Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes.

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Serval ID
serval:BIB_41654EAEAB53
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes.
Journal
Nature communications
Author(s)
Vigué L., Croce G., Petitjean M., Ruppé E., Tenaillon O., Weigt M.
ISSN
2041-1723 (Electronic)
ISSN-L
2041-1723
Publication state
Published
Issued date
12/07/2022
Peer-reviewed
Oui
Volume
13
Number
1
Pages
4030
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Abstract
Characterizing the effect of mutations is key to understand the evolution of protein sequences and to separate neutral amino-acid changes from deleterious ones. Epistatic interactions between residues can lead to a context dependence of mutation effects. Context dependence constrains the amino-acid changes that can contribute to polymorphism in the short term, and the ones that can accumulate between species in the long term. We use computational approaches to accurately predict the polymorphisms segregating in a panel of 61,157 Escherichia coli genomes from the analysis of distant homologues. By comparing a context-aware Direct-Coupling Analysis modelling to a non-epistatic approach, we show that the genetic context strongly constrains the tolerable amino acids in 30% to 50% of amino-acid sites. The study of more distant species suggests the gradual build-up of genetic context over long evolutionary timescales by the accumulation of small epistatic contributions.
Keywords
Escherichia coli/genetics, Mutation, Polymorphism, Genetic
Pubmed
Open Access
Yes
Create date
19/07/2022 14:43
Last modification date
28/07/2022 6:36
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