Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content

Abstract Inconsistent results on the association between evolutionary rates and amino acid composition of proteins have been reported in eukaryotes. However, there are few studies of how amino acid composition can influence evolutionary rates in bacteria. Thus, we constructed linear regression model...

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Autores principales:	Meng-Ze Du, Shuo Liu, Zhi Zeng, Labena Abraham Alemayehu, Wen Wei, Feng-Biao Guo
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/da1d30670e0f42e39817cfcbccaa00a1
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spelling	oai:doaj.org-article:da1d30670e0f42e39817cfcbccaa00a12021-12-02T16:08:04ZAmino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content10.1038/s41598-018-25364-12045-2322https://doaj.org/article/da1d30670e0f42e39817cfcbccaa00a12018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-25364-1https://doaj.org/toc/2045-2322Abstract Inconsistent results on the association between evolutionary rates and amino acid composition of proteins have been reported in eukaryotes. However, there are few studies of how amino acid composition can influence evolutionary rates in bacteria. Thus, we constructed linear regression models between composition frequencies of amino acids and evolutionary rates for bacteria. Compositions of all amino acids can on average explain 21.5% of the variation in evolutionary rates among 273 investigated bacterial organisms. In five model organisms, amino acid composition contributes more to variation in evolutionary rates than protein abundance, and frequency of optimal codons. The contribution of individual amino acid composition to evolutionary rate varies among organisms. The closer the GC-content of genome to its maximum or minimum, the better the correlation between the amino acid content and the evolutionary rate of proteins would appear in that genome. The types of amino acids that significantly contribute to evolutionary rates can be grouped into GC-rich and AT-rich amino acids. Besides, the amino acid with high composition also contributes more to evolutionary rates than amino acid with low composition in proteome. In summary, amino acid composition significantly contributes to the rate of evolution in bacterial organisms and this in turn is impacted by GC-content.Meng-Ze DuShuo LiuZhi ZengLabena Abraham AlemayehuWen WeiFeng-Biao GuoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-9 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Meng-Ze Du Shuo Liu Zhi Zeng Labena Abraham Alemayehu Wen Wei Feng-Biao Guo Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content
description	Abstract Inconsistent results on the association between evolutionary rates and amino acid composition of proteins have been reported in eukaryotes. However, there are few studies of how amino acid composition can influence evolutionary rates in bacteria. Thus, we constructed linear regression models between composition frequencies of amino acids and evolutionary rates for bacteria. Compositions of all amino acids can on average explain 21.5% of the variation in evolutionary rates among 273 investigated bacterial organisms. In five model organisms, amino acid composition contributes more to variation in evolutionary rates than protein abundance, and frequency of optimal codons. The contribution of individual amino acid composition to evolutionary rate varies among organisms. The closer the GC-content of genome to its maximum or minimum, the better the correlation between the amino acid content and the evolutionary rate of proteins would appear in that genome. The types of amino acids that significantly contribute to evolutionary rates can be grouped into GC-rich and AT-rich amino acids. Besides, the amino acid with high composition also contributes more to evolutionary rates than amino acid with low composition in proteome. In summary, amino acid composition significantly contributes to the rate of evolution in bacterial organisms and this in turn is impacted by GC-content.
format	article
author	Meng-Ze Du Shuo Liu Zhi Zeng Labena Abraham Alemayehu Wen Wei Feng-Biao Guo
author_facet	Meng-Ze Du Shuo Liu Zhi Zeng Labena Abraham Alemayehu Wen Wei Feng-Biao Guo
author_sort	Meng-Ze Du
title	Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content
title_short	Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content
title_full	Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content
title_fullStr	Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content
title_full_unstemmed	Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content
title_sort	amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic gc content
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/da1d30670e0f42e39817cfcbccaa00a1
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Amino acid compositions contribute to the proteins’ evolution under the influence of their abundances and genomic GC content

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