title: Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch.
abstract: Riboswitches are cis-acting elements that regulate gene expression by affecting transcriptional termination or translational initiation in response to binding of a metabolite. A typical riboswitch is made of an upstream aptamer domain and a downstream expression platform. Both domains participate in the folding and structural rearrangement in the absence or presence of its cognate metabolite. RNA polymerase pausing is a fundamental property of transcription that can influence RNA folding. Here we show that pausing plays an important role in the folding and conformational rearrangement of the Escherichia coli btuB riboswitch during transcription by the E. coli RNA polymerase. This riboswitch consists of an approximately 200 nucleotide, coenzyme B12 binding aptamer domain and an approximately 40 nucleotide expression platform that controls the ribosome access for translational initiation. We found that transcriptional pauses at strategic locations facilitate folding and structural rearrangement of the full-length riboswitch, but have minimal effect on the folding of the isolated aptamer domain. Pausing at these regulatory sites blocks the formation of alternate structures and plays a chaperoning role that couples folding of the aptamer domain and the expression platform. Pausing at strategic locations may be a general mechanism for coordinated folding and conformational rearrangements of riboswitch structures that underlie their response to environmental cues.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.
authors.forename: George A
authors.initials: GA
authors.lastname: Perdrizet
authors.forename: Irina
authors.initials: I
authors.lastname: Artsimovitch
authors.forename: Ran
authors.initials: R
authors.lastname: Furman
authors.forename: Tobin R
authors.initials: TR
authors.lastname: Sosnick
authors.forename: Tao
authors.initials: T
authors.lastname: Pan
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000502:physiology; D001483:Base Sequence; D003038:Cobamides / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000502:physiology; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics / Q000502:physiology*; D055029:Inverted Repeat Sequences; D026901:Membrane Transport Proteins / Q000737:chemistry* / Q000502:physiology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D009994:Osmolar Concentration; D010442:Peptide Chain Initiation, Translational; D059370:RNA Folding / Q000502:physiology*; D012318:RNA Polymerase I / Q000378:metabolism; D012045:Regulatory Sequences, Nucleic Acid; D012270:Ribosomes / Q000378:metabolism; D058928:Riboswitch / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D014158:Transcription, Genetic / Q000502:physiology*
chemical_list: D020121:5' Untranslated Regions; D052157:Aptamers, Nucleotide; D001425:Bacterial Outer Membrane Proteins; C044592:BtuB protein, E coli; D003038:Cobamides; D029968:Escherichia coli Proteins; D026901:Membrane Transport Proteins; D058928:Riboswitch; D012318:RNA Polymerase I; C000913:cobamamide