Structural flexibility of RNA as molecular basis for Hfq chaperone function.
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.
Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
Euripedes de Almeida
Ede A
Ribeiro
Mads
M
Beich-Frandsen
Petr V
PV
Konarev
Weifeng
W
Shang
Branislav
B
Vecerek
Georg
G
Kontaxis
Hermann
H
Hämmerle
Herwig
H
Peterlik
Dmitri I
DI
Svergun
Udo
U
Bläsi
Kristina
K
Djinović-Carugo
D029968:Escherichia coli Proteins / Q000737:chemistry*; D035001:Host Factor 1 Protein / Q000737:chemistry*; D008027:Light; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D058727:RNA, Small Untranslated / Q000737:chemistry*; D012542:Scattering, Radiation; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
C405431:DsrA RNA, E coli; D029968:Escherichia coli Proteins; C087373:Hfq protein, E coli; D035001:Host Factor 1 Protein; D058727:RNA, Small Untranslated