RNAchap

In all domains of life, non-coding RNAs have key roles in the function of the cell (gene silencing, host defense,...). Finding how these RNA species interact with other components of the cell remains a significant challenge. In both eukaryotic and prokaryotic organisms, protein-assisted base pairing allows each non-coding RNA (siRNA, sRNA, crispRNA) to identify a handful of mRNA targets within thousands of transcribed genes. In bacteria, Hfq was considered the only RNA chaperone able to assist trans-acting sRNAs, however another family of core-genome encoded RNA chaperone could contribute to non-coding RNA signalling. Recent studies by us and others showed that ProQ/FinO domain-containing proteins could indeed act as RNA chaperones. We identified and characterized the ProQ/FinO domain-containing protein RocC of Legionella pneumophila as a non-Hfq-like RNA chaperone of a trans-acting and multi-target sRNA, RocR. RocC stabilizes RocR and, together, they post-transcriptionally control the expression of genes that are important for natural transformation, a major mechanism of horizontal gene transfer. We here propose a project that builds on our data and that will keep us at the forefront of the sRNA field by unraveling the mechanism of this novel sRNA-based gene silencing system. To better understand the basic principle of silencing by a ProQ/FinO domain-containing RNA chaperone and its cognate sRNA, we will investigate, using biochemical and structural approaches, the sRNA remodelling activities of ProQ/FinO domain-containing RNA chaperones and the molecular mechanism of sRNA-mediated gene repression (Aim 1). Moreover, with its elegant simplicity, the RocC/R system seems to be a good candidate for a synthetic biology approach to design multi-target silencing strategies (Aim 2). Finally, as the RocC RNA chaperone is the central regulator of an important mechanism of genetic transfer, we will also study its regulation and its integration in the cell physiology (Aim 3).