@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},
abstract = {The evolution of multicellular metazoan organisms was marked by the inclusion of an extracellular matrix (ECM), a multicomponent, proteinaceous network between cells that contributes to the spatial arrangement of cells and the resulting tissue organization. [...].},
}

@article {pmid30622525,
year = {2018},
author = {Li, XG and Zhang, WJ and Xiao, X and Jian, HH and Jiang, T and Tang, HZ and Qi, XQ and Wu, LF},
title = {Pressure-Regulated Gene Expression and Enzymatic Activity of the Two Periplasmic Nitrate Reductases in the Deep-Sea Bacterium Shewanella piezotolerans WP3.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3173},
doi = {10.3389/fmicb.2018.03173},
pmid = {30622525},
issn = {1664-302X},
abstract = {Shewanella species are widely distributed in marine environments, from the shallow coasts to the deepest sea bottom. Most Shewanella species possess two isoforms of periplasmic nitrate reductases (NAP-α and NAP-β) and are able to generate energy through nitrate reduction. However, the contributions of the two NAP systems to bacterial deep-sea adaptation remain unclear. In this study, we found that the deep-sea denitrifier Shewanella piezotolerans WP3 was capable of performing nitrate respiration under high hydrostatic pressure (HHP) conditions. In the wild-type strain, NAP-β played a dominant role and was induced by both the substrate and an elevated pressure, whereas NAP-α was constitutively expressed at a relatively lower level. Genetic studies showed that each NAP system alone was sufficient to fully sustain nitrate-dependent growth and that both NAP systems exhibited substrate and pressure inducible expression patterns when the other set was absent. Biochemical assays further demonstrated that NAP-α had a higher tolerance to elevated pressure. Collectively, we report for the first time the distinct properties and contributions of the two NAP systems to nitrate reduction under different pressure conditions. The results will shed light on the mechanisms of bacterial HHP adaptation and nitrogen cycling in the deep-sea environment.},
}

@article {pmid30618841,
year = {2018},
author = {Huitzil, S and Sandoval-Motta, S and Frank, A and Aldana, M},
title = {Modeling the Role of the Microbiome in Evolution.},
journal = {Frontiers in physiology},
volume = {9},
number = {},
pages = {1836},
doi = {10.3389/fphys.2018.01836},
pmid = {30618841},
issn = {1664-042X},
abstract = {There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.},
}

@article {pmid30612623,
year = {2019},
author = {Bowman, JL and Briginshaw, LN and Florent, SN},
title = {Evolution and co-option of developmental regulatory networks in early land plants.},
journal = {Current topics in developmental biology},
volume = {131},
number = {},
pages = {35-53},
doi = {10.1016/bs.ctdb.2018.10.001},
pmid = {30612623},
issn = {1557-8933},
abstract = {Land plants evolved from an ancestral alga from which they inherited developmental and physiological characters. A key innovation of land plants is a life cycle with an alternation of generations, with both haploid gametophyte and diploid sporophyte generations having complex multicellular bodies. The origins of the developmental genetic programs patterning these bodies, whether inherited from an algal ancestor or evolved de novo, and whether programs were co-opted between generations, are largely open questions. We first provide a framework for land plant evolution and co-option of developmental regulatory pathways and then examine two cases in more detail.},
}

@article {pmid30612620,
year = {2019},
author = {Hackenberg, D and Twell, D},
title = {The evolution and patterning of male gametophyte development.},
journal = {Current topics in developmental biology},
volume = {131},
number = {},
pages = {257-298},
doi = {10.1016/bs.ctdb.2018.10.008},
pmid = {30612620},
issn = {1557-8933},
abstract = {The reproductive adaptations of land plants have played a key role in their terrestrial colonization and radiation. This encompasses mechanisms used for the production, dispersal and union of gametes to support sexual reproduction. The production of small motile male gametes and larger immotile female gametes (oogamy) in specialized multicellular gametangia evolved in the charophyte algae, the closest extant relatives of land plants. Reliance on water and motile male gametes for sexual reproduction was retained by bryophytes and basal vascular plants, but was overcome in seed plants by the dispersal of pollen and the guided delivery of non-motile sperm to the female gametes. Here we discuss the evolutionary history of male gametogenesis in streptophytes (green plants) and the underlying developmental biology, including recent advances in bryophyte and angiosperm models. We conclude with a perspective on research trends that promise to deliver a deeper understanding of the evolutionary and developmental mechanisms of male gametogenesis in plants.},
}

@article {pmid30612613,
year = {2019},
author = {Szövényi, P and Waller, M and Kirbis, A},
title = {Evolution of the plant body plan.},
journal = {Current topics in developmental biology},
volume = {131},
number = {},
pages = {1-34},
doi = {10.1016/bs.ctdb.2018.11.005},
pmid = {30612613},
issn = {1557-8933},
abstract = {Land plants evolved about 470 million years ago or even earlier, in a biological crust-dominated terrestrial flora. The origin of land plants was probably one of the most significant events in Earth's history, which ultimately contributed to the greening of the terrestrial environment and opened up the way for the diversification of both plant and non-plant lineages. Fossil and phylogenetic evidence suggest that land plants have evolved from fresh-water charophycean algae, which were physiologically, genetically, and developmentally potentiated to make the transition to land. Since all land plants have biphasic life cycles, in contrast to the haplontic life cycle of Charophytes, the evolution of land plants was linked to the origin of a multicellular sporophytic phase. Land plants have evolved complex body plans in a way that overall complexity increased toward the tip of the land plant tree of life. Early forms were unbranched, with terminal sporangia and simple rhizoid rooting structures but without vasculature and leaves. Later on, branched forms with lateral sporangia appeared and paved the route for the evolution for indeterminacy. Finally, leaves and roots evolved to enable efficient nutrient transport to support a large plant body. The fossil record also suggests that almost all plant organs, such as leaves and roots, evolved multiple times independently over the course of land plant evolution. In this review, we summarize the current knowledge on the evolution of the land plant body plan by combining evidence of the fossil record, phylogenetics, and developmental biology.},
}

@article {pmid30602438,
year = {2019},
author = {Murre, C},
title = {Helix-loop-helix proteins and the advent of cellular diversity: 30 years of discovery.},
journal = {Genes & development},
volume = {33},
number = {1-2},
pages = {6-25},
doi = {10.1101/gad.320663.118},
pmid = {30602438},
issn = {1549-5477},
abstract = {Helix-loop-helix (HLH) proteins are dimeric transcription factors that control lineage- and developmental-specific gene programs. Genes encoding for HLH proteins arose in unicellular organisms >600 million years ago and then duplicated and diversified from ancestral genes across the metazoan and plant kingdoms to establish multicellularity. Hundreds of HLH proteins have been identified with diverse functions in a wide variety of cell types. HLH proteins orchestrate lineage specification, commitment, self-renewal, proliferation, differentiation, and homing. HLH proteins also regulate circadian clocks, protect against hypoxic stress, promote antigen receptor locus assembly, and program transdifferentiation. HLH proteins deposit or erase epigenetic marks, activate noncoding transcription, and sequester chromatin remodelers across the chromatin landscape to dictate enhancer-promoter communication and somatic recombination. Here the evolution of HLH genes, the structures of HLH domains, and the elaborate activities of HLH proteins in multicellular life are discussed.},
}

@article {pmid30590727,
year = {2018},
author = {Tsitsekian, D and Daras, G and Alatzas, A and Templalexis, D and Hatzopoulos, P and Rigas, S},
title = {Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/ery440},
pmid = {30590727},
issn = {1460-2431},
abstract = {The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.},
}

@article {pmid30590062,
year = {2018},
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 = {},
number = {},
pages = {},
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 = {2018},
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 & differentiation},
volume = {},
number = {},
pages = {},
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)/ ; },
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 = {2018},
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},
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 {pmid30575840,
year = {2018},
author = {Cai, Y and Wang, Y and Xu, H and Cao, C and Zhu, R and Tang, X and Zhang, T and Pan, Y},
title = {Positive magnetic resonance angiography using ultrafine ferritin-based iron oxide nanoparticles.},
journal = {Nanoscale},
volume = {},
number = {},
pages = {},
doi = {10.1039/c8nr06812g},
pmid = {30575840},
issn = {2040-3372},
abstract = {Iron oxide nanoparticles with good biocompatibility can serve as safe magnetic resonance imaging contrast agents. Herein, we report that ultrafine ferritin-based iron oxide (hematite/maghemite) nanoparticles synthesized by controlled biomimetic mineralization using genetically recombinant human H chain ferritin can be used as a positive contrast agent in magnetic resonance angiography. The synthesized magnetoferritin with an averaged core size of 2.2 ± 0.7 nm (hereafter named M-HFn-2.2) shows a r1 value of 0.86 mM-1 s-1 and a r2/r1 ratio of 25.1 at a 7 T magnetic field. Blood pool imaging on mice using the M-HFn-2.2 nanoparticles that were injected through a tail vein by single injection at a dose of 0.54 mM Fe per kg mouse body weight enabled detecting detailed vascular nets at 3 minutes post-injection; the MR signal intensity continuously enhanced up to 2 hours post-injection, which is much longer than that of the commercial magnevist (Gd-DTPA) contrast. Moreover, biodistribution examination indicates that organs such as liver, spleen and kidney safely cleared the injected nanoparticles within one day after the injection, demonstrating no risk of iron overload in test mice. Therefore, this study sheds light on developing high-performance gadolinium free positive magnetic resonance contrast agents for biomedical applications.},
}

@article {pmid30568302,
year = {2018},
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 = {},
number = {},
pages = {},
doi = {10.1038/s41586-018-0801-z},
pmid = {30568302},
issn = {1476-4687},
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 {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 = {2018},
author = {Stein, WD},
title = {The ages of the cancer-associated genes.},
journal = {Seminars in oncology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.seminoncol.2018.11.001},
pmid = {30554805},
issn = {1532-8708},
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 = {},
number = {},
pages = {},
doi = {10.1016/j.cels.2018.11.003},
pmid = {30553725},
issn = {2405-4712},
abstract = {Constituents of multiprotein complexes are required at well-defined levels relative to each other. However, it remains unknown whether eukaryotic cells typically produce precise amounts of subunits, or instead rely on degradation to mitigate imprecise production. Here, we quantified the production rates of multiprotein complexes in unicellular and multicellular eukaryotes using ribosome profiling. By resolving read-mapping ambiguities, which occur for a large fraction of ribosome footprints and distort quantitation accuracy in eukaryotes, we found that obligate components of multiprotein complexes are produced in proportion to their stoichiometry, indicating that their abundances are already precisely tuned at the synthesis level. By systematically interrogating the impact of gene dosage variations in budding yeast, we found a general lack of negative feedback regulation protecting the normally precise rates of subunit synthesis. These results reveal a core principle of proteome homeostasis and highlight the evolution toward quantitative control at every step in the central dogma.},
}

@article {pmid30545356,
year = {2018},
author = {Herron, MD and Zamani-Dahaj, SA and Ratcliff, WC},
title = {Trait heritability in major transitions.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {145},
doi = {10.1186/s12915-018-0612-6},
pmid = {30545356},
issn = {1741-7007},
support = {NNA17BB05A//NASA Astrobiology Institute/ ; NNX15AR33G//National Aeronautics and Space Administration/ ; DEB-1723293//Division of Environmental Biology/ ; DEB-1456652//Division of Environmental Biology/ ; 43285//John Templeton Foundation/ ; },
abstract = {BACKGROUND: Increases in biological complexity and the origins of life's hierarchical organization are described by the "major transitions" 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.

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.

