Regulatory small RNA networks and bacterial pathogenesis

Tree JJ

School of Biotechnology and Biomolecular Sciences, UNSW, Sydney.

The transcriptomes of bacteria contain hundreds of short regulatory RNAs termed, small RNA (sRNA). These gene regulators control protein expression by modulating protein interactions with messanger RNAs (ribosomes, RNases, and termination factors), and by modulating mRNA structure. Small RNAs often base-pair with target mRNAs through regions of limited complementary making computational prediction of sRNA targets difficult. Recently, we have developed a proximity-dependant ligation technique termed RNase E-CLASH that allows recovery of bacterial sRNA-mRNA interactions occurring in vivo, profiling the sRNA interactome. We have used RNase E-CLASH to capture the sRNA interactome of the bacterial pathogen Enterohaemorrhagic E. coli (EHEC). We find that the major EHEC virulence factor, the Shiga toxin, unexpectedly encodes a regulatory sRNA within the toxin mRNA, that controls the general stress response pathway. RNase-CLASH is applicable to a broad range of bacteria and we demonstrate that the sRNA interactome can be recovered from multi-drug resistant Staphylococcus aureus, identifying novel regulators of antibiotic tolerance.