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 previously unknown ligands.
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
Daniel
D
Dar
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
Maya
M
Shamir
Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France. INSERM, U604, Paris, F-75015 France. Institut National de la Recherche Agronomique, USC2020, Paris, F-75015 France.
J R
JR
Mellin
Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France. INSERM, U604, Paris, F-75015 France. Institut National de la Recherche Agronomique, USC2020, Paris, F-75015 France.
Mikael
M
Koutero
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
Noam
N
Stern-Ginossar
Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris, F-75015 France. INSERM, U604, Paris, F-75015 France. Institut National de la Recherche Agronomique, USC2020, Paris, F-75015 France.
Pascale
P
Cossart
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel. rotem.sorek@weizmann.ac.il.
Rotem
R
Sorek
D020413:3' Untranslated Regions / Q000235:genetics; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001412:Bacillus subtilis / Q000187:drug effects / Q000235:genetics; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D013293:Enterococcus faecalis / Q000187:drug effects; D000069196:Gastrointestinal Microbiome / Q000187:drug effects / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008089:Listeria monocytogenes / Q000187:drug effects / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism; D058928:Riboswitch / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D061806:Transcription Termination, Genetic
D020413:3' Untranslated Regions; D000900:Anti-Bacterial Agents; D058928:Riboswitch