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Evolutionary Biology
Tea and coffee consumption in relation to DNA methylation in four European cohorts
May 23, 2017   Human Molecular Genetics
Ek WE, Tobi EW, Ahsan M, Lampa E, Ponzi E,   . . . . . .   , Vineis P, Lind L, Flanagan JM, Johansson Å, Epigenome-Wide Association study Consortium
Tea and coffee consumption in relation to DNA methylation in four European cohorts
May 23, 2017
Human Molecular Genetics
Lifestyle factors, such as food choices and exposure to chemicals, can alter DNA methylation and lead to changes in gene activity. Two such exposures with pharmacologically active components are coffee and tea consumption. Both coffee and tea has been suggested to play an important role in modulating disease-risk in humans by suppressing tumour progression, decreasing inflammation and influencing estrogen metabolism. These mechanisms may be mediated by changes in DNA methylation.To investigate if DNA methylation in blood is associated with coffee and tea consumption we performed a genome-wide DNA methylation study for coffee and tea consumption in four European cohorts (N = 3,096). DNA methylation was measured from whole blood at 421,695 CpG sites distributed throughout the genome and analysed in men and women both separately and together in each cohort. Meta-analyses of the results and additional regional-level analyses were performed.After adjusting for multiple testing, the meta-analysis revealed that two individual CpG-sites, mapping to DNAJC16 and TTC17, were differentially methylated in relation to tea consumption in women. No individual sites were associated in men or in the sex-combined analysis for tea or coffee. The regional analysis revealed that 28 regions were differentially methylated in relation to tea consumption in women. These regions contained genes known to interact with estradiol metabolism and cancer. No significant regions were found in the sex-combined and male-only analysis for either tea or coffee consumption. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
Recent evolutionary history of Chrysoperla externa (Hagen 1861) (Neuroptera: Chrysopidae) in Brazil
May 16, 2017   PloS One
Morales-Corrêa E Castro AC, Barbosa NCCP
Recent evolutionary history of Chrysoperla externa (Hagen 1861) (Neuroptera: Chrysopidae) in Brazil
May 16, 2017
PloS One
This work aimed to elucidate the distribution of Chrysoperla externa haplotypes and investigate whether it exhibits structure based on genetic composition as opposed to geographic location. The genetic diversity of C. externa, analyzed by AMOVA using the COI and 16S rRNA genes as mitochondrial markers, showed significant haplotype structure arising from genetic differences that was not associated with sampling location. This was reflected in the network grouping. Bayesian inference showed that haplotype distribution may have its origins in C. externa divergence into two distinct clades, which dispersed to various locations, and their subsequent diversification. The evolutionary history of C. externa may include multiple ancestral haplotypes differentiating within the same geographic area to generate the current broad genetic diversity, so that the earlier geographical history has been erased, and now we have highlighted its more recent genetic history.
A novel N-methyltransferase in Arabidopsis appears to feed a conserved pathway for nicotinate detoxification among land plants and is associated with lignin biosynthesis
May 23, 2017   Plant Physiology
Li W, Zhang F, Wu R, Jia L, Li G, Guo Y, Liu C, Wang G
A novel N-methyltransferase in Arabidopsis appears to feed a conserved pathway for nicotinate detoxification among land plants and is associated with lignin biosynthesis
May 23, 2017
Plant Physiology
The Preiss-Handler pathway, which salvages nicotinate (NA) for NAD synthesis, is an indispensable biochemical pathway in land plants. Various NA conjugations (mainly methylation and glycosylation) have been detected, and have long been proposed for NA detoxification in plants. Previously, we demonstrated that NA O-glucosylation functions as a mobilizable storage form for NAD biosynthesis in the Brassicaceae. However, little is known about the functions of other NA conjugations in plants. In this study, we firstly found that N-methylnicotinate is a ubiquitous NA conjugation in land plants. Further, we functionally identified a novel methyltransferase (At3g53140, NANMT), which is mainly responsible for N-methylnicotinate formation, from Arabidopsis. We also established that trigonelline (Tg) is a detoxification form of endogenous NA in plants. Combined phylogenetic analysis and enzymatic assays revealed that NA N-methylation activity was likely derived from duplication and subfunctionalization of an ancestral caffeic acid O-methyltransferase (COMT) gene in the course of land plant evolution. COMT enzymes, which function in S-lignin biosynthesis, also have weak NANMT activity. Our data suggest that NA detoxification conferred by NANMT and COMT might have facilitated the retention of the Preiss-Handler pathway in land plants. {copyright, serif} 2017 American Society of Plant Biologists. All rights reserved.
