A quest for biological roles of novel small RNAs discovered in a human pathogen: Helicobacter pylori – RARHePy

Gene regulation was up to recently believed to be exerted mainly by proteins. However it has become obvious that small non coding RNA may play an important role in the control of gene expression. The complete sequencing of many genomes from bacteria to mammals, led to the discovery of numerous RNAs, ranging from 20 to 500 nucleotides in length. For instance microRNAs (miRNAs) have recently emerged as a new class of post-transcriptional regulators of gene expression. In bacteria another class of small non coding RNAs (sRNA) has been identified. Like the eukaryotic miRNAs, sRNAs, expressed in response to a stress, are able to regulate selectively the expression of one or several genes by controlling the translation or the stability of the corresponding mRNAs. During the past few years, most of bacterial sRNAs known to date have been identified in the non-pathogenic bacteria Escherichia coli using both computational and experimental methods. Recently many new sRNA have been identified in pathogenic bacteria, such as the two gram positive bacteria Listeria monocytogenes and Staphylococcus aureus. To establish successful infections, bacterial pathogens may use sRNA to control precisely expression of their virulence genes in response to host signals. Strikingly, no regulatory small RNAs have yet been described in the gram-negative, microaerophilic, spiral-shaped bacterium named Helicobacter pylori that colonizes the gastric mucosa of humans. The aim of our project is to identify small non coding RNA that would be involved in the control of virulent gene expression in H. pylori. This bacterium is the aetiological agent of gastritis and peptic ulcers. The development of gastric carcinoma and MALT lymphoma is also strongly associated with long-term chronic H. pylori infection. About 50% of the world population is infected by H. pylori and 9,000 new cases of gastric cancer appear every year in France. The inflammation of the stomach, which is the natural reservoir in which H. pylori persists and grows, leads to lesions in the mucosa and genotoxic events in the gastric epithelial cells. Despite an efficient antibiotic treatment, H. pylori remains one of the most important human bacterial disease. Although several colonization and pathogenesis factors have been identified so far in H. pylori, the molecular mechanisms of the regulation of gene expression in this bacterium are largely unknown. How gene expression is modified to cope with changes in the environment or to facilitate chronic infections in the stomach is poorly defined. The aim of our project is to identify the function of novel sRNAs discovered in H. pylori and to study these sRNA in respect to the regulation of virulence factor gene expression. By the use of an experimental approach (RNomics), we expect to identify sRNA that are specifically induced or repressed during the colonization of the stomach (acidic stress) or in contact with the host epithelial gastric cells. Moreover in the second part of this project, we wish to identify which partners (messenger RNA, proteins or other cellular components) these sRNA are targeting. For this second objective we propose to use several combined approaches: comparative proteomics, bioinformatic searches for complementarities with messenger RNA, and sRNA-associated protein purifications.The discovery of cellular functions of sRNA in a pathogenic bacteria such as H. pylori should improve our global understanding of their role in RNA-mediated virulence gene regulation.