MBE Advance Access originally published online on April 6, 2009
Molecular Biology and Evolution 2009 26(7):1571-1580; doi:10.1093/molbev/msp070
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Research Articles |
Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins
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* Center for Computational Biology and Bioinformatics, The University of Texas at Austin
Section of Integrative Biology, The University of Texas at Austin
Institute for Cell and Molecular Biology, The University of Texas at Austin
E-mail: cwilke{at}mail.utexas.edu.
Accepted for publication March 27, 2009.
The mistranslation-induced protein misfolding hypothesis predicts that selection should prefer high-fidelity codons at sites at which translation errors are structurally disruptive and lead to protein misfolding and aggregation. To test this hypothesis, we analyzed the relationship between codon usage bias and protein structure in the genomes of four model organisms, Escherichia coli, yeast, fly, and mouse. Using both the Mantel–Haenszel procedure, which applies to categorical data, and a newly developed association test for continuous variables, we find that translationally optimal codons associate with buried residues and also with residues at sites where mutations lead to large changes in free energy (
G). In each species, only a subset of all amino acids show this signal, but most amino acids show the signal in at least one species. By repeating the analysis on a reduced data set that excludes interdomain linkers, we show that our results are not caused by an association of rare codons with solvent-accessible linker regions. Finally, we find that our results depend weakly on expression level; the association between optimal codons and buried sites exists at all expression levels, but increases in strength as expression level increases.
Key Words: codon usage bias • optimal codon • protein structure • protein evolution • translational accuracy selection
Michele Vendruscolo, Associate Editor