Epistasis and evolution: recent advances and an outlook for prediction

BMC Biology, Год журнала: 2023, Номер 21(1)

Опубликована: Май 24, 2023

Abstract As organisms evolve, the effects of mutations change as a result epistatic interactions with other accumulated along line descent. This can lead to shifts in adaptability or robustness that ultimately shape subsequent evolution. Here, we review recent advances measuring, modeling, and predicting epistasis evolutionary trajectories, both microbial cells single proteins. We focus on simple patterns global emerge this data, which be predicted by small number variables. The emergence these offers promise for efforts model predict

Язык: Английский

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Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation

eLife, Год журнала: 2020, Номер 9

Опубликована: Дек. 2, 2020

Building a genotype-phenotype-fitness map of adaptation is central goal in evolutionary biology. It difficult even when adaptive mutations are known because it hard to enumerate which phenotypes make these adaptive. We address this problem by first quantifying how the fitness hundreds yeast mutants responds subtle environmental shifts. then model number collectively influence decomposing patterns variation. find that small inferred can predict near their original glucose-limited evolution condition. Importantly, matter little at or condition strongly distant environments. This suggests locally modular - affecting environment where they evolved yet globally pleiotropic additional may reduce improve new

Язык: Английский

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Cohesion is established during DNA replication utilising chromosome associated cohesin rings as well as those loaded de novo onto nascent DNAs

eLife, Год журнала: 2020, Номер 9

Опубликована: Июнь 9, 2020

Sister chromatid cohesion essential for mitotic chromosome segregation is thought to involve the co-entrapment of sister DNAs within cohesin rings. Although can load onto chromosomes throughout cell cycle, it only builds during S phase. A key question whether generated by conversion complexes associated with un-replicated ahead replication forks into cohesive structures behind them, or from nucleoplasmic that loaded de novo nascent forks, a process would be dependent on cohesin’s Scc2 subunit. We show here in S. cerevisiae, both mechanisms exist and each requires different set replisome-associated proteins. Cohesion produced Tof1/Csm3, Ctf4 Chl1 but not while created Scc2-dependent loading at Ctf18-RFC complex. The association specific replisome proteins types establishment opens way mechanistic understanding an aspect DNA unique eukaryotic cells.

Язык: Английский

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Experimental evolution of dispersal: Unifying theory, experiments and natural systems

Journal of Animal Ecology, Год журнала: 2023, Номер 92(6), С. 1113 - 1123

Опубликована: Апрель 23, 2023

Abstract Dispersal is a central life history trait that affects the ecological and evolutionary dynamics of populations communities. The recent use experimental evolution for study dispersal promising avenue demonstrating valuable proofs concept, bringing insight into alternative strategies trade‐offs, testing repeatability outcomes. Practical constraints restrict studies to set typically small, short‐lived organisms reared in artificial laboratory conditions. Here, we argue despite these restrictions, inferences from can reinforce links between theoretical predictions empirical observations advance our understanding eco‐evolutionary consequences dispersal. We illustrate how applying an integrative framework theory, natural systems improve under more complex realistic biological scenarios, such as role biotic interactions syndromes.

Язык: Английский

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Evolutionary Repair Experiments as a Window to the Molecular Diversity of Life

Current Biology, Год журнала: 2020, Номер 30(10), С. R565 - R574

Опубликована: Май 1, 2020

Язык: Английский

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The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress