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 "for free," 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},
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},
doi = {10.1038/s41467-018-07728-3},
pmid = {30538242},
issn = {2041-1723},
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 {pmid29545531,
year = {2018},
author = {Moroni, M and Servin-Vences, MR and Fleischer, R and Sánchez-Carranza, O and Lewin, GR},
title = {Voltage gating of mechanosensitive PIEZO channels.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {1096},
pmid = {29545531},
issn = {2041-1723},
mesh = {Animals ; Cell Line ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster ; Evolution, Molecular ; Humans ; Ion Channels/genetics/*metabolism ; *Mechanotransduction, Cellular ; Mice ; Mutation, Missense ; Patch-Clamp Techniques ; Zebrafish ; Zebrafish Proteins/genetics/*metabolism ; },
abstract = {Mechanosensitive PIEZO ion channels are evolutionarily conserved proteins whose presence is critical for normal physiology in multicellular organisms. Here we show that, in addition to mechanical stimuli, PIEZO channels are also powerfully modulated by voltage and can even switch to a purely voltage-gated mode. Mutations that cause human diseases, such as xerocytosis, profoundly shift voltage sensitivity of PIEZO1 channels toward the resting membrane potential and strongly promote voltage gating. Voltage modulation may be explained by the presence of an inactivation gate in the pore, the opening of which is promoted by outward permeation. Older invertebrate (fly) and vertebrate (fish) PIEZO proteins are also voltage sensitive, but voltage gating is a much more prominent feature of these older channels. We propose that the voltage sensitivity of PIEZO channels is a deep property co-opted to add a regulatory mechanism for PIEZO activation in widely different cellular contexts.},
}

Animals
Cell Line
Drosophila Proteins/genetics/*metabolism
Drosophila melanogaster
Evolution, Molecular
Humans
Ion Channels/genetics/*metabolism
*Mechanotransduction, Cellular
Mice
Mutation, Missense
Patch-Clamp Techniques
Zebrafish
Zebrafish Proteins/genetics/*metabolism

@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},
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},
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 {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 & development ; Biological Evolution ; Biomarkers/analysis ; *Biota ; Ecosystem ; Europe ; *Fossils ; Geography ; Geologic Sediments/*chemistry/*microbiology ; Hydrocarbons/analysis ; Lipids/analysis ; Prochlorococcus/growth & development ; Synechococcus/growth & 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.},
}

Asia
Bacteria/growth & development
Biological Evolution
Biomarkers/analysis
*Biota
Ecosystem
Europe
*Fossils
Geography
Geologic Sediments/*chemistry/*microbiology
Hydrocarbons/analysis
Lipids/analysis
Prochlorococcus/growth & development
Synechococcus/growth & development

@article {pmid29427837,
year = {2018},
author = {Baldauf, SL and Romeralo, M and Fiz-Palacios, O and Heidari, N},
title = {A Deep Hidden Diversity of Dictyostelia.},
journal = {Protist},
volume = {169},
number = {1},
pages = {64-78},
doi = {10.1016/j.protis.2017.12.005},
pmid = {29427837},
issn = {1618-0941},
mesh = {*Biodiversity ; DNA Primers/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dictyostelium/classification/*genetics/isolation & purification ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Dictyostelia is a monophyletic group of transiently multicellular (sorocarpic) amoebae, whose study is currently limited to laboratory culture. This tends to favour faster growing species with robust sorocarps, while species with smaller more delicate sorocarps constitute most of the group's taxonomic breadth. The number of known species is also small (∼150) given Dictyostelia's molecular depth and apparent antiquity (>600 myr). Nonetheless, dictyostelid sequences are rarely recovered in culture independent sampling (ciPCR) surveys. We developed ciPCR primers to specifically target dictyostelid small subunit (SSU or 18S) rDNA and tested them on total DNAs extracted from a wide range of soils from five continents. The resulting clone libraries show mostly dictyostelid sequences (∼90%), and phylogenetic analyses of these sequences indicate novel lineages in all four dictyostelid families and most genera. This is especially true for the species-rich Heterostelium and Dictyosteliaceae but also the less species-rich Raperosteliaceae. However, the most novel deep branches are found in two very species-poor taxa, including the deepest branch yet seen in the highly divergent Cavenderiaceae. These results confirm a deep hidden diversity of Dictyostelia, potentially including novel morphologies and developmental schemes. The primers and protocols presented here should also enable more comprehensive studies of dictyostelid ecology.},
}

*Biodiversity
DNA Primers/genetics
DNA, Protozoan/genetics
DNA, Ribosomal/genetics
Dictyostelium/classification/*genetics/isolation & purification
Phylogeny
Polymerase Chain Reaction

@article {pmid30520011,
year = {2018},
author = {Rebolleda-Gómez, M and Travisano, M},
title = {Adaptation, chance, and history in experimental evolutionary reversals to unicellularity.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1111/evo.13654},
pmid = {30520011},
issn = {1558-5646},
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 re-organizations 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 paper 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. This article is protected by copyright. All rights reserved.},
}

@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},
doi = {10.3389/fphys.2018.01406},
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 = {},
number = {},
pages = {},
doi = {10.1038/s41586-018-0783-x},
pmid = {30518860},
issn = {1476-4687},
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 & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-018-0734-9},
pmid = {30510177},
issn = {2397-334X},
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},
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},
doi = {10.1038/s41467-018-07610-2},
pmid = {30498215},
issn = {2041-1723},
abstract = {Engineering multicellularity is one of the next breakthroughs for Synthetic Biology. A key bottleneck to building multicellular systems is the lack of a scalable signaling language with a large number of interfaces that can be used simultaneously. Here, we present a modular, scalable, intercellular signaling language in yeast based on fungal mating peptide/G-protein-coupled receptor (GPCR) pairs harnessed from nature. First, through genome-mining, we assemble 32 functional peptide-GPCR signaling interfaces with a range of dose-response characteristics. Next, we demonstrate that these interfaces can be combined into two-cell communication links, which serve as assembly units for higher-order communication topologies. Finally, we show 56 functional, two-cell links, which we use to assemble three- to six-member communication topologies and a three-member interdependent community. Importantly, our peptide-GPCR language is scalable and tunable by genetic encoding, requires minimal component engineering, and should be massively scalable by further application of our genome mining pipeline or directed evolution.},
}

@article {pmid30484227,
year = {2018},
author = {Trosko, JE},
title = {The Role of the Mitochondria in the Evolution of Stem Cells, Including MUSE Stem Cells and Their Biology.},
journal = {Advances in experimental medicine and biology},
volume = {1103},
number = {},
pages = {131-152},
doi = {10.1007/978-4-431-56847-6_7},
pmid = {30484227},
issn = {0065-2598},
abstract = {From the transition of single-cell organisms to multicellularity of metazoans, evolutionary pressures selected new genes and phenotypes to cope with the oxygenation of the Earth's environment, especially via the symbiotic acquisition of the mitochondrial organelle. There were many new genes and phenotypes that appeared, namely, stem cells, low-oxygen-micro-environments to house these genes ("niches"), 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 "induced pluripotent stem" cells, challenges to the origin of these "iPS" 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 "iPS" 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 = {2018},
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 = {},
number = {},
pages = {},
doi = {10.1038/s41564-018-0305-5},
pmid = {30478288},
issn = {2058-5276},
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},
doi = {10.1016/j.devcel.2018.09.023},
pmid = {30473004},
issn = {1878-1551},
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 = {0959-3330},
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 {pmid30445510,
year = {2018},
author = {Shekhar Saxena, A and Salomon, MP and Matsuba, C and Yeh, SD and Baer, CF},
title = {Evolution of the mutational process under relaxed selection in Caenorhabditis elegans.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msy213},
pmid = {30445510},
issn = {1537-1719},
abstract = {The mutational process varies at many levels, from within genomes to among taxa. Many mechanisms have been linked to variation in mutation, but understanding of the evolution of the mutational process is rudimentary. Physiological condition is often implicated as a source of variation in microbial mutation rate and may contribute to mutation rate variation in multicellular organisms.Deleterious mutations are a ubiquitous source of variation in condition. We test the hypothesis that the mutational process depends on the underlying mutation load in two groups of Caenorhabditis elegans mutation accumulation (MA) lines that differ in their starting mutation loads. "First-Order MA" (O1MA) lines maintained under minimal selection for ∼250 generations were divided into high-fitness and low-fitness groups and sets of "second-order MA" (O2MA) lines derived from each O1MA line were maintained for ∼150 additional generations. Genomes of 48 O2MA lines and their progenitors were sequenced. There is significant variation among O2MA lines in base-substitution rate (µbs), but no effect of initial fitness; the indel rate is greater in high-fitness O2MA lines. Overall, µbs is positively correlated with recombination and proximity to short tandem repeats and negatively correlated with 10 bp and 1 Kb GC content. However, probability of mutation is sufficiently predicted by the three-nucleotide motif alone. ∼90% of the variance in standing nucleotide variation is explained by mutability. Total mutation rate increased in the O2MA lines, as predicted by the "drift barrier" model of mutation rate evolution. These data, combined with experimental estimates of fitness, suggest that epistasis is synergistic.},
}

@article {pmid30444659,
year = {2018},
author = {Rebolleda-Gómez, M and Travisano, M},
title = {The Cost of Being Big: Local Competition, Importance of Dispersal, and Experimental Evolution of Reversal to Unicellularity.},
journal = {The American naturalist},
volume = {192},
number = {6},
pages = {731-744},
doi = {10.1086/700095},
pmid = {30444659},
issn = {1537-5323},
abstract = {Multicellularity provides multiple benefits. Nonetheless, unicellularity is ubiquitous, and there have been multiple cases of evolutionary reversal to a unicellular organization. In this article, we explore some of the costs of multicellularity as well as the possibility and dynamics of evolutionary reversals to unicellularity. We hypothesize that recently evolved multicellular organisms would face a high cost of increased competition for local resources in spatially structured environments because of larger size and increased cell densities. To test this hypothesis we conducted competition assays, computer simulations, and selection experiments using isolates of Saccharomyces cerevisiae that recently evolved multicellularity. In well-mixed environments, multicellular isolates had lower growth rates relative to their unicellular ancestor because of limitations of space and resource acquisition. In structured environments with localized resources, cells in both multicellular and unicellular isolates grew at a similar rate. Despite similar growth, higher local density of cells in multicellular groups led to increased competition and higher fitness costs in spatially structured environments. In structured environments all of the multicellular isolates rapidly evolved a predominantly unicellular life cycle, while in well-mixed environments reversal was more gradual. Taken together, these results suggest that a lack of dispersal, leading to higher local competition, might have been one of the main constraints in the evolution of early multicellular forms.},
}

@article {pmid30429351,
year = {2018},
author = {Ayoubian, H and Ludwig, N and Fehlmann, T and Menegatti, J and Gröger, L and Anastasiadou, E and Trivedi, P and Keller, A and Meese, E and Grässer, FA},
title = {Infection of cell lines derived from diffuse large B-cell lymphoma (DLBCL) with the Epstein-Barr virus (EBV) alters the miRNA loading of the Ago2-complex.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.01297-18},
pmid = {30429351},
issn = {1098-5514},
abstract = {Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoid tumor which is occasionally Epstein-Barr virus (EBV)-positive and is further subtyped as activated B-cell (ABC) and germinal center B-cell (GCB) DLBCL, which has implications for prognosis and treatment.We performed Ago2-RNA immunoprecipitation followed by high throughput RNA sequencing (Ago2-RIP-Seq) to capture functionally active miRNAs in EBV-negative ABC-DLBCL and GC-DLBCL cell lines and their EBV-infected counterparts. In parallel, total miRNomes of these cells were sequenced to capture the cellular miRNA profile for comparison with the functionally active profile. Selected miRNAs with differential abundance were validated using RT-qPCR and Northern Blot. We found 6 miRNAs with differential abundance (2 upregulated and 4 downregulated miRNAs) between EBV-neg. and pos. ABC-DLBCL, and 12 miRNAs with differential abundance (3 upregulated and 9 downregulated miRNAs) between EBV-neg and -pos GC-DLBCL. Eight and twelve miRNAs were confirmed using RT-qPCR in ABC-DLBCL and GC-DLBCL, respectively. Selected miRNs were analyzed in additional type I/II vs. type III EBV latency DLBCL cell lines. Furthermore, up regulation of miR-221-3p and down regulation of let-7c-5p in ABC-DLBCL and up regulation of miR-363-3p and down regulation of 423-5p in GC-DLBCL was verified using RIP-Northern blot.Our comprehensive sequence analysis of the DLBCL miRNomes identified sets of deregulated miRNAs in the Ago2-RIP-seq. Our Ago2-IP-seq miRNomes profile could be considered as an important data set for detection of deregulated functionally active miRNAs in DLBCL and could possibly lead to identification of miRNAs as biomarkers for classification of DLBCL or even as targets for personalized targeted treatment.Importance: Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive tumor of lymphoid origin which is occasionally Epstein-Barr virus (EBV)-positive. MicroRNAs are found in most multicellular organisms and even in viruses such as EBV. They regulate the synthesis of proteins by binding to their cognate messenger RNA (mRNA). MicroRNAs are tethered to their target mRNAs by "Argonaute" proteins. Here we compared the overall content of by differential loading of the Ago2-complex in comparison to the overall content of miRNAs in two DLBCL cell lines and their EBV-converted counterparts. In all cell lines, the Ago2-load was different from the overall expression of miRNAs. In addition, the loading of the Ago2-complex was changed upon infection with EBV. This indicates that the virus changes not only the overall content of miRNAs but also influences the expression of proteins by affecting the Ago-complexes.},
}

@article {pmid30427935,
year = {2018},
author = {Schneider, P and Greischar, MA and Birget, PLG and Repton, C and Mideo, N and Reece, SE},
title = {Adaptive plasticity in the gametocyte conversion rate of malaria parasites.},
journal = {PLoS pathogens},
volume = {14},
number = {11},
pages = {e1007371},
doi = {10.1371/journal.ppat.1007371},
pmid = {30427935},
issn = {1553-7374},
abstract = {Sexually reproducing parasites, such as malaria parasites, experience a trade-off between the allocation of resources to asexual replication and the production of sexual forms. Allocation by malaria parasites to sexual forms (the conversion rate) is variable but the evolutionary drivers of this plasticity are poorly understood. We use evolutionary theory for life histories to combine a mathematical model and experiments to reveal that parasites adjust conversion rate according to the dynamics of asexual densities in the blood of the host. Our model predicts the direction of change in conversion rates that returns the greatest fitness after perturbation of asexual densities by different doses of antimalarial drugs. The loss of a high proportion of asexuals is predicted to elicit increased conversion (terminal investment), while smaller losses are managed by reducing conversion (reproductive restraint) to facilitate within-host survival and future transmission. This non-linear pattern of allocation is consistent with adaptive reproductive strategies observed in multicellular organisms. We then empirically estimate conversion rates of the rodent malaria parasite Plasmodium chabaudi in response to the killing of asexual stages by different doses of antimalarial drugs and forecast the short-term fitness consequences of these responses. Our data reveal the predicted non-linear pattern, and this is further supported by analyses of previous experiments that perturb asexual stage densities using drugs or within-host competition, across multiple parasite genotypes. Whilst conversion rates, across all datasets, are most strongly influenced by changes in asexual density, parasites also modulate conversion according to the availability of red blood cell resources. In summary, increasing conversion maximises short-term transmission and reducing conversion facilitates in-host survival and thus, future transmission. Understanding patterns of parasite allocation to reproduction matters because within-host replication is responsible for disease symptoms and between-host transmission determines disease spread.},
}

@article {pmid30423096,
year = {2018},
author = {García-Jiménez, B and García, JL and Nogales, J},
title = {FLYCOP: metabolic modeling-based analysis and engineering microbial communities.},
journal = {Bioinformatics (Oxford, England)},
volume = {34},
number = {17},
pages = {i954-i963},
doi = {10.1093/bioinformatics/bty561},
pmid = {30423096},
issn = {1367-4811},
abstract = {Motivation: Synthetic microbial communities begin to be considered as promising multicellular biocatalysts having a large potential to replace engineered single strains in biotechnology applications, in pharmaceutical, chemical and living architecture sectors. In contrast to single strain engineering, the effective and high-throughput analysis and engineering of microbial consortia face the lack of knowledge, tools and well-defined workflows. This manuscript contributes to fill this important gap with a framework, called FLYCOP (FLexible sYnthetic Consortium OPtimization), which contributes to microbial consortia modeling and engineering, while improving the knowledge about how these communities work. FLYCOP selects the best consortium configuration to optimize a given goal, among multiple and diverse configurations, in a flexible way, taking temporal changes in metabolite concentrations into account.

