E. coli Variome

描述(由申请人提供)：我们建议通过分析多个菌株共有的基因正选择足迹，在全基因组和全人群范围内确定所有主要腹泻和肠外大肠杆菌致病类型的遗传变异。分析的主要重点将是详细描述在大肠杆菌核心基因的正选择下发生的并适应致病菌株的小核苷酸变异(点替换和插入)。我们的计划是组装具有病理类型代表性的大肠杆菌集合，包括从全球20,000多个大肠杆菌菌株中挑选出的大约2,500个分离物。将确定这些菌株的克隆多样性，并使用454技术对克隆不同的分离株进行高通量测序。250-300个大肠杆菌菌株(从头获得或在公共数据库中可用)的基因组将通过检测热点突变-影响相同氨基酸位置的重复(系统发育无关)突变-来分析阳性选择的足迹。热点突变预示着趋同进化--这是这种变化在特定环境中具有适应性意义的最强烈迹象之一。我们预计有数百个核心基因受到阳性选择的热点突变的影响。然后，将在全人群水平上验证特定热点突变与不同致病类型的遗传关联。此外，我们还将测试新的大肠杆菌基因分型标记的克隆分辨率，以便在临床和环境诊断中潜在应用。最后，将对参与调节大肠杆菌毒力因子的基因的正选择变异的功能效应进行研究。 公共卫生相关性：E.Coli Variome Project将汇编主要腹泻和肠道外E.Coli病原体的所有遗传变异，并分析多个菌株共享的基因的正选择足迹。核心基因的特定热点突变和新的基因分型标记之间的遗传学联系将在全人群水平上得到验证。最后，将对参与调节大肠杆菌毒力因子的基因的致病性适应性变异的功能效应进行研究。

DESCRIPTION (provided by applicant): We propose to determine on a genome-wide and population-wide scale genetic variations across all major diarrheal and extra-intestinal E. coli pathotypes, with the analysis of positive selection footprints in genes shared by multiple strains. The main focus of the analysis will be to characterize in detail small nucleotide variations (point substitutions and indels) that occur under positive selection in the core genes of E. coli and are adaptive to pathogenic strains. Our plan is to assemble pathotype-representative collection of E. coli that will encompass approximately 2,500 isolates selected from over 20,000 E. coli strains from around the globe. Clonal diversity of these strains will be determined and clonally diverse isolates will be subjected to high-throughput sequencing using 454 technology. Genomes of 250-300 E. coli strains (obtained de novo or available in public databases) will be analyzed for footprints of positive selection by detecting hot-spot mutations - repeated (phylogenetically-unlinked) mutations affecting the same amino acid position. Hot-spot mutations are indicative of convergent evolution - one of the strongest indications of the adaptive significance of such changes in specific environments. We expect that there are several hundred core genes affected by positively-selected hot-spot mutations. Genetic association of specific hot-spot mutations with different pathotypes will then be validated on a population-wide level. Also, we will test the clonal resolution of novel genotyping markers of E. coli for potential application in clinical and environmental diagnostics. Finally, functional effects of positively-selected variations will be investigated for genes involved in the regulation of E. coli virulence factors. PUBLIC HEALTH RELEVANCE: The E.coli Variome Project will compile all genetic variations across major diarrheal and extra-intestinal E.coli pathogens, with the analysis of positive selection footprints in genes shared by multiple strains. Genetics association of specific hot-spot mutations in core genes and novel genotyping markers will be validated on a population-wide level. Finally, function effects of pathogenicity-adaptive variations will be investigated for genes involved in the regulation of E.coli virulence factors.