A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli:: The search for the unit of selection
A genomic population genetics analysis of the pathogenic enterocyte effacement island in Escherichia coli:: The search for the unit of selection
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DOI：
10.1073/pnas.0408633102
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发表时间：
2005-02-01
影响因子：
11.1
通讯作者：
Souza, V
中科院分区：
文献类型：
--
作者：
Castillo, A;Eguiarte, LE;Souza, V
比较基因组分析是理解完整基因组的历史和组织的有力工具。群体遗传学的数学工具与基因组分析相结合，为剖析基因组进化中的异质性提供了强有力的方法。本研究提出了一个层次分析的肠上皮细胞和消失岛（35 kb），这是发现在肠致病性和肠出血性大肠杆菌和啮齿类柠檬酸杆菌菌株。对大肠杆菌肠上皮细胞的定位和消失进行了研究。大肠杆菌被认为是克隆生物体内的克隆单位，并预期作为单一单位进化。该分析通过确定（i）完整的致病岛，（ii）组织岛的五个操纵子，以及（iii）组成该基因座的41个基因中的每一个的不同功能水平的遗传多样性、GC含量和替换率来检查克隆假设。我们发现，有一个保守的区域，是由属于III型分泌系统的基因，这可能是水平转移的产品。一个更多样化的区域由分泌蛋白的基因和我们推断为E. coli基因组。这种遗传镶嵌似乎受到选择和突变的不同影响。我们的研究结果表明，重组和选择可能会打破这种结构，使不同的元素，充其量，在他们的进化弱耦合。这些观察表明，选择的单位不是完整的岛屿，而是组成岛屿的更小的单位。
Comparative genomic analysis is a powerful tool for understanding the history and organization of complete genomes. The mathematical tools of population genetics combined with genomic analysis provide a powerful approach to dissect heterogeneities in genome evolution. This study presents a hierarchical analysis of the enterocyte and effacement island (35 kb), which is found in the enteropathogenic and enterohemorrhagic strains in Escherichia coli and in Citrobacter rodentium. The locus of enterocyte and effacement in E. coli is considered to be a clonal unit inside a clonal organism and is expected to evolve as a single unit. This analysis examines the clonal assumption by determining genetic diversity, GC content, and the substitution rates at the different functional levels of (i) the complete pathogenic island, (it) the five operons in which the island is organized, and (iii) for each of the individual 41 genes that comprise the locus. We find that there is a conserved region that is composed of genes that belong to the type III secretion system and that may be products of horizontal transfer. A more diverse region is composed of genes for secreted proteins and genes that we infer to be original components of the E. coli genome. This genetic mosaic seems to be differentially affected by selection and mutation. Our results suggest that recombination and selection may be breaking this structure so that different elements are, at best, weakly coupled in their evolution. These observations suggest that the units of selection are not the complete island, but rather, much smaller units that comprise the island.