Molecular evolution in the gnd locus of Salmonella enterica

The gnd gene, the structural gene for 6-phosphogluconate dehydrogenase, wassequenced and analyzed in 34 isolates from different serovars of the sevensubspecies of Salmonella enterica to provide comparative information on theevolution in this gene, which has been studied extensively in Escherichiacoli. The gene tree obtained by the neighbor- joining method in generalgave separate branches for each subspecies, with the few exceptions readilyexplained by recombination. There is evidence of recombination involvingtransfer of long (more than 400 bp) and short (30-150 bp) segments of DNA.Four of the six long-segment transfers detected are at the 5' end of thegene, and in all four cases a variant of the chi sequence is located closeto the recombination junction and appears to have mediated therecombination events. We suggest that in these four cases and in a fifthcase with intersubspecies transfer of the whole gnd gene, the adjacent rfb(O antigen) locus may have been transferred in the same event. Theestimates of the number of synonymous substitutions per synonymous site,KS, and the number of nonsynonymous substitutions per nonsynonymous site,KA, within the E. coli and S. enterica gnd genes, and also between the twospecies show an interesting distribution, with KS being lower toward theends of the gene and KA in particular being lower in the first than in thesecond domain. In S. enterica, synonymous sites also seem to be subjectedto negative selection. The ratio of KA to KS was higher within S. entericaand E. coli than between them, which may indicate that intraspeciesvariation is essentially between clones and that mildly deleteriousmutations can be fixed within clones, which would thus raise KA withinspecies.