title: Study of E. coli Hfq's RNA annealing acceleration and duplex destabilization activities using substrates with different GC-contents.
abstract: Folding of RNA molecules into their functional three-dimensional structures is often supported by RNA chaperones, some of which can catalyse the two elementary reactions helix disruption and helix formation. Hfq is one such RNA chaperone, but its strand displacement activity is controversial. Whereas some groups found Hfq to destabilize secondary structures, others did not observe such an activity with their RNA substrates. We studied Hfq's activities using a set of short RNAs of different thermodynamic stabilities (GC-contents from 4.8% to 61.9%), but constant length. We show that Hfq's strand displacement as well as its annealing activity are strongly dependent on the substrate's GC-content. However, this is due to Hfq's preferred binding of AU-rich sequences and not to the substrate's thermodynamic stability. Importantly, Hfq catalyses both annealing and strand displacement with comparable rates for different substrates, hinting at RNA strand diffusion and annealing nucleation being rate-limiting for both reactions. Hfq's strand displacement activity is a result of the thermodynamic destabilization of the RNA through preferred single-strand binding whereas annealing acceleration is independent from Hfq's thermodynamic influence. Therefore, the two apparently disparate activities annealing acceleration and duplex destabilization are not in energetic conflict with each other.
authors.affiliation: Department for Biochemistry, Max F Perutz Laboratories, Dr-Bohrgasse 9, 1030 Vienna, Austria.
authors.forename: Martina
authors.initials: M
authors.lastname: Doetsch
authors.forename: Sabine
authors.initials: S
authors.lastname: Stampfl
authors.forename: Boris
authors.initials: B
authors.lastname: Fürtig
authors.forename: Mads
authors.initials: M
authors.lastname: Beich-Frandsen
authors.forename: Krishna
authors.initials: K
authors.lastname: Saxena
authors.forename: Meghan
authors.initials: M
authors.lastname: Lybecker
authors.forename: Renée
authors.initials: R
authors.lastname: Schroeder
mesh_terms: D001482:Base Composition; D003596:Cytosine / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000378:metabolism*; D006147:Guanine / Q000737:chemistry; D035001:Host Factor 1 Protein / Q000378:metabolism*; D010455:Peptides / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D059370:RNA Folding; D012330:RNA, Double-Stranded / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D054322:tat Gene Products, Human Immunodeficiency Virus / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D010455:Peptides; D012330:RNA, Double-Stranded; D054322:tat Gene Products, Human Immunodeficiency Virus; D006147:Guanine; D012313:RNA; D003596:Cytosine