Shi Shuo-Yong, Cai Xiao-Hui, Ding Da-fu
Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, China.
Acta Biochim Biophys Sin (Shanghai). 2005 Aug;37(8):561-6. doi: 10.1111/j.1745-7270.2005.00075.x.
Horizontal gene transfer (HGT), a process through which genomes acquire genetic materials from distantly related organisms, is believed to be one of the major forces in prokaryotic genome evolution. However, systematic investigation is still scarce to clarify two basic issues about HGT: (1) what types of genes are transferred; and (2) what influence HGT events over the organization and evolution of biological pathways. Genome-scale investigations of these two issues will advance the systematical understanding of HGT in the context of prokaryotic genome evolution. Having investigated 82 genomes, we constructed an HGT database across broad evolutionary timescales. We identified four function categories containing a high proportion of horizontally transferred genes: cell envelope, energy metabolism, regulatory functions, and transport/binding proteins. Such biased function distribution indicates that HGT is not completely random; instead, it is under high selective pressure, required by function restraints in organisms. Furthermore, we mapped the transferred genes onto the connectivity structure map of organism-specific pathways listed in Kyoto Encyclopedia of Genes and Genomes (KEGG). Our results suggest that recruitment of transferred genes into pathways is also selectively constrained because of the tuned interaction between original pathway members. Pathway organization structures still conserve well through evolution even with the recruitment of horizontally transferred genes. Interestingly, in pathways whose organization were significantly affected by HGT events, the operon-like arrangement of transferred genes was found to be prevalent. Such results suggest that operon plays an essential and directional role in the integration of alien genes into pathways.
水平基因转移（HGT）是基因组从远缘生物体获取遗传物质的过程，被认为是原核生物基因组进化的主要驱动力之一。然而，关于HGT的两个基本问题仍缺乏系统研究来阐明：（1）转移的基因类型有哪些；（2）HGT事件对生物途径的组织和进化有何影响。对这两个问题进行全基因组规模的研究将推动在原核生物基因组进化背景下对HGT的系统理解。在研究了82个基因组后，我们构建了一个跨越广泛进化时间尺度的HGT数据库。我们鉴定出四个功能类别，其中水平转移基因的比例很高：细胞包膜、能量代谢、调节功能以及转运/结合蛋白。这种有偏向性的功能分布表明HGT并非完全随机；相反，它受到生物体功能限制所要求的高选择压力的影响。此外，我们将转移的基因映射到京都基因与基因组百科全书（KEGG）中列出的特定生物体途径的连通性结构图上。我们的结果表明，由于原始途径成员之间经过调整的相互作用，将转移的基因招募到途径中也受到选择性限制。即使招募了水平转移基因，途径组织结构在进化过程中仍能很好地保留下来。有趣的是，在那些组织受到HGT事件显著影响的途径中，发现转移基因的操纵子样排列很普遍。这些结果表明操纵子在外源基因整合到途径中起着至关重要的定向作用。