Locally noisy autonomous agents improve global human coordination in network experiments
May 18, 2017   Nature Add nature.com free-link Cancel
Shirado H, Christakis NA
Locally noisy autonomous agents improve global human coordination in network experiments
May 18, 2017
Nature
Coordination in groups faces a sub-optimization problem and theory suggests that some randomness may help to achieve global optima. Here we performed experiments involving a networked colour coordination game in which groups of humans interacted with autonomous software agents (known as bots). Subjects (n = 4,000) were embedded in networks (n = 230) of 20 nodes, to which we sometimes added 3 bots. The bots were programmed with varying levels of behavioural randomness and different geodesic locations. We show that bots acting with small levels of random noise and placed in central locations meaningfully improve the collective performance of human groups, accelerating the median solution time by 55.6%. This is especially the case when the coordination problem is hard. Behavioural randomness worked not only by making the task of humans to whom the bots were connected easier, but also by affecting the gameplay of the humans among themselves and hence creating further cascades of benefit in global coordination in these heterogeneous systems.
Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations
May 18, 2017   Cancer Discovery
Huang FW, Mosquera JM, Garofalo A, Oh C, Baco M,   . . . . . .   , Mesirov J, Tamayo P, Rubin MA, Powell IJ, Garraway LA
Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations
May 18, 2017
Cancer Discovery
African-American men have the highest incidence and mortality from prostate cancer. Whether a biological basis exists for this disparity remains unclear. Exome sequencing (n=102) and targeted validation (n = 90) of localized primary hormone-naïve prostate cancer in African-American men identified several gene mutations not previously observed in this context, including recurrent loss-of-function mutations in ERF, an ETS transcriptional repressor, in 5% of cases. Analysis of existing prostate cancer cohorts revealed ERF deletions in 3% of primary prostate cancers and mutations or deletions in ERF in 3-5% of lethal castration-resistant prostate cancers. Knockdown of ERF confers increased anchorage-independent growth and generates a gene expression signature associated with oncogenic ETS activation and androgen signaling. Together, these results suggest that ERF is a prostate cancer tumor suppressor gene. More generally, our findings support the application of systematic cancer genomic characterization in settings of broader ancestral diversity to enhance discovery and, eventually, therapeutic applications. Copyright ©2017, American Association for Cancer Research.
Development of an R4 dual-site (R4DS) gateway cloning system enabling the efficient simultaneous cloning of two desired sets of promoters and open reading frames in a binary vector for plant research
May 18, 2017   PloS One
Aboulela M, Tanaka Y, Nishimura K, Mano S, Nishimura M, Ishiguro S, Kimura T, Nakagawa T
Development of an R4 dual-site (R4DS) gateway cloning system enabling the efficient simultaneous cloning of two desired sets of promoters and open reading frames in a binary vector for plant research
May 18, 2017
PloS One
Vast numbers of proteins work cooperatively to exert their functions in various cells. In order to understand the functions and molecular mechanisms of these proteins in plants, analyses of transgenic plants that concomitantly express two protein-coding genes are often required. We developed a novel Gateway cloning technology-compatible binary vector system, the R4 dual-site (R4DS) Gateway cloning system, which enables the easy and efficient cloning of two desired sets of promoters and open reading frames (ORFs) into a binary vector using promoter and ORF entry clones. In this system, C-terminal fusions with 17 kinds of tags including visible reporters and epitope tags are available for each ORF, and selection by four kinds of resistance markers is possible. We verified that the R4DS Gateway cloning system functioned well in Arabidopsis thaliana by observing the expression and localization patterns of fluorescent proteins fused with organelle-targeting signals and driven by stomatal-lineage specific promoters. We also confirmed that the two cloning sites in the R4DS Gateway cloning system were equivalent and independently regulated. The results obtained indicate that the R4DS Gateway cloning system facilitates detailed comparisons of the expression patterns of two promoters as well as co-localization and interaction analyses of two proteins in specific cells in plants.
