltz, BS}, title = {Adult neurogenesis in crayfish: origin, expansion and migration of neural progenitor lineages in a pseudostratified neuroepithelium.}, journal = {The Journal of comparative neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cne.24820}, pmid = {31743442}, issn = {1096-9861}, abstract = {Two decades after the discovery of adult-born neurons in the brains of decapod crustaceans, the deutocerebral proliferative system (DPS) producing these neural lineages has become a model of adult neurogenesis in invertebrates. Studies on crayfish have provided substantial insights into the anatomy, cellular dynamics and regulation of the DPS. Contrary to traditional thinking, recent evidence suggests that the neurogenic niche in the crayfish DPS lacks self-renewing stem cells, its cell pool being instead sustained via integration of hemocytes generated by the innate immune system. Here, we investigated the origin, division and migration patterns of the adult-born neural progenitor (NP) lineages in detail. We show that the niche cell pool is not only replenished by hemocyte integration but also by limited numbers of symmetric cell divisions with some characteristics reminiscent of interkinetic nuclear migration. Once specified in the niche, 1st generation NPs act as transit-amplifying intermediate NPs which eventually exit and produce multicellular clones as they move along migratory streams toward target brain areas. Different clones may migrate simultaneously in the streams but occupy separate tracks and show spatio-temporally flexible division patterns. Based on this, we propose an extended DPS model that emphasizes structural similarities to pseudostratified neuroepithelia in other arthropods and vertebrates. This model includes hemocyte integration and intrinsic cell proliferation to synergistically counteract niche cell pool depletion during the animal's lifespan. Further, we discuss parallels to recent findings on mammalian adult neurogenesis, as both systems seem to exhibit a similar decoupling of proliferative replenishment divisions and consuming neurogenic divisions. This article is protected by copyright. All rights reserved.}, }
@article {pmid31736534, year = {2019}, author = {Chen, J and Wang, N}, title = {Tissue cell differentiation and multicellular evolution via cytoskeletal stiffening in mechanically stressed microenvironments.}, journal = {Acta mechanica Sinica = Li xue xue bao}, volume = {35}, number = {2}, pages = {270-274}, doi = {10.1007/s10409-018-0814-8}, pmid = {31736534}, issn = {0567-7718}, abstract = {Evolution of eukaryotes from simple cells to complex multicellular organisms remains a mystery. Our postulate is that cytoskeletal stiffening is a necessary condition for evolution of complex multicellular organisms from early simple eukaryotes. Recent findings show that embryonic stem cells are as soft as primitive eukaryotes-amoebae and that differentiated tissue cells can be two orders of magnitude stiffer than embryonic stem cells. Soft embryonic stem cells become stiff as they differentiate into tissue cells of the complex multicellular organisms to match their microenvironment stiffness. We perhaps see in differentiation of embryonic stem cells (derived from inner cell mass cells) the echo of those early evolutionary events. Early soft unicellular organisms might have evolved to stiffen their cytoskeleton to protect their structural integrity from external mechanical stresses while being able to maintain form, to change shape, and to move.}, }
@article {pmid31723354, year = {2018}, author = {Jacobeen, S and Pentz, JT and Graba, EC and Brandys, CG and Ratcliff, WC and Yunker, PJ}, title = {Cellular packing, mechanical stress and the evolution of multicellularity.}, journal = {Nature physics}, volume = {14}, number = {}, pages = {286-290}, doi = {10.1038/s41567-017-0002-y}, pmid = {31723354}, issn = {1745-2473}, abstract = {The evolution of multicellularity set the stage for sustained increases in organismal complexity1-5. However, a fundamental aspect of this transition remains largely unknown: how do simple clusters of cells evolve increased size when confronted by forces capable of breaking intracellular bonds? Here we show that multicellular snowflake yeast clusters6-8 fracture due to crowding-induced mechanical stress. Over seven weeks (~291 generations) of daily selection for large size, snowflake clusters evolve to increase their radius 1.7-fold by reducing the accumulation of internal stress. During this period, cells within the clusters evolve to be more elongated, concomitant with a decrease in the cellular volume fraction of the clusters. The associated increase in free space reduces the internal stress caused by cellular growth, thus delaying fracture and increasing cluster size. This work demonstrates how readily natural selection finds simple, physical solutions to spatial constraints that limit the evolution of group size-a fundamental step in the evolution of multicellularity.}, }
@article {pmid31724951, year = {2019}, author = {Thattai, M}, title = {How contraction has shaped evolution.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.52805}, pmid = {31724951}, issn = {2050-084X}, abstract = {Two unicellular relatives of animals reveal that coordinated contractions of groups of cells using actomyosin predated animal multicellularity during evolution.}, }
@article {pmid31647412, year = {2019}, author = {Dudin, O and Ondracka, A and Grau-Bové, X and Haraldsen, AA and Toyoda, A and Suga, H and Bråte, J and Ruiz-Trillo, I}, title = {A unicellular relative of animals generates a layer of polarized cells by actomyosin-dependent cellularization.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.49801}, pmid = {31647412}, issn = {2050-084X}, support = {Consolidator Grant ERC-2012-Co-616960/ERC_/European Research Council/International ; MEXT KAKENHI 221S0002//Ministry of Education, Culture, Sports, Science and Technology/ ; MEXT KAKENHI 26891021//Ministry of Education, Culture, Sports, Science and Technology/ ; Young Research Talents grant 240284//Research Council of Norway/ ; P2LAP3_171815/SNSF_/Swiss National Science Foundation/Switzerland ; Individual fellowship MSCA-IF 746044//H2020 Marie Skłodowska-Curie Actions/ ; Individual fellowship MSCA-IF 747086//H2020 Marie Skłodowska-Curie Actions/ ; ERC-2012-Co -616960//European Research Council Consolidator Grant/ ; 221S0002//MEXT KAKENHI/ ; 26891021//MEXT KAKENHI/ ; 240284//Young Research Talents grant from the Research Council of Norway/ ; MSCA-IF 746044//Marie Sklodowska-Curie individual fellowship/ ; MSCA-IF 747086//Marie Sklodowska-Curie individual fellowship/ ; }, abstract = {In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly regulated transcriptional activation of genes involved in cell adhesion. Hereby we demonstrate the presence of a self-organized, clonally-generated, polarized layer of cells in a unicellular relative of animals.}, }
@article {pmid31714927, year = {2019}, author = {Hammond, MJ and Wang, T and Cummins, SF}, title = {Characterisation of early metazoan secretion through associated signal peptidase complex subunits, prohormone convertases and carboxypeptidases of the marine sponge (Amphimedon queenslandica).}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0225227}, doi = {10.1371/journal.pone.0225227}, pmid = {31714927}, issn = {1932-6203}, abstract = {Efficient communication between cells requires the ability to process precursor proteins into their mature and biologically active forms, prior to secretion into the extracellular space. Eukaryotic cells achieve this via a suite of enzymes that involve a signal peptidase complex, prohormone convertases and carboxypeptidases. Using genome and transcriptome data of the demosponge Amphimedon queenslandica, a universal ancestor to metazoan multicellularity, we endeavour to bridge the evolution of precursor processing machinery from single-celled eukaryotic ancestors through to the complex multicellular organisms that compromise Metazoa. The precursor processing repertoire as defined in this study of A. queenslandica consists of 3 defined signal peptidase subunits, 6 prohormone convertases and 1 carboxypeptidase, with 2 putative duplicates identified for signal peptidase complex subunits. Analysis of their gene expression levels throughout the sponge development enabled us to predict levels of activity. Some A. queenslandica precursor processing components belong to established functional clades while others were identified as having novel, yet to be discovered roles. These findings have clarified the presence of precursor processing machinery in the poriferans, showing the necessary machinery for the removal of precursor sequences, a critical post-translational modification required by multicellular organisms, and further sets a foundation towards understanding the molecular mechanism for ancient protein processing.}, }
@article {pmid30851154, year = {2019}, author = {Kalsoom, N and Zafar, M and Ahmad, M and Sultana, S and Usma, A and Jabeen, A}, title = {Investigating Schizocarp morphology as a taxonomic tool in study of Apiaceae family by utilizing LM and SEM techniques.}, journal = {Microscopy research and technique}, volume = {82}, number = {7}, pages = {1012-1020}, doi = {10.1002/jemt.23248}, pmid = {30851154}, issn = {1097-0029}, mesh = {Apiaceae/*anatomy &amp; histology/*classification ; Fruit/*anatomy &amp; histology/ultrastructure ; *Microscopy ; *Microscopy, Electron, Scanning ; Phylogeny ; Pollen ; }, abstract = {In present study, the schizocarp morphology of 14 species belonging to Apiaceae family has been investigated. Light microscopy (LM) and scanning electron microscopy (SEM) have been utilized to highlight qualitative and quantitative features of studied species. Variations have been observed in macro- and micro-morphological features such as color, shape, symmetry, length, width, apex, epicuticular projections, surface patterns, anticlinal, and periclinal wall patterns. Schizocarp shapes observed were oval, round, triangular, linear, elliptic, and globose. Fruit was either homomorphic or heteromorphic. Crystalloids, stellate hair, multicellular spines, and platelets were mostly observed epicuticular projections. Surface patterns on the fruit surface were striate, rugulate-striate, reticulate, and striato-knotted. Both macro- and micro-morphological characters can serve as an important tool in classifying Apiaceae family at various taxonomic ranks. Substantial variations observed can assist as useful constraints at various taxonomic levels as they provide reliable and constant details. Disparities observed in schizocarp features can pave a path for Apiaceae family classification based on phylogenetic and molecular studies.}, }
@article {pmid31709760, year = {2019}, author = {Collens, A and Kelley, E and Katz, LA}, title = {The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22915}, pmid = {31709760}, issn = {1552-5015}, support = {1541511//Division of Environmental Biology/ ; 1651908//Division of Environmental Biology/ ; R15HG010409/GM/NIGMS NIH HHS/United States ; R15HG010409/GF/NIH HHS/United States ; }, abstract = {John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.}, }
@article {pmid31707219, year = {2019}, author = {Stubbendieck, RM and Li, H and Currie, CR}, title = {Convergent evolution of signal-structure interfaces for maintaining symbioses.}, journal = {Current opinion in microbiology}, volume = {50}, number = {}, pages = {71-78}, doi = {10.1016/j.mib.2019.10.001}, pmid = {31707219}, issn = {1879-0364}, abstract = {Symbiotic microbes are essential to the ecological success and evolutionary diversification of multicellular organisms. The establishment and stability of bipartite symbioses are shaped by mechanisms ensuring partner fidelity between host and symbiont. In this minireview, we demonstrate how the interface of chemical signals and host structures influences fidelity between legume root nodules and rhizobia, Hawaiian bobtail squid light organs and Allivibrio fischeri, and fungus-growing ant crypts and Pseudonocardia. Subsequently, we illustrate the morphological diversity and widespread phylogenetic distribution of specialized structures used by hosts to house microbial symbionts, indicating the importance of signal-structure interfaces across the history of multicellular life. These observations, and the insights garnered from well-studied bipartite associations, demonstrate the need to concentrate on the signal-structure interface in complex and multipartite systems, including the human microbiome.}, }
