NON-CODING RNA-MEDIATED REGULATION IN THE ORAL MICROBIOME

Bacteria utilize a rich arsenal of regulation strategies to adjust their gene expression patterns in response to their rapidly changing environments. Among those, regulatory 5’ UTRs of genes and specifically riboswitches serve as an important and wide-spread mode of control in bacteria. These cis-acting RNA elements can prevent the formation of full transcripts by inducing premature transcriptional termination in response to specific metabolites. We have established an experimental approach, “meta-term-seq”, that identifies cis-acting RNA regulators across multiple bacteria and measures their condition-dependent function. We have previously demonstrated the power of this method by applying it to the oral microbiome, and discovered numerous regulators that are specifically responsive to antibiotics and control expression of antibiotics resistance related genes. We now expand the utility of “meta-term-seq” by employing it as a wide screening platform to systematically uncover RNA regulators which are responsive to a panel of stimuli across hundreds of bacteria. Our initial results point to several candidates that may represent novel ribowitches, and provide insights into the regulatory response of bacteria to different substances on the RNA level.