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Epistasis

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https://www.readbyqxmd.com/read/29163576/quantitative-trait-loci-and-maternal-effects-affecting-the-strong-grain-dormancy-of-wild-barley-hordeum-vulgare-ssp-spontaneum
#1
Shingo Nakamura, Mohammad Pourkheirandish, Hiromi Morishige, Mohammad Sameri, Kazuhiro Sato, Takao Komatsuda
Wild barley (Hordeum vulgare ssp. spontaneum) has strong grain dormancy, a trait that may enhance its survival in non-cultivated environments; by contrast, cultivated barley (Hordeum vulgare ssp. vulgare) has weaker dormancy, allowing uniform germination in cultivation. Malting barley cultivars have been bred for especially weak dormancy to optimize their use in malt production. Here, we analyzed the genetic mechanism of this difference in seed dormancy, using recombinant inbred lines (RILs) derived from a cross between the wild barley accession 'H602' and the malting barley cultivar 'Kanto Nakate Gold (KNG)'...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29158562/highly-expressed-genes-evolve-under-strong-epistasis-from-a-proteome-wide-scan-in-e-coli
#2
Pouria Dasmeh, Éric Girard, Adrian W R Serohijos
Epistasis or the non-additivity of mutational effects is a major force in protein evolution, but it has not been systematically quantified at the level of a proteome. Here, we estimated the extent of epistasis for 2,382 genes in E. coli using several hundreds of orthologs for each gene within the class Gammaproteobacteria. We found that the average epistasis is ~41% across genes in the proteome and that epistasis is stronger among highly expressed genes. This trend is quantitatively explained by the prevailing model of sequence evolution based on minimizing the fitness cost of protein unfolding and aggregation...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158332/ethylene-receptors-signal-via-a-non-canonical-pathway-to-regulate-abscisic-acid-responses
#3
Arkadipta Bakshi, Sarbottam Piya, Jessica C Fernandez, Christian Chervin, Tarek Hewezi, Brad Binder
Ethylene is a gaseous plant hormone perceived by a family of receptors in Arabidopsis thaliana including ETHYLENE RESPONSE1 (ETR1) and ETR2. Previously we showed that etr1-6 loss-of-function plants germinate better and etr2-3 loss-of-function plants germinate worse than wild-type under NaCl stress and in response to abscisic acid (ABA). In this study, we expanded these results by showing that ETR1 and ETR2 have contrasting roles in the control of germination under a variety of inhibitory conditions for seed germination such as treatment with KCl, CuSO4, ZnSO4, and ethanol...
November 20, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29154825/the-scf-ubiquitin-ligase-slimb-controls-nerfin-1-turnover-in-drosophila
#4
Xiaohui Lin, Feng Wang, Yuanpei Li, Chaojun Zhai, Guiping Wang, Xiaoting Zhang, Yang Gao, Tao Yi, Dan Sun, Shian Wu
The C2H2 type zinc-finger transcription factor Nerfin-1 expresses dominantly in Drosophila nervous system and plays an important role in early axon guidance decisions and preventing neurons dedifferentiation. Recently, increasing reports indicated that INSM1 (homologue to nerfin-1 in mammals) is a useful marker for prognosis of neuroendocrine tumors. The dynamic expression of Nerfin-1 is regulated post-transcriptionally by multiple microRNAs; however, its post-translational regulation is still unclear. Here we showed that the protein turnover of Nerfin-1 is regulated by Slimb, the substrate adaptor of SCF(Slimb) ubiquitin ligase complex...
November 14, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29146901/genome-driven-evolutionary-game-theory-helps-understand-the-rise-of-metabolic-interdependencies-in-microbial-communities
#5
Ali R Zomorrodi, Daniel Segrè
Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29143599/epistasis-physical-capacity-related-genes-and-exceptional-longevity-fndc5-gene-interactions-with-candidate-genes-foxoa3-and-apoe
#6
Noriyuki Fuku, Roberto Díaz-Peña, Yasumichi Arai, Yukiko Abe, Hirofumi Zempo, Hisashi Naito, Haruka Murakami, Motohiko Miyachi, Carlos Spuch, José A Serra-Rexach, Enzo Emanuele, Nobuyoshi Hirose, Alejandro Lucia
BACKGROUND: Forkhead box O3A (FOXOA3) and apolipoprotein E (APOE) are arguably the strongest gene candidates to influence human exceptional longevity (EL, i.e., being a centenarian), but inconsistency exists among cohorts. Epistasis, defined as the effect of one locus being dependent on the presence of 'modifier genes', may contribute to explain the missing heritability of complex phenotypes such as EL. We assessed the potential association of epistasis among candidate polymorphisms related to physical capacity, as well as antioxidant defense and cardiometabolic traits, and EL in the Japanese population...
