Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements
Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements
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DOI：
10.1128/jb.01524-10
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发表时间：
2011-08-01
影响因子：
3.2
通讯作者：
Ragan, Mark A.
中科院分区：
文献类型：
--
作者：
Chan, Cheong Xin;Beiko, Robert G.;Ragan, Mark A.
葡萄球菌分离株中广泛存在的抗生素耐药性和毒力部分归因于横向遗传转移（LGT），但对该属中LGT的更广泛程度知之甚少。在这里，我们报告了13个葡萄球菌基因组中遗传转移的模块化的第一个系统研究，这些葡萄球菌基因组涵盖了四个不同的命名物种。使用基于拓扑的系统发育方法，我们发现，在1354组同源基因中，368组（27.1%）基因组存在LGT的强证据，另外259组（19.1%）证据较弱。基因内转移和全基因转移对这些基因对参考系统发育的拓扑不一致贡献几乎相等。比较单拷贝和多拷贝基因组的遗传转移，我们观察到后者的LGT频率更高，而在全基因转移的情况下存在大量的功能偏差（在片段遗传转移的情况下几乎没有这种偏差）。我们发现的证据表明，横向转移，特别是整个基因的转移，不仅影响与抗生素、药物和重金属抗性相关的功能，以及膜运输，还影响与移动元件无关的核心信息和代谢功能。虽然序列相似性模式支持已识别物种的内聚，但金黄色葡萄球菌内的LGT似乎经常破坏克隆复合物。我们的研究结果表明，LGT和基因复制在葡萄球菌基因组的功能创新中起着重要作用。
The widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed in part to lateral genetic transfer (LGT), but little is known about the broader extent of LGT within this genus. Here we report the first systematic study of the modularity of genetic transfer among 13 Staphylococcus genomes covering four distinct named species. Using a topology-based phylogenetic approach, we found, among 1,354 sets of homologous genes examined, strong evidence of LGT in 368 (27.1%) gene sets, and weaker evidence in another 259 (19.1%). Within-gene and whole-gene transfer contribute almost equally to the topological discordance of these gene sets against a reference phylogeny. Comparing genetic transfer in single-copy and in multicopy gene sets, we observed a higher frequency of LGT in the latter, and a substantial functional bias in cases of whole-gene transfer (little such bias was observed in cases of fragmentary genetic transfer). We found evidence that lateral transfer, particularly of entire genes, impacts not only functions related to antibiotic, drug, and heavy-metal resistance, as well as membrane transport, but also core informational and metabolic functions not associated with mobile elements. Although patterns of sequence similarity support the cohesion of recognized species, LGT within S. aureus appears frequently to disrupt clonal complexes. Our results demonstrate that LGT and gene duplication play important parts in functional innovation in staphylococcal genomes.