Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives.
Cassette-like variation of restriction enzyme genes in Escherichia coli C and relatives.
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DOI：
10.1093/nar/gkh194
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发表时间：
2004-01
影响因子：
14.9
通讯作者：
M. H. Sibley;E. Raleigh
中科院分区：
文献类型：
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作者：
M. H. Sibley;E. Raleigh
比较细菌基因组学的一个令人惊讶的结果是发现大量的DNA存在于一种菌株中，但不存在于同一物种的另一种菌株中。我们详细研究了一个位置，基因的内容变化很大，限制性大肠杆菌中的集群。该区域被指定为移民控制区（ICR），因为在那里发现的限制功能的密度和可变性。为了更好地定义这个可变基因座的边界，我们确定了来自无限制性菌株大肠杆菌C的区域的序列。在这里，我们比较了跨越ICR位点的13.7 kb大肠杆菌C序列与来自5种大肠杆菌菌株和鼠伤寒沙门氏菌LT2的相应序列。为了讨论这种变异，我们采用术语“框架”来指相关谱系内基因组的稳定组成部分，而“迁移”基因是基因组的短暂居民。引人注目的是，七个不同的迁移DNA片段，编码不同的基因和基因片段，交替占据一个明确的位置，在七个菌株检查。侧翼框架基因yjiS和yjiA显示出近似正常的保守模式。观察到的模式与位点特异性重组酶的作用一致。由于没有邻近基因编码已知家族的可能重组酶，因此这样的重组酶必须是新家族的或未连锁的。
A surprising result of comparative bacterial genomics has been the large amount of DNA found to be present in one strain but not in another of the same species. We examine in detail one location where gene content varies extensively, the restriction cluster in Escherichia coli. This region is designated the Immigration Control Region (ICR) for the density and variability of restriction functions found there. To better define the boundaries of this variable locus, we determined the sequence of the region from a restrictionless strain, E.coli C. Here we compare the 13.7 kb E.coli C sequence spanning the site of the ICR with corresponding sequences from five E.coli strains and Salmonella typhimurium LT2. To discuss this variation, we adopt the term 'framework' to refer to genes that are stable components of genomes within related lineages, while 'migratory' genes are transient inhabitants of the genome. Strikingly, seven different migratory DNA segments, encoding different sets of genes and gene fragments, alternatively occupy a single well-defined location in the seven strains examined. The flanking framework genes, yjiS and yjiA, display approximately normal patterns of conservation. The patterns observed are consistent with the action of a site-specific recombinase. Since no nearby gene codes for a likely recombinase of known families, such a recombinase must be of a new family or unlinked.