DNA MISMATCH CORRECTION BY VERY SHORT PATCH REPAIR MAY HAVE ALTERED THE ABUNDANCE OF OLIGONUCLEOTIDES IN THE ESCHERICHIA-COLI GENOME
DNA MISMATCH CORRECTION BY VERY SHORT PATCH REPAIR MAY HAVE ALTERED THE ABUNDANCE OF OLIGONUCLEOTIDES IN THE ESCHERICHIA-COLI GENOME
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DOI：
10.1093/nar/20.7.1663
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发表时间：
1992-04-11
影响因子：
14.9
通讯作者：
MCCLELLAND, M
中科院分区：
文献类型：
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作者：
BHAGWAT, AS;MCCLELLAND, M
大肠杆菌K-12中有一种碱基错配纠正过程，称为非常短补丁（VSP）修复，当在某些序列环境中发现T:G与C:G错配时，它可以纠正T:G错配。两种底物错配（5'-CTWGG/3'-GGW' cc; W = A或T）发生在DNA中胞嘧啶甲基化的背景下，并降低了5-甲基胞嘧啶脱胺对胸腺嘧啶的致突变性作用。然而，已知VSP修复也可以修复T:G错配，这些错配预计不会由5-甲基胞嘧啶脱胺引起（例如ctag /GGTC）。在这些情况下，如果原始碱基对是T: a， VSP修复将导致T到C的转变。我们对大肠杆菌序列数据库进行了马尔可夫链分析，以确定后一类位点的修复是否改变了相关四核苷酸的丰度。结果与预测一致，即VSP修复倾向于耗尽含有“T”的序列（例如- ctag）的基因组，同时丰富相应的含有“C”的序列（CCAG）。此外，他们为肠道细菌基因组中含有限制性内切酶位点的CTAG的已知稀缺性提供了解释，并确定了VSP修复是塑造细菌基因组序列组成的一种力量。
A base mismatch correction process in E. coli K-12 called Very Short Patch (VSP) repair corrects T:G mismatches to C:G when found in certain sequence contexts. Two of the substrate mismatches (5'-CTWGG/3'-GGW'CC; W = A or T) occur in the context of cytosine methylation in DNA and reduce the mutagenic effects of 5-methylcytosine deamination to thymine. However, VSP repair is also known to repair T:G mismatches that are not expected to arise from 5-methylcytosine deamination (example-CTAG/GGTC). In these cases, if the original base pair were a T:A, VSP repair would cause a T to C transition. We have carried out Markov chain analysis of an E. coli sequence database to determine if repair at the latter class of sites has altered the abundance of the relevant tetranucleotides. The results are consistent with the prediction that VSP repair would tend to deplete the genome of the 'T' containing sequences (example-CTAG), while enriching it for the corresponding 'C' containing sequences (CCAG). Further, they provide an explanation for the known scarcity of CTAG containing restriction enzyme sites among the genomes of enteric bacteria and identify VSP repair as a force in shaping the sequence composition of bacterial genomes.