Sokurenko Evgeni V, Feldgarden Michael, Trintchina Elena, Weissman Scott J, Avagyan Serine, Chattopadhyay Sujay, Johnson James R, Dykhuizen Daniel E
Department of Microbiology, University of Washington, Seattle, WA, USA.
Mol Biol Evol. 2004 Jul;21(7):1373-83. doi: 10.1093/molbev/msh136. Epub 2004 Mar 24.
Spread of biological species from primary into novel habitats leads to within-species adaptive niche differentiation and is commonly driven by acquisition of point mutations in individual genes that increase fitness in the alternative environment. However, finding footprints of adaptive niche differentiation in specific genes remains a challenge. Here we describe a novel method to analyze the footprint of pathogenicity-adaptive, or pathoadaptive, mutations in the Escherichia coli gene encoding FimH-the major, mannose-sensitive adhesin. Analysis of distribution of mutations across the nodes and branches of the FimH phylogenetic network shows (1) zonal separation of evolutionary primary structural variants of FimH and recently derived ones, (2) dramatic differences in the ratio of synonymous and nonsynonymous changes between nodes from different zones, (3) evidence for replacement hot-spots in the FimH protein, (4) differential zonal distribution of FimH variants from commensal and uropathogenic E. coli, and (5) pathoadaptive functional changes in FimH brought by the mutations. The selective footprint in fimH indicates that the pathoadaptive niche differentiation of E. coli is either in its initial stages or undergoing an evolutionary "source/sink" dynamic.
生物物种从原生栖息地扩散到新栖息地会导致物种内部适应性生态位分化，通常是由单个基因中获得点突变驱动的，这些突变会增加在替代环境中的适应性。然而，在特定基因中发现适应性生态位分化的痕迹仍然是一项挑战。在这里，我们描述了一种新方法，用于分析编码FimH（主要的甘露糖敏感粘附素）的大肠杆菌基因中致病性适应性或致病适应性突变的痕迹。对FimH系统发育网络节点和分支上突变分布的分析表明：（1）FimH进化初级结构变体与最近衍生变体的区域分离；（2）不同区域节点之间同义变化与非同义变化比例的显著差异；（3）FimH蛋白中替换热点的证据；（4）共生大肠杆菌和尿路致病性大肠杆菌FimH变体的差异区域分布；（5）突变带来的FimH致病适应性功能变化。fimH中的选择性痕迹表明，大肠杆菌的致病适应性生态位分化要么处于初始阶段，要么正在经历进化的“源/汇”动态。
