Leplae Raphaël, Lima-Mendez Gipsi, Toussaint Ariane
SCMBB, Université Libre de Bruxelles, Bvd du Triomphe, Bruxelles, Belgium.
FEMS Microbiol Rev. 2006 Nov;30(6):980-94. doi: 10.1111/j.1574-6976.2006.00044.x.
Many plasmids are mobile genetic elements (MGEs) and, as other members of that group of DNA entities, their genomes display a mosaic and combinatorial structure, making their classification extremely difficult. As other MGEs, plasmids play a major role in horizontal transfer of genetic materials and genome reorganization. Yet, the full impact of such phenomenon on major properties of the host cell, such as pathogenicity, the ability to use new carbon sources or resistance to antibiotics, remains to be fully assessed. More and more complete plasmid genome sequences are available. However, in the absence of standards for storing plasmid sequence data and annotating genes and gene products on sequenced plasmid genomes, the resulting information remains rather limited. Using 503 sequenced plasmids organized in the ACLAME database, we discuss how, by structuring information on the genomes, their host and the proteins they code for, one can gain access to either global or more detailed analysis of the plasmid sequence information, as illustrated by a network representation of the relationships between plasmids.
许多质粒是可移动遗传元件（MGEs），并且作为该组DNA实体的其他成员，它们的基因组呈现出镶嵌和组合结构，这使得它们的分类极其困难。与其他MGEs一样，质粒在遗传物质的水平转移和基因组重组中起主要作用。然而，这种现象对宿主细胞主要特性（如致病性、利用新碳源的能力或对抗生素的抗性）的全面影响仍有待充分评估。越来越多完整的质粒基因组序列可供使用。然而，由于缺乏存储质粒序列数据以及对测序质粒基因组上的基因和基因产物进行注释的标准，所得到的信息仍然相当有限。利用在ACLAME数据库中整理的503个测序质粒，我们讨论了如何通过构建关于基因组、其宿主以及它们编码的蛋白质的信息，来获得对质粒序列信息的全局或更详细的分析，如质粒之间关系的网络表示所示。