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.

Code reproducing the study cases described in this manuscript are available on-line: https://github.com/beatrizgj/FLYCOP.

Supplementary information: Supplementary data are available at Bioinformatics online.},
}

@article {pmid30410727,
year = {2018},
author = {Morris, JJ},
title = {What is the hologenome concept of evolution?.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {},
doi = {10.12688/f1000research.14385.1},
pmid = {30410727},
issn = {2046-1402},
abstract = {All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host-microbiome ecosystem as a "holobiont". 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 "hologenome", or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.},
}

@article {pmid30410109,
year = {2018},
author = {Pönisch, W and Eckenrode, KB and Alzurqa, K and Nasrollahi, H and Weber, C and Zaburdaev, V and Biais, N},
title = {Pili mediated intercellular forces shape heterogeneous bacterial microcolonies prior to multicellular differentiation.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16567},
doi = {10.1038/s41598-018-34754-4},
pmid = {30410109},
issn = {2045-2322},
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},
doi = {10.1073/pnas.1815912115},
pmid = {30404915},
issn = {1091-6490},
abstract = {A hallmark of biological systems is that particular functions and outcomes are realized in specific contexts, such as when particular signals are received. One mechanism for mediating specificity is described by Fisher's "lock and key" metaphor, exemplified by enzymes that bind selectively to a particular substrate via specific finely tuned interactions. Another mechanism, more prevalent in multicellular organisms, relies on multivalent weak cooperative interactions. Its importance has recently been illustrated by the recognition that liquid-liquid phase transitions underlie the formation of membraneless condensates that perform specific cellular functions. Based on computer simulations of an evolutionary model, we report that the latter mechanism likely became evolutionarily prominent when a large number of tasks had to be performed specifically for organisms to function properly. We find that the emergence of weak cooperative interactions for mediating specificity results in organisms that can evolve to accomplish new tasks with fewer, and likely less lethal, mutations. We argue that this makes the system more capable of undergoing evolutionary changes robustly, and thus this mechanism has been repeatedly positively selected in increasingly complex organisms. Specificity mediated by weak cooperative interactions results in some useful cross-reactivity for related tasks, but at the same time increases susceptibility to misregulation that might lead to pathologies.},
}

@article {pmid30404807,
year = {2018},
author = {Palmer, WH and Joosten, J and Overheul, GJ and Jansen, PW and Vermeulen, M and Obbard, DJ and Van Rij, RP},
title = {Induction and suppression of NF-κB signalling by a DNA virus of Drosophila.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.01443-18},
pmid = {30404807},
issn = {1098-5514},
abstract = {Interactions between the insect immune system and RNA viruses have been extensively studied in Drosophila, where RNA interference, NF-κB and JAK-STAT pathways underlie antiviral immunity. In response to RNA interference, insect viruses have convergently evolved suppressors of this pathway that act by diverse mechanisms to permit viral replication. However, interactions between the insect immune system and DNA viruses have received less attention, primarily because few Drosophila-infecting DNA virus isolates are available. Here, we use a recently-isolated DNA virus of Drosophila melanogaster, Kallithea virus (family Nudiviridae), to probe known antiviral immune responses and virus evasion tactics in the context of DNA virus infection. We find that fly mutants for RNA interference and Immune deficiency (Imd), but not Toll, pathways are more susceptible to Kallithea virus infection. We identify the Kallithea virus-encoded protein gp83 as a potent inhibitor of Toll signalling, suggesting that Toll mediates antiviral defense against Kallithea virus infection, but that it is suppressed by the virus. We find that Kallithea virus gp83 inhibits Toll signalling through the regulation of NF-κB transcription factors. Furthermore, we find that gp83 of the closely related Drosophila innubila nudivirus (DiNV) suppresses D. melanogaster Toll signalling, suggesting an evolutionary conserved function of Toll in defense against DNA viruses. Together, these results provide a broad description of known antiviral pathways in the context of DNA virus infection and identify the first Toll pathway inhibitor in a Drosophila virus, extending the known diversity of insect virus-encoded immune inhibitors.IMPORTANCE Co-evolution of multicellular organisms and their natural viruses may lead to an intricate relationship in which host survival requires effective immunity, and virus survival depends on evasion of such responses. Insect antiviral immunity, and reciprocal virus immune suppression tactics, have been well-studied in Drosophila melanogaster, primarily during RNA, but not DNA, virus infection. Therefore, we describe interactions between a recently-isolated Drosophila DNA virus (Kallithea virus - KV) and immune processes known to control RNA viruses, such as RNAi and Imd pathways. We find that KV suppresses the Toll pathway, and identify gp83 as a KV-encoded protein that underlies this suppression. This immunosuppressive ability is conserved in another nudivirus, suggesting the Toll pathway has conserved antiviral activity against DNA nudiviruses, which have evolved suppressors in response. Together, these results indicate that DNA viruses induce and suppress NF-κB responses, and advance the application of KV as a model to study insect immunity.},
}

@article {pmid30396330,
year = {2018},
author = {Joo, S and Wang, MH and Lui, G and Lee, J and Barnas, A and Kim, E and Sudek, S and Worden, AZ and Lee, JH},
title = {Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida.},
journal = {BMC biology},
volume = {16},
number = {1},
pages = {136},
doi = {10.1186/s12915-018-0605-5},
pmid = {30396330},
issn = {1741-7007},
support = {Discovery Grant 418471-12//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada/ ; KCRC 2016M1A8A1925345//Ministry of Education, Science and Technology/ ; 0843119//Division of Integrative Organismal Systems/ ; 0843506//Division of Integrative Organismal Systems/ ; GBMF 3788//Gordon and Betty Moore Foundation/ ; CAREER-1453639//Directorate for Biological Sciences/ ; },
abstract = {BACKGROUND: Complex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Homeobox TFs in the TALE superclass are deeply embedded in the gene regulatory networks that orchestrate embryogenesis. Knotted-like homeobox (KNOX) TFs, homologous to animal MEIS, have been found to drive the haploid-to-diploid transition in both unicellular green algae and land plants via heterodimerization with other TALE superclass TFs, demonstrating remarkable functional conservation of a developmental TF across lineages that diverged one billion years ago. Here, we sought to delineate whether TALE-TALE heterodimerization is ancestral to eukaryotes.

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.

CONCLUSIONS: Our study indicates that the TF dyads consisting of KNOX/MEIS and PBC-containing TALEs must have evolved early in eukaryotic evolution. Based on our results, we hypothesize that in early eukaryotes, the TALE heterodimeric configuration provided transcription-on switches via dimerization-dependent subcellular localization, ensuring execution of the haploid-to-diploid transition only when the gamete fusion is correctly executed between appropriate partner gametes. The TALE switch then diversified in the several lineages that engage in a complex multicellular organization.},
}

@article {pmid30395805,
year = {2018},
author = {Ten Tusscher, K},
title = {Of mice and plants: Comparative developmental systems biology.},
journal = {Developmental biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ydbio.2018.10.024},
pmid = {30395805},
issn = {1095-564X},
abstract = {Multicellular animals and plants represent independent evolutionary experiments with complex multicellular bodyplans. Differences in their life history, a mobile versus sessile lifestyle, and predominant embryonic versus postembryonic development, have led to the evolution of highly different body plans. However, also many intriguing parallels exist. Extension of the vertebrate body axis and its segmentation into somites bears striking resemblance to plant root growth and the concomittant prepatterning of lateral root competent sites. Likewise, plant shoot phyllotaxis displays similarities with vertebrate limb and digit patterning. Additionally, both plants and animals use complex signalling systems combining systemic and local signals to fine tune and coordinate organ growth across their body. Identification of these striking examples of convergent evolution provides support for the existence of general design principles: the idea that for particular patterning demands, evolution is likely to arrive at highly similar developmental patterning mechanisms. Furthermore, focussing on these parallels may aid in identifying core mechanistic principles, often obscured by the highly complex nature of multiscale patterning processes.},
}

@article {pmid30389796,
year = {2018},
author = {Bull, JK and Flynn, JM and Chain, FJJ and Cristescu, ME},
title = {Fitness and Genomic Consequences of Chronic Exposure to Low Levels of Copper and Nickel in Daphnia pulex Mutation Accumulation Lines.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1534/g3.118.200797},
pmid = {30389796},
issn = {2160-1836},
abstract = {In at least some unicellular organisms, mutation rates are temporarily raised upon exposure to environmental stress, potentially contributing to the evolutionary response to stress. Whether this is true for multicellular organisms, however, has received little attention. This study investigated the effects of chronic mild stress, in the form of low-level copper and nickel exposure, on mutational processes in Daphnia pulex using a combination of mutation accumulation, whole genome sequencing and life-history assays. After over 100 generations of mutation accumulation, we found no effects of metal exposure on the rates of single nucleotide mutations and of loss of heterozygosity events, the two mutation classes that occurred in sufficient numbers to allow statistical analysis. Similarly, rates of decline in fitness, as measured by intrinsic rate of population increase and of body size at first reproduction, were negligibly affected by metal exposure. We can reject the possibility that Daphnia were insufficiently stressed to invoke genetic responses as we have previously shown rates of large-scale deletions and duplications are elevated under metal exposure in this experiment. Overall, the mutation accumulation lines did not significantly depart from initial values for phenotypic traits measured, indicating the lineage used was broadly mutationally robust. Taken together, these results indicate that the mutagenic effects of chronic low-level exposure to these metals are restricted to certain mutation classes and that fitness consequences are likely minor and therefore unlikely to be relevant in determining the evolutionary responses of populations exposed to these stressors.},
}

@article {pmid30386324,
year = {2018},
author = {Yap, GS and Gause, WC},
title = {Helminth Infections Induce Tissue Tolerance Mitigating Immunopathology but Enhancing Microbial Pathogen Susceptibility.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2135},
doi = {10.3389/fimmu.2018.02135},
pmid = {30386324},
issn = {1664-3224},
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 = {2018},
author = {Darris, C and Revert, F and Revert-Ros, F and Gozalbo-Rovira, R and Feigley, A and Fidler, A and Lopez-Pascual, E and Saus, J and Hudson, B},
title = {Unicellular ancestry and mechanisms of diversification of Goodpasture-antigen binding protein.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA118.006225},
pmid = {30377252},
issn = {1083-351X},
abstract = {The emergence of the basement membrane (BM), a specialized form of extracellular matrix, was essential in the unicellular transition to multicellularity. Yet, the mechanism is unknown. Goodpasture antigen-binding protein (GPBP), aBM protein, was uniquely poised to play diverse roles in this transition owing to its multiple isoforms (GPBP-1, -2 and -3) with varied intracellular and extracellular functions (ceramide trafficker and protein kinase). We sought to determine the evolutionary origin of GPBP isoforms. Our findings reveal the presence of GPBP in unicellular protists, with GPBP-2 as the most ancient isoform.In vertebrates GPBP-1 assumed extracellular function which is further enhanced by membrane bound GPBP-3 in mammalians, while GPBP-2 retained intracellular function. Moreover, GPBP-2 possesses a dual intracellular/extracellular functionin cnidarians, an early non-bilaterian group. We conclude that GPBP functioning both inside and outside the cell was of fundamental importance for the evolutionary transition to animal multicellularity and tissue evolution.},
}

@article {pmid30368592,
year = {2018},
author = {Niklas, KJ and Wayne, R and Benítez, M and Newman, SA},
title = {Polarity, planes of cell division, and the evolution of plant multicellularity.},
journal = {Protoplasma},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00709-018-1325-y},
pmid = {30368592},
issn = {1615-6102},
abstract = {Organisms as diverse as bacteria, fungi, plants, and animals manifest a property called "polarity." 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., "tip" growth in pollen tubes and fungal hyphae). The evolution of complex multicellular meristematic polarity required a third reorientation of axiation. These transitions show that polarity and the orientation of the future plane(s) of cell division are dyadic dynamical patterning modules that were critical for multicellular eukaryotic organisms.},
}