@article {pmid31702845, year = {2019}, author = {Grall, E and Tschopp, P}, title = {A sense of place, many times over - pattern formation and evolution of repetitive morphological structures.}, journal = {Developmental dynamics : an official publication of the American Association of Anatomists}, volume = {}, number = {}, pages = {}, doi = {10.1002/dvdy.131}, pmid = {31702845}, issn = {1097-0177}, abstract = {50 years ago, Lewis Wolpert introduced the concept of 'positional information' to explain how patterns form in a multicellular embryonic field. Using morphogen gradients, whose continuous distributions of positional values are discretized via thresholds into distinct cellular states, he provided, at the theoretical level, an elegant solution to the 'French Flag problem'. In the intervening years, many experimental studies have lent support to Wolpert's ideas. However, the embryonic patterning of highly repetitive morphological structures, as often occurring in nature, can reveal limitations in the strict implementation of his initial theory, given the number of distinct threshold values that would have to be specified. Here, we review how positional information is complemented to circumvent these inadequacies, to accommodate tissue growth and pattern periodicity. In particular, we focus on functional anatomical assemblies composed of such structures, like the vertebrate spine or tetrapod digits, where the resulting segmented architecture is intrinsically linked to periodic pattern formation and unidirectional growth. These systems integrate positional information and growth with additional patterning cues that, we suggest, increase robustness and evolvability. We discuss different experimental and theoretical models to study such patterning systems, and how the underlying processes are modulated over evolutionary timescales to enable morphological diversification. This article is protected by copyright. All rights reserved.}, }
@article {pmid31700531, year = {2019}, author = {Raven, N and Bramwell, G and Hamede, R and Thomas, F and Ujvari, B}, title = {Fifth International Biannual Evolution and Ecology of Cancer Conference (Cooperation, Conflict and Parasitism) meeting report-Wellcome Genome Campus, Hinxton, UK.}, journal = {Evolutionary applications}, volume = {12}, number = {10}, pages = {1863-1867}, doi = {10.1111/eva.12862}, pmid = {31700531}, issn = {1752-4571}, abstract = {The fifth biannual conference of the International Society of Evolution and Ecology of Cancer (ISEEC) was held between the 17th and 19th of July 2019 in Hinxton (UK) at the Wellcome Genome Campus. The main theme of the conference: cooperation, conflict and parasitism reflected our growing understanding of the role cancer has played in the evolution of multicellular organisms, as well as the urgent need of translating these Darwinian processes to treatment strategies. Below we provide a brief summary of each plenary sessions and other oral presentations, to bring the conference to the broader audience of evolutionary biology and applications.}, }
@article {pmid31689405, year = {2019}, author = {Coudert, Y and Harris, S and Charrier, B}, title = {Design Principles of Branching Morphogenesis in Filamentous Organisms.}, journal = {Current biology : CB}, volume = {29}, number = {21}, pages = {R1149-R1162}, doi = {10.1016/j.cub.2019.09.021}, pmid = {31689405}, issn = {1879-0445}, abstract = {The radiation of life on Earth was accompanied by the diversification of multicellular body plans in the eukaryotic kingdoms Animalia, Plantae, Fungi and Chromista. Branching forms are ubiquitous in nature and evolved repeatedly in the above lineages. The developmental and genetic basis of branch formation is well studied in the three-dimensional shoot and root systems of land plants, and in animal organs such as the lung, kidney, mammary gland, vasculature, etc. Notably, recent thought-provoking studies combining experimental analysis and computational modeling of branching patterns in whole animal organs have identified global patterning rules and proposed unifying principles of branching morphogenesis. Filamentous branching forms represent one of the simplest expressions of the multicellular body plan and constitute a key step in the evolution of morphological complexity. Similarities between simple and complex branching forms distantly related in evolution are compelling, raising the question whether shared mechanisms underlie their development. Here, we focus on filamentous branching organisms that represent major study models from three distinct eukaryotic kingdoms, including the moss Physcomitrella patens (Plantae), the brown alga Ectocarpus sp. (Chromista), and the ascomycetes Neurospora crassa and Aspergillus nidulans (Fungi), and bring to light developmental regulatory mechanisms and design principles common to these lineages. Throughout the review we explore how the regulatory mechanisms of branching morphogenesis identified in other models, and in particular animal organs, may inform our thinking on filamentous systems and thereby advance our understanding of the diverse strategies deployed across the eukaryotic tree of life to evolve similar forms.}, }
@article {pmid31687086, year = {2019}, author = {Poljsak, B and Kovac, V and Dahmane, R and Levec, T and Starc, A}, title = {Cancer Etiology: A Metabolic Disease Originating from Life's Major Evolutionary Transition?.}, journal = {Oxidative medicine and cellular longevity}, volume = {2019}, number = {}, pages = {7831952}, doi = {10.1155/2019/7831952}, pmid = {31687086}, issn = {1942-0994}, abstract = {A clear understanding of the origins of cancer is the basis of successful strategies for effective cancer prevention and management. The origin of cancer at the molecular and cellular levels is not well understood. Is the primary cause of the origin of cancer the genomic instability or impaired energy metabolism? An attempt was made to present cancer etiology originating from life's major evolutionary transition. The first evolutionary transition went from simple to complex cells when eukaryotic cells with glycolytic energy production merged with the oxidative mitochondrion (The Endosymbiosis Theory first proposed by Lynn Margulis in the 1960s). The second transition went from single-celled to multicellular organisms once the cells obtained mitochondria, which enabled them to obtain a higher amount of energy. Evidence will be presented that these two transitions, as well as the decline of NAD+ and ATP levels, are the root of cancer diseases. Restoring redox homeostasis and reactivation of mitochondrial oxidative metabolism are important factors in cancer prevention.}, }
@article {pmid31681764, year = {2019}, author = {Naumann, B and Burkhardt, P}, title = {Spatial Cell Disparity in the Colonial Choanoflagellate Salpingoeca rosetta.}, journal = {Frontiers in cell and developmental biology}, volume = {7}, number = {}, pages = {231}, doi = {10.3389/fcell.2019.00231}, pmid = {31681764}, issn = {2296-634X}, abstract = {Choanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to the co-existence of specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellate Salpingoeca rosetta that exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity of S. rosetta cells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial, and food vacuole volumes of 40 individual cells from four different S. rosetta rosette colonies and compared our findings to sponge choanocytes. Our analysis shows that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria, and food vacuoles. Furthermore, cell disparity within S. rosetta colonies is slightly higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.}, }
@article {pmid31680996, year = {2019}, author = {Arnellos, A and Keijzer, F}, title = {Bodily Complexity: Integrated Multicellular Organizations for Contraction-Based Motility.}, journal = {Frontiers in physiology}, volume = {10}, number = {}, pages = {1268}, doi = {10.3389/fphys.2019.01268}, pmid = {31680996}, issn = {1664-042X}, abstract = {Compared to other forms of multicellularity, the animal case is unique. Animals-barring some exceptions-consist of collections of cells that are connected and integrated to such an extent that these collectives act as unitary, large free-moving entities capable of sensing macroscopic properties and events. This animal configuration is so well-known that it is often taken as a natural one that 'must' have evolved, given environmental conditions that make large free-moving units 'obviously' adaptive. Here we question the seemingly evolutionary inevitableness of animals and introduce a thesis of bodily complexity: The multicellular organization characteristic for typical animals requires the integration of a multitude of intrinsic bodily features between its sensorimotor, physiological, and developmental aspects, and the related contraction-based tissue- and cellular-level events and processes. The evolutionary road toward this bodily complexity involves, we argue, various intermediate organizational steps that accompany and support the wider transition from cilia-based to contraction/muscle-based motility, and which remain insufficiently acknowledged. Here, we stress the crucial and specific role played by muscle-based and myoepithelial tissue contraction-acting as a physical platform for organizing both the multicellular transmission of mechanical forces and multicellular signaling-as key foundation of animal motility, sensing and maintenance, and development. We illustrate and discuss these bodily features in the context of the four basal animal phyla-Porifera, Ctenophores, Placozoans, and Cnidarians-that split off before the bilaterians, a supergroup that incorporates all complex animals.}, }
@article {pmid30177778, year = {2018}, author = {Waters, AJ and Capriotti, P and Gaboriau, DCA and Papathanos, PA and Windbichler, N}, title = {Rationally-engineered reproductive barriers using CRISPR &amp; CRISPRa: an evaluation of the synthetic species concept in Drosophila melanogaster.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13125}, pmid = {30177778}, issn = {2045-2322}, support = {335724//European Research Council/International ; }, mesh = {Animals ; Base Sequence ; CRISPR-Associated Protein 9/genetics/metabolism ; *CRISPR-Cas Systems ; Drosophila Proteins/*genetics ; Drosophila melanogaster/*genetics ; Female ; Gene Editing/*methods ; *Genes, Insect ; Genes, Lethal ; Genetic Fitness ; Genetic Loci ; *Genome, Insect ; Homeodomain Proteins/*genetics ; INDEL Mutation ; Male ; Population Control/methods ; Promoter Regions, Genetic ; RNA, Guide/genetics/metabolism ; Reproductive Isolation ; Sequence Alignment ; Transcription Factors/*genetics ; Transcriptional Activation ; }, abstract = {The ability to erect rationally-engineered reproductive barriers in animal or plant species promises to enable a number of biotechnological applications such as the creation of genetic firewalls, the containment of gene drives or novel population replacement and suppression strategies for genetic control. However, to date no experimental data exist that explores this concept in a multicellular organism. Here we examine the requirements for building artificial reproductive barriers in the metazoan model Drosophila melanogaster by combining CRISPR-based genome editing and transcriptional transactivation (CRISPRa) of the same loci. We directed 13 single guide RNAs (sgRNAs) to the promoters of 7 evolutionary conserved genes and used 11 drivers to conduct a misactivation screen. We identify dominant-lethal activators of the eve locus and find that they disrupt development by strongly activating eve outside its native spatio-temporal context. We employ the same set of sgRNAs to isolate, by genome editing, protective INDELs that render these loci resistant to transactivation without interfering with target gene function. When these sets of genetic components are combined we find that complete synthetic lethality, a prerequisite for most applications, is achievable using this approach. However, our results suggest a steep trade-off between the level and scope of dCas9 expression, the degree of genetic isolation achievable and the resulting impact on fly fitness. The genetic engineering strategy we present here allows the creation of single or multiple reproductive barriers and could be applied to other multicellular organisms such as disease vectors or transgenic organisms of economic importance.}, }
