Department of Microbial Ecology, University of Vienna, Vienna, Austria.
Mol Biol Evol. 2011 Dec;28(12):3253-70. doi: 10.1093/molbev/msr161. Epub 2011 Jun 20.
Chlamydiae are evolutionarily well-separated bacteria that live exclusively within eukaryotic host cells. They include important human pathogens such as Chlamydia trachomatis as well as symbionts of protozoa. As these bacteria are experimentally challenging and genetically intractable, our knowledge about them is still limited. In this study, we obtained the genome sequences of Simkania negevensis Z, Waddlia chondrophila 2032/99, and Parachlamydia acanthamoebae UV-7. This enabled us to perform the first comprehensive comparative and phylogenomic analysis of representative members of four major families of the Chlamydiae, including the Chlamydiaceae. We identified a surprisingly large core gene set present in all genomes and a high number of diverse accessory genes in those Chlamydiae that do not primarily infect humans or animals, including a chemosensory system in P. acanthamoebae and a type IV secretion system. In S. negevensis, the type IV secretion system is encoded on a large conjugative plasmid (pSn, 132 kb). Phylogenetic analyses suggested that a plasmid similar to the S. negevensis plasmid was originally acquired by the last common ancestor of all four families and that it was subsequently reduced, integrated into the chromosome, or lost during diversification, ultimately giving rise to the extant virulence-associated plasmid of pathogenic chlamydiae. Other virulence factors, including a type III secretion system, are conserved among the Chlamydiae to variable degrees and together with differences in the composition of the cell wall reflect adaptation to different host cells including convergent evolution among the four chlamydial families. Phylogenomic analysis focusing on chlamydial proteins with homology to plant proteins provided evidence for the acquisition of 53 chlamydial genes by a plant progenitor, lending further support for the hypothesis of an early interaction between a chlamydial ancestor and the primary photosynthetic eukaryote.
衣原体是进化上分离良好的细菌，仅在真核宿主细胞内生存。它们包括重要的人类病原体，如沙眼衣原体，以及原生动物的共生体。由于这些细菌在实验上具有挑战性且遗传上难以处理，因此我们对它们的了解仍然有限。在这项研究中，我们获得了 Simkania negevensis Z、Waddlia chondrophila 2032/99 和 Parachlamydia acanthamoebae UV-7 的基因组序列。这使我们能够对衣原体四个主要科的代表成员进行首次全面的比较和系统发育基因组分析，包括衣原体科。我们发现所有基因组中都存在一组令人惊讶的大型核心基因，而在那些主要不感染人类或动物的衣原体中存在大量多样化的辅助基因，包括 P. acanthamoebae 的化学感应系统和一种类型 IV 分泌系统。在 S. negevensis 中，类型 IV 分泌系统编码在一个大型的共轭质粒（pSn，132kb）上。系统发育分析表明，类似于 S. negevensis 质粒的质粒最初是由所有四个科的最后共同祖先获得的，随后在多样化过程中减少、整合到染色体中或丢失，最终导致了致病性衣原体现有的毒力相关质粒。其他毒力因子，包括 III 型分泌系统，在衣原体中不同程度地保守，与细胞壁组成的差异一起反映了对不同宿主细胞的适应，包括四个衣原体科之间的趋同进化。重点关注与植物蛋白同源的衣原体蛋白的系统发育基因组分析为 53 个衣原体基因由植物祖先进化而来提供了证据，进一步支持了衣原体祖先与最初的光合真核生物之间早期相互作用的假说。