@article {pmid30362942,
year = {2018},
author = {Castiglione, GM and Chang, BS},
title = {Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.35957},
pmid = {30362942},
issn = {2050-084X},
support = {Discovery grant//Natural Sciences and Engineering Research Council of Canada/International ; },
abstract = {Trade-offs between protein stability and activity can restrict access to evolutionary trajectories, but widespread epistasis may facilitate indirect routes to adaptation. This may be enhanced by natural environmental variation, but in multicellular organisms this process is poorly understood. We investigated a paradoxical trajectory taken during the evolution of tetrapod dim-light vision, where in the rod visual pigment rhodopsin, E122 was fixed 350 million years ago, a residue associated with increased active-state (MII) stability but greatly diminished rod photosensitivity. Here, we demonstrate that high MII stability could have likely evolved without E122, but instead, selection appears to have entrenched E122 in tetrapods via epistatic interactions with nearby coevolving sites. In fishes by contrast, selection may have exploited these epistatic effects to explore alternative trajectories, but via indirect routes with low MII stability. Our results suggest that within tetrapods, E122 and high MII stability cannot be sacrificed-not even for improvements to rod photosensitivity.},
}

@article {pmid30357728,
year = {2018},
author = {Fitzgerald, RS},
title = {O2/CO2: Biological Detection to Homeostatic Control.},
journal = {Advances in experimental medicine and biology},
volume = {1071},
number = {},
pages = {1-12},
doi = {10.1007/978-3-319-91137-3_1},
pmid = {30357728},
issn = {0065-2598},
abstract = {Oxygen (O2) and Carbon Dioxide (CO2) are the two gases to be detected and controlled. Of interest might be a query of the evolutionary origin of each. From the cooling of the Big Bang (~13.8 Billion Years Ago [BYA]) came a quark-gluon plasma from which protons and neutrons emerged, producing H, He, Li. As H and He collapsed into the first stars at ~13.3 BYA carbon and monatomic oxygen were generated. Some 3 billion years ago greater amounts of diatomic oxygen (O2) were provided by earth's photosynthesizing bacteria until earth's atmosphere had sufficient amounts to sustain the life processes of multicellular animals, and finally higher vertebrates. Origin of CO2 is somewhat unclear, though it probably came from the erupting early volcanoes. Photosynthesis produced sugars with O2 a waste product. Animal life took sugars and O2 needed for life. Clearly, animal detection and control of each was critical. Many chapters involving great heroes describe phases involved in detecting each, both in the CNS and in peripheral detectors. The carotid body (CB) has played a crucial role in the detection of each. What reflex responses the stimulated CB generates, and the mechanisms as to how it does so have been a fascinating story over the last 1.5 centuries, but principally over the last 50 years. Explorations to detect these gases have proceeded from the organismal/system/ organ levels down to the sub-cell and genetic levels.},
}

@article {pmid30348074,
year = {2018},
author = {Kin, K and Forbes, G and Cassidy, A and Schaap, P},
title = {Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {764},
doi = {10.1186/s12864-018-5146-3},
pmid = {30348074},
issn = {1471-2164},
support = {742288//H2020 European Research Council/ ; ALTF 295-2015//European Molecular Biology Organization/ ; H28-1002//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: A major hallmark of multicellular evolution is increasing complexity by the evolution of new specialized cell types. During Dictyostelid evolution novel specialization occurred within taxon group 4. We here aim to retrace the nature and ancestry of the novel "cup" cells by comparing their transcriptome to that of other cell types.

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.

CONCLUSIONS: This study reveals the unique transcriptomes of the mature cup, stalk and spore cells of D. discoideum and provides insight into the ancestry of cup cells and roles in signalling that were not previously realized. The data presented in this study will serve as an important resource for future studies into the regulation and evolution of cell type specialization.},
}

@article {pmid30336184,
year = {2018},
author = {Miller, WB and Torday, JS and Baluška, F},
title = {Biological evolution as defense of 'self'.},
journal = {Progress in biophysics and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pbiomolbio.2018.10.002},
pmid = {30336184},
issn = {1873-1732},
abstract = {Although the origin of self-referential consciousness is unknown, it can be argued that the instantiation of self-reference was the commencement 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 = {},
number = {},
pages = {},
doi = {10.1093/molbev/msy193},
pmid = {30325443},
issn = {1537-1719},
abstract = {Adenosine deaminases (ADAs) play a pivotal role in regulating the level of adenosine, an important signaling molecule that controls a variety of cellular responses. Two distinct ADAs, ADA1 and adenosine deaminase growth factor (ADGF aka ADA2), are known. Cytoplasmic ADA1 plays a key role in purine metabolism and is widely distributed from prokaryotes to mammals. On the other hand, secreted ADGF/ADA2 is a cell-signaling protein that was thought to be present only in multicellular organisms. Here, we discovered a bacterial homologue of ADGF/ADA2. Bacterial and eukaryotic ADGF/ADA2 possess the dimerization and PRB domains characteristic for the family, have nearly identical catalytic sites, and show similar catalytic characteristics. Most surprisingly, the bacterial enzyme has a signal sequence similar to that of eukaryotic ADGF/ADA2 and is specifically secreted into the extracellular space, where it may potentially control the level of extracellular adenosine. This finding provides the first example of evolution of an extracellular eukaryotic signaling protein from a secreted bacterial analogue with identical activity and suggests a potential role of ADGF/ADA2 in bacterial communication.},
}

@article {pmid30318349,
year = {2018},
author = {Bråte, J and Neumann, RS and Fromm, B and Haraldsen, AAB and Tarver, JE and Suga, H and Donoghue, PCJ and Peterson, KJ and Ruiz-Trillo, I and Grini, PE and Shalchian-Tabrizi, K},
title = {Unicellular Origin of the Animal MicroRNA Machinery.},
journal = {Current biology : CB},
volume = {28},
number = {20},
pages = {3288-3295.e5},
doi = {10.1016/j.cub.2018.08.018},
pmid = {30318349},
issn = {1879-0445},
abstract = {The emergence of multicellular animals was associated with an increase in phenotypic complexity and with the acquisition of spatial cell differentiation and embryonic development. Paradoxically, this phenotypic transition was not paralleled by major changes in the underlying developmental toolkit and regulatory networks. In fact, most of these systems are ancient, established already in the unicellular ancestors of animals [1-5]. In contrast, the Microprocessor protein machinery, which is essential for microRNA (miRNA) biogenesis in animals, as well as the miRNA genes themselves produced by this Microprocessor, have not been identified outside of the animal kingdom [6]. Hence, the Microprocessor, with the key proteins Pasha and Drosha, is regarded as an animal innovation [7-9]. Here, we challenge this evolutionary scenario by investigating unicellular sister lineages of animals through genomic and transcriptomic analyses. We identify in Ichthyosporea both Drosha and Pasha (DGCR8 in vertebrates), indicating that the Microprocessor complex evolved long before the last common ancestor of animals, consistent with a pre-metazoan origin of most of the animal developmental gene elements. Through small RNA sequencing, we also discovered expressed bona fide miRNA genes in several species of the ichthyosporeans harboring the Microprocessor. A deep, pre-metazoan origin of the Microprocessor and miRNAs comply with a view that the origin of multicellular animals was not directly linked to the innovation of these key regulatory components.},
}

@article {pmid30309963,
year = {2018},
author = {Armon, S and Bull, MS and Aranda-Diaz, A and Prakash, M},
title = {Ultrafast epithelial contractions provide insights into contraction speed limits and tissue integrity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {115},
number = {44},
pages = {E10333-E10341},
doi = {10.1073/pnas.1802934115},
pmid = {30309963},
issn = {1091-6490},
abstract = {By definition of multicellularity, all animals need to keep their cells attached and intact, despite internal and external forces. Cohesion between epithelial cells provides this key feature. To better understand fundamental limits of this cohesion, we study the epithelium mechanics of an ultrathin (∼25 μm) primitive marine animal Trichoplax adhaerens, composed essentially of two flat epithelial layers. With no known extracellular matrix and no nerves or muscles, T. adhaerens has been claimed to be the "simplest known living animal," 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 ("active cohesion"), 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 "Explosion".},
journal = {Integrative and comparative biology},
volume = {58},
number = {4},
pages = {605-622},
doi = {10.1093/icb/icy088},
pmid = {30295813},
issn = {1557-7023},
abstract = {Animals originated and evolved during a unique time in Earth history-the Neoproterozoic Era. This paper aims to discuss (1) when landmark events in early animal evolution occurred, and (2) the environmental context of these evolutionary milestones, and how such factors may have affected ecosystems and body plans. With respect to timing, molecular clock studies-utilizing a diversity of methodologies-agree that animal multicellularity had arisen by ∼800 million years ago (Ma) (Tonian period), the bilaterian body plan by ∼650 Ma (Cryogenian), and divergences between sister phyla occurred ∼560-540 Ma (late Ediacaran). Most purported Tonian and Cryogenian animal body fossils are unlikely to be correctly identified, but independent support for the presence of pre-Ediacaran animals is recorded by organic geochemical biomarkers produced by demosponges. This view of animal origins contrasts with data from the fossil record, and the taphonomic question of why animals were not preserved (if present) remains unresolved. Neoproterozoic environments demanding small, thin, body plans, and lower abundance/rarity in populations may have played a role. Considering environmental conditions, geochemical data suggest that animals evolved in a relatively low-oxygen ocean. Here, we present new analyses of sedimentary total organic carbon contents in shales suggesting that the Neoproterozoic ocean may also have had lower primary productivity-or at least lower quantities of organic carbon reaching the seafloor-compared with the Phanerozoic. Indeed, recent modeling efforts suggest that low primary productivity is an expected corollary of a low-O2 world. Combined with an inability to inhabit productive regions in a low-O2 ocean, earliest animal communities would likely have been more food limited than generally appreciated, impacting both ecosystem structure and organismal behavior. In light of this, we propose the "fire triangle" metaphor for environmental influences on early animal evolution. Moving toward consideration of all environmental aspects of the Cambrian radiation (fuel, heat, and oxidant) will ultimately lead to a more holistic view of the event.},
}

@article {pmid30288746,
year = {2018},
author = {Stiller, JW and Yang, C and Collén, J and Kowalczyk, N and Thompson, BE},
title = {Evolution and expression of core SWI/SNF genes in red algae.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.12795},
pmid = {30288746},
issn = {1529-8817},
support = {0741907//NSF Research Collaboration Network/ ; DE-AC02-05CH11231//U.S. Department of Energy Joint Genome Institute/ ; },
abstract = {Red algae are the oldest identifiable multicellular eukaryotes, with a fossil record dating back more than a billion years. During that time two major rhodophyte lineages, bangiophytes and florideophytes, have evolved varied levels of morphological complexity. These two groups are distinguished, in part, by different patterns of multicellular development, with florideophytes exhibiting a far greater diversity of morphologies. Interestingly, during their long evolutionary history, there is no record of a rhodophyte achieving the kinds of cellular and tissue-specific differentiation present in other multicellular algal lineages. To date, the genetic underpinnings of unique aspects of red algal development are largely unexplored; however, they must reflect the complements and patterns of expression of key regulatory genes. Here we report comparative evolutionary and gene expression analyses of core subunits of the SWI/SNF chromatin-remodeling complex, which is implicated in cell differentiation and developmental regulation in more well studied multicellular groups. Our results suggest that a single, canonical SWI/SNF complex was present in the rhodophyte ancestor, with gene duplications and evolutionary diversification of SWI/SNF subunits accompanying the evolution of multicellularity in the common ancestor of bangiophytes and florideophytes. Differences in how SWI/SNF chromatin remodeling evolved subsequently, in particular gene losses and more rapid divergence of SWI3 and SNF5 in bangiophytes, could help to explain why they exhibit a more limited range of morphological complexity than their florideophyte cousins.},
}

@article {pmid30283698,
year = {2018},
author = {Godwin, JL and Spurgin, LG and Michalczyk, Ł and Martin, OY and Lumley, AJ and Chapman, T and Gage, MJG},
title = {Lineages evolved under stronger sexual selection show superior ability to invade conspecific competitor populations.},
journal = {Evolution letters},
volume = {2},
number = {5},
pages = {511-523},
doi = {10.1002/evl3.80},
pmid = {30283698},
issn = {2056-3744},
abstract = {Despite limitations on offspring production, almost all multicellular species use sex to reproduce. Sex gives rise to sexual selection, a widespread force operating through competition and choice within reproduction, however, it remains unclear whether sexual selection is beneficial for total lineage fitness, or if it acts as a constraint. Sexual selection could be a positive force because of selection on improved individual condition and purging of mutation load, summing into lineages with superior fitness. On the other hand, sexual selection could negate potential net fitness through the actions of sexual conflict, or because of tensions between investment in sexually selected and naturally selected traits. Here, we explore these ideas using a multigenerational invasion challenge to measure consequences of sexual selection for the overall net fitness of a lineage. After applying experimental evolution under strong versus weak regimes of sexual selection for 77 generations with the flour beetle Tribolium castaneum, we measured the overall ability of introductions from either regime to invade into conspecific competitor populations across eight generations. Results showed that populations from stronger sexual selection backgrounds had superior net fitness, invading more rapidly and completely than counterparts from weak sexual selection backgrounds. Despite comprising only 10% of each population at the start of the invasion experiment, colonizations from strong sexual selection histories eventually achieved near-total introgression, almost completely eliminating the original competitor genotype. Population genetic simulations using the design and parameters of our experiment indicate that this invasion superiority could be explained if strong sexual selection had improved both juvenile and adult fitness, in both sexes. Using a combination of empirical and modeling approaches, our findings therefore reveal positive and wide-reaching impacts of sexual selection for net population fitness when facing the broad challenge of invading competitor populations across multiple generations.},
}

