Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement.
Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement.
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DOI：
10.1186/1471-2164-10-584
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发表时间：
2009-12-07
期刊：
影响因子：
4.4
通讯作者：
Thomson NR
中科院分区：
文献类型：
--
作者：
Jackson AP;Thomas GH;Parkhill J;Thomson NR
RHS基因是细菌基因组的显著特征，以前曾被认为与大肠杆菌的基因组重排有关。通过比较肠杆菌科的RHS谱系，这项研究对RHS的多样性和进化提供了强有力的解释，并提供了RHS多样性如何获得和丧失的机制模型。RHS基因在肠杆菌科中无处不在，由六个不同的结构谱系组成。在RHS谱系中存在着相当大的基因组间差异；例如，在肠沙门氏菌中，RHS仅限于可移动的元件，而在大肠杆菌中，随着较老的谱系被删除，一个RHS谱系通过转位而多样化。总体而言，比较基因组学揭示了不同属中频繁的、独立的基因得失，以及偶尔的横向基因转移。此外，我们证明了RHS的“核心”结构域和可变的C-末端在进化上是解耦的，并提出RHS的多样性是由与环状中间体的同源重组驱动的。现有的C-末端被侧向获得的替代物取代，产生了分离的‘尖端’的长阵列，表征了RHS基因座的外观。由于重复的基因获得和丢失，RHS谱系在肠杆菌基因组中具有高度的动态化。相反，RHS基因的一级结构在进化上是保守的，这表明RHS序列多样性不是由快速突变驱动的，而是由新的核心/末端组合相对缓慢的进化所驱动的。因此，我们预测，大量分离的RHS C-末端末端存在于同源异构体中，这些末端可能跨越分类边界传递。
Rhs genes are prominent features of bacterial genomes that have previously been implicated in genomic rearrangements in E. coli. By comparing rhs repertoires across the Enterobacteriaceae, this study provides a robust explanation of rhs diversification and evolution, and a mechanistic model of how rhs diversity is gained and lost. Rhs genes are ubiquitous and comprise six structurally distinct lineages within the Enterobacteriaceae. There is considerable intergenomic variation in rhs repertoire; for instance, in Salmonella enterica, rhs are restricted to mobile elements, while in Escherichia coli one rhs lineage has diversified through transposition as older lineages have been deleted. Overall, comparative genomics reveals frequent, independent gene gains and losses, as well as occasional lateral gene transfer, in different genera. Furthermore, we demonstrate that Rhs 'core' domains and variable C-termini are evolutionarily decoupled, and propose that rhs diversity is driven by homologous recombination with circular intermediates. Existing C-termini are displaced by laterally acquired alternatives, creating long arrays of dissociated 'tips' that characterize the appearance of rhs loci. Rhs repertoires are highly dynamic among Enterobacterial genomes, due to repeated gene gains and losses. In contrast, the primary structures of Rhs genes are evolutionarily conserved, indicating that rhs sequence diversity is driven, not by rapid mutation, but by the relatively slow evolution of novel core/tip combinations. Hence, we predict that a large pool of dissociated rhs C-terminal tips exists episomally and these are potentially transmitted across taxonomic boundaries.
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