Translation Comes First: Ancient and Convergent Selection of Codon Usage Bias Across Prokaryotic Genomes.
Codon usage
Genome evolution
Prokaryotes
Translational selection
Journal
Journal of molecular evolution
ISSN: 1432-1432
Titre abrégé: J Mol Evol
Pays: Germany
ID NLM: 0360051
Informations de publication
Date de publication:
12 2022
12 2022
Historique:
received:
09
03
2022
accepted:
12
09
2022
pubmed:
27
9
2022
medline:
11
11
2022
entrez:
26
9
2022
Statut:
ppublish
Résumé
Codon usage is the outcome of different evolutionary processes and can inform us about the conditions in which organisms live and evolve. Here, we present R_ENC', which is an improvement to the original S index developed by dos Reis et al. (2004). Our index is less sensitive to G+C content, which greatly affects synonymous codon usage in prokaryotes, making it better suited to detect selection acting on codon usage. We used R_ENC' to estimate the extent of selected codon usage bias in 1800 genomes representing 26 prokaryotic phyla. We found that Gammaproteobacteria, Betaproteobacteria, Actinobacteria, and Firmicutes are the phyla/subphyla showing more genomes with selected codon usage bias. In particular, we found that several lineages within Gammaproteobacteria and Firmicutes show a similar set of functional terms enriched in genes under selected codon usage bias, indicating convergent evolution. We also show that selected codon usage bias tends to evolve in genes coding for the translation machinery before other functional GO terms. Finally, we discuss the possibility to use R_ENC' to predict whether lineages evolved in copiotrophic or oligotrophic environments.
Identifiants
pubmed: 36156124
doi: 10.1007/s00239-022-10074-0
pii: 10.1007/s00239-022-10074-0
doi:
Substances chimiques
Codon
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
438-451Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
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