@article {pmid30281390,
year = {2018},
author = {Booth, DS and Szmidt-Middleton, H and King, N},
title = {Choanoflagellate transfection illuminates their cell biology and the ancestry of animal septins.},
journal = {Molecular biology of the cell},
volume = {},
number = {},
pages = {mbcE18080514},
doi = {10.1091/mbc.E18-08-0514},
pmid = {30281390},
issn = {1939-4586},
abstract = {As the closest living relatives of animals, choanoflagellates offer unique insights into animal origins and core mechanisms underlying animal cell biology. However, unlike traditional model organisms, such as yeast, flies and worms, choanoflagellates have been refractory to DNA delivery methods for expressing foreign genes. Here we report the establishment of a robust method for expressing transgenes in the choanoflagellate Salpingoeca rosetta, overcoming barriers that have previously hampered DNA delivery and expression. To demonstrate how this method accelerates the study of S. rosetta cell biology, we engineered a panel of fluorescent protein markers that illuminate key features of choanoflagellate cells. We then investigated the localization of choanoflagellate septins, a family of GTP-binding cytoskeletal proteins that are hypothesized to regulate multicellular rosette development in S. rosetta. Fluorescently tagged septins localized to the basal pole of S. rosetta single cells and rosettes in a pattern resembling septin localization in animal epithelia. The establishment of transfection in S. rosetta and its application to the study of septins represent critical advances in the growth of S. rosetta as an experimental model for investigating choanoflagellate cell biology, core mechanisms underlying animal cell biology, and the origin of animals.},
}

@article {pmid30280251,
year = {2018},
author = {Zhou, W and Gao, B and Zhu, S},
title = {Did cis- and trans-defensins derive from a common ancestor?.},
journal = {Immunogenetics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00251-018-1086-y},
pmid = {30280251},
issn = {1432-1211},
support = {31570773//National Natural Science Foundation of China/ ; 31870766//National Natural Science Foundation of China/ ; },
abstract = {Defensins are small, cysteine-rich, cationic antimicrobial peptides, serving as effectors of the innate immune system and modulators of the adaptive immune system. They extensively exist in multicellular organisms and are divided into cis and trans according to their disulfide bridge connectivity patterns. It has been proposed that these two types of defensins convergently originated from different ancestors. Here, we report the discovery of a structural signature involved in the formation of the cysteine-stabilized α-helix/β-sheet (CSαβ) fold of the cis-defensins in some trans-β-defensins, with only one amino acid indel (CXC vs. CC. C, cysteine; X, any amino acid). The indel of the X residue in the structural signature provides a possible explanation as to why cis- and trans-defensins possess different folds and connectivity patterns of disulfide bridges formed in evolution. Although our attempt to convert the structure type of a present-day trans-defensin with the X residue deleted was unsuccessful due to the low solubility of the synthetic peptide, a combination of data from structural signature, function, and phylogenetic distribution suggests that these defensins may have descended from a common ancestor. In this evolutionary scenario, we propose that a progenitor cis-scaffold might gradually evolve into a trans-defensin after deleting the X residue in specific lineages. This proposal adds a new dimension to more deeply studying the evolutionary relationship of defensins with different folds and of other distantly related proteins.},
}

@article {pmid30271390,
year = {2018},
author = {Teng, Z and Zhang, Y and Zhang, W and Pan, H and Xu, J and Huang, H and Xiao, T and Wu, LF},
title = {Diversity and Characterization of Multicellular Magnetotactic Prokaryotes From Coral Reef Habitats of the Paracel Islands, South China Sea.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2135},
doi = {10.3389/fmicb.2018.02135},
pmid = {30271390},
issn = {1664-302X},
abstract = {While multicellular magnetotactic prokaryotes (MMPs) are ubiquitous in marine environments, the diversity of MMPs in sediments of coral reef ecosystems has rarely been reported. In this study, we made an investigation on the diversity and characteristics of MMPs in sediments at 11 stations in coral reef habitats of the Paracel Islands. The results showed that MMPs were present at nine stations, with spherical mulberry-like MMPs (s-MMPs) found at all stations and ellipsoidal pineapple-like MMPs (e-MMPs) found at seven stations. The maximum abundance of MMPs was 6 ind./cm3. Phylogenetic analysis revealed the presence of one e-MMP species and five s-MMP species including two species of a new genus. The results indicate that coral reef habitats of the Paracel Islands have a high diversity of MMPs that bio-mineralize multiple intracellular chains of iron crystals and play important role in iron cycling in such oligotrophic environment. These observations provide new perspective of the diversity of MMPs in general and expand knowledge of the occurrence of MMPs in coral reef habitats.},
}

@article {pmid30270425,
year = {2018},
author = {Joshi, J and Guttal, V},
title = {Demographic noise and cost of greenbeard can facilitate greenbeard cooperation.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1111/evo.13615},
pmid = {30270425},
issn = {1558-5646},
support = {DBT-IISc partnership program//Department of Biotechnology , Ministry of Science and Technology/ ; DST-FIST//Department of Science and Technology, Ministry of Science and Technology/ ; Mathematical Biology Phase II (SR/S4/MS:799/12)//Department of Science and Technology, Ministry of Science and Technology/ ; ICTS/Prog-PGE2018/03//International Centre for Theoretical Sciences/ ; },
abstract = {Cooperation among organisms, where cooperators suffer a personal cost to benefit others, is ubiquitous in nature. Greenbeard is a key mechanism for the evolution of cooperation, where a single gene or a set of linked genes codes for both cooperation and a phenotypic tag (metaphorically called "green beard"). Greenbeard cooperation is typically thought to decline over time since defectors can also evolve the tag. However, models of tag-based cooperation typically ignore two key realistic features: populations are finite, and that phenotypic tags can be costly. We develop an analytical model for coevolutionary dynamics of two evolvable traits in finite populations with mutations: costly cooperation and a costly tag. We show that an interplay of demographic noise and cost of the tag can induce coevolutionary cycling, where the evolving population does not reach a steady state but spontaneously switches between cooperative tag-carrying and noncooperative tagless states. Such dynamics allows the tag to repeatedly reappear even after it is invaded by defectors. Thus, we highlight the surprising possibility that the cost of the tag, together with demographic noise, can facilitate the evolution of greenbeard cooperation. We discuss implications of these findings in the context of the evolution of quorum sensing and multicellularity.},
}

@article {pmid30254228,
year = {2018},
author = {Chen, X and Köllner, TG and Shaulsky, G and Jia, Q and Dickschat, JS and Gershenzon, J and Chen, F},
title = {Diversity and Functional Evolution of Terpene Synthases in Dictyostelid Social Amoebae.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {14361},
doi = {10.1038/s41598-018-32639-0},
pmid = {30254228},
issn = {2045-2322},
abstract = {Dictyostelids, or social amoebae, have a unique life style in forming multicellular fruiting bodies from unicellular amoeboids upon starvation. Recently, dictyostelids were found to contain terpene synthase (TPS) genes, a gene type of secondary metabolism previously known to occur only in plants, fungi and bacteria. Here we report an evolutionary functional study of dictyostelid TPS genes. The number of TPS genes in six species of dictyostelids examined ranges from 1 to 19; and the model species Dictyostelium purpureum contains 12 genes. Using in vitro enzyme assays, the 12 TPS genes from D. purpureum were shown to encode functional enzymes with distinct product profiles. The expression of the 12 TPS genes in D. purpureum is developmentally regulated. During multicellular development, D. purpureum releases a mixture of volatile terpenes dominated by sesquiterpenes that are the in vitro products of a subset of the 12 TPS genes. The quality and quantity of the terpenes released from D. purpureum, however, bear little resemblance to those of D. discoideum, a closely related dictyostelid. Despite these variations, the conserved clade of dictyostelid TPSs, which have an evolutionary distance of more than 600 million years, has the same biochemical function, catalyzing the formation of a sesquiterpene protoillud-7-ene. Taken together, our results indicate that the dynamic evolution of dictyostelid TPS genes includes both purifying selection of an orthologous group and species-specific expansion with functional divergence. Consequently, the terpenes produced by these TPSs most likely have conserved as well as species-adaptive biological functions as chemical languages in dictyostelids.},
}

@article {pmid30231028,
year = {2018},
author = {Lau, AYT and Cheng, X and Cheng, CK and Nong, W and Cheung, MK and Chan, RH and Hui, JHL and Kwan, HS},
title = {Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0198234},
doi = {10.1371/journal.pone.0198234},
pmid = {30231028},
issn = {1932-6203},
abstract = {Coprinopsis cinerea is a model mushroom particularly suited for the study of fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) have been extensively studied in animals and plants for their essential roles in post-transcriptional regulation of gene expression, miRNAs in fungi are less well characterized and their potential roles in controlling mushroom development remain unknown. To identify miRNA-like RNAs (milRNAs) in C. cinerea and explore their expression patterns during the early developmental transition of mushroom development, small RNA libraries of vegetative mycelium and primordium were generated and putative milRNA candidates were identified following the standards of miRNA prediction in animals and plants. Two out of 22 novel predicted milRNAs, cci-milR-12c and cci-milR-13e-5p, were validated by northern blot and stem-loop reverse transcription real-time PCR. Cci-milR-12c was differentially expressed whereas the expression levels of cci-milR-13e-5p were similar in the two developmental stages. Target prediction of the validated milRNAs resulted in genes associated with fruiting body development, including pheromone, hydrophobin, cytochrome P450, and protein kinase. Essential genes for miRNA biogenesis, including three coding for Dicer-like (DCL), one for Argonaute (AGO), one for AGO-like and one for quelling deficient-2 (QDE-2) proteins, were also identified in the C. cinerea genome. Phylogenetic analysis showed that the DCL and AGO proteins of C. cinerea were more closely related to those in other basidiomycetes and ascomycetes than to those in animals and plants. Taken together, our findings provided the first evidence for milRNAs in the model mushroom and their potential roles in regulating fruiting body development. New information on the evolutionary relationship of milRNA biogenesis proteins across kingdoms has also provided new insights for guiding further functional and evolutionary studies of miRNAs.},
}

@article {pmid30225080,
year = {2018},
author = {Herron, MD and Ratcliff, WC and Boswell, J and Rosenzweig, F},
title = {Genetics of a de novo origin of undifferentiated multicellularity.},
journal = {Royal Society open science},
volume = {5},
number = {8},
pages = {180912},
doi = {10.1098/rsos.180912},
pmid = {30225080},
issn = {2054-5703},
abstract = {The evolution of multicellularity was a major transition in evolution and set the stage for unprecedented increases in complexity, especially in land plants and animals. Here, we explore the genetics underlying a de novo origin of multicellularity in a microbial evolution experiment carried out on the green alga Chlamydomonas reinhardtii. We show that large-scale changes in gene expression underlie the transition to a multicellular life cycle. Among these, changes to genes involved in cell cycle and reproductive processes were overrepresented, as were changes to C. reinhardtii-specific and volvocine-specific genes. These results suggest that the genetic basis for the experimental evolution of multicellularity in C. reinhardtii has both lineage-specific and shared features, and that the shared features have more in common with C. reinhardtii's relatives among the volvocine algae than with other multicellular green algae or land plants.},
}

@article {pmid30220504,
year = {2018},
author = {De Clerck, O and Kao, SM and Bogaert, KA and Blomme, J and Foflonker, F and Kwantes, M and Vancaester, E and Vanderstraeten, L and Aydogdu, E and Boesger, J and Califano, G and Charrier, B and Clewes, R and Del Cortona, A and D'Hondt, S and Fernandez-Pozo, N and Gachon, CM and Hanikenne, M and Lattermann, L and Leliaert, F and Liu, X and Maggs, CA and Popper, ZA and Raven, JA and Van Bel, M and Wilhelmsson, PKI and Bhattacharya, D and Coates, JC and Rensing, SA and Van Der Straeten, D and Vardi, A and Sterck, L and Vandepoele, K and Van de Peer, Y and Wichard, T and Bothwell, JH},
title = {Insights into the Evolution of Multicellularity from the Sea Lettuce Genome.},
journal = {Current biology : CB},
volume = {28},
number = {18},
pages = {2921-2933.e5},
doi = {10.1016/j.cub.2018.08.015},
pmid = {30220504},
issn = {1879-0445},
abstract = {We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva's rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance "green tides." 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 & integrative biology},
volume = {11},
number = {3},
pages = {1-9},
doi = {10.1080/19420889.2018.1489184},
pmid = {30214674},
issn = {1942-0889},
abstract = {In the legacy of Thomas Henry Huxley, and his 'epigenetic' philosophy of biology, cells are proposed to represent a trinity of three memory-storing media: Senome, Epigenome, and Genome that together comprise a cell-wide informational architecture. Our current preferential focus on the Genome needs to be complemented by a similar focus on the Epigenome and a here proposed Senome, representing the sum of all the sensory experiences of the cognitive cell and its sensing apparatus. Only then will biology be in a position to embrace the whole complexity of the eukaryotic cell, understanding its true nature which allows the communicative assembly of cells in the form of sentient multicellular organisms.},
}

@article {pmid30212236,
year = {2018},
author = {Zhang, L and Vijg, J},
title = {Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging.},
journal = {Annual review of genetics},
volume = {52},
number = {},
pages = {397-419},
doi = {10.1146/annurev-genet-120417-031501},
pmid = {30212236},
issn = {1545-2948},
abstract = {DNA mutations as a consequence of errors during DNA damage repair, replication, or mitosis are the substrate for evolution. In multicellular organisms, mutations can occur in the germline and also in somatic tissues, where they are associated with cancer and other chronic diseases and possibly with aging. Recent advances in high-throughput sequencing have made it relatively easy to study germline de novo mutations, but in somatic cells, the vast majority of mutations are low-abundant and can be detected only in clonal lineages, such as tumors, or single cells. Here we review recent results on somatic mutations in normal human and animal tissues with a focus on their possible functional consequences.},
}