@article {pmid31667165, year = {2019}, author = {Fortunato, A and Aktipis, A}, title = {Social feeding behavior of Trichoplax adhaerens.}, journal = {Frontiers in ecology and evolution}, volume = {7}, number = {}, pages = {}, doi = {10.3389/fevo.2019.00019}, pmid = {31667165}, issn = {2296-701X}, abstract = {Animals have evolved different foraging strategies in which some animals forage independently and others forage in groups. The evolution of social feeding does not necessarily require cooperation; social feeding can be a beneficial individual-level strategy if it provides mutualistic benefits, for example though increasing the efficiency of resource extraction or processing. We found that Trichoplax adhaerens, the simplest multicellular animal ever described, engages in social feeding behavior. T. adhaerens lacks muscle tissue, nervous and digestive systems - yet is capable of aggregating and forming groups of closely connected individuals who collectively feed. The tight physical interactions between the animals are transitory and appear to serve the goal of staying connected to neighbors during the external digestion of algae when enzymes are released on the biofilm and nutrients are absorbed through the ventral epithelium. We found that T. adhaerens are more likely to engage in social feeding when the concentrations of algae are high - both in a semi-natural conditions and in vitro. It is surprising that T. adhaerens - an organism without a nervous system - is able to engage in this social feeding behavior. Whether this behavior is cooperative is still an open question. Nevertheless, the social feeding behavior of T. adhaerens, an early multicellular animal, suggests that sociality may have played an important role in the early evolution of animals. It also suggests that T. adhaerens could be used as a simple model organism for exploring questions regarding ecology and sociobiology.}, }
@article {pmid31662428, year = {2019}, author = {Du, H and Zhang, W and Zhang, W and Zhang, W and Pan, H and Pan, Y and Bazylinski, DA and Wu, LF and Xiao, T and Lin, W}, title = {Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, doi = {10.1128/mSystems.00315-19}, pmid = {31662428}, issn = {2379-5077}, abstract = {The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry. Current genomic data from magnetotactic bacteria (MTB), the only prokaryotes known to be capable of sensing the Earth's geomagnetic field, suggests an ancient origin of magnetotaxis in the domain Bacteria Vertical inheritance, followed by multiple independent magnetosome gene cluster loss, is considered to be one of the major forces that drove the evolution of magnetotaxis at or above the class or phylum level, although the evolutionary trajectories at lower taxonomic ranks (e.g., within the class level) remain largely unstudied. Here we report the isolation, cultivation, and sequencing of a novel magnetotactic spirillum belonging to the genus Terasakiella (Terasakiella sp. strain SH-1) within the class Alphaproteobacteria The complete genome sequence of Terasakiella sp. strain SH-1 revealed an unexpected duplication event of magnetosome genes within the mamAB operon, a group of genes essential for magnetosome biomineralization and magnetotaxis. Intriguingly, further comparative genomic analysis suggests that the duplication of mamAB genes is a common feature in the genomes of alphaproteobacterial MTB. Taken together, with the additional finding that gene duplication appears to have also occurred in some magnetotactic members of the Deltaproteobacteria, our results indicate that gene duplication plays an important role in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain BacteriaIMPORTANCE A diversity of organisms can sense the geomagnetic field for the purpose of navigation. Magnetotactic bacteria are the most primitive magnetism-sensing organisms known thus far and represent an excellent model system for the study of the origin, evolution, and mechanism of microbial magnetoreception (or magnetotaxis). The present study is the first report focused on magnetosome gene cluster duplication in the Alphaproteobacteria, which suggests the important role of gene duplication in the evolution of magnetotaxis in the Alphaproteobacteria and perhaps the domain Bacteria A novel scenario for the evolution of magnetotaxis in the Alphaproteobacteria is proposed and may provide new insights into evolution of magnetoreception of higher species.}, }
@article {pmid31209289, year = {2019}, author = {Morrissey, EM and Mau, RL and Hayer, M and Liu, XA and Schwartz, E and Dijkstra, P and Koch, BJ and Allen, K and Blazewicz, SJ and Hofmockel, K and Pett-Ridge, J and Hungate, BA}, title = {Evolutionary history constrains microbial traits across environmental variation.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {7}, pages = {1064-1069}, doi = {10.1038/s41559-019-0918-y}, pmid = {31209289}, issn = {2397-334X}, mesh = {Biological Evolution ; Carbon ; *Ecosystem ; Nitrogen ; *Soil ; }, abstract = {Organisms influence ecosystems, from element cycling to disturbance regimes, to trophic interactions and to energy partitioning. Microorganisms are part of this influence, and understanding their ecology in nature requires studying the traits of these organisms quantitatively in their natural habitats-a challenging task, but one which new approaches now make possible. Here, we show that growth rate and carbon assimilation rate of soil microorganisms are influenced more by evolutionary history than by climate, even across a broad climatic gradient spanning major temperate life zones, from mixed conifer forest to high-desert grassland. Most of the explained variation (~50% to ~90%) in growth rate and carbon assimilation rate was attributable to differences among taxonomic groups, indicating a strong influence of evolutionary history, and taxonomic groupings were more predictive for organisms responding to resource addition. With added carbon and nitrogen substrates, differences among taxonomic groups explained approximately eightfold more variance in growth rate than did differences in ecosystem type. Taxon-specific growth and carbon assimilation rates were highly intercorrelated across the four ecosystems, constrained by the taxonomic identity of the organisms, such that plasticity driven by environment was limited across ecosystems varying in temperature, precipitation and dominant vegetation. Taken together, our results suggest that, similar to multicellular life, the traits of prokaryotes in their natural habitats are constrained by evolutionary history to a greater degree than environmental variation.}, }
@article {pmid31649660, year = {2019}, author = {Smith, NC and Rise, ML and Christian, SL}, title = {A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {2292}, doi = {10.3389/fimmu.2019.02292}, pmid = {31649660}, issn = {1664-3224}, abstract = {The immune system is composed of two subsystems-the innate immune system and the adaptive immune system. The innate immune system is the first to respond to pathogens and does not retain memory of previous responses. Innate immune responses are evolutionarily older than adaptive responses and elements of innate immunity can be found in all multicellular organisms. If a pathogen persists, the adaptive immune system will engage the pathogen with specificity and memory. Several components of the adaptive system including immunoglobulins (Igs), T cell receptors (TCR), and major histocompatibility complex (MHC), are assumed to have arisen in the first jawed vertebrates-the Gnathostomata. This review will discuss and compare components of both the innate and adaptive immune systems in Gnathostomes, particularly in Chondrichthyes (cartilaginous fish) and in Osteichthyes [bony fish: the Actinopterygii (ray-finned fish) and the Sarcopterygii (lobe-finned fish)]. While many elements of both the innate and adaptive immune systems are conserved within these species and with higher level vertebrates, some elements have marked differences. Components of the innate immune system covered here include physical barriers, such as the skin and gastrointestinal tract, cellular components, such as pattern recognition receptors and immune cells including macrophages and neutrophils, and humoral components, such as the complement system. Components of the adaptive system covered include the fundamental cells and molecules of adaptive immunity: B lymphocytes (B cells), T lymphocytes (T cells), immunoglobulins (Igs), and major histocompatibility complex (MHC). Comparative studies in fish such as those discussed here are essential for developing a comprehensive understanding of the evolution of the immune system.}, }
@article {pmid31649059, year = {2019}, author = {Duttke, SH and Chang, MW and Heinz, S and Benner, C}, title = {Identification and dynamic quantification of regulatory elements using total RNA.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.253492.119}, pmid = {31649059}, issn = {1549-5469}, abstract = {The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 million years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.}, }
@article {pmid30270182, year = {2018}, author = {Thomas, GWC and Wang, RJ and Puri, A and Harris, RA and Raveendran, M and Hughes, DST and Murali, SC and Williams, LE and Doddapaneni, H and Muzny, DM and Gibbs, RA and Abee, CR and Galinski, MR and Worley, KC and Rogers, J and Radivojac, P and Hahn, MW}, title = {Reproductive Longevity Predicts Mutation Rates in Primates.}, journal = {Current biology : CB}, volume = {28}, number = {19}, pages = {3193-3197.e5}, pmid = {30270182}, issn = {1879-0445}, support = {HHSN272201200031C/AI/NIAID NIH HHS/United States ; P40 OD010938/OD/NIH HHS/United States ; }, mesh = {Animals ; Aotidae/genetics ; Genetic Fitness/*genetics ; Genetics, Population/methods ; Genome/genetics ; Humans ; Longevity/*genetics ; Mutation ; *Mutation Rate ; Pedigree ; Population Density ; Primates/genetics ; Reproduction ; }, abstract = {Mutation rates vary between species across several orders of magnitude, with larger organisms having the highest per-generation mutation rates. Hypotheses for this pattern typically invoke physiological or population-genetic constraints imposed on the molecular machinery preventing mutations [1]. However, continuing germline cell division in multicellular eukaryotes means that organisms with longer generation times and of larger size will leave more mutations to their offspring simply as a byproduct of their increased lifespan [2, 3]. Here, we deeply sequence the genomes of 30 owl monkeys (Aotus nancymaae) from six multi-generation pedigrees to demonstrate that paternal age is the major factor determining the number of de novo mutations in this species. We find that owl monkeys have an average mutation rate of 0.81 × 10-8 per site per generation, roughly 32% lower than the estimate in humans. Based on a simple model of reproductive longevity that does not require any changes to the mutational machinery, we show that this is the expected mutation rate in owl monkeys. We further demonstrate that our model predicts species-specific mutation rates in other primates, including study-specific mutation rates in humans based on the average paternal age. Our results suggest that variation in life history traits alone can explain variation in the per-generation mutation rate among primates, and perhaps among a wide range of multicellular organisms.}, }
@article {pmid31624206, year = {2019}, author = {Brunet, T and Larson, BT and Linden, TA and Vermeij, MJA and McDonald, K and King, N}, title = {Light-regulated collective contractility in a multicellular choanoflagellate.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6463}, pages = {326-334}, doi = {10.1126/science.aay2346}, pmid = {31624206}, issn = {1095-9203}, abstract = {Collective cell contractions that generate global tissue deformations are a signature feature of animal movement and morphogenesis. However, the origin of collective contractility in animals remains unclear. While surveying the Caribbean island of Curaçao for choanoflagellates, the closest living relatives of animals, we isolated a previously undescribed species (here named Choanoeca flexa sp. nov.) that forms multicellular cup-shaped colonies. The colonies rapidly invert their curvature in response to changing light levels, which they detect through a rhodopsin-cyclic guanosine monophosphate pathway. Inversion requires actomyosin-mediated apical contractility and allows alternation between feeding and swimming behavior. C. flexa thus rapidly converts sensory inputs directly into multicellular contractions. These findings may inform reconstructions of hypothesized animal ancestors that existed before the evolution of specialized sensory and contractile cells.}, }
