Structural Flexibility of RNA As Molecular Basis for Hfq Chaperone Function

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2012 Jun 22

PMID 22718981

Citations 19

Authors

Euripedes de Almeida Ribeiro Jr

Mads Beich-Frandsen

Petr V Konarev

Weifeng Shang

Branislav Vecerek

Georg Kontaxis

Hermann Hammerle

Herwig Peterlik

Dmitri I Svergun

Udo Blasi

Kristina Djinovic-Carugo

Affiliations

Soon will be listed here.

Abstract

In enteric bacteria, many small regulatory RNAs (sRNAs) associate with the RNA chaperone host factor Q (Hfq) and often require the protein for regulation of target mRNAs. Previous studies suggested that the hexameric Escherichia coli Hfq (Hfq(Ec)) binds sRNAs on the proximal site, whereas the distal site has been implicated in Hfq-mRNA interactions. Employing a combination of small angle X-ray scattering, nuclear magnetic resonance and biochemical approaches, we report the structural analysis of a 1:1 complex of Hfq(Ec) with a 34-nt-long subsequence of a natural substrate sRNA, DsrA (DsrA(34)). This sRNA is involved in post-transcriptional regulation of the E. coli rpoS mRNA encoding the stationary phase sigma factor RpoS. The molecular envelopes of Hfq(Ec) in complex with DsrA(34) revealed an overall asymmetric shape of the complex in solution with the protein maintaining its doughnut-like structure, whereas the extended DsrA(34) is flexible and displays an ensemble of different spatial arrangements. These results are discussed in terms of a model, wherein the structural flexibility of RNA ligands bound to Hfq stochastically facilitates base pairing and provides the foundation for the RNA chaperone function inherent to Hfq.

Citing Articles

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Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq.

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References

Soper T, Doxzen K, Woodson S . Major role for mRNA binding and restructuring in sRNA recruitment by Hfq. RNA. 2011; 17(8):1544-50. PMC: 3153977. DOI: 10.1261/rna.2767211. View

Otaka H, Ishikawa H, Morita T, Aiba H . PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action. Proc Natl Acad Sci U S A. 2011; 108(32):13059-64. PMC: 3156202. DOI: 10.1073/pnas.1107050108. View

Jousselin A, Metzinger L, Felden B . On the facultative requirement of the bacterial RNA chaperone, Hfq. Trends Microbiol. 2009; 17(9):399-405. DOI: 10.1016/j.tim.2009.06.003. View

Farrow N, Zhang O, Szabo A, Torchia D, Kay L . Spectral density function mapping using 15N relaxation data exclusively. J Biomol NMR. 1995; 6(2):153-62. DOI: 10.1007/BF00211779. View

Schumacher M, Pearson R, Moller T, Valentin-Hansen P, Brennan R . Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein. EMBO J. 2002; 21(13):3546-56. PMC: 126077. DOI: 10.1093/emboj/cdf322. View

Flores S, Altman R . Turning limited experimental information into 3D models of RNA. RNA. 2010; 16(9):1769-78. PMC: 2924536. DOI: 10.1261/rna.2112110. View

Darfeuille F, Unoson C, Vogel J, Wagner E . An antisense RNA inhibits translation by competing with standby ribosomes. Mol Cell. 2007; 26(3):381-92. DOI: 10.1016/j.molcel.2007.04.003. View

Wang W, Wang L, Zou Y, Zhang J, Gong Q, Wu J . Cooperation of Escherichia coli Hfq hexamers in DsrA binding. Genes Dev. 2011; 25(19):2106-17. PMC: 3197208. DOI: 10.1101/gad.16746011. View

Sauter C, Basquin J, Suck D . Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli. Nucleic Acids Res. 2003; 31(14):4091-8. PMC: 167641. DOI: 10.1093/nar/gkg480. View

10.

Hyeon C, Dima R, Thirumalai D . Size, shape, and flexibility of RNA structures. J Chem Phys. 2006; 125(19):194905. DOI: 10.1063/1.2364190. View

11.

Round A, Franke D, Moritz S, Huchler R, Fritsche M, Malthan D . Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33. J Appl Crystallogr. 2014; 41(Pt 5):913-917. PMC: 4233401. DOI: 10.1107/S0021889808021018. View

12.

Sauer E, Weichenrieder O . Structural basis for RNA 3'-end recognition by Hfq. Proc Natl Acad Sci U S A. 2011; 108(32):13065-70. PMC: 3156190. DOI: 10.1073/pnas.1103420108. View

13.

Moon K, Gottesman S . Competition among Hfq-binding small RNAs in Escherichia coli. Mol Microbiol. 2011; 82(6):1545-62. PMC: 7394283. DOI: 10.1111/j.1365-2958.2011.07907.x. View

14.

Caliskan G, Hyeon C, Perez-Salas U, Briber R, Woodson S, Thirumalai D . Persistence length changes dramatically as RNA folds. Phys Rev Lett. 2006; 95(26):268303. DOI: 10.1103/PhysRevLett.95.268303. View

15.

Beich-Frandsen M, Vecerek B, Konarev P, Sjoblom B, Kloiber K, Hammerle H . Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq. Nucleic Acids Res. 2011; 39(11):4900-15. PMC: 3113564. DOI: 10.1093/nar/gkq1346. View

16.

Svergun D . Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J. 1999; 76(6):2879-86. PMC: 1300260. DOI: 10.1016/S0006-3495(99)77443-6. View

17.

Flores S, Wan Y, Russell R, Altman R . Predicting RNA structure by multiple template homology modeling. Pac Symp Biocomput. 2009; :216-27. PMC: 2872935. DOI: 10.1142/9789814295291_0024. View

18.

Bernado P, Mylonas E, Petoukhov M, Blackledge M, Svergun D . Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc. 2007; 129(17):5656-64. DOI: 10.1021/ja069124n. View

19.

Wilusz C, Wilusz J . Eukaryotic Lsm proteins: lessons from bacteria. Nat Struct Mol Biol. 2005; 12(12):1031-6. DOI: 10.1038/nsmb1037. View

20.

Doetsch M, Furtig B, Gstrein T, Stampfl S, Schroeder R . The RNA annealing mechanism of the HIV-1 Tat peptide: conversion of the RNA into an annealing-competent conformation. Nucleic Acids Res. 2011; 39(10):4405-18. PMC: 3105384. DOI: 10.1093/nar/gkq1339. View