Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus.
Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus.
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DOI：
10.1186/1471-2164-11-568
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发表时间：
2010-10-15
期刊：
影响因子：
4.4
通讯作者：
Gaudriault S
中科院分区：
文献类型：
--
作者：
Ogier JC;Calteau A;Forst S;Goodrich-Blair H;Roche D;Rouy Z;Suen G;Zumbihl R;Givaudan A;Tailliez P;Médigue C;Gaudriault S
灵活的基因组促进了细菌的进化，通常被组织成多态的菌株特异性片段，称为基因组可塑性区域（RGPs）。利用新的网络工具RGPFinder，研究了细菌基因组中的可塑性单元，详细描述了属于肠杆菌科并与无脊椎动物（昆虫和线虫）相互作用的两个Photorhabdus和两个Xenorhabdus菌株的rgp。在研究的四个基因组中，rgp约占60%。我们将RGP分为基因组岛（GIs）、噬菌体（prophages）和两类不具有经典移动遗传元件（MGEs）特征但含有DNA重组酶编码基因（RGPmob）或无显著特征（RGPnone）的RGP。这些新类别占rgp的大部分，并且可能是高变区，具有退化的移动机制的古代mge或移动机制尚未描述的非规范mge。我们提供的证据表明，不仅是GIs和噬菌体，还有RGPmob和RGPnone都具有由模块组成的马赛克结构。一个模块是一个基因块，长度为0.5 - 60kb，在不同肠杆菌科中显示一个保守的基因组组织。模块是涉及宿主/环境相互作用（22-31%）、代谢（22-27%）、细胞内或细胞间DNA迁移（13-30%）、耐药性（4-5%）和抗生素合成（3-6%）的功能单元。最后，通过计算机比较和PCR多重分析表明，这些模块在细菌基因组形成过程中充当可塑性单元，在光habdus克隆变异中充当缺失单元。这使我们认为，在短期和长期的基因组进化过程中，这些模块，而不是整个RGP，才是细菌基因组可塑性的真正单位。
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.
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影响因子：
64.8
作者：
Beaber, JW;Hochhut, B;Waldor, MK
通讯作者：
Waldor, MK
影响因子：
4.4
作者：
BOEMARE, NE;BOYERGIGLIO, MH;BREHELIN, M
通讯作者：
BREHELIN, M
DOI：
10.1073/pnas.1731982100
发表时间：
2003-09-02
影响因子：
11.1
作者：
Buell, CR;Joardar, V;Collmer, A
通讯作者：
Collmer, A
DOI：
10.1073/pnas.0408633102
发表时间：
2005-02-01
影响因子：
11.1
作者：
Castillo, A;Eguiarte, LE;Souza, V
通讯作者：
Souza, V
影响因子：
3.2
作者：
Cowles, Charles E.;Goodrich-Blair, Heidi
通讯作者：
Goodrich-Blair, Heidi