Thus there are two alleles at this position, represented by the presence of C or U at the third codon position, that will be labelled B1 and B2. For simplicity consider a haploid model, which will be the appropriate model in E. coli , suppose that individuals carrying B2 have relative fitness 1 - s compared with those carrying B1, and that there is a mutation rate u from B1 to B2 and v in the other direction. Hartl et al. The nature of selection Selection on codon usage could act either through speed of translation or accuracy of translation. I shall consider these factors in turn.
Rare codons take longer to translate than common codons.
The rate of synthesis of a particular protein is not appreciably affected by usage of common or rare codons. However, one would expect the use of a rare codon in a particular gene to slow down the total rate of protein production. This is five orders of magnitude greater than the selection coefficient against rare glycine codons estimated in ribosomal protein genes at the end of the previous section, which is puzzling. Preferred codons may enhance not only the speed but also the accuracy of translation. He compared codons which are conserved at the amino acid level between two species of Drosophila with codons in the same gene at which an amino acid substitution has occurred, and found that the bias for the preferred codon was higher in the conserved than the nonconserved codons.