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Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq

Beich-Frandsen, Mads, Večerek, Branislav, Konarev, Petr V., Sjöblom, Björn, Kloiber, Karin, Hämmerle, Hermann, Rajkowitsch, Lukas, Miles, Andrew J., Kontaxis, Georg, Wallace, B.A., Svergun, Dimitri I., Konrat, Robert, Bläsi, Udo, Djinović-Carugo, Kristina
Nucleic acids research 2011 v.39 no.11 pp. 4900-4915
Escherichia coli, X-radiation, bacteria, bioinformatics, chemical elements, chemical interactions, circular dichroism spectroscopy, messenger RNA, nuclear magnetic resonance spectroscopy, proteins
The hexameric Escherichia coli RNA chaperone Hfq (HfqEc) is involved in riboregulation of target mRNAs by small trans-encoded RNAs. Hfq proteins of different bacteria comprise an evolutionarily conserved core, whereas the C-terminus is variable in length. Although the structure of the conserved core has been elucidated for several Hfq proteins, no structural information has yet been obtained for the C-terminus. Using bioinformatics, nuclear magnetic resonance spectroscopy, synchrotron radiation circular dichroism (SRCD) spectroscopy and small angle X-ray scattering we provide for the first time insights into the conformation and dynamic properties of the C-terminal extension of HfqEc. These studies indicate that the C-termini are flexible and extend laterally away from the hexameric core, displaying in this way features typical of intrinsically disordered proteins that facilitate intermolecular interactions. We identified a minimal, intrinsically disordered region of the C-terminus supporting the interactions with longer RNA fragments. This minimal region together with rest of the C-terminal extension provides a flexible moiety capable of tethering long and structurally diverse RNA molecules. Furthermore, SRCD spectroscopy supported the hypothesis that RNA fragments exceeding a certain length interact with the C-termini of HfqEc.