An evolutionary switch in ND2 enables Src kinase regulation of NMDA receptors
May 16, 2017   Nature Communications
Scanlon DP, Bah A, Krzeminski M, Zhang W, Leduc-Pessah HL, Dong YN, Forman-Kay JD, Salter MW
An evolutionary switch in ND2 enables Src kinase regulation of NMDA receptors
May 16, 2017
Nature Communications
The non-receptor tyrosine kinase Src is a key signalling hub for upregulating the function of N-methyl D-aspartate receptors (NMDARs). Src is anchored within the NMDAR complex via NADH dehydrogenase subunit 2 (ND2), a mitochondrially encoded adaptor protein. The interacting regions between Src and ND2 have been broadly identified, but the interaction between ND2 and the NMDAR has remained elusive. Here we generate a homology model of ND2 and dock it onto the NMDAR via the transmembrane domain of GluN1. This interaction is enabled by the evolutionary loss of three helices in bilaterian ND2 proteins compared to their ancestral homologues. We experimentally validate our model and demonstrate that blocking this interaction with an ND2 fragment identified in our experimental studies prevents Src-mediated upregulation of NMDAR currents in neurons. Our findings establish the mode of interaction between an NMDAR accessory protein with one of the core subunits of the receptor.
Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases
May 15, 2017   Nature Communications
Wollenberg Valero KC, Garcia-Porta J, Rodríguez A, Arias M, Shah A, Randrianiaina RD, Brown JL, Glaw F, Amat F, Künzel S, Metzler D, Isokpehi RD, Vences M
Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases
May 15, 2017
Nature Communications
Anuran amphibians undergo major morphological transitions during development, but the contribution of their markedly different life-history phases to macroevolution has rarely been analysed. Here we generate testable predictions for coupling versus uncoupling of phenotypic evolution of tadpole and adult life-history phases, and for the underlying expression of genes related to morphological feature formation. We test these predictions by combining evidence from gene expression in two distantly related frogs, Xenopus laevis and Mantidactylus betsileanus, with patterns of morphological evolution in the entire radiation of Madagascan mantellid frogs. Genes linked to morphological structure formation are expressed in a highly phase-specific pattern, suggesting uncoupling of phenotypic evolution across life-history phases. This gene expression pattern agrees with uncoupled rates of trait evolution among life-history phases in the mantellids, which we show to have undergone an adaptive radiation. Our results validate a prevalence of uncoupling in the evolution of tadpole and adult phenotypes of frogs.
Mistranslation can enhance fitness through purging of deleterious mutations
May 19, 2017   Nature Communications
Bratulic S, Toll-Riera M, Wagner A
Mistranslation can enhance fitness through purging of deleterious mutations
May 19, 2017
Nature Communications
Phenotypic mutations are amino acid changes caused by mistranslation. How phenotypic mutations affect the adaptive evolution of new protein functions is unknown. Here we evolve the antibiotic resistance protein TEM-1 towards resistance on the antibiotic cefotaxime in an Escherichia coli strain with a high mistranslation rate. TEM-1 populations evolved in such strains endow host cells with a general growth advantage, not only on cefotaxime but also on several other antibiotics that ancestral TEM-1 had been unable to deactivate. High-throughput sequencing of TEM-1 populations shows that this advantage is associated with a lower incidence of weakly deleterious genotypic mutations. Our observations show that mistranslation is not just a source of noise that delays adaptive evolution. It could even facilitate adaptive evolution by exacerbating the effects of deleterious mutations and leading to their more efficient purging. The ubiquity of mistranslation and its effects render mistranslation an important factor in adaptive protein evolution.