eLife, Год журнала: 2020, Номер 9

Опубликована: Фев. 11, 2020

Many biological features are conserved and thus considered to be resistant evolutionary change. While rapid genetic adaptation following the removal of genes has been observed, we often lack a mechanistic understanding how happens. We used budding yeast, Saccharomyces cerevisiae, investigate plasticity chromosome metabolism, network modules. experimentally evolved cells constitutively experiencing DNA replication stress caused by absence Ctf4, protein that coordinates enzymatic activities at forks. Parallel populations adapted stress, over 1000 generations, acquiring multiple, concerted mutations. These mutations altered two metabolism modules, sister chromatid cohesion, inactivated third, damage checkpoint. The selected define functionally reproducible trajectory. suggest implications for genome evolution in natural cancer.All plants, animals fungi share common ancestor, though they have become very distinct billions years, all essential machinery needed grow divide. At heart this is complex interaction proteins involved replication, process duplicating material every time cell divides. needs done with great care, error rates as small one mistake billion. Otherwise, can accumulate genome, causing problems long-term survival. Despite overall principles remaining same, underlying mechanisms vary across different organisms. Given precision complexity replicating DNA, it was not clear had differences. Fumasoni Murray set out answer forcing strain yeast evolve removing gene an important, but essential, component replication. were still able reproduce, hampered mutation. studied after reproduced thousand giving enough acquire new would allow compensate initial defects. In eight separate samples, made many same changes order overcome original segregation third feature normally protect against accumulation damaged DNA. findings show pathways controlled, laboratory environment quickly processes damaged. behavior mutated mimicked cancer cells, which struggling adapt their machinery. Studying follows perturbations could help researchers better deal challenges treatment development antibiotic resistance bacteria, well leading deeper both biology.

Язык: Английский

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Can gene-inactivating mutations lead to evolutionary novelty?

Current Biology, Год журнала: 2020, Номер 30(10), С. R465 - R471

Опубликована: Май 1, 2020

Язык: Английский

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Evolutionary stalling and a limit on the power of natural selection to improve a cellular module

Proceedings of the National Academy of Sciences, Год журнала: 2020, Номер 117(31), С. 18582 - 18590

Опубликована: Июль 17, 2020

Significance Cellular modules, such as the translation machinery (TM), are key units of adaptive evolution because fitness depends on their performance. In rapidly evolving populations, natural selection may not be able to improve all modules simultaneously mutations in different compete against each other. We hypothesize that adaptation some would stall, despite availability beneficial mutations. empirically demonstrate evolutionary stalling TM module experimental populations Escherichia coli . Natural initially improved TM, but its focus shifted away other cellular before TM’s performance was fully restored. This work shows rapid shifts can slow down improvement individual components nature.

Язык: Английский

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Mutational robustness changes during long-term adaptation in laboratory budding yeast populations

eLife, Год журнала: 2022, Номер 11

Опубликована: Июль 26, 2022

As an adapting population traverses the fitness landscape, its local neighborhood (i.e., collection of effects single-step mutations) can change shape because interactions with mutations acquired during evolution. These changes to distribution affect both rate adaptation and accumulation deleterious mutations. However, while numerous models landscapes have been proposed in literature, empirical data on how this evolution remains limited. In study, we directly measure landscape laboratory adaptation. Using a barcode-based mutagenesis system, 91 specific gene disruption genetic backgrounds spanning 8000-10,000 generations two constant environments. We find that mean decreases one environment, indicating reduction mutational robustness, but does not other. show these distribution-level patterns result from differences relative frequency certain epistasis at level individual mutations, including fitness-correlated idiosyncratic epistasis.

Язык: Английский

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Metaboverse enables automated discovery and visualization of diverse metabolic regulatory patterns

Nature Cell Biology, Год журнала: 2023, Номер 25(4), С. 616 - 625

Опубликована: Апрель 1, 2023

Abstract Metabolism is intertwined with various cellular processes, including controlling cell fate, influencing tumorigenesis, participating in stress responses and more. a complex, interdependent network, local perturbations can have indirect effects that are pervasive across the metabolic network. Current analytical technical limitations long created bottleneck data interpretation. To address these shortcomings, we developed Metaboverse, user-friendly tool to facilitate exploration hypothesis generation. Here introduce algorithms leverage network extract complex reaction patterns from data. minimize impact of missing measurements within methods enable pattern recognition multiple reactions. Using identify previously undescribed metabolite signature correlated survival outcomes early stage lung adenocarcinoma patients. yeast model, suggesting an adaptive role citrate homeostasis during mitochondrial dysfunction facilitated by transporter, Ctp1. We demonstrate Metaboverse augments user’s ability meaningful multi-omics datasets develop actionable hypotheses.

Язык: Английский

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