Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7
Effect of repeat copy number on variable-number tandem repeat mutations in Escherichia coli O157:H7
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DOI：
10.1128/jb.00001-06
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发表时间：
2006-06-01
影响因子：
3.2
通讯作者：
Keim, Paul
中科院分区：
文献类型：
--
作者：
Vogler, Amy J.;Keys, Christine;Keim, Paul
可变数目串联重复序列（VNTR）位点已显示出显着的能力，区分最近出现的克隆病原体大肠杆菌O 157：H7的分离株，使它们成为一个非常有用的分子流行病学工具。然而，人们对这些序列突变的速率、影响突变速率的因素或这些位点发生突变的机制知之甚少。在此，我们测量了28个VNTR基因座的突变率，并研究了重复拷贝数和错配修复对突变率的影响，使用体外产生的10个E。coli O 157：H7菌株。我们发现单基因座突变率高达7.0 × 10 ~（-4）突变/代，28个基因座的组合突变率为6.4 × 10 ~（-4）突变/代。我们观察到的单重复和多重复突变与滑动链错配突变模型一致，以及少量的大重复拷贝数突变与重组介导的事件一致。阵列内的重复拷贝数与最易突变的位点O 157 -10（r（2）= 0.565，P = 0.0196）和所有突变位点的突变率均强相关。O 157 -10基因座的合并模型与排除O 157 -10基因座的合并模型的相关系数分别为r（2）= 0.833和r（2）= 0.452，P < 0.0001。错配修复缺陷不影响28个重复单位大小> 5 bp的VNTR中任何一个的突变率，尽管多聚（G）同源序列在mutS菌株中不稳定。最后，我们描述了VNTR突变的一般模型，包括插入和缺失，单重复和多重复突变，以及基于我们的经验突变率数据的相对频率。
Variable-number tandem repeat (VNTR) loci have shown a remarkable ability to discriminate among isolates of the recently emerged clonal pathogen Escherichia coli O157:H7, making them a very useful molecular epidemiological tool. However, little is known about the rates at which these sequences mutate, the factors that affect mutation rates, or the mechanisms by which mutations occur at these loci. Here, we measure mutation rates for 28 VNTR loci and investigate the effects of repeat copy number and mismatch repair on mutation rate using in vitro-generated populations for 10 E. coli O157:H7 strains. We find single-locus rates as high as 7.0 X 10(-4) mutations/generation and a combined 28-locus rate of 6.4 X 10(-4) mutations/generation. We observed single- and multirepeat mutations that were consistent with a slipped-strand mispairing mutation model, as well as a smaller number of large repeat copy number mutations that were consistent with recombination-mediated events. Repeat copy number within an array was strongly correlated with mutation rate both at the most mutable locus, O157-10 (r(2) = 0.565, P = 0.0196), and across all mutating loci. The combined locus model was significant whether locus O157-10 was included (r(2) = 0.833, P < 0.0001) or excluded (r(2) = 0.452, P < 0.0001) from the analysis. Deficient mismatch repair did not affect mutation rate at any of the 28 VNTRs with repeat unit sizes of > 5 bp, although a poly(G) homomeric tract was destabilized in the mutS strain. Finally, we describe a general model for VNTR mutations that encompasses insertions and deletions, single- and multiple-repeat-mutations, and their relative frequencies based upon our empirical mutation rate data.