@article {pmid31617664, year = {2019}, author = {Nanjundiah, V}, title = {Many roads lead to Rome: Neutral phenotypes in microorganisms.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22909}, pmid = {31617664}, issn = {1552-5015}, abstract = {John Bonner pointed out that microorganisms differ in several ways, some of which may reflect neutral phenotypic evolution. For making his case, Bonner referred to interspecies differences and morphological traits. Here we consider intraspecies differences and physiological traits. As a case-study, we examine the production of an extracellular cyclic 3 ' ,5 ' monophosphate phosphodiesterase in the cellular slime mold Dictyostelium discoideum. Temporal profiles of phosphodiesterase activity differ significantly between wild-type strains. From that we argue that the inference drawn initially from studies on a single wild-type, namely that the profile displayed by it pointed to an adaptive role, was mistaken. We generalize the conclusion to suggest that physiological differences exhibited by microorganisms of the same species may, but need not, reflect adaptations to different environments. Rather, the differences could be related to the fact that microorganisms live in groups whose composition can vary between homogeneous (clonal) and heterogeneous (polyclonal). More than one physiological profile is consistent with the normal development of the group in a given environment; the alternatives are neutral. When studying microbial physiology and behavior, it is expected that the observations are made on a clonal population; genetic (and so phenotypic) heterogeneity is carefully guarded against. As the example from D. discoideum shows, an unintended consequence of overlooking phenotypic heterogeneity is that one can fall into the trap of accepting a seemingly plausible, but possibly erroneous, adaptive explanation for a &quot;normal&quot; wild-type phenotype.}, }
@article {pmid31617575, year = {2019}, author = {Wan, TM and Iyer, DN and Ng, L}, title = {Roles of microRNAs as non-invasive biomarker and therapeutic target in colorectal cancer.}, journal = {Histology and histopathology}, volume = {}, number = {}, pages = {18171}, doi = {10.14670/HH-18-171}, pmid = {31617575}, issn = {1699-5848}, support = {-//-/ ; }, 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 {pmid29487180, year = {2018}, author = {Cardon, ZG and Peredo, EL and Dohnalkova, AC and Gershone, HL and Bezanilla, M}, title = {A model suite of green algae within the Scenedesmaceae for investigating contrasting desiccation tolerance and morphology.}, journal = {Journal of cell science}, volume = {131}, number = {7}, pages = {}, doi = {10.1242/jcs.212233}, pmid = {29487180}, issn = {1477-9137}, mesh = {Cell Nucleus/chemistry/genetics/ultrastructure ; Chlorophyceae/classification/*genetics/growth &amp; development ; Chlorophyta/*genetics/growth &amp; development/ultrastructure ; Cytokinesis/genetics ; Ecosystem ; Golgi Apparatus/chemistry/ultrastructure ; Light ; Photosynthesis/*genetics ; *Phylogeny ; Reactive Oxygen Species/metabolism ; Time-Lapse Imaging ; }, abstract = {Microscopic green algae inhabiting desert microbiotic crusts are remarkably diverse phylogenetically, and many desert lineages have independently evolved from aquatic ancestors. Here we worked with five desert and aquatic species within the family Scenedesmaceae to examine mechanisms that underlie desiccation tolerance and release of unicellular versus multicellular progeny. Live cell staining and time-lapse confocal imaging coupled with transmission electron microscopy established that the desert and aquatic species all divide by multiple (rather than binary) fission, although progeny were unicellular in three species and multicellular (joined in a sheet-like coenobium) in two. During division, Golgi complexes were localized near nuclei, and all species exhibited dynamic rotation of the daughter cell mass within the mother cell wall at cytokinesis. Differential desiccation tolerance across the five species, assessed from photosynthetic efficiency during desiccation/rehydration cycles, was accompanied by differential accumulation of intracellular reactive oxygen species (ROS) detected using a dye sensitive to intracellular ROS. Further comparative investigation will aim to understand the genetic, ultrastructural and physiological characteristics supporting unicellular versus multicellular coenobial morphology, and the ability of representatives in the Scenedesmaceae to colonize ecologically diverse, even extreme, habitats.}, }
@article {pmid31613422, year = {2019}, author = {Love, AC}, title = {Evolution evolving? Reflections on big questions.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22907}, pmid = {31613422}, issn = {1552-5015}, abstract = {John Bonner managed a long and productive career that balanced specialized inquiry into cellular slime molds with general investigations of big questions in evolutionary biology, such as the origins of multicellular development and the evolution of complexity. This commentary engages with his final paper (&quot;The evolution of evolution&quot;), which argues that the evolutionary process has changed through the history of life. In particular, Bonner emphasizes the possibility that natural selection plays different roles at different size scales. I identify some underlying assumptions in his argument and evaluate its cogency to both foster future discussion and emulate the intellectual example set by Bonner over a lifetime. This endeavor is important beyond Bonner's own theoretical disposition because similar issues are visible in controversies about the possibility of an extended evolutionary synthesis.}, }
@article {pmid31604443, year = {2019}, author = {Ramon-Mateu, J and Ellison, ST and Angelini, TE and Martindale, MQ}, title = {Regeneration in the ctenophore Mnemiopsis leidyi occurs in the absence of a blastema, requires cell division, and is temporally separable from wound healing.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {80}, doi = {10.1186/s12915-019-0695-8}, pmid = {31604443}, issn = {1741-7007}, support = {IOS-1755364//National Science Foundation (NSF)/ ; }, abstract = {BACKGROUND: The ability to regenerate is a widely distributed but highly variable trait among metazoans. A variety of modes of regeneration has been described for different organisms; however, many questions regarding the origin and evolution of these strategies remain unanswered. Most species of ctenophore (or &quot;comb jellies&quot;), a clade of marine animals that branch off at the base of the animal tree of life, possess an outstanding capacity to regenerate. However, the cellular and molecular mechanisms underlying this ability are unknown. We have used the ctenophore Mnemiopsis leidyi as a system to study wound healing and adult regeneration and provide some first-time insights of the cellular mechanisms involved in the regeneration of one of the most ancient extant group of multicellular animals.<br><br>RESULTS: We show that cell proliferation is activated at the wound site and is indispensable for whole-body regeneration. Wound healing occurs normally in the absence of cell proliferation forming a scar-less wound epithelium. No blastema-like structure is generated at the cut site, and pulse-chase experiments and surgical intervention show that cells originating in the main regions of cell proliferation (the tentacle bulbs) do not seem to contribute to the formation of new structures after surgical challenge, suggesting a local source of cells during regeneration. While exposure to cell-proliferation blocking treatment inhibits regeneration, the ability to regenerate is recovered when the treatment ends (days after the original cut), suggesting that ctenophore regenerative capabilities are constantly ready to be triggered and they are somehow separable of the wound healing process.<br><br>CONCLUSIONS: Ctenophore regeneration takes place through a process of cell proliferation-dependent non-blastemal-like regeneration and is temporally separable of the wound healing process. We propose that undifferentiated cells assume the correct location of missing structures and differentiate in place. The remarkable ability to replace missing tissue, the many favorable experimental features (e.g., optical clarity, high fecundity, rapid regenerative performance, stereotyped cell lineage, sequenced genome), and the early branching phylogenetic position in the animal tree, all point to the emergence of ctenophores as a new model system to study the evolution of animal regeneration.}, }
@article {pmid31601898, year = {2019}, author = {Agić, H and Högström, AES and Moczydłowska, M and Jensen, S and Palacios, T and Meinhold, G and Ebbestad, JOR and Taylor, WL and Høyberget, M}, title = {Organically-preserved multicellular eukaryote from the early Ediacaran Nyborg Formation, Arctic Norway.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14659}, doi = {10.1038/s41598-019-50650-x}, pmid = {31601898}, issn = {2045-2322}, support = {VR2016-06810//Vetenskapsrådet (Swedish Research Council)/ ; }, abstract = {Eukaryotic multicellularity originated in the Mesoproterozoic Era and evolved multiple times since, yet early multicellular fossils are scarce until the terminal Neoproterozoic and often restricted to cases of exceptional preservation. Here we describe unusual organically-preserved fossils from mudrocks, that provide support for the presence of organisms with differentiated cells (potentially an epithelial layer) in the late Neoproterozoic. Cyathinema digermulense gen. et sp. nov. from the Nyborg Formation, Vestertana Group, Digermulen Peninsula in Arctic Norway, is a new carbonaceous organ-taxon which consists of stacked tubes with cup-shaped ends. It represents parts of a larger organism (multicellular eukaryote or a colony), likely with greater preservation potential than its other elements. Arrangement of open-ended tubes invites comparison with cells of an epithelial layer present in a variety of eukaryotic clades. This tissue may have benefitted the organism in: avoiding overgrowth, limiting fouling, reproduction, or water filtration. C. digermulense shares characteristics with extant and fossil groups including red algae and their fossils, demosponge larvae and putative sponge fossils, colonial protists, and nematophytes. Regardless of its precise affinity, C. digermulense was a complex and likely benthic marine eukaryote exhibiting cellular differentiation, and a rare occurrence of early multicellularity outside of Konservat-Lagerstätten.}, }
@article {pmid31521503, year = {2019}, author = {Kieninger, AK and Forchhammer, K and Maldener, I}, title = {A nanopore array in the septal peptidoglycan hosts gated septal junctions for cell-cell communication in multicellular cyanobacteria.}, journal = {International journal of medical microbiology : IJMM}, volume = {}, number = {}, pages = {151303}, doi = {10.1016/j.ijmm.2019.03.007}, pmid = {31521503}, issn = {1618-0607}, abstract = {Some filamentous cyanobacteria are phototrophic bacteria with a true multicellular life style. They show patterned cell differentiation with the distribution of metabolic tasks between different cell types. This life style requires a system of cell-cell communication and metabolite exchange along the filament. During our study of the cell wall of species Nostoc punctiforme and Anabaena sp. PCC 7120 we discovered regular perforations in the septum between neighboring cells, which we called nanopore array. AmiC-like amidases are drilling the nanopores with a diameter of 20 nm, and are essential for communication and cell differentiation. NlpD-like regulators of AmiC activity and septum localized proteins SepJ, FraC and FraD are also involved in correct nanopore formation. By focused ion beam (FIB) milling and electron cryotomography we could visualize the septal junctions, which connect adjacent cells and pass thru the nanopores. They consist of cytoplasmic caps, which are missing in the fraD mutant, a plug inside the cytoplasmic membrane and a tube like conduit. A destroyed membrane potential and other stress factors lead to a conformational change in the cap structure and loss of cell-cell communication. These gated septal junctions of cyanobacteria are ancient structures that represent an example of convergent evolution, predating metazoan gap junctions.}, }
@article {pmid31339482, year = {2019}, author = {Guo, JS and Zhang, Z and Qiao, M and Yu, ZF}, title = {Phalangispora sinensis sp. nov. from Yunnan, China and two new members of Wiesneriomycetaceae.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {69}, number = {10}, pages = {3207-3213}, doi = {10.1099/ijsem.0.003612}, pmid = {31339482}, issn = {1466-5034}, mesh = {Ascomycota/*classification/isolation &amp; purification ; China ; DNA, Fungal/genetics ; Mycological Typing Techniques ; *Phylogeny ; Sequence Analysis, DNA ; Spores, Fungal ; *Water Microbiology ; }, abstract = {Phalangispora sinensis, an aquatic hyphomycete collected from south-western PR China, is described as a new species. This new species is characterized by having multicellular branched conidia composed of a curved main axis and one or two laterals, with the laterals arising from the third or fourth cell of the base of the main axis. Combined analyses of the LSU, SSU, RPB2 and TEF1 gene sequence data revealed that Phalangispora and another aquatic hyphomycete genus, Setosynnema, belonged to Wiesneriomycetaceae, Tubeufiales, Dothideomycetes, Ascomycota.}, }
