Structural flexibility of RNA as molecular basis for Hfq chaperone function

Author(s)

Euripedes De Almeida Ribeiro, Mads Beich-Frandsen, Peter V. Konarev, Weifeng Shang, Branislav Vecerek, Georg Kontaxis, Hermann Konrad Hämmerle, Herwig Peterlik, Dimitri I. Svergun, Udo Bläsi, Kristina Djinovic-Carugo

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.

Organisation(s)

Department of Structural and Computational Biology, Department of Microbiology, Immunobiology and Genetics, Dynamics of Condensed Systems

External organisation(s)

European Molecular Biology Laboratory

Journal

Nucleic Acids Research

Volume

40

Pages

8072-8084

No. of pages

13

ISSN

0305-1048

DOI

https://doi.org/10.1093/nar/gks510

Publication date

06-2012

Peer reviewed

Yes

Austrian Fields of Science 2012

103009 Solid state physics, 103015 Condensed matter, 103018 Materials physics

Portal url

https://ucrisportal.univie.ac.at/en/publications/ced9d6bb-c38c-4889-89b4-5a87fea86845