Optimal codon identities in bacteria: implications from the conflicting results of two different methods.

A correlation method was recently adopted to identify selection-favored 'optimal' codons from 675 bacterial genomes. Surprisingly, the identities of these optimal codons were found to track the bacterial GC content, leading to a conclusion that selection would generally shape the codon usa...

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Autores principales:	Bin Wang, Zhu-Qing Shao, Ying Xu, Jing Liu, Yuan Liu, Yue-Yu Hang, Jian-Qun Chen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8872ea99ead84b78b16d3c2f505b27e8
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spelling	oai:doaj.org-article:8872ea99ead84b78b16d3c2f505b27e82021-11-18T06:49:09ZOptimal codon identities in bacteria: implications from the conflicting results of two different methods.1932-620310.1371/journal.pone.0022714https://doaj.org/article/8872ea99ead84b78b16d3c2f505b27e82011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21829489/?tool=EBIhttps://doaj.org/toc/1932-6203A correlation method was recently adopted to identify selection-favored 'optimal' codons from 675 bacterial genomes. Surprisingly, the identities of these optimal codons were found to track the bacterial GC content, leading to a conclusion that selection would generally shape the codon usages to the same direction as the overall mutation does. Raising several concerns, here we report a thorough comparative study on 203 well-selected bacterial species, which strongly suggest that the previous conclusion is likely an illusion. Firstly, the previous study did not preclude species that are suffering weak or no selection pressures on their codon usages. For these species, as showed in this study, the optimal codon identities are prone to be incorrect and follow GC content. Secondly, the previous study only adopted the correlation method, without considering another method to test the reliability of inferred optimal codons. Actually by definition, optimal codons can also be identified by simply comparing codon usages between high- and low-expression genes. After using both methods to identify optimal codons for the selected species, we obtained highly conflicting results, suggesting at least one method is misleading. Further we found a critical problem of correlation method at the step of calculating gene bias level. Due to a failure of accurately defining the background mutation, the problem would result in wrong optimal codon identities. In other words, partial mutational effects on codon choices were mistakenly regarded as selective influences, leading to incorrect and biased optimal codon identities. Finally, considering the translational dynamics, optimal codons identified by comparison method can be well-explained by tRNA compositions, whereas optimal codons identified by correlation method can not be. For all above reasons, we conclude that real optimal codons actually do not track the genomic GC content, and correlation method is misleading in identifying optimal codons and better be avoided.Bin WangZhu-Qing ShaoYing XuJing LiuYuan LiuYue-Yu HangJian-Qun ChenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 7, p e22714 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bin Wang Zhu-Qing Shao Ying Xu Jing Liu Yuan Liu Yue-Yu Hang Jian-Qun Chen Optimal codon identities in bacteria: implications from the conflicting results of two different methods.
description	A correlation method was recently adopted to identify selection-favored 'optimal' codons from 675 bacterial genomes. Surprisingly, the identities of these optimal codons were found to track the bacterial GC content, leading to a conclusion that selection would generally shape the codon usages to the same direction as the overall mutation does. Raising several concerns, here we report a thorough comparative study on 203 well-selected bacterial species, which strongly suggest that the previous conclusion is likely an illusion. Firstly, the previous study did not preclude species that are suffering weak or no selection pressures on their codon usages. For these species, as showed in this study, the optimal codon identities are prone to be incorrect and follow GC content. Secondly, the previous study only adopted the correlation method, without considering another method to test the reliability of inferred optimal codons. Actually by definition, optimal codons can also be identified by simply comparing codon usages between high- and low-expression genes. After using both methods to identify optimal codons for the selected species, we obtained highly conflicting results, suggesting at least one method is misleading. Further we found a critical problem of correlation method at the step of calculating gene bias level. Due to a failure of accurately defining the background mutation, the problem would result in wrong optimal codon identities. In other words, partial mutational effects on codon choices were mistakenly regarded as selective influences, leading to incorrect and biased optimal codon identities. Finally, considering the translational dynamics, optimal codons identified by comparison method can be well-explained by tRNA compositions, whereas optimal codons identified by correlation method can not be. For all above reasons, we conclude that real optimal codons actually do not track the genomic GC content, and correlation method is misleading in identifying optimal codons and better be avoided.
format	article
author	Bin Wang Zhu-Qing Shao Ying Xu Jing Liu Yuan Liu Yue-Yu Hang Jian-Qun Chen
author_facet	Bin Wang Zhu-Qing Shao Ying Xu Jing Liu Yuan Liu Yue-Yu Hang Jian-Qun Chen
author_sort	Bin Wang
title	Optimal codon identities in bacteria: implications from the conflicting results of two different methods.
title_short	Optimal codon identities in bacteria: implications from the conflicting results of two different methods.
title_full	Optimal codon identities in bacteria: implications from the conflicting results of two different methods.
title_fullStr	Optimal codon identities in bacteria: implications from the conflicting results of two different methods.
title_full_unstemmed	Optimal codon identities in bacteria: implications from the conflicting results of two different methods.
title_sort	optimal codon identities in bacteria: implications from the conflicting results of two different methods.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/8872ea99ead84b78b16d3c2f505b27e8
work_keys_str_mv	AT binwang optimalcodonidentitiesinbacteriaimplicationsfromtheconflictingresultsoftwodifferentmethods AT zhuqingshao optimalcodonidentitiesinbacteriaimplicationsfromtheconflictingresultsoftwodifferentmethods AT yingxu optimalcodonidentitiesinbacteriaimplicationsfromtheconflictingresultsoftwodifferentmethods AT jingliu optimalcodonidentitiesinbacteriaimplicationsfromtheconflictingresultsoftwodifferentmethods AT yuanliu optimalcodonidentitiesinbacteriaimplicationsfromtheconflictingresultsoftwodifferentmethods AT yueyuhang optimalcodonidentitiesinbacteriaimplicationsfromtheconflictingresultsoftwodifferentmethods AT jianqunchen optimalcodonidentitiesinbacteriaimplicationsfromtheconflictingresultsoftwodifferentmethods
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Optimal codon identities in bacteria: implications from the conflicting results of two different methods.

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