title: Characterization of the full-length btuB riboswitch from Klebsiella pneumoniae.
abstract: Riboswitches are cis-regulatory RNA elements on the mRNA level that control the expression of the downstream coding region. The interaction of the riboswitch with its specific metabolite, which is related to the function of the controlled gene, induces a structural change of the RNA architecture. Consequently, gene regulation is induced by un/masking of the ribosome binding site (RBS). In the genome of Klebsiella pneumoniae a sequence was identified by bioinformatics and proposed to be a B12 riboswitch regulated by coenzyme B12. Here we study this new coenzyme B12-dependent riboswitch system by in-line probing and ITC. The riboswitch sequence includes the whole expression platform as well as RBS. In-line probing experiments were performed to investigate the structural rearrangement of this 243-nt long RNA sequence while Isothermal Titration Calorimetry (ITC) yielded the thermodynamic parameters of the interaction between the riboswitch and its metabolite. The interaction of coenzyme B12 with the butB riboswitch of K. pneumoniae is an exothermic process with a 1:1 binding stoichiometry and binding affinities of log KA=6.73±0.02 at 15°C and log KA=6.00±0.09 at 30°C.
authors.affiliation: Department of Chemistry, University of the Balearic Islands, Carretera Valldemossa km 7.5, Palma de Mallorca E-07122, Spain.
authors.forename: J
authors.initials: J
authors.lastname: Palou-Mir
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
authors.forename: A
authors.initials: A
authors.lastname: Musiari
authors.affiliation: Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
authors.forename: R K O
authors.initials: RK
authors.lastname: Sigel
authors.affiliation: Department of Chemistry, University of the Balearic Islands, Carretera Valldemossa km 7.5, Palma de Mallorca E-07122, Spain. Electronic address: miquel.barcelo@uib.es.
authors.forename: M
authors.initials: M
authors.lastname: Barceló-Oliver
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D003038:Cobamides / Q000737:chemistry*; D019295:Computational Biology; D007700:Kinetics; D007711:Klebsiella pneumoniae / Q000737:chemistry* / Q000235:genetics; D009690:Nucleic Acid Conformation; D012270:Ribosomes / Q000737:chemistry / Q000235:genetics; D058928:Riboswitch; D013816:Thermodynamics
chemical_list: D003038:Cobamides; D058928:Riboswitch; C000913:cobamamide
keywords: Coenzyme B(12); ITC; In-line probing; RNA; btuB riboswitch