Selective differences among translation termination codons

The frequency of use of the three alternative translation termination codons has been examined in 165 Escherichia coli, 52 Bacillus subtilis and 106 Saccharomyces cerevisiae genes. Genes were first categorised according to their degree of bias in sense codon usage. In each species there is a very strong bias in favour of UAA (over UAG and UGA) in genes where sense codon usage is highly biased. This bias declines, principally with an increase in the use of UGA, in genes with lower sense codon bias. It appears that selection operating during translation may maintain the bias in stop codon usage. Such selection could result from the greater availability of UAA-cognate release factor(s), or from a lower frequency of translational readthrough at UAA.