Identification Of Small RNAs In Escherichia Coli O157:H7

sRNA(small RNA), also called ncRNA(non-coding RNA), are widespread in variety of organisms, ranging from eukaryotes to prokaryotes. To date, more than 200 sRNA genes have been found in bacteria. Among them, approximate 80 sRNA genes were found in E.coli, which has been most investigated.sRNAs are involved in a diverse range of functions, from structural through regulatory to catalysis, affecting a large variety of processes in organisms, including RNA progressing, mRNA stability, translation, protein stability and secretion. A single sRNA can regulate multiple genes and have profound effects on cell physiology. sRNAs act via several mechanisms. Most of them base-pair with target mRNAs, and were assisted by RNA chaperone Hfq.The bacterium Escherichia coli O157: H7 is a worldwide threat to public health and has been implicated in many outbreaks of haemorrhagic colitis, some of which included fatalities caused by haemolytic uraemic syndrome. The severity of disease, the lack of effective treatment and the potential for large-scale outbreaks from contaminated food supplies have propelled intensive research on the pathogenesis and detection of. As sRNAs play extensive roles in bacteria, including bacterial virulence, here we search for the sRNAs in E.coli O157: H7. It might sheds new insight into the pathogenicity and the physiology of O157: H7, and open a way to understand the molecular mechanisms underlying the O157: H7 infection.At present, researches of sRNA mainly based on bioinformatical prediction and molecular biological experiments. Toward the goal of developing an efficient method for predicting unknown sRNA genes in the completed E.coli O157: H7 genome, we adopted a bioinformatics approach to search for them. As a starting point for detecting novel sRNAs in E.coli O157: H7, we considered a number of common properties of the previously identified sRNAs that might serve as a guide to identify genes encoding new sRNAs. And then we developed a computational strategy employing transcription signals and genomic features of the known sRNA-encoding genes. The search, for which we used restrictive criteria, has led to the prediction of 53 putative sRNA-encoding genes in E.coli O157: H7 EDL933, and 65 in E.coli O157: H7 str. Sakai. These genes were all located in intergenic regions. Then we tested 49 candidate sRNAs in E.coli O157: H7 EDL933 experimentally. The method for experimental validation is hybridization, which comprises dot blot and northern blot. The oligonucleotides used as probes for the hybridization were designed to be complementary to sequences of the predicted sRNAs, with restrictive sizes. The synthesized probes were non-isotopically labeled with DIG, which is a nucleic acid intercalating reagent.Here we report on the discovery of 10 genes encoding small RNAs in E. coli O157: H7 EDL933. All the newly discovered sRNAs express in exponential phase. To our knowledge, this is the first report of such genomic search for sRNAs in E.coli O157: H7. The result suggests that our methodology may have the potential to discover more novel sRNA genes in other bacteria.