INRA, UMR 1133, Laboratoire EMIP, Place Eugène Bataillon, F-34095 Montpellier, France.
BMC Genomics. 2010 Oct 15;11:568. doi: 10.1186/1471-2164-11-568.
Flexible genomes facilitate bacterial evolution and are classically organized into polymorphic strain-specific segments called regions of genomic plasticity (RGPs). Using a new web tool, RGPFinder, we investigated plasticity units in bacterial genomes, by exhaustive description of the RGPs in two Photorhabdus and two Xenorhabdus strains, belonging to the Enterobacteriaceae and interacting with invertebrates (insects and nematodes).
RGPs account for about 60% of the genome in each of the four genomes studied. We classified RGPs into genomic islands (GIs), prophages and two new classes of RGP without the features of classical mobile genetic elements (MGEs) but harboring genes encoding enzymes catalyzing DNA recombination (RGPmob), or with no remarkable feature (RGPnone). These new classes accounted for most of the RGPs and are probably hypervariable regions, ancient MGEs with degraded mobilization machinery or non canonical MGEs for which the mobility mechanism has yet to be described. We provide evidence that not only the GIs and the prophages, but also RGPmob and RGPnone, have a mosaic structure consisting of modules. A module is a block of genes, 0.5 to 60 kb in length, displaying a conserved genomic organization among the different Enterobacteriaceae. Modules are functional units involved in host/environment interactions (22-31%), metabolism (22-27%), intracellular or intercellular DNA mobility (13-30%), drug resistance (4-5%) and antibiotic synthesis (3-6%). Finally, in silico comparisons and PCR multiplex analysis indicated that these modules served as plasticity units within the bacterial genome during genome speciation and as deletion units in clonal variants of Photorhabdus.
This led us to consider the modules, rather than the entire RGP, as the true unit of plasticity in bacterial genomes, during both short-term and long-term genome evolution.
灵活的基因组促进了细菌的进化，并且经典地组织成称为基因组可塑性区域（RGP）的多态菌株特异性片段。使用新的网络工具 RGPFinder，我们通过 exhaustive 描述 Photorhabdus 和 Xenorhabdus 两种菌株中的 RGPs，研究了细菌基因组中的可塑性单元，这两种菌株属于肠杆菌科并与无脊椎动物（昆虫和线虫）相互作用。
RGPs 约占研究的四个基因组中每个基因组的 60%。我们将 RGPs 分为基因组岛（GI）、噬菌体和两个没有经典移动遗传元件（MGE）特征但含有编码催化 DNA 重组酶的基因的新 RGP 类（RGPmob），或没有显著特征（RGPnone）。这些新类占大多数 RGPs，可能是高度可变的区域，是移动机制尚未描述的古老 MGEs 或非典型 MGEs。我们提供的证据表明，不仅 GI 和噬菌体，而且 RGPmob 和 RGPnone，都具有由模块组成的镶嵌结构。模块是一个基因块，长度为 0.5 到 60kb，在不同的肠杆菌科中显示出保守的基因组组织。模块是参与宿主/环境相互作用（22-31%）、代谢（22-27%）、细胞内或细胞间 DNA 流动性（13-30%）、耐药性（4-5%）和抗生素合成（3-6%）的功能单元。最后，计算机比较和 PCR 多重分析表明，这些模块在细菌基因组的物种形成过程中作为细菌基因组中的可塑性单元，并且在 Photorhabdus 的克隆变体中作为缺失单元。
这使我们考虑将模块而不是整个 RGP 作为细菌基因组在短期和长期基因组进化过程中的真正可塑性单元。
