Journal Article

Universal Pattern and Diverse Strengths of Successive Synonymous Codon Bias in Three Domains of Life, Particularly Among Prokaryotic Genomes

Feng-Biao Guo, Yuan-Nong Ye, Hai-Long Zhao, Dan Lin and Wen Wei

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 19, issue 6, pages 477-485
Published in print December 2012 | ISSN: 1340-2838
Published online November 2012 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dss027

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There has been significant progress in understanding the process of protein translation in recent years. One of the best examples is the discovery of usage bias in successive synonymous codons and its role in eukaryotic translation efficiency. We observed here a similar type of bias in the other two life domains, bacteria and archaea, although the bias strength was much smaller than in eukaryotes. Among 136 prokaryotic genomes, 98 were found to have significant bias from random use of successive synonymous codons with Z scores larger than three. Furthermore, significantly different bias strengths were found between prokaryotes grouped by various genomic or biochemical characteristics. Interestingly, the bias strength measured by a general Z score could be fitted well (R = 0.83, P < 10−15) by three genomic variables: genome size, G + C content, and tRNA gene number based on multiple linear regression. A different distribution of synonymous codon pairs between protein-coding genes and intergenic sequences suggests that bias is caused by translation selection. The present results indicate that protein translation is tuned by codon (pair) usage, and the intensity of the regulation is associated with genome size, tRNA gene number, and G + C content.

Keywords: successive synonymous codon bias; comparative analysis; prokaryotic genomes; Z scores; translation efficiency

Journal Article.  5049 words.  Illustrated.

Subjects: Genetics and Genomics

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