期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 26, 期 7, 页码 1571-1580出版社
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msp070
关键词
codon usage bias; optimal codon; protein structure; protein evolution; translational accuracy selection
资金
- NIH [R01 AI065960]
- NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES [R01AI065960] Funding Source: NIH RePORTER
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 (delta delta 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.
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