The silent impact: codon usage bias and protein evolution in bacteria

Bias in synonymous codon usage has been reported across all kingdoms of life. Evidence across species suggests that codon usage bias is often driven by selective pressures, typically for translational efficiency. These selective pressures have been shown to depress the rate at which synonymous sites evolve. We hypothesise that selection on synonymous codon use could also slow the rate of protein evolution if two amino acids have different preferred codons. We test this hypothesis by looking at patterns of protein evolution using polymorphism and substitution data in bacteria. We found that non-synonymous mutations that change from unpreferred to preferred codons are more common than the opposite, but only amongst codons that vary substantially in their preference level. Overall, selection on codon bias seems to have little influence over non-synonymous polymorphism or substitution patterns.