Chew on this
May 19, 2017   Science (New York, N.Y.)
Beard KC
Chew on this
May 19, 2017
Science (New York, N.Y.)
Higher predation risk for insect prey at low latitudes and elevations
May 19, 2017   Science (New York, N.Y.)
Roslin T, Hardwick B, Novotny V, Petry WK, Andrew NR,   . . . . . .   , van Nouhuys S, Vandvik V, Weissflog A, Zhukovich V, Slade EM
Higher predation risk for insect prey at low latitudes and elevations
May 19, 2017
Science (New York, N.Y.)
Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic trend in attack rates by birds or mammals. These matching gradients at global and regional scales suggest consistent drivers of biotic interaction strength, a finding that needs to be integrated into general theories of herbivory, community organization, and life-history evolution. Copyright © 2017, American Association for the Advancement of Science.
A maternal-effect selfish genetic element in Caenorhabditis elegans
May 12, 2017   Science (New York, N.Y.)
Ben-David E, Burga A, Kruglyak L
A maternal-effect selfish genetic element in Caenorhabditis elegans
May 12, 2017
Science (New York, N.Y.)
Selfish genetic elements spread in natural populations and have an important role in genome evolution. We discovered a selfish element causing embryonic lethality in crosses between wild strains of the nematode Caenorhabditis elegans The element is made up of sup-35, a maternal-effect toxin that kills developing embryos, and pha-1, its zygotically expressed antidote. pha-1 has long been considered essential for pharynx development on the basis of its mutant phenotype, but this phenotype arises from a loss of suppression of sup-35 toxicity. Inactive copies of the sup-35/pha-1 element show high sequence divergence from active copies, and phylogenetic reconstruction suggests that they represent ancestral stages in the evolution of the element. Our results suggest that other essential genes identified by genetic screens may turn out to be components of selfish elements. Copyright © 2017, American Association for the Advancement of Science.
Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome
May 16, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang TH,   . . . . . .   , Putra A, Drautz-Moses DI, Schuster SC, Herrera-Estrella L, Albert VA
Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome
May 16, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
Utricularia gibba, the humped bladderwort, is a carnivorous plant that retains a tiny nuclear genome despite at least two rounds of whole genome duplication (WGD) since common ancestry with grapevine and other species. We used a third-generation genome assembly with several complete chromosomes to reconstruct the two most recent lineage-specific ancestral genomes that led to the modern U. gibba genome structure. Patterns of subgenome dominance in the most recent WGD, both architectural and transcriptional, are suggestive of allopolyploidization, which may have generated genomic novelty and led to instantaneous speciation. Syntenic duplicates retained in polyploid blocks are enriched for transcription factor functions, whereas gene copies derived from ongoing tandem duplication events are enriched in metabolic functions potentially important for a carnivorous plant. Among these are tandem arrays of cysteine protease genes with trap-specific expression that evolved within a protein family known to be useful in the digestion of animal prey. Further enriched functions among tandem duplicates (also with trap-enhanced expression) include peptide transport (intercellular movement of broken-down prey proteins), ATPase activities (bladder-trap acidification and transmembrane nutrient transport), hydrolase and chitinase activities (breakdown of prey polysaccharides), and cell-wall dynamic components possibly associated with active bladder movements. Whereas independently polyploid Arabidopsis syntenic gene duplicates are similarly enriched for transcriptional regulatory activities, Arabidopsis tandems are distinct from those of U. gibba, while still metabolic and likely reflecting unique adaptations of that species. Taken together, these findings highlight the special importance of tandem duplications in the adaptive landscapes of a carnivorous plant genome.
