Lercher Martin J, Pál Csaba
Department of Computer Science, Heinrich-Heine-University, Düsseldorf, Germany.
Mol Biol Evol. 2008 Mar;25(3):559-67. doi: 10.1093/molbev/msm283. Epub 2007 Dec 24.
Adaptation of bacteria to new or changing environments is often associated with the uptake of foreign genes through horizontal gene transfer. However, it has remained unclear how (and how fast) new genes are integrated into their host's cellular networks. Combining the regulatory and protein interaction networks of Escherichia coli with comparative genomics tools, we provide the first systematic analysis of this issue. Genes transferred recently have fewer interaction partners compared to nontransferred genes in both regulatory and protein interaction networks. Thus, horizontally transferred genes involved in complex regulatory and protein-protein interactions are rarely favored by selection. Only few protein-protein interactions are gained after the initial integration of genes following the transfer event. In contrast, transferred genes are gradually integrated into the regulatory network of their host over evolutionary time. During adaptation to the host cellular environment, horizontally transferred genes recruit existing transcription factors of the host, reflected in the fast evolutionary rates of the cis-regulatory regions of transferred genes. Further, genes resulting from increasingly ancient transfer events show increasing numbers of transcriptional regulators as well as improved coregulation with interacting proteins. Fine-tuned integration of horizontally transferred genes into the regulatory network spans more than 8-22 million years and encompasses accelerated evolution of regulatory regions, stabilization of protein-protein interactions, and changes in codon usage.
细菌对新环境或变化环境的适应通常与通过水平基因转移摄取外源基因有关。然而，新基因如何（以及多快）整合到宿主细胞网络中仍不清楚。我们结合大肠杆菌的调控和蛋白质相互作用网络以及比较基因组学工具，首次对这个问题进行了系统分析。在调控和蛋白质相互作用网络中，与未转移基因相比，最近转移的基因具有更少的相互作用伙伴。因此，参与复杂调控和蛋白质 - 蛋白质相互作用的水平转移基因很少受到选择青睐。在转移事件后基因最初整合后，仅获得了很少的蛋白质 - 蛋白质相互作用。相反，随着进化时间的推移，转移基因逐渐整合到宿主的调控网络中。在适应宿主细胞环境的过程中，水平转移基因招募宿主现有的转录因子，这反映在转移基因顺式调控区域的快速进化速率上。此外，源于越来越古老转移事件的基因显示出越来越多的转录调节因子，以及与相互作用蛋白质更好的共调节。水平转移基因精细地整合到调控网络中跨越了800 - 2200万年，包括调控区域的加速进化、蛋白质 - 蛋白质相互作用的稳定以及密码子使用的变化。
