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Selection on codon usage for error minimization at the protein level.

Marco Archetti¹

¹Département de Biologie, Section Ecologie et Evolution, Université de Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland. marco.archetti@unifr.ch

Journal of Molecular Evolution

|November 24, 2004

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Genes in fruit flies and rodents show a preference for specific DNA building blocks (codons) that reduce errors during protein production. This suggests natural selection favors error minimization in coding sequences.

Area of Science:

Evolutionary biology
Genetics
Molecular biology

Background:

Synonymous codons vary in their ability to mitigate mutation and mistranslation errors.
This variation may influence codon preference in protein-coding genes to minimize protein-level error impact.

Purpose of the Study:

To investigate if protein-coding genes exhibit a preference for codons that minimize errors.
To explore the relationship between codon error minimization and factors like CG content, codon usage bias, and nucleotide substitution rates.

Main Methods:

Developed a theoretical measure of codon error minimization based on amino acid similarity.
Calculated the degree of error minimization for genes in Drosophila melanogaster and rodents.
Analyzed correlations between error minimization, CG content, codon usage bias, and nucleotide substitution rates.

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Main Results:

Drosophila and rodent genes preferentially use codons that minimize errors.
This preference is not solely attributable to mutation bias.
Error minimization correlates with codon usage bias and nonsynonymous substitution rates.

Conclusions:

Natural selection for protein-level error minimization influences the evolution of coding sequences in Drosophila and rodents.
The findings highlight a selective pressure acting on codon usage beyond simple mutation or translation efficiency.