Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes
Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes
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DOI：
10.1101/gr.089615.108
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发表时间：
2009-10-01
期刊：
影响因子：
7
通讯作者：
Hayashi, Tetsuya
中科院分区：
文献类型：
--
作者：
Ooka, Tadasuke;Ogura, Yoshitoshi;Hayashi, Tetsuya
可移动遗传元件在细菌基因组的进化和多样化中起着重要的作用。在肠出血性大肠杆菌O157中，影响基因组多样性的一个主要因素是前驱体，它产生了在O157基因组中观察到的大部分大小结构多态(LSSP)。在这里，我们描述了对大量小尺寸结构多态(SSSP)的系统分析结果，这些SSSP是通过比较8个临床分离株的基因组和一个测序菌株O157 Sakai而检测到的。大多数SSSP是由只与两个插入序列(IS)元件IS629和ISEC8相关的遗传事件产生的，并鉴定了一些被这些事件失活或缺失的基因。还检测到IS629的简单切除和IS629切除形成的小缺失(足迹)，这两种情况在细菌中很少描述。此外，IS元件的分布高度偏向于前噬菌体、原噬菌体样整合元件和质粒。基于这些和我们以前的结果，我们得出结论，除了前驱体外，这两个IS元件是O157菌株基因组多样化的主要贡献者，LSSP主要由噬菌体产生，SSSP主要由IS元件产生。我们还认为IS元件可能在进入噬菌体和质粒的失活和固定化中发挥作用。综上所述，我们的结果揭示了IS元素对细菌基因组多样化的真正影响，并突出了它们在基因组进化中的新作用。
Mobile genetic elements play important roles in the evolution and diversification of bacterial genomes. In enterohemorrhagic Escherichia coli O157, a major factor that affects genomic diversity is prophages, which generate most of the large-size structural polymorphisms (LSSPs) observed in O157 genomes. Here, we describe the results of a systematic analysis of numerous small-size structural polymorphisms (SSSPs) that were detected by comparing the genomes of eight clinical isolates with a sequenced strain, O157 Sakai. Most of the SSSPs were generated by genetic events associated with only two insertion sequence (IS) elements, IS629 and ISEc8, and a number of genes that were inactivated or deleted by these events were identified. Simple excisions of IS629 and small deletions (footprints) formed by the excision of IS629, both of which are rarely described in bacteria, were also detected. In addition, the distribution of IS elements was highly biased toward prophages, prophage-like integrative elements, and plasmids. Based on these and our previous results, we conclude that, in addition to prophages, these two IS elements are major contributors to the genomic diversification of O157 strains and that LSSPs have been generated mainly by bacteriophages and SSSPs by IS elements. We also suggest that IS elements possibly play a role in the inactivation and immobilization of incoming phages and plasmids. Taken together, our results reveal the true impact of IS elements on the diversification of bacterial genomes and highlight their novel role in genome evolution.