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

• Published in: Nucleic acids research 2011-06, Vol.39 (11), p.4900-4915
• Main Authors: Beich-Frandsen, Mads, Ve erek, 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, Djinovi -Carugo, Kristina
• Format: Article
• Language: English
• Subjects: Circular Dichroism; Computational Biology; Escherichia coli; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Host Factor 1 Protein - chemistry; Host Factor 1 Protein - genetics; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; RNA - chemistry; Sequence Deletion; Structural Biology
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkq1346

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.