November 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29136190/the-genotype-phenotype-relationships-in-the-light-of-natural-selection
#7
Han Chen, Chung-I Wu, Xionglei He
Although any genotype-phenotype relationships are a result of evolution, little is known about how natural selection and neutral drift, two distinct driving forces of evolution, operate to shape the relationships. By analysing ∼500 yeast quantitative traits we reveal a basic "supervisor-worker" gene architecture underlying a trait. Supervisors are often identified by "perturbational" approaches (such as gene deletion), while workers, which usually show small and statistically insignificant deletion effects, are tracked primarily by "observational" approaches that examine the correlation between gene activity and trait value across a number of conditions...
November 9, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29130883/regulatory-network-structure-determines-patterns-of-intermolecular-epistasis
#8
Mato Lagator, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, Călin C Guet
Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site...
November 13, 2017: ELife
https://www.readbyqxmd.com/read/29127445/negative-epistasis-in-experimental-rna-fitness-landscapes
#9
REVIEW
Devin P Bendixsen, Bjørn Østman, Eric J Hayden
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast...
November 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29114909/an-ancestry-based-approach-for-detecting-interactions
#10
Danny S Park, Itamar Eskin, Eun Yong Kang, Eric R Gamazon, Celeste Eng, Christopher R Gignoux, Joshua M Galanter, Esteban Burchard, Chun J Ye, Hugues Aschard, Eleazar Eskin, Eran Halperin, Noah Zaitlen
BACKGROUND: Epistasis and gene-environment interactions are known to contribute significantly to variation of complex phenotypes in model organisms. However, their identification in human association studies remains challenging for myriad reasons. In the case of epistatic interactions, the large number of potential interacting sets of genes presents computational, multiple hypothesis correction, and other statistical power issues. In the case of gene-environment interactions, the lack of consistently measured environmental covariates in most disease studies precludes searching for interactions and creates difficulties for replicating studies...
November 8, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/29114080/a-role-for-the-f-box-protein-hawaiian-skirt-in-plant-microrna-function
#11
Patricia L M Lang, Michael D Christie, Ezgi S Dogan, Rebecca Schwab, Jörg Hagmann, Anna-Lena Van de Weyer, Detlef Weigel, Emanuele Scacchi
As regulators of gene expression in multicellular organisms, microRNAs (miRNAs) are crucial for growth and development. While a plethora of factors involved in their biogenesis and action in Arabidopsis thaliana has been described, these processes and their fine-tuning are not fully understood. Here, we used plants expressing an artificial miRNA target mimic (MIM) to screen for negative regulators of miR156. We identified a new mutant allele of the F-box gene HAWAIIAN SKIRT (HWS; At3G61590), hws-5, as a suppressor of the MIM156-induced developmental and molecular phenotypes...
November 7, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29113978/additive-phenotypes-underlie-epistasis-of-fitness-effects
#12
Andrew M Sackman, Darin R Rokyta
Gene interactions, or epistasis, play a large role in determining evolutionary outcomes. The ruggedness of fitness landscapes, and thus the predictability of evolution and the accessibility of high-fitness genotypes, is determined largely by the pervasiveness of epistasis and the degree of correlation between similar genotypes. We created all possible pairings of three sets of five beneficial first-step mutations fixed during adaptive walks under three different regimes: selection on growth rate alone, on growth rate and thermal stability, and on growth rate and pH stability...
November 7, 2017: Genetics
https://www.readbyqxmd.com/read/29112968/fitness-cost-of-reassortment-in-human-influenza
#13
Mara Villa, Michael Lässig
Reassortment, which is the exchange of genome sequence between viruses co-infecting a host cell, plays an important role in the evolution of segmented viruses. In the human influenza virus, reassortment happens most frequently between co-existing variants within the same lineage. This process breaks genetic linkage and fitness correlations between viral genome segments, but the resulting net effect on viral fitness has remained unclear. In this paper, we determine rate and average selective effect of reassortment processes in the human influenza lineage A/H3N2...
November 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29100081/compensatory-mutations-and-epistasis-for-protein-function
#14
REVIEW
Jay F Storz
Adaptive protein evolution may be facilitated by neutral amino acid mutations that confer no benefit when they first arise but which potentiate subsequent function-altering mutations via direct or indirect structural mechanisms. Theoretical and empirical results indicate that such compensatory interactions (intramolecular epistasis) can exert a strong influence on trajectories of protein evolution. For this reason, assessing the form and prevalence of intramolecular epistasis and characterizing biophysical mechanisms of compensatory interaction are important research goals at the nexus of structural biology and molecular evolution...