@article {pmid30177944,
year = {2018},
author = {Yruela, I and Contreras-Moreira, B and Dunker, AK and Niklas, KJ},
title = {Evolution of Protein Ductility in Duplicated Genes of Plants.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1216},
doi = {10.3389/fpls.2018.01216},
pmid = {30177944},
issn = {1664-462X},
abstract = {Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of diverse phylogenetic lineages have revealed: (1) that protein ductility increases in concert with organismic complexity, and (2) that distributions of IDPs and IDRs along the chromosomes of plant species are non-random and correlate with variations in the rates of the genetic recombination and chromosomal rearrangement. Here, we show that approximately 50% of aligned residues in paralogs across a spectrum of algae, bryophytes, monocots, and eudicots are IDRs and that a high proportion (ca. 60%) are in disordered segments greater than 30 residues. When three types of IDRs are distinguished (i.e., identical, similar and variable IDRs) we find that species with large numbers of chromosome and endoduplicated genes exhibit paralogous sequences with a higher frequency of identical IDRs, whereas species with small chromosomes numbers exhibit paralogous sequences with a higher frequency of similar and variable IDRs. These results are interpreted to indicate that genome duplication events influence the distribution of IDRs along protein sequences and likely favor the presence of identical IDRs (compared to similar IDRs or variable IDRs). We discuss the evolutionary implications of gene duplication events in the context of ductile/disordered residues and segments, their conservation, and their effects on functionality.},
}

@article {pmid30172691,
year = {2018},
author = {Olejarz, J and Kaveh, K and Veller, C and Nowak, MA},
title = {Selection for synchronized cell division in simple multicellular organisms.},
journal = {Journal of theoretical biology},
volume = {457},
number = {},
pages = {170-179},
doi = {10.1016/j.jtbi.2018.08.038},
pmid = {30172691},
issn = {1095-8541},
abstract = {The evolution of multicellularity was a major transition in the history of life on earth. Conditions under which multicellularity is favored have been studied theoretically and experimentally. But since the construction of a multicellular organism requires multiple rounds of cell division, a natural question is whether these cell divisions should be synchronous or not. We study a population model in which there compete simple multicellular organisms that grow by either synchronous or asynchronous cell divisions. We demonstrate that natural selection can act differently on synchronous and asynchronous cell division, and we offer intuition for why these phenotypes are generally not neutral variants of each other.},
}

@article {pmid30171399,
year = {2018},
author = {Liu, Y and Liu, D and Khan, AR and Liu, B and Wu, M and Huang, L and Wu, J and Song, G and Ni, H and Ying, H and Yu, H and Gan, Y},
title = {NbGIS regulates glandular trichome initiation through GA signaling in tobacco.},
journal = {Plant molecular biology},
volume = {98},
number = {1-2},
pages = {153-167},
doi = {10.1007/s11103-018-0772-3},
pmid = {30171399},
issn = {1573-5028},
support = {31570183; 31529001; 31661143004//National Natural Science Foundation of China/ ; LZ15C020001//Zhejiang Provincial Natural Science Foundation of China/ ; 2015CB150200//Major State Basic Research Development Program/ ; 2016YFD0100701//the National Key R & 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 & development/*metabolism ; Trichomes/*growth & 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.},
}

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 & development/*metabolism
Trichomes/*growth & development/*metabolism/ultrastructure

@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.},
}

Animals
Biological Evolution
Cnidaria/*parasitology
Host-Parasite Interactions
Myxozoa/genetics/*physiology
Parasites

@article {pmid30159848,
year = {2018},
author = {Chi, C and Wang, L and Lan, W and Zhao, L and Su, Y},
title = {PpV, acting via the JNK pathway, represses apoptosis during normal development of Drosophila wing.},
journal = {Apoptosis : an international journal on programmed cell death},
volume = {23},
number = {9-10},
pages = {554-562},
doi = {10.1007/s10495-018-1479-2},
pmid = {30159848},
issn = {1573-675X},
support = {201612010//Fundamental Research Funds for the Central Universities/ ; 201762003//Fundamental Research Funds for the Central Universities/ ; 201562029//Fundamental Research Funds for the Central Universities/ ; 31701274//National Natural Science Foundation of China/ ; 2017M612349//China Postdoctoral Science Foundation/ ; },
abstract = {Apoptosis is one of the main fundamental biological processes required for development of multicellular organisms. Inappropriate regulation of apoptosis can lead to severe developmental abnormalities and diseases. Therefore, the control of apoptosis, not only for its activation but also for its inhibition, is critically important during development. In contrast to the extensive studies of apoptosis induction, its inhibitory mechanisms that are even more vital in certain populations of cells actually are very far from being well understood. Here we report an inhibitory role of protein phosphatase V (PpV), a serine/threonine protein phosphatase, in controlling the apoptosis during Drosophila wing development. We observed that inhibition of ppv by RNAi in wing imaginal discs induced ectopic cell death and caspase activation, thus, resulted in a defective adult wing. Moreover, knocking-down ppv triggered the activation of c-Jun N-terminal kinase (JNK) signal, an evolutionarily conserved intracellular signaling that has been implicated to modulate the apoptotic machinery in many biological and experimental systems. Disrupting the JNK signal transduction was adequate to suppress the ppv effects for wing development. Together, we provided the evidence to demonstrate that ppv is required for normal wing development in maintaining the silence of apoptotic signal possibly through JNK pathway.},
}

@article {pmid30149856,
year = {2018},
author = {Strauss, J and Wilkinson, C and Vidilaseris, K and Harborne, SPD and Goldman, A},
title = {A Simple Strategy to Determine the Dependence of Membrane-Bound Pyrophosphatases on K+ as a Cofactor.},
journal = {Methods in enzymology},
volume = {607},
number = {},
pages = {131-156},
doi = {10.1016/bs.mie.2018.04.018},
pmid = {30149856},
issn = {1557-7988},
abstract = {Membrane-bound pyrophosphatases (mPPases) couple pyrophosphate hydrolysis to H+ and/or Na+ pumping across membranes and are found in all domains of life except for multicellular animals including humans. They are important for development and stress resistance in plants. Furthermore, mPPases play a role in virulence of human pathogens that cause severe diseases such as malaria and African sleeping sickness. Sequence analysis, functional studies, and recently solved crystal structures have contributed to the understanding of the mPPase catalytic cycle. However, several key mechanistic features remain unknown. During evolution, several subgroups of mPPases differing in their pumping specificity and cofactor dependency arose. mPPases are classified into one of five subgroups, usually by sequence analysis. However, classification based solely on sequence has been inaccurate in several instances due to our limited understanding of the molecular mechanism of mPPases. Thus, pumping specificity and cofactor dependency of mPPases require experimental confirmation. Here, we describe a simple method for the determination of K+ dependency in mPPases using a hydrolytic activity assay. By coupling these dependency studies with site-directed mutagenesis, we have begun to build a better understanding of the molecular mechanisms of mPPases. We optimized the assay for thermostable mPPases that are commonly used as model systems in our lab, but the method is equally applicable to mesophilic mPPases with minor modifications.},
}

@article {pmid30134151,
year = {2018},
author = {Stone, R and Portegys, T and Mikhailovsky, G and Alicea, B},
title = {Origins of the Embryo: Self-organization through cybernetic regulation.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biosystems.2018.08.005},
pmid = {30134151},
issn = {1872-8324},
abstract = {The construction of an embryo from a single cell precursor is a highly complex process. Evolutionary emergence of the first embryos is even more complex, and involves both a transition to multicellularity along with the establishment of developmental mechanisms. We propose that embryogenesis relies on a community of cells conforming to a regulatory model of emergent multicellularity. This model draws together multiple threads in the scientific literature, from complexity theory to cybernetics, and from thermodynamic entropy to artificial life. All of these strands come together to inform a model of goal-oriented regulation for emergent structures in early life. This is an important step in the evolution of early life, as well as the emergence of complex life in the earliest habitats. Our model, called the cybernetic embryo, allows for a systems-level view of the embryogenetic process.},
}

@article {pmid30125231,
year = {2018},
author = {Hanschen, ER and Herron, MD and Wiens, JJ and Nozaki, H and Michod, RE},
title = {Multicellularity Drives the Evolution of Sexual Traits.},
journal = {The American naturalist},
volume = {192},
number = {3},
pages = {E93-E105},
doi = {10.1086/698301},
pmid = {30125231},
issn = {1537-5323},
abstract = {From the male peacock's tail plumage to the floral displays of flowering plants, traits related to sexual reproduction are often complex and exaggerated. Why has sexual reproduction become so complicated? Why have such exaggerated sexual traits evolved? Early work posited a connection between multicellularity and sexual traits such as anisogamy (i.e., the evolution of small sperm and large eggs). Anisogamy then drives the evolution of other forms of sexual dimorphism. Yet the relationship between multicellularity and the evolution of sexual traits has not been empirically tested. Given their extensive variation in both multicellular complexity and sexual systems, the volvocine green algae offer a tractable system for understanding the interrelationship of multicellular complexity and sex. Here we show that species with greater multicellular complexity have a significantly larger number of derived sexual traits, including anisogamy, internal fertilization, and secondary sexual dimorphism. Our results demonstrate that anisogamy repeatedly evolved from isogamous multicellular ancestors and that anisogamous species are larger and produce larger zygotes than isogamous species. In the volvocine algae, the evolution of multicellularity likely drives the evolution of anisogamy, and anisogamy subsequently drives secondary sexual dimorphism. Multicellularity may set the stage for the overall diversity of sexual complexity throughout the Tree of Life.},
}

@article {pmid30109121,
year = {2018},
author = {Wang, X and Zhu, W and Chang, P and Wu, H and Liu, H and Chen, J},
title = {Merge and separation of NuA4 and SWR1 complexes control cell fate plasticity in Candida albicans.},
journal = {Cell discovery},
volume = {4},
number = {},
pages = {45},
doi = {10.1038/s41421-018-0043-0},
pmid = {30109121},
issn = {2056-5968},
support = {R01 AI099190/AI/NIAID NIH HHS/United States ; R01 GM117111/GM/NIGMS NIH HHS/United States ; },
abstract = {Phenotypic plasticity is common in development. Candida albicans, a polymorphic fungal pathogen of humans, possesses the unique ability to achieve rapid and reversible cell fate between unicellular form (yeast) and multicellular form (hypha) in response to environmental cues. The NuA4 histone acetyltransferase activity and Hda1 histone deacetylase activity have been reported to be required for hyphal initiation and maintenance. However, how Hda1 and NuA4 regulate hyphal elongation is not clear. NuA4 histone acetyltransferase and SWR1 chromatin remodeling complexes are conserved from yeast to human, which may have merged together to form a larger TIP60 complex since the origin of metazoan. In this study, we show a dynamic merge and separation of NuA4 and SWR1 complexes in C. albicans. NuA4 and SWR1 merge together in yeast state and separate into two distinct complexes in hyphal state. We demonstrate that acetylation of Eaf1 K173 controls the interaction between the two complexes. The YEATS domain of Yaf9 in C. albicans can recognize an acetyl-lysine of the Eaf1 and mediate the Yaf9-Eaf1 interaction. The reversible acetylation and deacetylation of Eaf1 by Esa1 and Hda1 control the merge and separation of NuA4 and SWR1, and this regulation is triggered by Brg1 recruitment of Hda1 to chromatin in response nutritional signals that sustain hyphal elongation. We have also observed an orchestrated promoter association of Esa1, Hda1, Swr1, and H2A.Z during the reversible yeast-hyphae transitions. This is the first discovery of a regulated merge of the NuA4 and SWR1 complexes that controls cell fate determination and this regulation may be conserved in polymorphic fungi.},
}

@article {pmid30103474,
year = {2018},
author = {Mattick, JS},
title = {The State of Long Non-Coding RNA Biology.},
journal = {Non-coding RNA},
volume = {4},
number = {3},
pages = {},
doi = {10.3390/ncrna4030017},
pmid = {30103474},
issn = {2311-553X},
abstract = {Transcriptomic studies have demonstrated that the vast majority of the genomes of mammals and other complex organisms is expressed in highly dynamic and cell-specific patterns to produce large numbers of intergenic, antisense and intronic long non-protein-coding RNAs (lncRNAs). Despite well characterized examples, their scaling with developmental complexity, and many demonstrations of their association with cellular processes, development and diseases, lncRNAs are still to be widely accepted as major players in gene regulation. This may reflect an underappreciation of the extent and precision of the epigenetic control of differentiation and development, where lncRNAs appear to have a central role, likely as organizational and guide molecules: most lncRNAs are nuclear-localized and chromatin-associated, with some involved in the formation of specialized subcellular domains. I suggest that a reassessment of the conceptual framework of genetic information and gene expression in the 4-dimensional ontogeny of spatially organized multicellular organisms is required. Together with this and further studies on their biology, the key challenges now are to determine the structure⁻function relationships of lncRNAs, which may be aided by emerging evidence of their modular structure, the role of RNA editing and modification in enabling epigenetic plasticity, and the role of RNA signaling in transgenerational inheritance of experience.},
}

