Distribution of centromere-like parS sites in bacteria:: Insights from comparative genomics
Distribution of centromere-like parS sites in bacteria:: Insights from comparative genomics
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DOI：
10.1128/jb.01239-07
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发表时间：
2007-12-01
影响因子：
3.2
通讯作者：
Waldor, Matthew K.
中科院分区：
文献类型：
--
作者：
Livny, Jonathan;Yamaichi, Yoshiharu;Waldor, Matthew K.
低拷贝数质粒向子代细胞的分配通常依赖于作用于类着丝粒parS位点的ParA和ParB蛋白。类似的染色体编码的par基因座可能也有助于染色体分离。在此，我们使用生物信息学方法在400个原核生物基因组中搜索染色体parS位点。尽管用于搜索parS位点的共有序列矩阵源自两种革兰氏阳性菌，但在来自细菌所有分支的69%的菌株染色体上都鉴定出了假定的parS位点。未发现含有parS位点的菌株聚集在原核生物进化树相对较少的分支中。在绝大多数情况下，parS位点是在染色体的近原点区域被鉴定出来的。parS位点在多种细菌中的广泛保守性表明，par基因座在细菌染色体进化的早期就已经形成，并且某些菌株中parS、ParA和/或ParB的缺失可能反映了在进化后期这些基因座中的一个或多个的丢失。此外，parS高度保守的近原点位置表明par基因座主要致力于调控涉及细菌染色体原点区域的过程。在含有多条染色体的物种中，在次生染色体上发现的parS位点与在其主染色体上发现的位点有显著差异，这表明多部分基因组的染色体分离需要不同的复制子特异性par基因座。此外，次生染色体上的parS位点在不同物种之间不是很保守，这表明次生染色体的进化历史比主染色体的更加多样化。
Partitioning of low-copy-number plasmids to daughter cells often depends on ParA and ParB proteins acting on centromere-like parS sites. Similar chromosome-encoded par loci likely also contribute to chromosome segregation. Here, we used bioinformatic approaches to search for chromosomal parS sites in 400 prokaryotic genomes. Although the consensus sequence matrix used to search for parS sites was derived from two gram-positive species, putative parS sites were identified on the chromosomes of 69% of strains from all branches of bacteria. Strains that were not found to contain parS sites clustered among relatively few branches of the prokaryotic evolutionary tree. In the vast majority of cases, parS sites were identified in origin-proximal regions of chromosomes. The widespread conservation of parS sites across diverse bacteria suggests that par loci evolved very early in the evolution of bacterial chromosomes and that the absence of parS, parA, and/or parB in certain strains likely reflects the loss of one of more of these loci much later in evolution. Moreover, the highly conserved origin-proximal position of parS suggests par loci are primarily devoted to regulating processes that involve the origin region of bacterial chromosomes. In species containing multiple chromosomes, the parS sites found on secondary chromosomes diverge significantly from those found on their primary chromosomes, suggesting that chromosome segregation of multipartite genomes requires distinct replicon-specific par loci. Furthermore, parS sites on secondary chromosomes are not well conserved among different species, suggesting that the evolutionary histories of secondary chromosomes are more diverse than those of primary chromosomes.