The general form of Hamilton's rule makes no predictions and cannot be tested empirically
May 17, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Nowak MA, McAvoy A, Allen B, Wilson EO
The general form of Hamilton's rule makes no predictions and cannot be tested empirically
May 17, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
Hamilton's rule asserts that a trait is favored by natural selection if the benefit to others, [Formula: see text], multiplied by relatedness, [Formula: see text], exceeds the cost to self, [Formula: see text] Specifically, Hamilton's rule states that the change in average trait value in a population is proportional to [Formula: see text] This rule is commonly believed to be a natural law making important predictions in biology, and its influence has spread from evolutionary biology to other fields including the social sciences. Whereas many feel that Hamilton's rule provides valuable intuition, there is disagreement even among experts as to how the quantities [Formula: see text], [Formula: see text], and [Formula: see text] should be defined for a given system. Here, we investigate a widely endorsed formulation of Hamilton's rule, which is said to be as general as natural selection itself. We show that, in this formulation, Hamilton's rule does not make predictions and cannot be tested empirically. It turns out that the parameters [Formula: see text] and [Formula: see text] depend on the change in average trait value and therefore cannot predict that change. In this formulation, which has been called "exact and general" by its proponents, Hamilton's rule can "predict" only the data that have already been given.
Collective action and the evolution of social norm internalization
May 23, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Gavrilets S, Richerson PJ
Collective action and the evolution of social norm internalization
May 23, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
Human behavior is strongly affected by culturally transmitted norms and values. Certain norms are internalized (i.e., acting according to a norm becomes an end in itself rather than merely a tool in achieving certain goals or avoiding social sanctions). Humans' capacity to internalize norms likely evolved in our ancestors to simplify solving certain challenges-including social ones. Here we study theoretically the evolutionary origins of the capacity to internalize norms. In our models, individuals can choose to participate in collective actions as well as punish free riders. In making their decisions, individuals attempt to maximize a utility function in which normative values are initially irrelevant but play an increasingly important role if the ability to internalize norms emerges. Using agent-based simulations, we show that norm internalization evolves under a wide range of conditions so that cooperation becomes "instinctive." Norm internalization evolves much more easily and has much larger effects on behavior if groups promote peer punishment of free riders. Promoting only participation in collective actions is not effective. Typically, intermediate levels of norm internalization are most frequent but there are also cases with relatively small frequencies of "oversocialized" individuals willing to make extreme sacrifices for their groups no matter material costs, as well as "undersocialized" individuals completely immune to social norms. Evolving the ability to internalize norms was likely a crucial step on the path to large-scale human cooperation.
Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality
May 23, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Wei G, Lai Y, Wang G, Chen H, Li F, Wang S
Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality
May 23, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
The insect gut microbiota plays crucial roles in modulating the interactions between the host and intestinal pathogens. Unlike viruses, bacteria, and parasites, which need to be ingested to cause disease, entomopathogenic fungi infect insects through the cuticle and proliferate in the hemolymph. However, interactions between the gut microbiota and entomopathogenic fungi are unknown. Here we show that the pathogenic fungus Beauveria bassiana interacts with the gut microbiota to accelerate mosquito death. After topical fungal infection, mosquitoes with gut microbiota die significantly faster than mosquitoes without microbiota. Furthermore, fungal infection causes dysbiosis of mosquito gut microbiota with a significant increase in gut bacterial load and a significant decrease in bacterial diversity. In particular, the opportunistic pathogenic bacterium Serratia marcescens overgrows in the midgut and translocates to the hemocoel, which promotes fungal killing of mosquitoes. We further reveal that fungal infection down-regulates antimicrobial peptide and dual oxidase expression in the midgut. Duox down-regulation in the midgut is mediated by secretion of the toxin oosporein from B. bassiana Our findings reveal the important contribution of the gut microbiota in B. bassiana-killing activity, providing new insights into the mechanisms of fungal pathogenesis in insects.