@article {pmid31589243, year = {2019}, author = {Arcas, A and Wilkinson, DG and Nieto, MÁ}, title = {The evolutionary history of Ephs and ephrins: towards multicellular organisms.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msz222}, pmid = {31589243}, issn = {1537-1719}, abstract = {Eph receptor (Eph) and ephrin signalling regulates fundamental developmental processes through both forward and reverse signalling triggered upon cell-cell contact. In vertebrates, they are both classified into classes A and B, and some representatives have been identified in many metazoan groups, where their expression and functions have been well studied. We have extended previous phylogenetic analyses and examined the presence of Eph and ephrins in the tree of life to determine their origin and evolution. We have found that (i) premetazoan choanoflagellates may already have rudimental Eph/ephrin signalling as they have an Eph-/ephrin-like pair and homologues of downstream signalling genes; (ii) both forward and reverse downstream signalling might already occur in Porifera since sponges have most genes involved in these types of signalling; (iii) the non-vertebrate metazoan Eph is a type-B receptor that can bind ephrins regardless of their membrane anchoring structure, glycosylphosphatidylinositol or transmembrane; (iv) Eph/ephrin cross-class binding is specific to Gnathostomata and (v) kinase-dead Eph receptors can be traced back to Gnathostomata. We conclude that Eph/ephrin signalling is of older origin than previously believed. We also examined the presence of protein domains associated with functional characteristics and the appearance and conservation of downstream signalling pathways to understand the original and derived functions of Ephs and ephrins. We find that the evolutionary history of these gene families points to an ancestral function in cell-cell interactions that could contribute to the emergence of multicellularity and, in particular, to the required segregation of cell populations.}, }
@article {pmid31587642, year = {2019}, author = {López-Escardó, D and Grau-Bové, X and Guillaumet-Adkins, A and Gut, M and Sieracki, ME and Ruiz-Trillo, I}, title = {Reconstruction of protein domain evolution using single-cell amplified genomes of uncultured choanoflagellates sheds light on the origin of animals.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1786}, pages = {20190088}, doi = {10.1098/rstb.2019.0088}, pmid = {31587642}, issn = {1471-2970}, abstract = {Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovations and how they appeared, we need the broadest taxon sampling possible, especially among early-branching animals and their unicellular relatives. Here, we take advantage of single-cell genomics to expand our understanding of the genomic diversity of choanoflagellates, the sister-group to animals. With these genomes, we have performed an updated and taxon-rich reconstruction of protein evolution from the Last Eukaryotic Common Ancestor (LECA) to animals. Our novel data re-defines the origin of some genes previously thought to be metazoan-specific, like the POU transcription factor, which we show appeared earlier in evolution. Moreover, our data indicate that the acquisition of new genes at the stem of Metazoa was mainly driven by duplications and protein domain rearrangement processes at the stem of Metazoa. Furthermore, our analysis allowed us to reveal protein domains that are essential to the maintenance of animal multicellularity. Our analyses also demonstrate the utility of single-cell genomics from uncultured taxa to address evolutionary questions. This article is part of a discussion meeting issue 'Single cell ecology'.}, }
@article {pmid31568885, year = {2019}, author = {Thakur, R and Shiratori, T and Ishida, KI}, title = {Taxon-rich Multigene Phylogenetic Analyses Resolve the Phylogenetic Relationship Among Deep-branching Stramenopiles.}, journal = {Protist}, volume = {170}, number = {5}, pages = {125682}, doi = {10.1016/j.protis.2019.125682}, pmid = {31568885}, issn = {1618-0941}, abstract = {Stramenopiles are one of the major eukaryotic assemblages. This group comprises a wide range of species including photosynthetic unicellular and multicellular algae, fungus-like osmotrophic organisms and many free-living phagotrophic flagellates. However, the phylogeny of the Stramenopiles, especially relationships among deep-branching heterotrophs, has not yet been resolved because of a lack of adequate transcriptomic data for representative lineages. In this study, we performed multigene phylogenetic analyses of deep-branching Stramenopiles with improved taxon sampling. We sequenced transcriptomes of three deep-branching Stramenopiles: Incisomonas marina, Pseudophyllomitus vesiculosus and Platysulcus tardus. Phylogenetic analyses using 120 protein-coding genes and 56 taxa indicated that Pl. tardus is sister to all other Stramenopiles while Ps. vesiculosus is sister to MAST-4 and form a robust clade with the Labyrinthulea. The resolved phylogenetic relationships of deep-branching Stramenopiles provide insights into the ancestral traits of the Stramenopiles.}, }
@article {pmid31568790, year = {2019}, author = {Newman, SA}, title = {Cell differentiation: what have we learned in 50 years?.}, journal = {Journal of theoretical biology}, volume = {}, number = {}, pages = {110031}, doi = {10.1016/j.jtbi.2019.110031}, pmid = {31568790}, issn = {1095-8541}, abstract = {I revisit two theories of cell differentiation in multicellular organisms published a half-century ago, Stuart Kauffman's global gene regulatory dynamics (GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory network (MGRN) model, in light of newer knowledge of mechanisms of gene regulation in the metazoans (animals). The two models continue to inform hypotheses and computational studies of differentiation of lineage-adjacent cell types. However, their shared notion (based on bacterial regulatory systems) of gene switches and networks built from them, have constrained progress in understanding the dynamics and evolution of differentiation. Recent work has described unique write-read-rewrite chromatin-based expression encoding in eukaryotes, as well metazoan-specific processes of gene activation and silencing in condensed-phase, enhancer-recruiting regulatory hubs, employing disordered proteins, including transcription factors, with context-dependent identities. These findings suggest an evolutionary scenario in which the origination of differentiation in animals, rather than depending exclusively on adaptive natural selection, emerged as a consequence of a type of multicellularity in which the novel metazoan gene regulatory apparatus was readily mobilized to amplify and exaggerate inherent cell functions of unicellular ancestors. The plausibility of this hypothesis is illustrated by the evolution of the developmental role of Grainyhead-like in the formation of epithelium.}, }
@article {pmid31565856, year = {2019}, author = {Gilbert, SF}, title = {Evolutionary transitions revisited: Holobiont evo-devo.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22903}, pmid = {31565856}, issn = {1552-5015}, support = {//Swarthmore College Faculty Research Grant/ ; }, abstract = {John T. Bonner lists four essential transformations in the evolution of life: the emergence of the eukaryotic cell, meiosis, multicellularity, and the nervous system. This paper analyses the mechanisms for those transitions in light of three of Dr. Bonner's earlier hypotheses: (a) that the organism is its life cycle, (b) that evolution consists of alterations of the life cycle, and (c) that development extends beyond the body and into interactions with other organisms. Using the notion of the holobiont life cycle, this paper attempts to show that these evolutionary transitions can be accomplished through various means of symbiosis. Perceiving the organism both as an interspecies consortium and as a life cycle supports a twofold redefinition of the organism as a holobiont constructed by integrating together the life cycles of several species. These findings highlight the importance of symbiosis and the holobiont development in analyses of evolution.}, }
@article {pmid31563945, year = {2019}, author = {Hernández-Hernández, V and Benítez, M and Boudaoud, A}, title = {Interplay between turgor pressure and plasmodesmata during plant development.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erz434}, pmid = {31563945}, issn = {1460-2431}, abstract = {Plasmodesmata traverse cell walls, generating connections between neighboring cells. They allow intercellular movement of molecules such as transcription factors, hormones, and sugars, and thus create a symplasmic continuity within a tissue. One important factor that determines plasmodesmal permeability is their aperture which is regulated during developmental and physiological processes. Regulation of aperture has been shown to affect developmental events such as vascular differentiation in the root, initiation of lateral roots, or transition to flowering. Extensive research has unraveled molecular factors involved in the regulation of plasmodesmal permeability. Nevertheless, many plant developmental processes appear to involve feedbacks mediated by mechanical forces, raising the question of whether mechanical forces and plasmodesmal permeability affect each other. Here, we review experimental data on how one of these forces, turgor pressure, and plasmodesmal permeability may mutually influence each other during plant development, and we discuss the questions raised by these data. Addressing such questions will improve our knowledge of how cellular patterns emerge during development, shedding light on the evolution of complex multicellular plants.}, }
@article {pmid31552662, year = {2020}, author = {Wanninger, A and Wollesen, T}, title = {Methods in Brain Development of Molluscs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2047}, number = {}, pages = {311-324}, doi = {10.1007/978-1-4939-9732-9_17}, pmid = {31552662}, issn = {1940-6029}, abstract = {Representatives of the phylum Mollusca have long been important models in neurobiological research. Recently, the routine application of immunocytochemistry and gene expression analyses in combination with confocal laserscanning microscopy has allowed fast generation of highly detailed reconstructions of neural structures of even the smallest multicellular animals, including early developmental stages. As a consequence, large-scale comparative analyses of neurogenesis-an important prerequisite for inferences concerning the evolution of animal nervous systems-are now possible in a reasonable amount of time. Herein, we describe immunocytochemical staining and in situ hybridization protocols for both, whole-mount preparations of developmental stages-usually 70-300 μm in size-as well as for vibratome and cryostat sections of complex brains. Although our procedures have been optimized for marine molluscs, they may easily be adapted to other (marine) organisms by the creative neurobiologist.}, }
@article {pmid31542284, year = {2019}, author = {Barger, SR and James, ML and Pellenz, CD and Krendel, M and Sirotkin, V}, title = {Human myosin 1e tail but not motor domain replaces fission yeast Myo1 domains to support myosin-I function during endocytosis.}, journal = {Experimental cell research}, volume = {}, number = {}, pages = {111625}, doi = {10.1016/j.yexcr.2019.111625}, pmid = {31542284}, issn = {1090-2422}, abstract = {In both unicellular and multicellular organisms, long-tailed class I myosins function in clathrin-mediated endocytosis. Myosin 1e (Myo1e) in vertebrates and Myo1 in fission yeast have similar domain organization, yet whether these proteins or their individual protein domains are functionally interchangeable remains unknown. In an effort to assess functional conservation of class I myosins, we tested whether human Myo1e could replace Myo1 in fission yeast Schizosaccharomyces pombe and found that it was unable to substitute for yeast Myo1. To determine if any individual protein domain is responsible for the inability of Myo1e to function in yeast, we created human-yeast myosin-I chimeras. By functionally testing these chimeric myosins in vivo, we concluded that the Myo1e motor domain is unable to function in yeast, even when combined with the yeast Myo1 tail and a full complement of yeast regulatory light chains. Conversely, the Myo1e tail, when attached to the yeast Myo1 motor domain, supports localization to endocytic actin patches and partially rescues the endocytosis defect in myo1Δ cells. Further dissection showed that both the TH1 and TH2-SH3 domains in the human Myo1e tail are required for localization and function of chimeric myosin-I at endocytic sites. Overall, this study provides insights into the role of individual myosin-I domains, expands the utility of fission yeast as a simple model system to study the effects of disease-associated MYO1E mutations, and supports a model of co-evolution between a myosin motor and its actin track.}, }
