Régulation ARN-dépendante dans deux bactéries pathogènes gram positive, Listeria monocytogenes et Staphylococcus aureus – BACREGRNA

Bacteria have the properties to inhabit numerous ecological niches and should experience rapidly varying life conditions. This is particularly true for pathogenic bacteria which have to survive in various environmental conditions imposed by the host. Therefore basic research is required to decipher the networks of intracellular physiological processes unique to bacteria, to analyze the way they sense, transmit the external signals, and regulate their metabolism. In the past few years, several studies have unraveled the role of bacterial RNAs in gene regulation, primarily in E. coli and enterobacteria. With the development of bioinformatic tools and genetic screens, novel riboswitches and ncRNAs have been discovered at a staggering rate in many other bacteria. These RNAs bring the missing links in the regulatory pathways that allow the bacteria to sense the population density, to modulate the cell surface composition, to adjust the metabolism during cell growth, and to regulate virulence gene expression. Many of these regulatory events occur at the post-transcriptional level and involve changes in the structures of 5' untranslated region of mRNAs, which have freely evolved a plethora of binding sites for trans-acting ligands. In addition, proteins have been shown to assist the folding of RNA and RNA-dependent regulation. A good example in enterobacteria is with the widely spread Sm-like Hfq protein, which is associated with many trans-acting ncRNAs that directly bind to target mRNAs. Thus, the variety of mRNA regulatory signals and of trans-acting regulators (proteins, regulatory RNA, metabolites, ions) allows the bacteria to integrate a large range of internal and external signals. As regulatory RNAs continue to be discovered in bacteria, detailed understanding of their structures and functions will undoubtedly reveal surprising ways to regulate gene expression. Although a large number of studies have been focused on Gram-negative bacteria, few studies have unraveled the importance of RNA-dependent regulation in Gram-positive bacteria which comprises several major human pathogens. There is also accumulating evidence that Gram-positive and Gram-negative bacteria have evolved different regulatory mechanisms, as well as RNA decay mechanisms. The proposed G+REGRNA project will deal with novel aspects of RNA-dependent regulation in two major pathogenic Gram-positive bacteria, Listeria monocytogenes which is a typical intracellular pathogen, and Staphylococcus aureus which is mainly a pyogenic and toxigenic extracellular pathogen. The three teams have made several original and major contributions to this field, and have recently identified novel non coding RNAs (ncRNAs) in both pathogenic bacteria. The strength of this network lies also in the combination of complementary expertises in molecular microbiology, bacterial physiology, RNA biology, biochemistry and structural biology. The G+REGRNA partners will join to better understand the function of RNAs in gene regulation of two major pathogenic Gram-positive bacteria (Fig. 1). This proposal will address the biological functions of RNAs that have been recently discovered by the partners and will analyze the regulatory networks in which they are involved. We will identify the signaling pathways, characterize the primary targets of the ncRNAs and their generated downstream effects, and elucidate their biological implications. Furthermore, the interaction and the structures of the regulatory RNAs with their targets will be studied at the molecular level, as well as the proteins that are required for their activity or which inhibit their action (helper protein, ribonucleases, RNA-binding protein'). We will also identify the mechanism of regulation and will have a particular focus for RNAs that regulate gene expression by novel mechanisms. A special focus will be on RNAs that regulate virulence gene expression as well as stress-related responses and metabolic adaptation. The originality of the present project resides at different levels. At the fundamental level, we will obtain a more complete picture of the conserved and species-specific regulatory networks involved in virulence and adaptation, and deep mechanistic insights. The understanding of the RNA-dependent regulatory mechanisms and the rules that dictate specific recognition between RNAs and targets at the molecular level may also pave the way to find alternative strategies to repress bacterial gene expression and/or decrease pathogenicity.