title: A kissing loop is important for btuB riboswitch ligand sensing and regulatory control.
abstract: RNA-based genetic regulation is exemplified by metabolite-binding riboswitches that modulate gene expression through conformational changes. Crystal structures show that the Escherichia coli btuB riboswitch contains a kissing loop interaction that is in close proximity to the bound ligand. To analyze the role of the kissing loop interaction in the riboswitch regulatory mechanism, we used RNase H cleavage assays to probe the structure of nascent riboswitch transcripts produced by the E. coli RNA polymerase. By monitoring the folding of the aptamer, kissing loop, and riboswitch expression platform, we established the conformation of each structural component in the absence or presence of bound adenosylcobalamin. We found that the kissing loop interaction is not essential for ligand binding. However, we showed that kissing loop formation improves ligand binding efficiency and is required to couple ligand binding to the riboswitch conformational changes involved in regulating gene expression. These results support a mechanism by which the btuB riboswitch modulates the formation of a tertiary structure to perform metabolite sensing and regulate gene expression.
authors.affiliation: From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada.
authors.forename: Antony
authors.initials: A
authors.lastname: Lussier
authors.affiliation: From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada.
authors.forename: Laurène
authors.initials: L
authors.lastname: Bastet
authors.affiliation: From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada.
authors.forename: Adrien
authors.initials: A
authors.lastname: Chauvier
authors.affiliation: From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada Daniel.Lafontaine@USherbrooke.ca.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Lafontaine
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001692:Biological Transport; D003038:Cobamides / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008024:Ligands; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D016914:Ribonuclease H / Q000737:chemistry / Q000378:metabolism; D058928:Riboswitch; D014158:Transcription, Genetic
chemical_list: D001425:Bacterial Outer Membrane Proteins; C044592:BtuB protein, E coli; D003038:Cobamides; D029968:Escherichia coli Proteins; D008024:Ligands; D026901:Membrane Transport Proteins; D012329:RNA, Bacterial; D058928:Riboswitch; D016914:Ribonuclease H; C000913:cobamamide
keywords: RNA structure; adenosylcobalamin (AdoCbl); gene regulation; riboswitch; structure-function; translation control