@article {pmid31540916, year = {2019}, author = {Pukhlyakova, EA and Kirillova, AO and Kraus, YA and Zimmermann, B and Technau, U}, title = {Cadherin switch marks germ layer formation in the diploblastic sea anemone Nematostella vectensis.}, journal = {Development (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1242/dev.174623}, pmid = {31540916}, issn = {1477-9129}, abstract = {Morphogenesis is a shape-building process during development of multicellular organisms. During this process the establishment and modulation of cell-cell contacts play an important role. Cadherins, the major cell adhesion molecules, form adherens junctions connecting epithelial cells. Numerous studies in Bilateria have shown that cadherins are associated with the regulation of cell differentiation, cell shape changes, cell migration and tissue morphogenesis. To date, the role of Cadherins in non-bilaterians is unknown. Here, we study the expression and the function of two paralogous classical cadherins, cadherin1 and cadherin3, in the diploblastic animal, the sea anemone Nematostella vectensis We show that a cadherin switch is accompanying the formation of germ layers. Using specific antibodies, we show that both cadherins are localized to adherens junctions at apical and basal positions in ectoderm and endoderm. During gastrulation, partial EMT of endodermal cells is marked by a step-wise down-regulation of cadherin3 and up-regulation of cadherin1. Knockdown experiments show that both cadherins are required for maintenance of tissue integrity and tissue morphogenesis. Thus, both sea anemones and bilaterians use independently duplicated cadherins combinatorially for tissue morphogenesis and germ layer differentiation.}, }
@article {pmid31540472, year = {2019}, author = {Denes, V and Geck, P and Mester, A and Gabriel, R}, title = {Pituitary Adenylate Cyclase-Activating Polypeptide: 30 Years in Research Spotlight and 600 Million Years in Service.}, journal = {Journal of clinical medicine}, volume = {8}, number = {9}, pages = {}, doi = {10.3390/jcm8091488}, pmid = {31540472}, issn = {2077-0383}, abstract = {Emerging from the depths of evolution, pituitary adenylate cyclase-activating polypeptide (PACAP) and its receptors (i.e., PAC1, VPAC1, VPAC2) are present in multicellular organisms from Tunicates to humans and govern a remarkable number of physiological processes. Consequently, the clinical relevance of PACAP systems spans a multifaceted palette that includes more than 40 disorders. We aimed to present the versatility of PACAP1-38 actions with a focus on three aspects: (1) when PACAP1-38 could be a cause of a malfunction, (2) when PACAP1-38 could be the cure for a malfunction, and (3) when PACAP1-38 could either improve or impair biology. PACAP1-38 is implicated in the pathophysiology of migraine and post-traumatic stress disorder whereas an outstanding protective potential has been established in ischemia and in Alzheimer's disease. Lastly, PACAP receptors could mediate opposing effects both in cancers and in inflammation. In the light of the above, the duration and concentrations of PACAP agents must be carefully set at any application to avoid unwanted consequences. An enormous amount of data accumulated since its discovery (1989) and the first clinical trials are dated in 2017. Thus in the field of PACAP research: &quot;this is not the end, not even the beginning of the end, but maybe the end of the beginning.&quot;}, }
@article {pmid31534207, year = {2019}, author = {Moger-Reischer, R and Lennon, JT}, title = {Microbial ageing and longevity.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41579-019-0253-y}, pmid = {31534207}, issn = {1740-1534}, abstract = {Longevity reflects the ability to maintain homeostatic conditions necessary for life as an organism ages. A long-lived organism must contend not only with environmental hazards but also with internal entropy and macromolecular damage that result in the loss of fitness during ageing, a phenomenon known as senescence. Although central to many of the core concepts in biology, ageing and longevity have primarily been investigated in sexually reproducing, multicellular organisms. However, growing evidence suggests that microorganisms undergo senescence, and can also exhibit extreme longevity. In this Review, we integrate theoretical and empirical insights to establish a unified perspective on senescence and longevity. We discuss the evolutionary origins, genetic mechanisms and functional consequences of microbial ageing. In addition to having biomedical implications, insights into microbial ageing shed light on the role of ageing in the origin of life and the upper limits to longevity.}, }
@article {pmid31532063, year = {2019}, author = {Powell, R and O'Malley, MA}, title = {Metabolic and microbial perspectives on the &quot;evolution of evolution&quot;.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {}, number = {}, pages = {}, doi = {10.1002/jez.b.22898}, pmid = {31532063}, issn = {1552-5015}, abstract = {Identifying and theorizing major turning points in the history of life generates insights into not only world-changing evolutionary events but also the processes that bring these events about. In his treatment of these issues, Bonner identifies the evolution of sex, multicellularity, and nervous systems as enabling the &quot;evolution of evolution,&quot; which involves fundamental transformations in how evolution occurs. By contextualizing his framework within two decades of theorizing about major transitions in evolution, we identify some basic problems that Bonner's theory shares with much of the prevailing literature. These problems include implicit progressivism, theoretical disunity, and a limited ability to explain major evolutionary transformations. We go on to identify events and processes that are neglected by existing views. In contrast with the &quot;vertical&quot; focus on replication, hierarchy, and morphology that preoccupies most of the literature on major transitions, we propose a &quot;horizontal&quot; dimension in which metabolism and microbial innovations play a central explanatory role in understanding the broad-scale organization of life.}, }
@article {pmid31529373, year = {2019}, author = {Erwin, DH}, title = {Tempos and modes of collectivity in the history of life.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12064-019-00303-4}, pmid = {31529373}, issn = {1611-7530}, support = {NNA13AA90A//NASA Astrobiology Institute/ ; }, abstract = {Collective integration and processing of information have increased through the history of life, through both the formation of aggregates in which the entities may have very different properties and which jointly coarse-grained environmental variables (ranging from widely varying metabolism in microbial consortia to the ecological diversity of species on reefs) and through collectives of similar entities (such as cells within an organism or social groups). Such increases have been implicated in significant transitions in the history of life, including aspects of the origin of life, the generation of pangenomes among microbes and microbial communities such as stromatolites, multicellularity and social insects. This contribution provides a preliminary overview of the dominant modes of collective information processing in the history of life, their phylogenetic distribution and extent of convergence, and the effects of new modes for integrating and acting upon information on the tempo of evolutionary change.}, }
@article {pmid31521200, year = {2019}, author = {Rausch, P and Rühlemann, M and Hermes, BM and Doms, S and Dagan, T and Dierking, K and Domin, H and Fraune, S and von Frieling, J and Hentschel, U and Heinsen, FA and Höppner, M and Jahn, MT and Jaspers, C and Kissoyan, KAB and Langfeldt, D and Rehman, A and Reusch, TBH and Roeder, T and Schmitz, RA and Schulenburg, H and Soluch, R and Sommer, F and Stukenbrock, E and Weiland-Bräuer, N and Rosenstiel, P and Franke, A and Bosch, T and Baines, JF}, title = {Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {133}, doi = {10.1186/s40168-019-0743-1}, pmid = {31521200}, issn = {2049-2618}, support = {CRC 1182//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as &quot;metaorganisms.&quot; The goal of the Collaborative Research Center &quot;Origin and Function of Metaorganisms&quot; is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.<br><br>METHODS: In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.<br><br>CONCLUSION: While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3 V4 over the V1 V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.}, }
@article {pmid31517991, year = {2019}, author = {de Araújo Silva-Cardoso, IM and Meira, FS and Gomes, ACMM and Scherwinski-Pereira, JE}, title = {Histology, histochemistry and ultrastructure of pre-embryogenic cells determined for direct somatic embryogenesis in the palm tree Syagrus oleracea.}, journal = {Physiologia plantarum}, volume = {}, number = {}, pages = {}, doi = {10.1111/ppl.13026}, pmid = {31517991}, issn = {1399-3054}, abstract = {Somatic embryogenesis in palm trees is, in general, a slow and highly complex process, with a predominance of the indirect route and, consequently, a lack of knowledge about the direct route. We present new knowledge related to the morphological, histochemical, and ultrastructural aspects of the transition from somatic to embryogenic cells and direct formation of somatic embryos from mature zygotic embryos of Syagrus oleracea, a palm tree. The results support the general concept that 2,4-dichlorophenoxyacetic acid plays a critical role for the formation of somatic embryos of direct and multicellular origin. Seven days in medium with auxin were enough for the identification of embryogenic cells. These cells had a set of characteristics that fit them into the concept of totipotent stem cells. At fourteen days in induction medium, nodular formations were observed in the distal region of inoculated embryos, which evolved into globular somatic embryos. At 120 days in induction medium, the quality of the somatic embryos was compromised. The dynamics of the mobilization of reserve compounds was also demonstrated, with emphasis on starch and protein as energy sources required for the embryogenic process. This study shows for the first time the anatomical and ultrastructural events involved in direct somatic embryogenesis in a palm tree and incites the scientific community to return to the discussion of classical concepts related to direct somatic embryogenesis, especially regarding the characteristics and location of determined pre-embryogenic cells. This article is protected by copyright. All rights reserved.}, }
@article {pmid31501435, year = {2019}, author = {Kiss, E and Hegedüs, B and Virágh, M and Varga, T and Merényi, Z and Kószó, T and Bálint, B and Prasanna, AN and Krizsán, K and Kocsubé, S and Riquelme, M and Takeshita, N and Nagy, LG}, title = {Comparative genomics reveals the origin of fungal hyphae and multicellularity.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4080}, doi = {10.1038/s41467-019-12085-w}, pmid = {31501435}, issn = {2041-1723}, abstract = {Hyphae represent a hallmark structure of multicellular fungi. The evolutionary origins of hyphae and of the underlying genes are, however, hardly known. By systematically analyzing 72 complete genomes, we here show that hyphae evolved early in fungal evolution probably via diverse genetic changes, including co-option and exaptation of ancient eukaryotic (e.g. phagocytosis-related) genes, the origin of new gene families, gene duplications and alterations of gene structure, among others. Contrary to most multicellular lineages, the origin of filamentous fungi did not correlate with expansions of kinases, receptors or adhesive proteins. Co-option was probably the dominant mechanism for recruiting genes for hypha morphogenesis, while gene duplication was apparently less prevalent, except in transcriptional regulators and cell wall - related genes. We identified 414 novel gene families that show correlated evolution with hyphae and that may have contributed to its evolution. Our results suggest that hyphae represent a unique multicellular organization that evolved by limited fungal-specific innovations and gene duplication but pervasive co-option and modification of ancient eukaryotic functions.}, }
