Molecular Biology and Evolution, Vol 4, 426-444, Copyright © 1987 by Society for Molecular Biology and Evolution
M Gouy
This investigation of the codon context of enterobacteria, plasmid, and
phage protein genes was based on a search for correlations between the
presence of one base type at codon position III and the presence of another
base type at some other position in adjacent codons. Enterobacterial genes
were compared with eukaryotic sequences for codon context effects. In
enterobacterial genes, base usage at codon position III is correlated with
the third position of the upstream adjacent codon and with all three
positions of the downstream codon. Plasmid genes are free of context
biases. Phage genes are heterogeneous: MS2 codons have no biased context,
whereas lambda genes partly follow the trends of the host bacterium, and T7
genes have biased codon contexts that differ from those of the host. It has
been reported that two successive third-codon positions tend to be occupied
by two purines or two pyrimidines in Escherichia coli genes of low
expression level. Here, the extent to which highly expressed protein genes
can modulate base usage at two successive codon positions III, given the
constraints on codon usage and protein sequence that act on them, was
quantified. This demonstrates that the above-mentioned favored patterns are
not a characteristic of weakly expressed genes but occur in all genes in
which codon context can vary appreciably. The correlation between
successive third-codon positions is a distinct feature of enterobacteria
and of some phages, one that may result from adaptation of gene structure
to translational efficiency. Conversely, codon context in yeast and human
genes is biased--but for reasons unrelated to translation.
ORIGINAL ARTICLE
Codon contexts in enterobacterial and coliphage genes
Institut d'Evolution Moleculaire, Universite Claude Bernard, Villeurbanne, France.
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