@article {pmid30102347,
year = {2018},
author = {Gaouda, H and Hamaji, T and Yamamoto, K and Kawai-Toyooka, H and Suzuki, M and Noguchi, H and Minakuchi, Y and Toyoda, A and Fujiyama, A and Nozaki, H and Smith, DR},
title = {Exploring the Limits and Causes of Plastid Genome Expansion in Volvocine Green Algae.},
journal = {Genome biology and evolution},
volume = {10},
number = {9},
pages = {2248-2254},
doi = {10.1093/gbe/evy175},
pmid = {30102347},
issn = {1759-6653},
abstract = {Plastid genomes are not normally celebrated for being large. But researchers are steadily uncovering algal lineages with big and, in rare cases, enormous plastid DNAs (ptDNAs), such as volvocine green algae. Plastome sequencing of five different volvocine species has revealed some of the largest, most repeat-dense plastomes on record, including that of Volvox carteri (∼525 kb). Volvocine algae have also been used as models for testing leading hypotheses on organelle genome evolution (e.g., the mutational hazard hypothesis), and it has been suggested that ptDNA inflation within this group might be a consequence of low mutation rates and/or the transition from a unicellular to multicellular existence. Here, we further our understanding of plastome size variation in the volvocine line by examining the ptDNA sequences of the colonial species Yamagishiella unicocca and Eudorina sp. NIES-3984 and the multicellular Volvox africanus, which are phylogenetically situated between species with known ptDNA sizes. Although V. africanus is closely related and similar in multicellular organization to V. carteri, its ptDNA was much less inflated than that of V. carteri. Synonymous- and noncoding-site nucleotide substitution rate analyses of these two Volvox ptDNAs suggest that there are drastically different plastid mutation rates operating in the coding versus intergenic regions, supporting the idea that error-prone DNA repair in repeat-rich intergenic spacers is contributing to genome expansion. Our results reinforce the idea that the volvocine line harbors extremes in plastome size but ultimately shed doubt on some of the previously proposed hypotheses for ptDNA inflation within the lineage.},
}

@article {pmid30099198,
year = {2018},
author = {Lazzari, G and Nicolas, V and Matsusaki, M and Akashi, M and Couvreur, P and Mura, S},
title = {Multicellular spheroid based on a triple co-culture: A novel 3D model to mimic pancreatic tumor complexity.},
journal = {Acta biomaterialia},
volume = {78},
number = {},
pages = {296-307},
doi = {10.1016/j.actbio.2018.08.008},
pmid = {30099198},
issn = {1878-7568},
abstract = {The preclinical drug screening of pancreatic cancer treatments suffers from the absence of appropriate models capable to reproduce in vitro the heterogeneous tumor microenvironment and its stiff desmoplasia. Driven by this pressing need, we describe in this paper the conception and the characterization of a novel 3D tumor model consisting of a triple co-culture of pancreatic cancer cells (PANC-1), fibroblasts (MRC-5) and endothelial cells (HUVEC), which assembled to form a hetero-type multicellular tumor spheroid (MCTS). By histological analyses and Selective Plain Illumination Microscopy (SPIM) we have monitored the spatial distribution of each cell type and the evolution of the spheroid composition. Results revealed the presence of a core rich in fibroblasts and fibronectin in which endothelial cells were homogeneously distributed. The integration of the three cell types enabled to reproduce in vitro with fidelity the influence of the surrounding environment on the sensitivity of cancer cells to chemotherapy. To our knowledge, this is the first time that a scaffold-free pancreatic cancer spheroid model combining both tumor and multiple stromal components has been designed. It holds the possibility to become an advantageous tool for a pertinent assessment of the efficacy of various therapeutic strategies.

STATEMENT OF SIGNIFICANCE: Pancreatic tumor microenvironment is characterized by abundant fibrosis and aberrant vasculature. Aiming to reproduce in vitro these features, cancer cells have been already co-cultured with fibroblasts or endothelial cells separately but the integration of both these essential components of the pancreatic tumor microenvironment in a unique system, although urgently needed, was still missing. In this study, we successfully integrated cellular and acellular microenvironment components (i.e., fibroblasts, endothelial cells, fibronectin) in a hetero-type scaffold-free multicellular tumor spheroid. This new 3D triple co-culture model closely mimicked the resistance to treatments observed in vivo, resulting in a reduction of cancer cell sensitivity to the anticancer treatment.},
}

@article {pmid30089142,
year = {2018},
author = {Tverskoi, D and Makarenkov, V and Aleskerov, F},
title = {Modeling functional specialization of a cell colony under different fecundity and viability rates and resource constraint.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201446},
doi = {10.1371/journal.pone.0201446},
pmid = {30089142},
issn = {1932-6203},
abstract = {The emergence of functional specialization is a core problem in biology. In this work we focus on the emergence of reproductive (germ) and vegetative viability-enhancing (soma) cell functions (or germ-soma specialization). We consider a group of cells and assume that they contribute to two different evolutionary tasks, fecundity and viability. The potential of cells to contribute to fitness components is traded off. As embodied in current models, the curvature of the trade-off between fecundity and viability is concave in small-sized organisms and convex in large-sized multicellular organisms. We present a general mathematical model that explores how the division of labor in a cell colony depends on the trade-off curvatures, a resource constraint and different fecundity and viability rates. Moreover, we consider the case of different trade-off functions for different cells. We describe the set of all possible solutions of the formulated mathematical programming problem and show some interesting examples of optimal specialization strategies found for our objective fitness function. Our results suggest that the transition to specialized organisms can be achieved in several ways. The evolution of Volvocalean green algae is considered to illustrate the application of our model. The proposed model can be generalized to address a number of important biological issues, including the evolution of specialized enzymes and the emergence of complex organs.},
}

@article {pmid30086318,
year = {2018},
author = {Furumizu, C and Hirakawa, Y and Bowman, JL and Sawa, S},
title = {3D Body Evolution: Adding a New Dimension to Colonize the Land.},
journal = {Current biology : CB},
volume = {28},
number = {15},
pages = {R838-R840},
doi = {10.1016/j.cub.2018.06.040},
pmid = {30086318},
issn = {1879-0445},
abstract = {Complex multicellular plant bodies evolved in both generations of land plants. A new study demonstrates that CLAVATA3-like peptides function via conserved receptors in Physcomitrella patens as key molecules for morphological innovation of 3D growth in land plants.},
}

@article {pmid30082786,
year = {2018},
author = {Li, Z and Fu, X and Wang, Y and Liu, R and He, Y},
title = {Polycomb-mediated gene silencing by the BAH-EMF1 complex in plants.},
journal = {Nature genetics},
volume = {50},
number = {9},
pages = {1254-1261},
doi = {10.1038/s41588-018-0190-0},
pmid = {30082786},
issn = {1546-1718},
abstract = {Polycomb proteins implement genome-wide transcriptional repression in multicellular organisms. The evolutionarily conserved Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) that is read and effected by Polycomb repressive complex 1 (PRC1) in animals, but the interpretation of this mark remains unclear in plants. Here we report that in the eudicot Arabidopsis thaliana two homologous BAH (Bromo adjacent homology) domain-containing proteins form a plant-specific complex with EMBRYONIC FLOWER 1 (EMF1), and that the BAH-EMF1 complex (BAH-EMF1c) reads and effects the H3K27me3 mark and mediates genome-wide transcriptional repression. Furthermore, in the monocot rice a homolog of the Arabidopsis BAH-domain proteins also binds methylated H3K27 and forms a complex with the rice homolog of EMF1, suggesting that BAH-EMF1c is conserved in flowering plants. Therefore, our results show that the plant-specific BAH-EMF1c fulfills PRC1-like functions in higher plants, suggesting a convergent evolution of PRC1 activity in plants and animals.},
}

@article {pmid30078827,
year = {2018},
author = {Oka, M and Yoneda, Y},
title = {Importin α: functions as a nuclear transport factor and beyond.},
journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences},
volume = {94},
number = {7},
pages = {259-274},
doi = {10.2183/pjab.94.018},
pmid = {30078827},
issn = {1349-2896},
mesh = {Active Transport, Cell Nucleus ; Animals ; Cell Nucleus/*metabolism ; Humans ; Neurons/cytology/metabolism ; Nuclear Pore/metabolism ; alpha Karyopherins/*metabolism ; },
abstract = {Nucleocytoplasmic transport is an essential process in eukaryotes. The molecular mechanisms underlying nuclear transport that involve the nuclear transport receptor, small GTPase Ran, and the nuclear pore complex are highly conserved from yeast to humans. On the other hand, it has become clear that the nuclear transport system diverged during evolution to achieve various physiological functions in multicellular eukaryotes. In this review, we first summarize the molecular mechanisms of nuclear transport and how these were elucidated. Then, we focus on the diverse functions of importin α, which acts not merely an import factor but also as a multi-functional protein contributing to a variety of cellular functions in higher eukaryotes.},
}

Active Transport, Cell Nucleus
Animals
Cell Nucleus/*metabolism
Humans
Neurons/cytology/metabolism
Nuclear Pore/metabolism
alpha Karyopherins/*metabolism

@article {pmid30072980,
year = {2018},
author = {Sharma, G and Burrows, LL and Singer, M},
title = {Diversity and Evolution of Myxobacterial Type IV Pilus Systems.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1630},
doi = {10.3389/fmicb.2018.01630},
pmid = {30072980},
issn = {1664-302X},
abstract = {Type IV pili (T4P) are surface-exposed protein fibers that play key roles in the bacterial life cycle via surface attachment/adhesion, biofilm formation, motility, and development. The order Myxococcales (myxobacteria) are members of the class Deltaproteobacteria and known for their large genome size and complex social behaviors, including gliding motility, fruiting body formation, biofilm production, and prey hunting. Myxococcus xanthus, the best-characterized member of the order, relies on the appropriate expression of 17 type IVa (T4aP) genes organized in a single cluster plus additional genes (distributed throughout the genome) for social motility and development. Here, we compared T4aP genes organization within the myxobacteria to understand their evolutionary origins and diversity. We found that T4aP genes are organized as large clusters in suborder Cystobacterineae, whereas in other two suborders Sorangiineae and Nannocystineae, these genes are dispersed throughout the genome. Based on the genomic organization, the phylogeny of conserved proteins, and synteny studies among 28 myxobacterial and 66 Proteobacterial genomes, we propose an evolutionary model for the origin of myxobacterial T4aP genes independently from other orders in class Deltaproteobacteria. Considering a major role for T4P, this study further proposes the origins and evolution of social motility in myxobacteria and provides a foundation for understanding how complex-behavioral traits, such as gliding motility, multicellular development, etc., might have evolved in this diverse group of complex organisms.},
}

@article {pmid30068565,
year = {2018},
author = {Bornens, M},
title = {Cell polarity: having and making sense of direction-on the evolutionary significance of the primary cilium/centrosome organ in Metazoa.},
journal = {Open biology},
volume = {8},
number = {8},
pages = {},
doi = {10.1098/rsob.180052},
pmid = {30068565},
issn = {2046-2441},
abstract = {Cell-autonomous polarity in Metazoans is evolutionarily conserved. I assume that permanent polarity in unicellular eukaryotes is required for cell motion and sensory reception, integration of these two activities being an evolutionarily constrained function. Metazoans are unique in making cohesive multicellular organisms through complete cell divisions. They evolved a primary cilium/centrosome (PC/C) organ, ensuring similar functions to the basal body/flagellum of unicellular eukaryotes, but in different cells, or in the same cell at different moments. The possibility that this innovation contributed to the evolution of individuality, in being instrumental in the early specification of the germ line during development, is further discussed. Then, using the example of highly regenerative organisms like planarians, which have lost PC/C organ in dividing cells, I discuss the possibility that part of the remodelling necessary to reach a new higher-level unit of selection in multi-cellular organisms has been triggered by conflicts among individual cell polarities to reach an organismic polarity. Finally, I briefly consider organisms with a sensorimotor organ like the brain that requires exceedingly elongated polarized cells for its activity. I conclude that beyond critical consequences for embryo development, the conservation of cell-autonomous polarity in Metazoans had far-reaching implications for the evolution of individuality.},
}

@article {pmid30066215,
year = {2018},
author = {Stencel, A and Wloch-Salamon, DM},
title = {Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation.},
journal = {Theory in biosciences = Theorie in den Biowissenschaften},
volume = {137},
number = {2},
pages = {197-206},
doi = {10.1007/s12064-018-0268-3},
pmid = {30066215},
issn = {1611-7530},
support = {2018/28/T/HS1/00201//Narodowe Centrum Nauki/ ; Opus 2017/25/B/NZ8/01035//Narodowe Centrum Nauki/ ; DS/762 - K/ZDS/007338//Uniwersytet Jagielloński w Krakowie/ ; },
abstract = {Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated. In this paper, we argue, firstly, that only a very small number of symbiotic microorganisms are sufficiently integrated into multicellular organisms to act in concert with them as units of selection, thus rendering claims that holobionts are units of selection invalid. Secondly, even though holobionts are not units of selection, they can still constitute genuine units from an evolutionary perspective, provided we accept certain constraints: mainly, they should be considered units of co-operation. Thirdly, we propose a reconciliation of the role of symbiotic microorganisms with the theory of speciation through the use of a developed framework. Mainly, we will argue that, in order to understand the role of microorganisms in the speciation of multicellular organisms, it is not necessary to consider holobionts units of selection; it is sufficient to consider them units of co-operation.},
}

