title: Structural model of an mRNA in complex with the bacterial chaperone Hfq.
abstract: The Sm-like protein Hfq (host factor Q-beta phage) facilitates regulation by bacterial small noncoding RNAs (sRNAs) in response to stress and other environmental signals. Here, we present a low-resolution model of Escherichia coli Hfq bound to the rpoS mRNA, a bacterial stress response gene that is targeted by three different sRNAs. Selective 2'-hydroxyl acylation and primer extension, small-angle X-ray scattering, and Monte Carlo molecular dynamics simulations show that the distal face and lateral rim of Hfq interact with three sites in the rpoS leader, folding the RNA into a compact tertiary structure. These interactions are needed for sRNA regulation of rpoS translation and position the sRNA target adjacent to an sRNA binding region on the proximal face of Hfq. Our results show how Hfq specifically distorts the structure of the rpoS mRNA to enable sRNA base pairing and translational control.
authors.affiliation: Cell, Molecular and Developmental Biology and Biophysics Program, Johns Hopkins University, Baltimore, MD 21218;
authors.forename: Yi
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899;
authors.forename: Joseph E
authors.initials: JE
authors.lastname: Curtis
authors.affiliation: Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702; and.
authors.forename: Xianyang
authors.initials: X
authors.lastname: Fang
authors.affiliation: T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 swoodson@jhu.edu.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Woodson
mesh_terms: D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D035001:Host Factor 1 Protein / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D053838:Scattering, Small Angle; D012808:Sigma Factor / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D014961:X-Ray Diffraction
chemical_list: D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D012808:Sigma Factor
keywords: Lsm protein; RNA–protein interactions; SAXS; bacterial posttranscriptional control; small noncoding RNA