Codon bias in Escherichia coli: the influence of codon context on mutation and selection.

The codon bias in Escherichia coli for all two-fold degenerate amino acids was studied as dependent on the context from the six bases in the nearest surrounding codons. By comparing the results in genes at different expression levels, effects that are due to differences in mutation rates can be distinguished from those that are due to selection. Selective effects on the codon bias is found mostly from the first neighbouring base in the 3'direction, while neighbouring bases further away influence mostly the mutational bias. In some cases it is also possible to identify specific molecular processes, repair or avoidance of frame shift, that lead to the context dependence of the bias.