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Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome

Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalact...

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Autores principales: Ma, Yan-Ping, Ke, Hao, Liang, Zhi-Ling, Liu, Zhen-Xing, Hao, Le, Ma, Jiang-Yao, Li, Yu-Gu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813141/
https://www.ncbi.nlm.nih.gov/pubmed/26927064
http://dx.doi.org/10.3390/ijms17030277
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author Ma, Yan-Ping
Ke, Hao
Liang, Zhi-Ling
Liu, Zhen-Xing
Hao, Le
Ma, Jiang-Yao
Li, Yu-Gu
author_facet Ma, Yan-Ping
Ke, Hao
Liang, Zhi-Ling
Liu, Zhen-Xing
Hao, Le
Ma, Jiang-Yao
Li, Yu-Gu
author_sort Ma, Yan-Ping
collection PubMed
description Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts.
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spelling pubmed-48131412016-04-06 Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome Ma, Yan-Ping Ke, Hao Liang, Zhi-Ling Liu, Zhen-Xing Hao, Le Ma, Jiang-Yao Li, Yu-Gu Int J Mol Sci Article Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts. MDPI 2016-02-24 /pmc/articles/PMC4813141/ /pubmed/26927064 http://dx.doi.org/10.3390/ijms17030277 Text en © 2016 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons by Attribution (CC-BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ma, Yan-Ping
Ke, Hao
Liang, Zhi-Ling
Liu, Zhen-Xing
Hao, Le
Ma, Jiang-Yao
Li, Yu-Gu
Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome
title Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome
title_full Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome
title_fullStr Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome
title_full_unstemmed Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome
title_short Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome
title_sort multiple evolutionary selections involved in synonymous codon usages in the streptococcus agalactiae genome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4813141/
https://www.ncbi.nlm.nih.gov/pubmed/26927064
http://dx.doi.org/10.3390/ijms17030277
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