title: Three-state mechanism couples ligand and temperature sensing in riboswitches.
abstract: Riboswitches are cis-acting gene-regulatory RNA elements that can function at the level of transcription, translation and RNA cleavage. The commonly accepted molecular mechanism for riboswitch function proposes a ligand-dependent conformational switch between two mutually exclusive states. According to this mechanism, ligand binding to an aptamer domain induces an allosteric conformational switch of an expression platform, leading to activation or repression of ligand-related gene expression. However, many riboswitch properties cannot be explained by a pure two-state mechanism. Here we show that the regulation mechanism of the adenine-sensing riboswitch, encoded by the add gene on chromosome II of the human Gram-negative pathogenic bacterium Vibrio vulnificus, is notably different from a two-state switch mechanism in that it involves three distinct stable conformations. We characterized the temperature and Mg(2+) dependence of the population ratios of the three conformations and the kinetics of their interconversion at nucleotide resolution. The observed temperature dependence of a pre-equilibrium involving two structurally distinct ligand-free conformations of the add riboswitch conferred efficient regulation over a physiologically relevant temperature range. Such robust switching is a key requirement for gene regulation in bacteria that have to adapt to environments with varying temperatures. The translational adenine-sensing riboswitch represents the first example, to our knowledge, of a temperature-compensated regulatory RNA element.
authors.affiliation: Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany.
authors.forename: Anke
authors.initials: A
authors.lastname: Reining
authors.forename: Senada
authors.initials: S
authors.lastname: Nozinovic
authors.forename: Kai
authors.initials: K
authors.lastname: Schlepckow
authors.forename: Florian
authors.initials: F
authors.lastname: Buhr
authors.forename: Boris
authors.initials: B
authors.lastname: Fürtig
authors.forename: Harald
authors.initials: H
authors.lastname: Schwalbe
mesh_terms: D000225:Adenine / Q000378:metabolism; D001483:Base Sequence; D015964:Gene Expression Regulation, Bacterial; D008024:Ligands; D008274:Magnesium / Q000737:chemistry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D058928:Riboswitch; D013696:Temperature; D041261:Vibrio vulnificus / Q000235:genetics
chemical_list: D008024:Ligands; D012329:RNA, Bacterial; D058928:Riboswitch; D008274:Magnesium; D000225:Adenine