The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome.
Mycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M....
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doaj-44bbe582d6b640c5a60694d159bf3eb12020-11-25T01:24:21ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-01910e10894910.1371/journal.pone.0108949The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome.Jian-hua ZhouYao-zhong DingYing HeYue-feng ChuPing ZhaoLi-ya MaXin-jun WangXue-rui LiYong-sheng LiuMycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M. bovis (three strains' genomes) were analyzed. The overall nucleotide content of genes in the M. bovis genome is AT-rich. Although the G and C contents at the third codon position of genes in the leading strand differ from those in the lagging strand (p<0.05), the 59 synonymous codon usage patterns of genes in the leading strand are highly similar to those in the lagging strand. The over-represented codons and the under-represented codons were identified. A comparison of the synonymous codon usage pattern of M. bovis and cattle (susceptible host) indicated the independent formation of synonymous codon usage of M. bovis. Principal component analysis revealed that (i) strand-specific mutational bias fails to affect the synonymous codon usage pattern in the leading and lagging strands, (ii) mutation pressure from nucleotide content plays a role in shaping the overall codon usage, and (iii) the major trend of synonymous codon usage has a significant correlation with the gene expression level that is estimated by the codon adaptation index. The plot of the effective number of codons against the G+C content at the third codon position also reveals that mutation pressure undoubtedly contributes to the synonymous codon usage pattern of M. bovis. Additionally, the formation of the overall codon usage is determined by certain evolutionary selections for gene function classification (30S protein, 50S protein, transposase, membrane protein, and lipoprotein) and translation elongation region of genes in M. bovis. The information could be helpful in further investigations of evolutionary mechanisms of the Mycoplasma family and heterologous expression of its functionally important proteins.http://europepmc.org/articles/PMC4211681?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jian-hua Zhou Yao-zhong Ding Ying He Yue-feng Chu Ping Zhao Li-ya Ma Xin-jun Wang Xue-rui Li Yong-sheng Liu |
spellingShingle |
Jian-hua Zhou Yao-zhong Ding Ying He Yue-feng Chu Ping Zhao Li-ya Ma Xin-jun Wang Xue-rui Li Yong-sheng Liu The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. PLoS ONE |
author_facet |
Jian-hua Zhou Yao-zhong Ding Ying He Yue-feng Chu Ping Zhao Li-ya Ma Xin-jun Wang Xue-rui Li Yong-sheng Liu |
author_sort |
Jian-hua Zhou |
title |
The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. |
title_short |
The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. |
title_full |
The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. |
title_fullStr |
The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. |
title_full_unstemmed |
The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome. |
title_sort |
effect of multiple evolutionary selections on synonymous codon usage of genes in the mycoplasma bovis genome. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2014-01-01 |
description |
Mycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M. bovis (three strains' genomes) were analyzed. The overall nucleotide content of genes in the M. bovis genome is AT-rich. Although the G and C contents at the third codon position of genes in the leading strand differ from those in the lagging strand (p<0.05), the 59 synonymous codon usage patterns of genes in the leading strand are highly similar to those in the lagging strand. The over-represented codons and the under-represented codons were identified. A comparison of the synonymous codon usage pattern of M. bovis and cattle (susceptible host) indicated the independent formation of synonymous codon usage of M. bovis. Principal component analysis revealed that (i) strand-specific mutational bias fails to affect the synonymous codon usage pattern in the leading and lagging strands, (ii) mutation pressure from nucleotide content plays a role in shaping the overall codon usage, and (iii) the major trend of synonymous codon usage has a significant correlation with the gene expression level that is estimated by the codon adaptation index. The plot of the effective number of codons against the G+C content at the third codon position also reveals that mutation pressure undoubtedly contributes to the synonymous codon usage pattern of M. bovis. Additionally, the formation of the overall codon usage is determined by certain evolutionary selections for gene function classification (30S protein, 50S protein, transposase, membrane protein, and lipoprotein) and translation elongation region of genes in M. bovis. The information could be helpful in further investigations of evolutionary mechanisms of the Mycoplasma family and heterologous expression of its functionally important proteins. |
url |
http://europepmc.org/articles/PMC4211681?pdf=render |
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