A general model of codon bias due to GC mutational bias.

<h4>Background</h4>In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position,...

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Autores principales:	Gareth A Palidwor, Theodore J Perkins, Xuhua Xia
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e9a2077d48854f60bd975893266a6a1d
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spelling	oai:doaj.org-article:e9a2077d48854f60bd975893266a6a1d2021-11-18T07:02:49ZA general model of codon bias due to GC mutational bias.1932-620310.1371/journal.pone.0013431https://doaj.org/article/e9a2077d48854f60bd975893266a6a1d2010-10-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21048949/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position, the overall GC bias of a genome or genomic region is highly correlated with GC3, a measure of third position GC content. For individual amino acids as well, G/C ending codons usage generally increases with increasing GC bias and decreases with increasing AT bias. Arginine and leucine, amino acids that allow GC-changing synonymous substitutions in the first and third codon positions, have codons which may be expected to show different usage patterns.<h4>Principal findings</h4>In analyzing codon usage bias in hundreds of prokaryotic and plant genomes and in human genes, we find that two G-ending codons, AGG (arginine) and TTG (leucine), unlike all other G/C-ending codons, show overall usage that decreases with increasing GC bias, contrary to the usual expectation that G/C-ending codon usage should increase with increasing genomic GC bias. Moreover, the usage of some codons appears nonlinear, even nonmonotone, as a function of GC bias. To explain these observations, we propose a continuous-time Markov chain model of GC-biased synonymous substitution. This model correctly predicts the qualitative usage patterns of all codons, including nonlinear codon usage in isoleucine, arginine and leucine. The model accounts for 72%, 64% and 52% of the observed variability of codon usage in prokaryotes, plants and human respectively. When codons are grouped based on common GC content, 87%, 80% and 68% of the variation in usage is explained for prokaryotes, plants and human respectively.<h4>Conclusions</h4>The model clarifies the sometimes-counterintuitive effects that GC mutational bias can have on codon usage, quantifies the influence of GC mutational bias and provides a natural null model relative to which other influences on codon bias may be measured.Gareth A PalidworTheodore J PerkinsXuhua XiaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 10, p e13431 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gareth A Palidwor Theodore J Perkins Xuhua Xia A general model of codon bias due to GC mutational bias.
description	<h4>Background</h4>In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position, the overall GC bias of a genome or genomic region is highly correlated with GC3, a measure of third position GC content. For individual amino acids as well, G/C ending codons usage generally increases with increasing GC bias and decreases with increasing AT bias. Arginine and leucine, amino acids that allow GC-changing synonymous substitutions in the first and third codon positions, have codons which may be expected to show different usage patterns.<h4>Principal findings</h4>In analyzing codon usage bias in hundreds of prokaryotic and plant genomes and in human genes, we find that two G-ending codons, AGG (arginine) and TTG (leucine), unlike all other G/C-ending codons, show overall usage that decreases with increasing GC bias, contrary to the usual expectation that G/C-ending codon usage should increase with increasing genomic GC bias. Moreover, the usage of some codons appears nonlinear, even nonmonotone, as a function of GC bias. To explain these observations, we propose a continuous-time Markov chain model of GC-biased synonymous substitution. This model correctly predicts the qualitative usage patterns of all codons, including nonlinear codon usage in isoleucine, arginine and leucine. The model accounts for 72%, 64% and 52% of the observed variability of codon usage in prokaryotes, plants and human respectively. When codons are grouped based on common GC content, 87%, 80% and 68% of the variation in usage is explained for prokaryotes, plants and human respectively.<h4>Conclusions</h4>The model clarifies the sometimes-counterintuitive effects that GC mutational bias can have on codon usage, quantifies the influence of GC mutational bias and provides a natural null model relative to which other influences on codon bias may be measured.
format	article
author	Gareth A Palidwor Theodore J Perkins Xuhua Xia
author_facet	Gareth A Palidwor Theodore J Perkins Xuhua Xia
author_sort	Gareth A Palidwor
title	A general model of codon bias due to GC mutational bias.
title_short	A general model of codon bias due to GC mutational bias.
title_full	A general model of codon bias due to GC mutational bias.
title_fullStr	A general model of codon bias due to GC mutational bias.
title_full_unstemmed	A general model of codon bias due to GC mutational bias.
title_sort	general model of codon bias due to gc mutational bias.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/e9a2077d48854f60bd975893266a6a1d
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_version_	1718424013078790144

A general model of codon bias due to GC mutational bias.

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