REGULATORY RNA IN BACTERIA - BIOLOGY AND MECHANISMS

Bacterial small RNAs (sRNAs) post-transcriptional regulate numerous genes. We work on fundamental mechanistic and biological questions. Three sRNAs, IstR1 and OmrA/B, are topics for future work. IstR1 inhibits translation of TisB, a toxin that induces persisters.

IstR1 acts by preventing "ribosome standby", a mechanism that allows translation of structurally blocked mRNAs, e.g. tisB mRNA.

Here, we will use biochemistry and biophysics to elucidate the full anatomy of this standby site, involving an RNA pseudoknot, the role of r-protein S1 in RNA structure unwinding, and trapping of 30S subunits towards the sequestered initiation site (CLIP-seq, FRET, single-molecule experiments). Secondly, we study the genome-wideprevalence of standby.

UV-crosslinking/RNA-Trap/RNA-seq will map RNA fragments on standby-30S, and identify their features.OmrA/B are paralogs that redundantly target csgD, flgM, and dgcM, affecting motility/ biofilm lifestyles.

These sibling RNAs have started to evolve specialization on some targets, which will be assessed for candidate metabolic genes (nutritional sensing for motility/biofilm decisions). An exciting new, unexplored, project is "RNA toxicity". Some RNAs, when highly expressed, are toxic. OmrA/B are ideal to analyze mechanisms: A, but not B, stops bacterial cell growth.

By random mutagenesis and positive selection for non-toxic OmrA, toxicity determinants will be identified. The application expands on the plausible mechanisms and how to test them.