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MBE Advance Access originally published online on November 13, 2006
Molecular Biology and Evolution 2007 24(2):374-381; doi:10.1093/molbev/msl166
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Synonymous Codon Usage in Escherichia coli: Selection for Translational Accuracy

Nina Stoletzki*,{dagger} and Adam Eyre-Walker{dagger},{ddagger}

* Ludwig-Maximilan Universität, Biocenter, Planegg-Martinsried, Germany
{dagger} Center for Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
{ddagger} National Evolutionary Synthesis Center, Durham, North Carolina

E-mail: nstoletzki{at}googlemail.com.

Accepted for publication November 2, 2006.

In many organisms, selection acts on synonymous codons to improve translation. However, the precise basis of this selection remains unclear in the majority of species. Selection could be acting to maximize the speed of elongation, to minimize the costs of proofreading, or to maximize the accuracy of translation. Using several data sets, we find evidence that codon use in Escherichia coli is biased to reduce the costs of both missense and nonsense translational errors. Highly conserved sites and genes have higher codon bias than less conserved ones, and codon bias is positively correlated to gene length and production costs, both indicating selection against missense errors. Additionally, codon bias increases along the length of genes, indicating selection against nonsense errors. Doublet mutations or replacement substitutions do not explain our observations. The correlations remain when we control for expression level and for conflicting selection pressures at the start and end of genes. Considering each amino acid by itself confirms our results. We conclude that selection on synonymous codon use in E. coli is largely due to selection for translational accuracy, to reduce the costs of both missense and nonsense errors.

Key Words: synonymous codon use • translational accuracy • translational selection

Kenneth Wolfe, Associate Editor


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