Thampapillai G, Lan R, Reeves P R
Department of Microbiology, University of Sydney, New South Wales, Australia.
Mol Biol Evol. 1994 Nov;11(6):813-28. doi: 10.1093/oxfordjournals.molbev.a040165.
The gnd gene, the structural gene for 6-phosphogluconate dehydrogenase, was sequenced and analyzed in 34 isolates from different serovars of the seven subspecies of Salmonella enterica to provide comparative information on the evolution in this gene, which has been studied extensively in Escherichia coli. The gene tree obtained by the neighbor-joining method in general gave separate branches for each subspecies, with the few exceptions readily explained by recombination. There is evidence of recombination involving transfer 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 the gene, and in all four cases a variant of the chi sequence is located close to the recombination junction and appears to have mediated the recombination events. We suggest that in these four cases and in a fifth case with intersubspecies transfer of the whole gnd gene, the adjacent rfb (O antigen) locus may have been transferred in the same event. The estimates 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 two species show an interesting distribution, with KS being lower toward the ends of the gene and KA in particular being lower in the first than in the second domain. In S. enterica, synonymous sites also seem to be subjected to negative selection. The ratio of KA to KS was higher within S. enterica and E. coli than between them, which may indicate that intraspecies variation is essentially between clones and that mildly deleterious mutations can be fixed within clones, which would thus raise KA within species.
对来自肠炎沙门氏菌七个亚种不同血清型的34个分离株中的6-磷酸葡萄糖酸脱氢酶结构基因gnd进行了测序和分析，以提供该基因进化的比较信息，该基因在大肠杆菌中已得到广泛研究。通过邻接法获得的基因树通常为每个亚种给出单独的分支，少数例外情况可通过重组轻松解释。有证据表明存在涉及长（超过400 bp）和短（30 - 150 bp）DNA片段转移的重组。检测到的六个长片段转移中有四个位于基因的5'端，在所有这四种情况下，chi序列的一个变体位于重组连接点附近，似乎介导了重组事件。我们认为，在这四种情况以及整个gnd基因发生亚种间转移的第五种情况下，相邻的rfb（O抗原）位点可能在同一事件中被转移。大肠杆菌和肠炎沙门氏菌gnd基因内部以及两个物种之间每个同义位点的同义替换数（KS）和每个非同义位点的非同义替换数（KA）的估计显示出有趣的分布，KS在基因末端较低，特别是KA在第一个结构域比第二个结构域低。在肠炎沙门氏菌中，同义位点似乎也受到负选择。肠炎沙门氏菌和大肠杆菌内部的KA与KS之比高于它们之间的比值，这可能表明种内变异本质上是克隆之间的变异，并且轻度有害的突变可以在克隆内固定，从而提高物种内的KA。
