A. Eyrewalker et M. Bulmer, REDUCED SYNONYMOUS SUBSTITUTION RATE AT THE START OF ENTEROBACTERIAL GENES, Nucleic acids research, 21(19), 1993, pp. 4599-4603
Synonymous codon usage is less biased at the start of Escherichia coli
genes than elsewhere. The rate of synonymous substitution between E.c
oli and Salmonella typhimurium is substantially reduced near the start
of the gene, which suggests the presence of an additional selection p
ressure which competes with the selection for codons which are most ra
pidly translated. Possible competing sources of selection are the pres
ence of secondary ribosome binding sites downstream from the start cod
on, the avoidance of mRNA secondary structure near the start of the ge
ne and the use of sub-optimal codons to regulate gene expression. We p
rovide evidence against the last of these possibilities. We also show
that there is a decrease in the frequency of A, and an increase in the
frequency of G along the E. coli genes at all three codon positions.
We argue that these results are most consistent with selection to avoi
d mRNA secondary structure.