Association of the φ nucleotide with codon bias, amino acid usage and expressivity:: differences between Bacillus subtilis and Escherichia coli

By measuring the non-randomness in Shine-Dalgarno regions it was recently shown that the compositional non-randomness peaks approximately 10 nucleotides upstream of the start codons. This position, termed the phi position, was furthermore shown to be associated with certain characteristics of the gene/protein and start codon usage. This raises the question whether codon usage in general is associated with the phi position. In this study, the connection between the phi nucleotide and general codon usage, both gene-wide and at the level of individual amino acids, was studied in Eschericia coli and Bacillus subtilis. E coli but not B. subtilis shows a strong general association between the phi position and codon usage bias. In both species, the genes with higher expressivity show stronger conservation in the Shine-Dalgarno region compared to the genes with lower expressivity.