Absence of translationally selected synonymous codon usage bias in Helicobacter pylori

Synonymous codon usage in the complete genome of Helicobacter pylori was in vestigated. The moderate A+T-richness of the genome (G+C = 39 mol%) is refl ected in the overall synonymous codon usage but the frequencies of some cod ons cannot be explained by simple mutational biases. A low level of heterog eneity among genes was observed, but this does not appear to be due to vary ing mutational bias or translational selection. Some of the heterogeneity w as due to amino acid composition variation among the encoded proteins, and some may be attributable to recent acquisition of genes from other species. Since Hel. pylori codon usage is not dominated by biased mutation patterns , the absence of evidence for translationally mediated selection among syno nymous codons is striking. This has implications with regard to the life hi story of this species, and in particular suggests that Hel. pylori strains are not subject to periods of competitive exponential growth. Despite the l ack of selected codon usage, base composition immediately after the transla tion initiation site is skewed, consistent with selection against secondary structure formation in this region.