Solitary bees reduce investment in communication compared with their social relatives
May 23, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Wittwer B, Hefetz A, Simon T, Murphy LEK, Elgar MA, Pierce NE, Kocher SD
Solitary bees reduce investment in communication compared with their social relatives
May 23, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
Social animals must communicate to define group membership and coordinate social organization. For social insects, communication is predominantly mediated through chemical signals, and as social complexity increases, so does the requirement for a greater diversity of signals. This relationship is particularly true for advanced eusocial insects, including ants, bees, and wasps, whose chemical communication systems have been well-characterized. However, we know surprisingly little about how these communication systems evolve during the transition between solitary and group living. Here, we demonstrate that the sensory systems associated with signal perception are evolutionarily labile. In particular, we show that differences in signal production and perception are tightly associated with changes in social behavior in halictid bees. Our results suggest that social species require a greater investment in communication than their solitary counterparts and that species that have reverted from eusociality to solitary living have repeatedly reduced investment in these potentially costly sensory perception systems.
Evolutionary steps involving counterion displacement in a tunicate opsin
May 23, 2017   Proceedings Of The National Academy Of Sciences Of The United States Of America
Kojima K, Yamashita T, Imamoto Y, Kusakabe TG, Tsuda M, Shichida Y
Evolutionary steps involving counterion displacement in a tunicate opsin
May 23, 2017
Proceedings Of The National Academy Of Sciences Of The United States Of America
Ci-opsin1 is a visible light-sensitive opsin present in the larval ocellus of an ascidian, Ciona intestinalis This invertebrate opsin belongs to the vertebrate visual and nonvisual opsin groups in the opsin phylogenetic tree. Ci-opsin1 contains candidate counterions (glutamic acid residues) at positions 113 and 181; the former is a newly acquired position in the vertebrate visual opsin lineage, whereas the latter is an ancestral position widely conserved among invertebrate opsins. Here, we show that Glu113 and Glu181 in Ci-opsin1 act synergistically as counterions, which imparts molecular properties to Ci-opsin1 intermediate between those of vertebrate- and invertebrate-type opsins. Synergy between the counterions in Ci-opsin1 was demonstrated by E113Q and E181Q mutants that exhibit a pH-dependent spectral shift, whereas only the E113Q mutation in vertebrate rhodopsin yields this spectral shift. On absorbing light, Ci-opsin1 forms an equilibrium between two intermediates with protonated and deprotonated Schiff bases, namely the MI-like and MII-like intermediates, respectively. Adding G protein caused the equilibrium to shift toward the MI-like intermediate, indicating that Ci-opsin1 has a protonated Schiff base in its active state, like invertebrate-type opsins. Ci-opsin1's G protein activation efficiency is between the efficiencies of vertebrate- and invertebrate-type opsins. Interestingly, the E113Y and E181S mutations change the molecular properties of Ci-opsin1 into those resembling invertebrate-type or bistable opsins and vertebrate ancient/vertebrate ancient-long or monostable opsins, respectively. These results strongly suggest that acquisition of counterion Glu113 changed the molecular properties of visual opsin in a vertebrate/tunicate common ancestor as a crucial step in the evolution of vertebrate visual opsins.
Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness
May 15, 2017   PLoS Genetics
Hendler A, Medina EM, Kishkevich A, Abu-Qarn M, Klier S, Buchler NE, de Bruin RAM, Aharoni A
Gene duplication and co-evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness
May 15, 2017
PLoS Genetics
Transcriptional regulatory networks play a central role in optimizing cell survival. How DNA binding domains and cis-regulatory DNA binding sequences have co-evolved to allow the expansion of transcriptional networks and how this contributes to cellular fitness remains unclear. Here we experimentally explore how the complex G1/S transcriptional network evolved in the budding yeast Saccharomyces cerevisiae by examining different chimeric transcription factor (TF) complexes. Over 200 G1/S genes are regulated by either one of the two TF complexes, SBF and MBF, which bind to specific DNA binding sequences, SCB and MCB, respectively. The difference in size and complexity of the G1/S transcriptional network across yeast species makes it well suited to investigate how TF paralogs (SBF and MBF) and DNA binding sequences (SCB and MCB) co-evolved after gene duplication to rewire and expand the network of G1/S target genes. Our data suggests that whilst SBF is the likely ancestral regulatory complex, the ancestral DNA binding element is more MCB-like. G1/S network expansion took place by both cis- and trans- co-evolutionary changes in closely related but distinct regulatory sequences. Replacement of the endogenous SBF DNA-binding domain (DBD) with that from more distantly related fungi leads to a contraction of the SBF-regulated G1/S network in budding yeast, which also correlates with increased defects in cell growth, cell size, and proliferation.
Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba
May 22, 2017   PLoS Genetics
Rogers RL, Shao L, Thornton KR
Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba
May 22, 2017
PLoS Genetics
One common hypothesis to explain the impacts of tandem duplications is that whole gene duplications commonly produce additive changes in gene expression due to copy number changes. Here, we use genome wide RNA-seq data from a population sample of Drosophila yakuba to test this 'gene dosage' hypothesis. We observe little evidence of expression changes in response to whole transcript duplication capturing 5' and 3' UTRs. Among whole gene duplications, we observe evidence that dosage sharing across copies is likely to be common. The lack of expression changes after whole gene duplication suggests that the majority of genes are subject to tight regulatory control and therefore not sensitive to changes in gene copy number. Rather, we observe changes in expression level due to both shuffling of regulatory elements and the creation of chimeric structures via tandem duplication. Additionally, we observe 30 de novo gene structures arising from tandem duplications, 23 of which form with expression in the testes. Thus, the value of tandem duplications is likely to be more intricate than simple changes in gene dosage. The common regulatory effects from chimeric gene formation after tandem duplication may explain their contribution to genome evolution.
Evolutionary forces affecting synonymous variations in plant genomes
May 22, 2017   PLoS Genetics
Clément Y, Sarah G, Holtz Y, Homa F, Pointet S,   . . . . . .   , Santoni S, Labouisse JP, Pham JL, David J, Glémin S
Evolutionary forces affecting synonymous variations in plant genomes
May 22, 2017
PLoS Genetics
Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.
On the mechanistic nature of epistasis in a canonical cis-regulatory element
May 18, 2017   ELife
Lagator M, Paixao T, Barton N, Bollback JP, Guet CC
On the mechanistic nature of epistasis in a canonical cis-regulatory element
May 18, 2017
ELife
Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for. .
Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome
May 12, 2017   ELife
Dorrell RG, Gile G, McCallum G, Méheust R, Bapteste EP, Klinger CM, Brillet-Guéguen L, Freeman KD, Richter DJ, Bowler C
Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome
May 12, 2017
ELife
Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25% of its phylogenetically tractable proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history.
A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases
May 20, 2017   ELife
Bradshaw N, Levdikov VM, Zimanyi CM, Gaudet R, Wilkinson AJ, Losick R
A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases
May 20, 2017
ELife
PP2C phosphatases control biological processes including stress responses, development, and cell division in all kingdoms of life. Diverse regulatory domains adapt PP2C phosphatases to specific functions, but how these domains control phosphatase activity was unknown. We present structures representing active and inactive states of the PP2C phosphatase SpoIIE from Bacillus subtilis. Based on structural analyses and genetic and biochemical experiments, we identify an α-helical switch that shifts a carbonyl oxygen into the active site to coordinate a metal cofactor. Our analysis indicates that this switch is widely conserved among PP2C family members, serving as a platform to control phosphatase activity in response to diverse inputs. Remarkably, the switch is shared with proteasomal proteases, which we identify as evolutionary and structural relatives of PP2C phosphatases. Although these proteases use an unrelated catalytic mechanism, rotation of equivalent helices controls protease activity by movement of the equivalent carbonyl oxygen into the active site.
Global clues to the nature of genomic mutations in humans
May 17, 2017   ELife
Scally A
Global clues to the nature of genomic mutations in humans
May 17, 2017
ELife
An analysis of worldwide human genetic variation reveals the footprints of ancient changes in genomic mutation processes.

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