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Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids

Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here,...

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Detalles Bibliográficos
Autores principales: Wald, Naama, Alroy, Maya, Botzman, Maya, Margalit, Hanah
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424539/
https://www.ncbi.nlm.nih.gov/pubmed/22581775
http://dx.doi.org/10.1093/nar/gks348
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author Wald, Naama
Alroy, Maya
Botzman, Maya
Margalit, Hanah
author_facet Wald, Naama
Alroy, Maya
Botzman, Maya
Margalit, Hanah
author_sort Wald, Naama
collection PubMed
description Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon–anticodon interaction, all consistent with more efficient translation.
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spelling pubmed-34245392012-08-22 Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids Wald, Naama Alroy, Maya Botzman, Maya Margalit, Hanah Nucleic Acids Res Computational Biology Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon–anticodon interaction, all consistent with more efficient translation. Oxford University Press 2012-08 2012-05-11 /pmc/articles/PMC3424539/ /pubmed/22581775 http://dx.doi.org/10.1093/nar/gks348 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Computational Biology
Wald, Naama
Alroy, Maya
Botzman, Maya
Margalit, Hanah
Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids
title Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids
title_full Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids
title_fullStr Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids
title_full_unstemmed Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids
title_short Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids
title_sort codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids
topic Computational Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3424539/
https://www.ncbi.nlm.nih.gov/pubmed/22581775
http://dx.doi.org/10.1093/nar/gks348
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