November 5, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29078365/molecular-ensembles-make-evolution-unpredictable
#15
Zachary R Sailer, Michael J Harms
Evolutionary prediction is of deep practical and philosophical importance. Here we show, using a simple computational protein model, that protein evolution remains unpredictable, even if one knows the effects of all mutations in an ancestral protein background. We performed a virtual deep mutational scan-revealing the individual and pairwise epistatic effects of every mutation to our model protein-and then used this information to predict evolutionary trajectories. Our predictions were poor. This is a consequence of statistical thermodynamics...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29077520/marr-family-transcription-factor-hpar-controls-expression-of-the-vgrr-vgrs-operon-of-xanthomonas-campestris-pv-campestris
#16
Yue Pan, Fang Liang, Ru-Jiao Li, Wei Qian
MarR-family transcription factors (TFs), which regulate the expression of virulence factors and other physiological pathways in pathogenic bacteria, are regarded as ideal molecular targets for the development of novel antimicrobial strategies. In the plant bacterial pathogen Xanthomonas campestris pv. campestris, HpaR, a typical MarR-family TF, is associated with bacterial virulence, but its mechanism of virulence regulation remains unclear. Here, we dissected the HpaR regulon using high-throughput RNA sequencing and chromatin immunoprecipitation sequencing...
October 27, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29075131/diversity-and-evolution-of-drug-resistance-mechanisms-in-mycobacterium-tuberculosis
#17
REVIEW
Mashael Al-Saeedi, Sahal Al-Hajoj
Despite the efficacy of antibiotics to protect humankind against many deadly pathogens, such as Mycobacterium tuberculosis, nothing can prevent the emergence of drug-resistant strains. Several mechanisms facilitate drug resistance in M. tuberculosis including compensatory evolution, epistasis, clonal interference, cell wall integrity, efflux pumps, and target mimicry. In this study, we present recent findings relevant to these mechanisms, which can enable the discovery of new drug targets and subsequent development of novel drugs for treatment of drug-resistant M...
2017: Infection and Drug Resistance
https://www.readbyqxmd.com/read/29066469/polygenicity-and-epistasis-underlie-fitness-proximal-traits-in-the-caenorhabditis-elegans-multiparental-experimental-evolution-cemee-panel
#18
Luke M Noble, Ivo Chelo, Thiago Guzella, Bruno Afonso, David D Riccardi, Patrick Ammerman, Adel Dayarian, Sara Carvalho, Anna Crist, Ania Pino-Querido, Boris Shraiman, Matthew V Rockman, Henrique Teotónio
Understanding the genetic basis of complex traits remains a major challenge in biology. Polygenicity, phenotypic plasticity and epistasis contribute to phenotypic variance in ways that are rarely clear. This uncertainty can be problematic for estimating heritability, for predicting individual phenotypes from genomic data, and for parameterizing models of phenotypic evolution. Here we report an advanced recombinant inbred line (RIL) quantitative trait locus (QTL) mapping panel for the hermaphroditic nematode Caenorhabditis elegans, the C...
October 24, 2017: Genetics
https://www.readbyqxmd.com/read/29062121/sequence-entropy-of-folding-and-the-absolute-rate-of-amino-acid-substitutions
#19
Richard A Goldstein, David D Pollock
Adequate representations of protein evolution should consider how the acceptance of mutations depends on the sequence context in which they arise. However, epistatic interactions among sites in a protein result in hererogeneities in the substitution rate, both temporal and spatial, that are beyond the capabilities of current models. Here we use parallels between amino acid substitutions and chemical reaction kinetics to develop an improved theory of protein evolution. We constructed a mechanistic framework for modelling amino acid substitution rates that uses the formalisms of statistical mechanics, with principles of population genetics underlying the analysis...
October 23, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29057891/exhaustive-search-for-epistatic-effects-on-the-human-methylome
#20
Tobias Egli, Vanja Vukojevic, Thierry Sengstag, Martin Jacquot, Rubén Cabezón, David Coynel, Virginie Freytag, Angela Heck, Christian Vogler, Dominique J-F de Quervain, Andreas Papassotiropoulos, Annette Milnik
Studies assessing the existence and magnitude of epistatic effects on complex human traits provide inconclusive results. The study of such effects is complicated by considerable increase in computational burden, model complexity, and model uncertainty, which in concert decrease model stability. An additional source introducing significant uncertainty with regard to the detection of robust epistasis is the biological distance between the genetic variation and the trait under study. Here we studied CpG methylation, a genetically complex molecular trait that is particularly close to genomic variation, and performed an exhaustive search for two-locus epistatic effects on the CpG-methylation signal in two cohorts of healthy young subjects...
October 20, 2017: Scientific Reports
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