Hazen Tracy H, Daugherty Sean C, Shetty Amol, Mahurkar Anup A, White Owen, Kaper James B, Rasko David A
Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA.
Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA.
Front Microbiol. 2015 Jun 12;6:569. doi: 10.3389/fmicb.2015.00569. eCollection 2015.
Enteropathogenic Escherichia coli (EPEC) are a leading cause of diarrheal illness among infants in developing countries. E. coli isolates classified as typical EPEC are identified by the presence of the locus of enterocyte effacement (LEE) and the bundle-forming pilus (BFP), and absence of the Shiga-toxin genes, while the atypical EPEC also encode LEE but do not encode BFP or Shiga-toxin. Comparative genomic analyses have demonstrated that EPEC isolates belong to diverse evolutionary lineages and possess lineage- and isolate-specific genomic content. To investigate whether this genomic diversity results in significant differences in global gene expression, we used an RNA sequencing (RNA-Seq) approach to characterize the global transcriptomes of the prototype typical EPEC isolates E2348/69, B171, C581-05, and the prototype atypical EPEC isolate E110019. The global transcriptomes were characterized during laboratory growth in two different media and three different growth phases, as well as during adherence of the EPEC isolates to human cells using in vitro tissue culture assays. Comparison of the global transcriptomes during these conditions was used to identify isolate- and growth phase-specific differences in EPEC gene expression. These analyses resulted in the identification of genes that encode proteins involved in survival and metabolism that were coordinately expressed with virulence factors. These findings demonstrate there are isolate- and growth phase-specific differences in the global transcriptomes of EPEC prototype isolates, and highlight the utility of comparative transcriptomics for identifying additional factors that are directly or indirectly involved in EPEC pathogenesis.
肠致病性大肠杆菌（EPEC）是发展中国家婴儿腹泻疾病的主要病因。被归类为典型EPEC的大肠杆菌分离株可通过肠细胞损伤位点（LEE）和束状菌毛（BFP）的存在以及志贺毒素基因的缺失来鉴定，而非典型EPEC也编码LEE，但不编码BFP或志贺毒素。比较基因组分析表明，EPEC分离株属于不同的进化谱系，并拥有谱系和分离株特异性的基因组内容。为了研究这种基因组多样性是否会导致全球基因表达的显著差异，我们使用RNA测序（RNA-Seq）方法来表征典型EPEC原型分离株E2348/69、B171、C581-05以及非典型EPEC原型分离株E110019的全球转录组。在两种不同培养基和三个不同生长阶段的实验室培养过程中，以及使用体外组织培养试验检测EPEC分离株与人细胞的黏附过程中，对全球转录组进行了表征。通过比较这些条件下的全球转录组，以确定EPEC基因表达中分离株和生长阶段特异性的差异。这些分析鉴定出了与毒力因子协同表达的、编码参与生存和代谢的蛋白质的基因。这些发现表明，EPEC原型分离株的全球转录组存在分离株和生长阶段特异性的差异，并突出了比较转录组学在识别直接或间接参与EPEC发病机制的其他因素方面的效用。
