Large-Scale Analysis of Plasmid Relationships through Gene-Sharing Networks
Large-Scale Analysis of Plasmid Relationships through Gene-Sharing Networks
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DOI：
10.1093/molbev/msr292
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发表时间：
2012-04-01
影响因子：
10.7
通讯作者：
Fondi, Marco
中科院分区：
文献类型：
--
作者：
Tamminen, Manu;Virta, Marko;Fondi, Marco
质粒是微生物群落中遗传交换的容器。已知它们在不同宿主生物之间转移并从染色体和/或其他质粒获取不同的遗传元件。因此，它们通过在不同群落之间快速传播各种遗传特性，构成微生物进化的重要元素。一个典型的例子是抗生素抗性（AR）基因的传播，导致多重耐药致病菌株的出现。为了全面分析质粒的进化动态，我们构建了一个大图，其中 2,343 个质粒（节点）根据彼此共享的蛋白质连接起来。对这个基因共享网络的分析揭示了网络聚类和相应微生物的系统发育类别之间的整体一致性，这可能是由于遥远的系统发育群体之间水平基因转移的遗传障碍造成的。栖息地并不是聚类的关键因素，因为来自不同环境的生物体的质粒经常被发现嵌入在同一簇中。对网络指标的分析揭示了质粒移动性与其在网络中的中心性之间存在统计学上显着的相关性，这为移动质粒在微生物群落中传播基因特别重要的观察提供了支持。最后，我们的研究揭示了放线菌和伽玛变形菌之间广泛的（之前未描述的）AR基因共享，这表明前者可能代表了后者AR基因的重要库。
Plasmids are vessels of genetic exchange in microbial communities. They are known to transfer between different host organisms and acquire diverse genetic elements from chromosomes and/or other plasmids. Therefore, they constitute an important element in microbial evolution by rapidly disseminating various genetic properties among different communities. A paradigmatic example of this is the dissemination of antibiotic resistance (AR) genes that has resulted in the emergence of multiresistant pathogenic bacterial strains. To globally analyze the evolutionary dynamics of plasmids, we built a large graph in which 2,343 plasmids (nodes) are connected according to the proteins shared by each other. The analysis of this gene-sharing network revealed an overall coherence between network clustering and the phylogenetic classes of the corresponding microorganisms, likely resulting from genetic barriers to horizontal gene transfer between distant phylogenetic groups. Habitat was not a crucial factor in clustering as plasmids from organisms inhabiting different environments were often found embedded in the same cluster. Analyses of network metrics revealed a statistically significant correlation between plasmid mobility and their centrality within the network, providing support to the observation that mobile plasmids are particularly important in spreading genes in microbial communities. Finally, our study reveals an extensive (and previously undescribed) sharing of AR genes between Actinobacteria and Gammaproteobacteria, suggesting that the former might represent an important reservoir of AR genes for the latter.