title: Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches.
abstract: Riboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations.
authors.affiliation: a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Sondés
authors.initials: S
authors.lastname: Guedich
authors.affiliation: a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Barbara
authors.initials: B
authors.lastname: Puffer-Enders
authors.affiliation: b IBMC-CNRS, Régulations post-transcriptionnelles et nutrition, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Baltzinger
authors.affiliation: c EMBL Grenoble Outstation , Grenoble , France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Hoffmann
authors.affiliation: a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Cyrielle
authors.initials: C
authors.lastname: Da Veiga
authors.affiliation: d IBMC-CNRS, Evolution des ARN non codants chez la levure, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Jossinet
authors.affiliation: e Université de Bordeaux, Institut Européen de Chimie et Biologie, ARNA laboratory; INSERM-U1212; CNRS-UMR5320 ; Bordeaux , France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Thore
authors.affiliation: a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bec
authors.affiliation: a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Eric
authors.initials: E
authors.lastname: Ennifar
authors.affiliation: a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Burnouf
authors.affiliation: a IBMC-CNRS, Biophysique et Biologie Structurale, Architecture et Réactivité de l'ARN, Université de Strasbourg , Strasbourg , France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Dumas
mesh_terms: D004926:Escherichia coli / Q000235:genetics*; D017665:Hydroxyl Radical / Q000378:metabolism; D007700:Kinetics; D058928:Riboswitch; D013816:Thermodynamics; D013835:Thiamine Pyrophosphate / Q000235:genetics*
chemical_list: D058928:Riboswitch; D017665:Hydroxyl Radical; D013835:Thiamine Pyrophosphate
keywords: Kinetic Regulation; kinITC; pyrophosphate; riboswitches; thiamine