@article {pmid30065707,
year = {2018},
author = {Chen, H and Zhang, SD and Chen, L and Cai, Y and Zhang, WJ and Song, T and Wu, LF},
title = {Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {1569},
doi = {10.3389/fmicb.2018.01569},
pmid = {30065707},
issn = {1664-302X},
abstract = {Magnetotactic bacteria (MTB) are a diverse group of microorganisms capable of using geomagnetic fields for navigation. This magnetotactic behavior can help microorganisms move toward favorable habitats for optimal growth and reproduction. A comprehensive understanding of the magnetotactic mechanism at molecular levels requires highly efficient genomic editing tools, which remain underdeveloped in MTB. Here, we adapted an engineered CRISPR-Cas9 system for efficient inactivation of genes in a widely used MTB model strain, Magnetospirillum magneticum AMB-1. By combining a nuclease-deficient Cas9 (dCas9) and single-guide RNA (sgRNA), a CRISPR interference system was successfully developed to repress amb0994 expression. Furthermore, we constructed an in-frame deletion mutant of amb0994 by developing a CRISPR-Cas9 system. This mutant produces normal magnetosomes; however, its response to abrupt magnetic field reversals is faster than wild-type strain. This behavioral difference is probably a consequence of altered flagella function, as suggested with our dynamics simulation study by modeling M. magneticum AMB-1 cell as an ellipsoid. These data indicate that, Amb0994 is involved in the cellular response to magnetic torque changes via controlling flagella. In summary, this study, besides contributing to a better understanding of magnetotaxis mechanism, demonstrated the CRISPR-(d)Cas9 system as a useful genetic tool for efficient genome editing in MTB.},
}

@article {pmid30061903,
year = {2018},
author = {Benítez, M and Hernández-Hernández, V and Newman, SA and Niklas, KJ},
title = {Dynamical Patterning Modules, Biogeneric Materials, and the Evolution of Multicellular Plants.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {871},
doi = {10.3389/fpls.2018.00871},
pmid = {30061903},
issn = {1664-462X},
abstract = {Comparative analyses of developmental processes across a broad spectrum of organisms are required to fully understand the mechanisms responsible for the major evolutionary transitions among eukaryotic photosynthetic lineages (defined here as the polyphyletic algae and the monophyletic land plants). The concepts of dynamical patterning modules (DPMs) and biogeneric materials provide a framework for studying developmental processes in the context of such comparative analyses. In the context of multicellularity, DPMs are defined as sets of conserved gene products and molecular networks, in conjunction with the physical morphogenetic and patterning processes they mobilize. A biogeneric material is defined as mesoscale matter with predictable morphogenetic capabilities that arise from complex cellular conglomerates. Using these concepts, we outline some of the main events and transitions in plant evolution, and describe the DPMs and biogeneric properties associated with and responsible for these transitions. We identify four primary DPMs that played critical roles in the evolution of multicellularity (i.e., the DPMs responsible for cell-to-cell adhesion, identifying the future cell wall, cell differentiation, and cell polarity). Three important conclusions emerge from a broad phyletic comparison: (1) DPMs have been achieved in different ways, even within the same clade (e.g., phycoplastic cell division in the Chlorophyta and phragmoplastic cell division in the Streptophyta), (2) DPMs had their origins in the co-option of molecular species present in the unicellular ancestors of multicellular plants, and (3) symplastic transport mediated by intercellular connections, particularly plasmodesmata, was critical for the evolution of complex multicellularity in plants.},
}

@article {pmid30061561,
year = {2018},
author = {Stewart, AD and Rice, WR},
title = {Arrest of sex-specific adaptation during the evolution of sexual dimorphism in Drosophila.},
journal = {Nature ecology & evolution},
volume = {2},
number = {9},
pages = {1507-1513},
doi = {10.1038/s41559-018-0613-4},
pmid = {30061561},
issn = {2397-334X},
abstract = {Sexually antagonistic selection arises when a trait expressed in both sexes (a shared trait) is selected towards different, sex-specific optima. Sex-discordant selection causes different alleles to be favoured in each sex (intralocus sexual conflict). A key parameter responsible for generating this conflict is the intersexual genetic correlation (rMF), which determines the degree to which heritable genetic variation for the shared trait produces a similar phenotype in both sexes. A strong, positive rMF interferes with adaptation when there is sex-discordant selection. In principle, the rMF can evolve in response to sex-discordant selection: the faster it declines, the faster the resolution of intralocus sexual conflict. Here, we use Drosophila melanogaster to quantify the time scale over which a strong, positive rMF impedes a response to sex-discordant selection for a canonical quantitative trait (body size) with an exceptionally long (250 generations) selection experiment for a complex multicellular organism. We found that, compared with rapid and substantial evolution under sex-concordant selection, a high rMF arrested sex-specific adaptation for 100 generations in females and a minimum of 250 generations in males. Our study demonstrates that a high rMF can lead to a protracted period of adaptive stalemate during the evolution of sexual dimorphism.},
}

@article {pmid30059538,
year = {2018},
author = {Waldron, FM and Stone, GN and Obbard, DJ},
title = {Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes.},
journal = {PLoS genetics},
volume = {14},
number = {7},
pages = {e1007533},
doi = {10.1371/journal.pgen.1007533},
pmid = {30059538},
issn = {1553-7404},
abstract = {RNA interference (RNAi)-related pathways target viruses and transposable element (TE) transcripts in plants, fungi, and ecdysozoans (nematodes and arthropods), giving protection against infection and transmission. In each case, this produces abundant TE and virus-derived 20-30nt small RNAs, which provide a characteristic signature of RNAi-mediated defence. The broad phylogenetic distribution of the Argonaute and Dicer-family genes that mediate these pathways suggests that defensive RNAi is ancient, and probably shared by most animal (metazoan) phyla. Indeed, while vertebrates had been thought an exception, it has recently been argued that mammals also possess an antiviral RNAi pathway, although its immunological relevance is currently uncertain and the viral small RNAs (viRNAs) are not easily detectable. Here we use a metagenomic approach to test for the presence of viRNAs in five species from divergent animal phyla (Porifera, Cnidaria, Echinodermata, Mollusca, and Annelida), and in a brown alga-which represents an independent origin of multicellularity from plants, fungi, and animals. We use metagenomic RNA sequencing to identify around 80 virus-like contigs in these lineages, and small RNA sequencing to identify viRNAs derived from those viruses. We identified 21U small RNAs derived from an RNA virus in the brown alga, reminiscent of plant and fungal viRNAs, despite the deep divergence between these lineages. However, contrary to our expectations, we were unable to identify canonical (i.e. Drosophila- or nematode-like) viRNAs in any of the animals, despite the widespread presence of abundant micro-RNAs, and somatic transposon-derived piwi-interacting RNAs. We did identify a distinctive group of small RNAs derived from RNA viruses in the mollusc. However, unlike ecdysozoan viRNAs, these had a piRNA-like length distribution but lacked key signatures of piRNA biogenesis. We also identified primary piRNAs derived from putatively endogenous copies of DNA viruses in the cnidarian and the echinoderm, and an endogenous RNA virus in the mollusc. The absence of canonical virus-derived small RNAs from our samples may suggest that the majority of animal phyla lack an antiviral RNAi response. Alternatively, these phyla could possess an antiviral RNAi response resembling that reported for vertebrates, with cryptic viRNAs not detectable through simple metagenomic sequencing of wild-type individuals. In either case, our findings show that the antiviral RNAi responses of arthropods and nematodes, which are highly divergent from each other and from that of plants and fungi, are also highly diverged from the most likely ancestral metazoan state.},
}

@article {pmid30028958,
year = {2018},
author = {Campbell, FC and Loughrey, MB and McClements, J and Deevi, RK and Javadi, A and Rainey, L},
title = {Mechanistic Insights into Colorectal Cancer Phenomics from Fundamental and Organotypic Model Studies.},
journal = {The American journal of pathology},
volume = {188},
number = {9},
pages = {1936-1948},
doi = {10.1016/j.ajpath.2018.05.021},
pmid = {30028958},
issn = {1525-2191},
abstract = {Colorectal cancer (CRC) diagnosis and prognostic stratification are based on histopathologic assessment of cell or nuclear pleomorphism, aberrant mitotic figures, altered glandular architecture, and other phenomic abnormalities. This complexity is driven by oncogenic perturbation of tightly coordinated spatiotemporal signaling to disrupt multiple scales of tissue organization. This review clarifies molecular and cellular mechanisms underlying common CRC histologic features and helps understand how the CRC genome controls core aspects of tumor aggressiveness. It further explores a spatiotemporal framework for CRC phenomics based on regulation of living cells in fundamental and organotypic model systems. The review also discusses tissue homeostasis, considers distinct classes of oncogenic perturbations, and evolution of cellular or multicellular cancer phenotypes. It further explores the molecular controls of cribriform, micropapillary, and high-grade CRC morphology in organotypic culture models and assesses relevant translational studies. In addition, the review delves into complexities of morphologic plasticity whereby a single molecular signature generates heterogeneous cancer phenotypes, and, conversely, morphologically homogeneous tumors show substantive molecular diversity. Principles outlined may aid mechanistic interpretation of omics data in a setting of cancer pathology, provide insight into CRC consensus molecular subtypes, and better define principles for CRC prognostic stratification.},
}

@article {pmid29992410,
year = {2018},
author = {Leong, SP and Aktipis, A and Maley, C},
title = {Cancer initiation and progression within the cancer microenvironment.},
journal = {Clinical & experimental metastasis},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10585-018-9921-y},
pmid = {29992410},
issn = {1573-7276},
abstract = {Within the cancer microenvironment, the growth and proliferation of cancer cells in the primary site as well as in the metastatic site represent a global biological phenomenon. To understand the growth, proliferation and progression of cancer either by local expansion and/or metastasis, it is important to understand the cancer microenvironment and host response to cancer growth. Melanoma is an excellent model to study the interaction of cancer initiation and growth in relationship to its microenvironment. Social evolution with cooperative cellular groups within an organism is what gives rise to multicellularity in the first place. Cancer cells evolve to exploit their cellular environment. The foundations of multicellular cooperation break down in cancer because those cells that misbehave have an evolutionary advantage over their normally behaving neighbors. It is important to classify evolutionary and ecological aspects of cancer growth, thus, data for cancer growth and outcomes need to be collected to define these parameters so that accurate predictions of how cancer cells may proliferate and metastasize can be developed.},
}

@article {pmid29966484,
year = {2018},
author = {Liao, Z and Kjellin, J and Hoeppner, MP and Grabherr, M and Söderbom, F},
title = {Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.},
journal = {RNA biology},
volume = {15},
number = {7},
pages = {937-954},
doi = {10.1080/15476286.2018.1481697},
pmid = {29966484},
issn = {1555-8584},
abstract = {Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3'-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.},
}

@article {pmid29961831,
year = {2018},
author = {Zhao, J and Yuan, S and Gao, B and Zhu, S},
title = {Molecular diversity of fungal inhibitor cystine knot peptides evolved by domain repeat and fusion.},
journal = {FEMS microbiology letters},
volume = {365},
number = {15},
pages = {},
doi = {10.1093/femsle/fny158},
pmid = {29961831},
issn = {1574-6968},
abstract = {Peptides with the inhibitor cystine knot (ICK) motif are extensively present in animals and plants where they exert a diversity of biological functions. However, few studies have been undertaken on this class of peptides in fungi. In this work, we identify a total of 386 fungal ICK peptides and proteins containing this motif by computational data mining of fungal genome databases, which exhibit 14 different exon-intron structures. According to their domain architectures, these proteins are classified into three distinct structural types, including single domains, tandem repeat domains and fusion domains, in which six families belonging to single or tandem repeat domains show remarkable sequence similarity to those from animals and plants, suggesting their orthologous relationship. Extremely high molecular diversity in fungal ICKs might be attributable to different genetic mechanisms, such as gene/domain duplication and fusion. This work not only enlarges the number of ICK peptides in multicellular organisms, but also uncovers their complex evolutionary history in a specific lineage.},
}

@article {pmid29954963,
year = {2018},
author = {Pennisi, E},
title = {Is cancer a breakdown of multicellularity?.},
journal = {Science (New York, N.Y.)},
volume = {360},
number = {6396},
pages = {1391},
doi = {10.1126/science.360.6396.1391},
pmid = {29954963},
issn = {1095-9203},
mesh = {*Biological Evolution ; Carcinogenesis/genetics/*pathology ; Gene Regulatory Networks ; Humans ; Neoplasms/genetics/*pathology ; },
}

*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 & evolution},
volume = {2},
number = {7},
pages = {1176-1188},
doi = {10.1038/s41559-018-0575-6},
pmid = {29942020},
issn = {2397-334X},
abstract = {A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement cell-type-specific functions. However, the evolution of metazoan cell types and their underlying gene regulatory programmes remains largely uncharacterized. Here, we use whole-organism single-cell RNA sequencing to map cell-type-specific transcription in Porifera (sponges), Ctenophora (comb jellies) and Placozoa species. We describe the repertoires of cell types in these non-bilaterian animals, uncovering diverse instances of previously unknown molecular signatures, such as multiple types of peptidergic cells in Placozoa. Analysis of the regulatory programmes of these cell types reveals variable levels of complexity. In placozoans and poriferans, sequence motifs in the promoters are predictive of cell-type-specific programmes. By contrast, the generation of a higher diversity of cell types in ctenophores is associated with lower specificity of promoter sequences and the existence of distal regulatory elements. Our findings demonstrate that metazoan cell types can be defined by networks of transcription factors and proximal promoters, and indicate that further genome regulatory complexity may be required for more diverse cell type repertoires.},
}