Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria

Riboswitches and attenuators are cis-regulatory RNA elements, most of which control bacterial gene expression via metabolite-mediated, premature transcription termination. We developed an unbiased experimental approach for genome-wide discovery of such ribo-regulators in bacteria. We also devised an experimental platform that quantitatively measures the in-vivo activity of all such regulators in parallel, and enables rapid screening for ribo-regulators that respond to metabolites of choice. Using this approach we detected numerous antibiotic-responsive ribo-regulators that control antibiotic resistance genes in pathogens and in the human microbiome. Studying one such regulator in Listeria monocytogenes revealed an attenuation mechanism mediated by antibiotic-stalled ribosomes. Our results expose broad roles for conditional termination in regulating antibiotic resistance, and provide a tool for discovering riboswitches and attenuators that respond to novel ligands.