SYNONYMOUS CODON USAGE IN KLUYVEROMYCES-LACTIS

The nature and variation of synonymous codon usage in 47 open reading frames from Kluyveromyces lactis have been investigated. Using multiva riate statistical analysis, a single major trend among K. lactis genes was identified that differentiates among genes by expression level: h ighly expressed genes have high codon usage bias, while genes of low e xpression level have low bias. A relatively minor secondary trend diff erentiates among genes according to G+C content at silent sites. In th ese respects, K. lactis is similar to both Saccharomyces cerevisiae an d Candida albicans, and the same 'optimal' codons appear to be selecte d in highly expressed genes in all three species. In addition, silent sites in K. lactis and S. cerevisiae have similar G+C contents, but in C albicans genes they are more A+T-rich. Thus, in all essential featu res, codon usage in K. lactis is very similar to that in S. cerevisiae , even though silent sites in genes compared between these two species have undergone sufficient mutation to be saturated with changes. We c onclude that the factors influencing overall codon usage, namely mutat ional biases and the abundances of particular tRNAs, have not diverged between the two species. Nevertheless, in a few cases, codon usage di ffers between homologous genes from K. lactis and S. cerevisae. The st rength of codon usage bias in cytochrome c genes differs considerably, presumably because of different expression patterns in the two specie s. Two other, linked, genes have very different G+C content at silent sites in the two species, which may be a reflection of their chromosom al locations. Correspondence analysis was used to identify two open re ading frames with highly atypical codon usage that are probably not ge nes.