title: Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation.
abstract: On the basis of nascent transcript sequencing, it has been postulated but never demonstrated that transcriptional pausing at translation start sites is important for gene regulation. Here we show that the Escherichia coli thiamin pyrophosphate (TPP) thiC riboswitch contains a regulatory pause site in the translation initiation region that acts as a checkpoint for thiC expression. By biochemically probing nascent transcription complexes halted at defined positions, we find a narrow transcriptional window for metabolite binding, in which the downstream boundary is delimited by the checkpoint. We show that transcription complexes at the regulatory pause site favour the formation of a riboswitch intramolecular lock that strongly prevents TPP binding. In contrast, cotranscriptional metabolite binding increases RNA polymerase pausing and induces Rho-dependent transcription termination at the checkpoint. Early transcriptional pausing may provide a general mechanism, whereby transient transcriptional windows directly coordinate the sensing of environmental cues and bacterial mRNA regulation.
authors.affiliation: Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, J1K 2R1 Quebec, Canada.
authors.forename: Adrien
authors.initials: A
authors.lastname: Chauvier
authors.affiliation: Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, J1K 2R1 Quebec, Canada.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Picard-Jean
authors.affiliation: Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, J1K 2R1 Quebec, Canada.
authors.forename: Jean-Christophe
authors.initials: JC
authors.lastname: Berger-Dancause
authors.affiliation: Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, J1K 2R1 Quebec, Canada.
authors.forename: Laurène
authors.initials: L
authors.lastname: Bastet
authors.affiliation: INRS-Institut Armand-Frappier, Laval, H7V 1B7 Quebec, Canada.
authors.forename: Mohammad Reza
authors.initials: MR
authors.lastname: Naghdi
authors.affiliation: Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, J1K 2R1 Quebec, Canada.
authors.forename: Audrey
authors.initials: A
authors.lastname: Dubé
authors.affiliation: Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, J1K 2R1 Quebec, Canada.
authors.forename: Pierre
authors.initials: P
authors.lastname: Turcotte
authors.affiliation: INRS-Institut Armand-Frappier, Laval, H7V 1B7 Quebec, Canada.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Perreault
authors.affiliation: Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, J1K 2R1 Quebec, Canada.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Lafontaine
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D018387:Codon, Initiator; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D009154:Mutation; D014176:Protein Biosynthesis; D011487:Protein Conformation; D016914:Ribonuclease H / Q000235:genetics / Q000378:metabolism; D058928:Riboswitch / Q000235:genetics*; D013835:Thiamine Pyrophosphate / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D018387:Codon, Initiator; D029968:Escherichia coli Proteins; C534627:Rho protein, E coli; D058928:Riboswitch; C105797:ThiC protein, Bacteria; D016914:Ribonuclease H; D013835:Thiamine Pyrophosphate