@article {pmid31480977, year = {2019}, author = {Fisher, RM and Regenberg, B}, title = {Multicellular group formation in Saccharomyces cerevisiae.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1910}, pages = {20191098}, doi = {10.1098/rspb.2019.1098}, pmid = {31480977}, issn = {1471-2954}, abstract = {Understanding how and why cells cooperate to form multicellular organisms is a central aim of evolutionary biology. Multicellular groups can form through clonal development (where daughter cells stick to mother cells after division) or by aggregation (where cells aggregate to form groups). These different ways of forming groups directly affect relatedness between individual cells, which in turn can influence the degree of cooperation and conflict within the multicellular group. It is hard to study the evolution of multicellularity by focusing only on obligately multicellular organisms, like complex animals and plants, because the factors that favour multicellular cooperation cannot be disentangled, as cells cannot survive and reproduce independently. We support the use of Saccharomyces cerevisiae as an ideal model for studying the very first stages of the evolution of multicellularity. This is because it can form multicellular groups both clonally and through aggregation and uses a family of proteins called 'flocculins' that determine the way in which groups form, making it particularly amenable to laboratory experiments. We briefly review current knowledge about multicellularity in S. cerevisiae and then propose a framework for making predictions about the evolution of multicellular phenotypes in yeast based on social evolution theory. We finish by explaining how S. cerevisiae is a particularly useful experimental model for the analysis of open questions concerning multicellularity.}, }
@article {pmid31474536, year = {2019}, author = {Gonçalves, AP and Heller, J and Span, EA and Rosenfield, G and Do, HP and Palma-Guerrero, J and Requena, N and Marletta, MA and Glass, NL}, title = {Allorecognition upon Fungal Cell-Cell Contact Determines Social Cooperation and Impacts the Acquisition of Multicellularity.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2019.07.060}, pmid = {31474536}, issn = {1879-0445}, abstract = {Somatic cell fusion and conspecific cooperation are crucial social traits for microbial unicellular-to-multicellular transitions, colony expansion, and substrate foraging but are also associated with risks of parasitism. We identified a cell wall remodeling (cwr) checkpoint that acts upon cell contact to assess genetic compatibility and regulate cell wall dissolution during somatic cell fusion in a wild population of the filamentous fungus Neurospora crassa. Non-allelic interactions between two linked loci, cwr-1 and cwr-2, were necessary and sufficient to block cell fusion: cwr-1 encodes a polysaccharide monooxygenase (PMO), a class of enzymes associated with extracellular degradative capacities, and cwr-2 encodes a predicted transmembrane protein. Mutations of sites in CWR-1 essential for PMO catalytic activity abolished the block in cell fusion between formerly incompatible strains. In Neurospora, alleles cwr-1 and cwr-2 were highly polymorphic, fell into distinct haplogroups, and showed trans-species polymorphisms. Distinct haplogroups and trans-species polymorphisms at cwr-1 and cwr-2 were also identified in the distantly related genus Fusarium, suggesting convergent evolution. Proteins involved in chemotropic processes showed extended localization at contact sites, suggesting that cwr regulates the transition between chemotropic growth and cell wall dissolution. Our work revealed an allorecognition surveillance system based on kind discrimination that inhibits cooperative behavior in fungi by blocking cell fusion upon contact, contributing to fungal immunity by preventing formation of chimeras between genetically non-identical colonies.}, }
@article {pmid31463010, year = {2019}, author = {Vostinar, AE and Goldsby, HJ and Ofria, C}, title = {Suicidal selection: Programmed cell death can evolve in unicellular organisms due solely to kin selection.}, journal = {Ecology and evolution}, volume = {9}, number = {16}, pages = {9129-9136}, doi = {10.1002/ece3.5460}, pmid = {31463010}, issn = {2045-7758}, abstract = {Abstract: Unicellular organisms can engage in a process by which a cell purposefully destroys itself, termed programmed cell death (PCD). While it is clear that the death of specific cells within a multicellular organism could increase inclusive fitness (e.g., during development), the origin of PCD in unicellular organisms is less obvious. Kin selection has been shown to help maintain instances of PCD in existing populations of unicellular organisms; however, competing hypotheses exist about whether additional factors are necessary to explain its origin. Those factors could include an environmental shift that causes latent PCD to be expressed, PCD hitchhiking on a large beneficial mutation, and PCD being simply a common pathology. Here, we present results using an artificial life model to demonstrate that kin selection can, in fact, be sufficient to give rise to PCD in unicellular organisms. Furthermore, when benefits to kin are direct-that is, resources provided to nearby kin-PCD is more beneficial than when benefits are indirect-that is, nonkin are injured, thus increasing the relative amount of resources for kin. Finally, when considering how strict organisms are in determining kin or nonkin (in terms of mutations), direct benefits are viable in a narrower range than indirect benefits.<br><br>Open Research Badges: This article has been awarded Open Data and Open Materials Badges. All materials and data are publicly accessible via the Open Science Framework at https://github.com/anyaevostinar/SuicidalAltruismDissertation/tree/master/LongTerm.}, }
@article {pmid31462290, year = {2019}, author = {Romero-Mujalli, D and Jeltsch, F and Tiedemann, R}, title = {Elevated mutation rates are unlikely to evolve in sexual species, not even under rapid environmental change.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {175}, doi = {10.1186/s12862-019-1494-0}, pmid = {31462290}, issn = {1471-2148}, support = {not applicable//Universität Potsdam/ ; }, abstract = {BACKGROUND: Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats.<br><br>RESULTS: The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats.<br><br>CONCLUSIONS: Given that 50% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become - at least locally - extinct.}, }
@article {pmid31456065, year = {2019}, author = {Cleri, F}, title = {Agent-based model of multicellular tumor spheroid evolution including cell metabolism.}, journal = {The European physical journal. E, Soft matter}, volume = {42}, number = {8}, pages = {112}, doi = {10.1140/epje/i2019-11878-7}, pmid = {31456065}, issn = {1292-895X}, abstract = {Computational models aiming at the spatio-temporal description of cancer evolution are a suitable framework for testing biological hypotheses from experimental data, and generating new ones. Building on our recent work (J. Theor. Biol. 389, 146 (2016)) we develop a 3D agent-based model, capable of tracking hundreds of thousands of interacting cells, over time scales ranging from seconds to years. Cell dynamics is driven by a Monte Carlo solver, incorporating partial differential equations to describe chemical pathways and the activation/repression of &quot;genes&quot;, leading to the up- or down-regulation of specific cell markers. Each cell-agent of different kind (stem, cancer, stromal etc.) runs through its cycle, undergoes division, can exit to a dormant, senescent, necrotic state, or apoptosis, according to the inputs from its systemic network. The basic network at this stage describes glucose/oxygen/ATP cycling, and can be readily extended to cancer-cell specific markers. Eventual accumulation of chemical/radiation damage to each cell's DNA is described by a Markov chain of internal states, and by a damage-repair network, whose evolution is linked to the cell systemic network. Aimed at a direct comparison with experiments of tumorsphere growth from stem cells, the present model will allow to quantitatively study the role of transcription factors involved in the reprogramming and variable radio-resistance of simulated cancer-stem cells, evolving in a realistic computer simulation of a growing multicellular tumorsphere.}, }
@article {pmid31446445, year = {2019}, author = {Annunziata, R and Andrikou, C and Perillo, M and Cuomo, C and Arnone, MI}, title = {Development and evolution of gut structures: from molecules to function.}, journal = {Cell and tissue research}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00441-019-03093-9}, pmid = {31446445}, issn = {1432-0878}, support = {215781//Marie Curie ITN EVONET/ ; }, abstract = {The emergence of a specialized system for food digestion and nutrient absorption was a crucial innovation for multicellular organisms. Digestive systems with different levels of complexity evolved in different animals, with the endoderm-derived one-way gut of most bilaterians to be the prevailing and more specialized form. While the molecular events regulating the early phases of embryonic tissue specification have been deeply investigated in animals occupying different phylogenetic positions, the mechanisms underlying gut patterning and gut-associated structures differentiation are still mostly obscure. In this review, we describe the main discoveries in gut and gut-associated structures development in echinoderm larvae (mainly for sea urchin and, when available, for sea star) and compare them with existing information in vertebrates. An impressive degree of conservation emerges when comparing the transcription factor toolkits recruited for gut cells and tissue differentiation in animals as diverse as echinoderms and vertebrates, thus suggesting that their function emerged in the deuterostome ancestor.}, }
@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 &amp; 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 {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}, support = {F32 GM122419/GM/NIGMS NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; R24 RR032670/RR/NCRR NIH HHS/United States ; }, 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 {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 &quot;neutral phenotypes&quot; and &quot;neutral morphologies&quot; 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}, 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 = {572}, number = {7768}, pages = {249-253}, 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 {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 {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}, support = {Programme Bettencourt//Ecole Doctorale FIRE/ ; //Ecole normale supérieure/ ; //Centre National de la Recherche Scientifique/ ; PANDA/ERC_/European Research Council/International ; /ERC_/European Research Council/International ; //École Normale Supérieure/ ; }, 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.}, }
@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 {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 = {18}, number = {17}, pages = {2040-2054}, 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 = {3}, number = {8}, pages = {1197-1205}, 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 = {3}, number = {7}, pages = {1018-1029}, 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 = {205}, number = {4}, pages = {619-627}, 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}, mesh = {Archaea/cytology/enzymology/*metabolism ; Bacteria/cytology/enzymology/*metabolism ; Cell Membrane/*metabolism ; *Electron Transport ; *Energy Metabolism ; Membrane Proteins/*chemistry/*metabolism ; }, 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 {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 = {570}, number = {7762}, pages = {519-522}, 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. Approximately 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 ultrathin 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 behaviour. Together these results unveil the unique structure and function property of ellipsoidal MMPs.}, }
