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MBE Advance Access published online on March 24, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh133
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted March 8, 2004
© 2004 Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved.

Original Articles

Evolution of Prokaryotic DNA: Intra- and Extragenic Divergences Observed with Orthologues from Three Related Species

Anders Fuglsang 1*

1 Danish University of Pharmaceutical Sciences, Institute of Pharmacology, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark

* To whom correspondence should be addressed. E-mail: anfu{at}dfh.dk.


  Abstract

This study compared orthologous gene pairs from Escherichia coli K12, E. coli O157:H7 EDL933, Salmonella typhimurium LT2 and Yersinia pestis CO92, using only homologues of equal length, and differing nucleotides were counted and mapped. The data showed very clearly how the rates of divergence change with intra- and extragenic position. The rate of synonymous mutation is lowest near start codons and near stop codons and, a little surprisingly, the opposite seemed to be true for non-synonymous substitutions. Analysis outside genes reveals that nucleotide divergences occur less frequently upstream of start codons than downstream of stop codons, and a remarkable drop in divergences is seen for two of the datasets around N=9 nucleotides upstream of start codons, i.e. the Shine-Dalgarno region changes at a lower rate. The explanation is likely to be the link between expressivity and sequence complementarity to the 3'-end of 16S ribosomal rRNA. The latter is highly conserved across many bacterial and archaebacterial species.

Key Words: Sequence alignment, Shine-Dalgarno regions, mutation, molecular evolution, codon usage bias, expressivity


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