Journal of Molecular Evolution

, Volume 33, Issue 1, pp 23-33

First online:

Determinants of DNA sequence divergence betweenEscherichia coli andSalmonella typhimurium: Codon usage, map position, and concerted evolution

  • Paul M. SharpAffiliated withDepartment of Genetics, Trinity College

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The nature and extent of DNA sequence divergence between homologous proteincoding genes fromEscherichia coli andSalmonella typhimurium have been examined. The degree of divergence varies greatly among genes at both synonymous (silent) and nonsynonymous sites. Much of the variation in silent substitution rates can be explained by natural selection on synonymous codon usage, varying in intensity with gene expression level. Silent substitution rates also vary significantly with chromosomal location, with genes nearoriC having lower divergence. Certain genes have been examined in more detail. In particular, the duplicate genes encoding elongation factor Tu,tufA andtufB, fromS. typhimurium have been compared to theirE. coli homologues. As expected these very highly expressed genes have high codon usage bias and have diverged very little between the two species. Interestingly, these genes, which are widely spaced on the bacterial chromosome, also appear to be undergoing concerted evolution, i.e., there has been exchange between the loci subsequent to the divergence of the two species.

Key words

Molecular clocks Enterobacteria Elongation factor Tu Genome evolution Synonymous codon usage