Synonymous codon usage inBacillus subtilisreflects both translational selection and mutational biases

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Abstract
Codon usage data for 56 Bacillus subtilis genes show that synonynous codon usage in B.subtilis is less biased than in Escherlchia coli, or in Saccharomyces cerevisiae. Nevertheless, certain genes with a high codon bias can be identified by correspondence analysis, and also by various indices of codon bias. These genes are very highly expressed, and a general trend (a decrease) in codon bias across genes seems to correspond to decreasing expression level. This, then, may be a general phenoaenon in unicellular organisms. The unusually small effect of translational selection on the pattern of codon usage in lowly expressed genes in B.subtilis yields similar dinucleotide frequencies among different codon positions, and on complementary strands. These patterns could arise through selection on DNA structure, but more probably are largely determined by mutation. This prevalence of mutational bias could lead to difficulties in assessing whether open reading frames encode proteins.