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Selection on Codon Usage for Error Minimization at the Protein Level

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Abstract

Given the structure of the genetic code, synonymous codons differ in their capacity to minimize the effects of errors due to mutation or mistranslation. I suggest that this may lead, in protein-coding genes, to a preference for codons that minimize the impact of errors at the protein level. I develop a theoretical measure of error minimization for each codon, based on amino acid similarity. This measure is used to calculate the degree of error minimization for 82 genes of Drosophila melanogaster and 432 rodent genes and to study its relationship with CG content, the degree of codon usage bias, and the rate of nucleotide substitution. I show that (i) Drosophila and rodent genes tend to prefer codons that minimize errors; (ii) this cannot be merely the effect of mutation bias; (iii) the degree of error minimization is correlated with the degree of codon usage bias; (iv) the amino acids that contribute more to codon usage bias are the ones for which synonymous codons differ more in the capacity to minimize errors; and (v) the degree of error minimization is correlated with the rate of nonsynonymous substitution. These results suggest that natural selection for error minimization at the protein level plays a role in the evolution of coding sequences in Drosophila and rodents.

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Acknowledgments

Nick Smith provided the substitution rates used by Smith and Hurst (1997).

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Authors and Affiliations

  1. Département de Biologie, Section Ecologie et Evolution, Université de Fribourg, Chemin du Musée, 10, 1700, Fribourg, Switzerland

    Marco Archetti

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  1. Marco Archetti
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Correspondence to Marco Archetti.

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Reviewing Editor: Dr. Massimo Di Giulio

Appendix

Appendix

Table AI wR N values for different values of the parameters for 82 Drosophila melanogaster genes
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Archetti, M. Selection on Codon Usage for Error Minimization at the Protein Level. J Mol Evol 59, 400–415 (2004). https://doi.org/10.1007/s00239-004-2634-7

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