@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}, 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 = {Secreted Flavin Cofactors for Anaerobic Respiration of Fumarate and Urocanate by Shewanella oneidensis: Cost and Role.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {16}, 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, both as 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, and the fitness cost of flavin secretion has not been quantified. We demonstrate that deletion of the inner membrane flavin adenine dinucleotide (FAD) exporter Bfe results in a 23% slower growth rate than that of the wild type during fumarate respiration and an 80 to 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, in 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 = {11}, number = {4}, pages = {130-141}, 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 = {P20 GM113132/GM/NIGMS NIH HHS/United States ; MCB 1817342//National Science Foundation (NSF)/International ; P20-GM113132//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; 31003A_169377//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/International ; STANTO15RO//Cystic Fibrosis Foundation (CF Foundation)/International ; }, mesh = {*Bacterial Adhesion ; *Biofilms ; Caulobacter crescentus/*physiology ; *Hydrodynamics ; }, 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 = {476}, number = {}, pages = {62-73}, 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 = {570}, number = {7760}, pages = {232-235}, 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 = {18}, number = {4}, 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 = {28}, number = {12}, pages = {3089-3100}, doi = {10.1111/mec.15117}, pmid = {31055860}, issn = {1365-294X}, support = {170201//UBO/VRIP/ ; 201730E063//Consejo Superior de Investigaciones Científicas/ ; N 16-55-16007//Russian Foundation for Basic Research/ ; 11170927//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1170815//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 310003A_143960//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 31003A_163254//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; P2NEP3_178543//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 2015-05174//Swedish Research Council/ ; }, abstract = {Recent studies show that soil eukaryotic diversity is immense and dominated by micro-organisms. However, it is unclear to what extent the processes that shape the distribution of diversity in plants and animals also apply to micro-organisms. 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 phylogeographical 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 habitats. 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 habitats. 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 micro-organisms, propagule dispersal is slow enough that historical processes may contribute to their diversification and phylogeographical patterns and may partly explain their very high overall diversity.}, }
@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 Deltaproteobacteria Strain, WYHR-1, from a Freshwater Lake.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {14}, 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) represent 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, 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 = {332}, number = {6}, pages = {171-178}, 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}, mesh = {Amino Acid Sequence ; Animals ; Ctenophora/*metabolism ; Ephrins/*metabolism ; Evolution, Molecular ; Humans ; Ligands ; Phylogeny ; Porifera/*metabolism ; Protein Binding ; Protein Domains ; Receptors, Eph Family/chemistry/*metabolism ; *Signal Transduction ; }, 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 = {125}, number = {14}, pages = {2409-2422}, doi = {10.1002/cncr.32053}, pmid = {31012964}, issn = {1097-0142}, support = {1S10RR15768-01//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/ ; 1 S10 RR 15768-01//U.S. Public Health Service/ ; }, 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 = {28}, number = {9}, pages = {2136-2154}, 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/Intramural NASA/Intramural NASA/United States ; NNA17BB05A/NASA/National Aeronautics and Space Administration/United States ; 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 ; T32 DK007569/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 = {26}, number = {2}, pages = {183-192}, doi = {10.1093/dnares/dsz002}, pmid = {30918953}, issn = {1756-1663}, mesh = {Caulerpa/*genetics ; Chlorophyta/genetics ; Embryophyta/genetics ; *Evolution, Molecular ; Gene Expression Profiling ; Genes, Homeobox/*genetics ; *Genome, Plant ; Genomics ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, 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 {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 {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 {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}, mesh = {Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; *Biomarkers, Tumor ; Clinical Studies as Topic ; Disease Management ; Drug Evaluation, Preclinical ; Female ; Humans ; *Molecular Targeted Therapy/methods ; Neoplasm Invasiveness ; Neoplasm Metastasis ; Neoplasm Staging ; Neoplastic Stem Cells/drug effects/metabolism/pathology ; Ovarian Neoplasms/*etiology/pathology/*therapy ; Standard of Care ; Treatment Outcome ; }, 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}, mesh = {Alleles ; *Evolution, Molecular ; *Genes, Bacterial ; Microbial Interactions/*genetics ; Myxococcus xanthus/*genetics ; Nucleotidyltransferases/genetics ; Phenotype ; *Selection, Genetic ; *Soil Microbiology ; }, 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}, mesh = {Animals ; Biological Evolution ; *Chromatin Assembly and Disassembly ; Chromosomal Proteins, Non-Histone/genetics/history/metabolism ; DNA/*genetics/history/metabolism ; Eukaryotic Cells/cytology/metabolism ; *Genome ; Genomics/methods ; Histones/genetics/history/metabolism ; History, 21st Century ; History, Ancient ; Humans ; Nucleosomes/chemistry/*genetics/metabolism ; Prokaryotic Cells/cytology/metabolism ; Transcription Factors/genetics/history/metabolism ; *Transcription, Genetic ; }, 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}, mesh = {Animals ; Anthozoa/genetics/metabolism ; *Biological Evolution ; Hydra/physiology ; Invertebrates/*genetics ; Multigene Family ; Thrombospondins/*genetics/metabolism ; }, 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}, support = {R15 GM122032/GM/NIGMS NIH HHS/United States ; }, 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 = {47}, number = {8}, pages = {e48}, 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 = {13}, number = {5}, pages = {597-605}, 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}, mesh = {*Biological Evolution ; Genes, Microbial ; *Genome, Bacterial ; *Genome, Fungal ; *Multigene Family ; Oxidoreductases/genetics ; *PDZ Domains ; Peptide Hydrolases/genetics ; Protein Biosynthesis ; Stress, Physiological ; }, 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}, mesh = {Animals ; Chromatin/classification/*genetics ; DNA-Binding Proteins/genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/*genetics ; *Evolution, Molecular ; Histone Code ; }, 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 {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 {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 ; }, mesh = {Animals ; *Evolution, Molecular ; *Genes, p53 ; Phylogeny ; *Selection, Genetic ; Vertebrates/*genetics ; }, 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}, mesh = {Animals ; Automation ; Drug Evaluation, Preclinical ; Humans ; Kidney/diagnostic imaging/drug effects ; *Lab-On-A-Chip Devices ; Liver/diagnostic imaging/drug effects ; Optical Imaging/*instrumentation ; Rats ; }, 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 = {2385-2070}, 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}, mesh = {Alternative Splicing ; Animals ; *Evolution, Molecular ; *Exons ; *Genome ; *Introns ; *Transcriptome ; }, 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}, mesh = {*Biological Evolution ; Embryophyta/*genetics/*growth &amp; development ; *Gene Expression Regulation, Plant ; *Gene Regulatory Networks ; Plant Proteins/*genetics ; }, 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 ; }, mesh = {*Biological Evolution ; *Gametogenesis, Plant ; *Plant Physiological Phenomena ; *Plants ; Pollen/*cytology/*physiology ; }, 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}, mesh = {*Biological Evolution ; Embryophyta/genetics/*growth &amp; development ; Phylogeny ; Plant Leaves/genetics/*growth &amp; development ; Plant Roots/genetics/*growth &amp; development ; }, 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 = {2019}, 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 = {70}, number = {7}, pages = {2185-2197}, 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 = {P30 DK063720/DK/NIDDK NIH HHS/United States ; R01 DK097441/DK/NIDDK NIH HHS/United States ; R01 DK108822/DK/NIDDK NIH HHS/United States ; P30 DK098722/DK/NIDDK NIH HHS/United States ; R01 DK112268/DK/NIDDK NIH HHS/United States ; }, mesh = {Acclimatization ; Adipose Tissue, Beige/*cytology/*metabolism ; Adipose Tissue, White/cytology/metabolism ; Animals ; Cell Differentiation ; Cell Survival ; *Cold Temperature ; *Cold-Shock Response ; Energy Metabolism ; GA-Binding Protein Transcription Factor/metabolism ; *Glycolysis ; Homeostasis ; Male ; Mice ; *Muscle Development ; MyoD Protein/metabolism ; Myoblasts/cytology ; Receptors, Adrenergic, beta/metabolism ; }, 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}, support = {R35 GM124732/GM/NIGMS NIH HHS/United States ; T32 GM007287/GM/NIGMS NIH HHS/United States ; }, 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}, mesh = {Adult Stem Cells/cytology ; *Biological Evolution ; Cell Differentiation ; Humans ; Induced Pluripotent Stem Cells/cytology ; Mitochondria/*physiology ; Pluripotent Stem Cells/*cytology ; }, 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 ; }, mesh = {Animals ; *Biological Evolution ; Caenorhabditis elegans/*genetics ; DNA Copy Number Variations ; Genetic Fitness ; *Genetic Load ; Microsatellite Repeats ; *Mutation ; Recombination, Genetic ; Selection, Genetic ; }, 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}, mesh = {*Biological Evolution ; *Cell Division ; *Cell Polarity ; Meristem/cytology ; Phylogeny ; Plant Cells/*metabolism ; }, 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}, mesh = {Animals ; Atmosphere ; Carbon Dioxide/*analysis/physiology ; *Homeostasis ; Oxygen/*analysis/physiology ; Photosynthesis ; }, 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}, mesh = {Adenosine Deaminase/*genetics ; Amino Acid Sequence ; Bacterial Proteins/*genetics ; Drosophila Proteins/genetics ; *Evolution, Molecular ; Intercellular Signaling Peptides and Proteins/genetics ; Multigene Family ; Phylogeny ; }, 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}, support = {80NSSC18K1085//Intramural NASA/United States ; }, 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/International ; DE-AC02-05CH11231//U.S. Department of Energy Joint Genome Institute/International ; }, 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}, mesh = {Defensins/*chemistry/genetics ; Evolution, Molecular ; Phylogeny ; Protein Folding ; Protein Structure, Secondary ; }, 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 {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 {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 ; }, mesh = {Aging/*genetics/pathology ; Clonal Evolution/genetics ; Genetic Diseases, Inborn/*genetics/pathology ; Genome, Human/*genetics ; Germ-Line Mutation/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Mutagenesis/*genetics ; Mutation/genetics ; }, 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}, 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}, support = {NNA17BB05A/ImNASA/Intramural NASA/United States ; T32 GM084905/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Chlamydomonas reinhardtii/*genetics ; Meiosis ; *Sex Characteristics ; Volvox/*genetics ; }, 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}, mesh = {Cell Death ; Cell Line, Tumor ; Cell Survival ; Coculture Techniques ; Fibroblasts/cytology/metabolism ; Human Umbilical Vein Endothelial Cells/cytology/metabolism ; Humans ; *Models, Biological ; Pancreatic Neoplasms/*pathology ; Spheroids, Cellular/*pathology ; Tumor Microenvironment ; }, 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}, support = {C9136/A15342//Cancer Research UK/United Kingdom ; MR/L015110/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Colorectal Neoplasms/*pathology ; *Disease Models, Animal ; Humans ; Organ Culture Techniques/*methods ; }, 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}, mesh = {Aging/*genetics ; *Epigenesis, Genetic ; Humans ; Peptides/*genetics ; RNA, Long Noncoding ; }, 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 = {U01 CA176287/CA/NCI NIH HHS/United States ; U01 CA217864/CA/NCI NIH HHS/United States ; R35 CA210018/CA/NCI NIH HHS/United States ; R01 CA184510/CA/NCI NIH HHS/United States ; F31 CA206459/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}, mesh = {Humans ; *Neoplasms ; }, }
@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}, mesh = {*Biological Evolution ; DNA Methylation ; *DNA Transposable Elements ; Epigenesis, Genetic ; Gene Duplication ; Gene Expression Regulation ; *Genome Size ; Rhodophyta/*genetics ; }, 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}, mesh = {ATP-Binding Cassette Transporters/*genetics/*metabolism ; Anabaena/*genetics/growth &amp; development/metabolism ; Bacterial Proteins/*genetics/*metabolism ; Base Sequence ; Evolution, Molecular ; Gene Expression Regulation, Bacterial ; Genetic Variation ; Genome, Bacterial ; Genomics ; Mutation ; Polymorphism, Single Nucleotide ; Sequence Deletion ; }, 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?