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

By Mads Beich-Frandsen, Branislav Večerek, Petr V. Konarev, Björn Sjöblom, Karin Kloiber, Hermann Hämmerle, Lukas Rajkowitsch, Andrew J. Miles, Georg Kontaxis, B. A. Wallace, Dimitri I. Svergun, Robert Konrat, Udo Bläsi and Kristina Djinović-Carugo


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

Topics: Structural Biology
Publisher: Oxford University Press
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Provided by: PubMed Central

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  1. (2006). A reference database for circular dichroism spectroscopy covering fold and secondary structure space.
  2. (1995). Activation of alpha-toxin translation in Staphylococcus aureus by the trans-encoded antisense RNA,
  3. (1993). Amino acid type determination in the sequential assignment procedure of uniformly 13 C/15 N-enriched proteins.
  4. (2007). An Hfq-like protein in archaea: crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii.
  5. (1999). Analyzing protein circular dichroism spectra for accurate secondary structures.
  6. (2004). Anchor residues in protein-protein interactions.
  7. (2007). ATSAS 2.1-towards automated and web-supported small-angle scattering data analysis.
  8. (2008). Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33.
  9. (2008). Backbone assignment of osteopontin, a cytokine and cell attachment protein implicated in tumorigenesis.
  10. (1994). Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation.
  11. (2006). Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq.
  12. (2003). Calibration and standardisation of synchrotron radiation circular dichroism and conventional circular dichroism spectrophotometers.
  13. (2004). CDtool-an integrated software package for circular dichroism spectroscopic data processing, analysis, and archiving.
  14. (2003). Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs.
  15. (2002). Coupling of folding and binding for unstructured proteins.
  16. (2007). Coupling RNA annealing and strand displacement: a FRET-based microplate reader assay for RNA chaperone activity.
  17. (1995). CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates.
  18. (1998). Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr.
  19. (2009). Cyanobacteria contain a structural homologue of the Hfq protein with altered RNA-binding properties.
  20. (2009). DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering.
  21. (2010). Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes.
  22. (2004). DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data.
  23. (2010). E. coli DNA associated with isolated Hfq interacts with Hfq’s distal surface and C-terminal domain.
  24. (2004). Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs.
  25. (1981). Estimation of globular protein secondary structure from circular dichroism.
  26. (1990). Estimation of protein secondary structure and error analysis from circular dichroism spectra.
  27. (2000). Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.
  28. (2010). Expression, crystallization and preliminary crystallographic analysis of RNA-binding protein Hfq (YmaH) from Bacillus subtilis in complex with an RNA aptamer.
  29. (1982). Folding of the mitochondrial proton adenosinetriphosphatase proteolipid channel in phospholipid vesicles.
  30. (2004). Functional effects of variants of the RNA chaperone Hfq.
  31. (2002). Functional replacement of the Escherichia coli hfq gene by the homologue of Pseudomonas aeruginosa.
  32. (1982). General theory.
  33. (2005). Global rigid body modeling of macromolecular complexes against small-angle scattering data.
  34. (1991). GNOM-a program package for small-angle scattering data processing.
  35. (2001). Hfq is necessary for regulation by the untranslated RNA DsrA.
  36. (2006). Hfq-dependent alterations of the transcriptome profile and effects on quorum sensing in Pseudomonas aeruginosa.
  37. (2002). Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction.
  38. (1993). HNCACB, a high-sensitivity 3 D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha- and beta-carbon resonances in proteins.
  39. (2000). HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.
  40. (2003). Interaction of the RNA chaperone Hfq with mRNAs: direct and indirect roles of Hfq in iron metabolism of Escherichia coli.
  41. (2006). Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes.
  42. (2001). Intrinsically disordered protein.
  43. (2005). Intrinsically unstructured proteins and their functions.
  44. (2007). MacPyMOL: A PyMOL-based Molecular Graphics Application for MacOS X. DeLano Scientific LLC,
  45. (2005). Micros for microbes: non-coding regulatory RNAs in bacteria.
  46. (2009). Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level.
  47. (1995). NMRPipe: a multidimensional spectral processing system based on UNIX pipes.
  48. (2008). Noncoding RNA control of the making and breaking of sugars.
  49. (2009). On the facultative requirement of the bacterial RNA chaperone,
  50. (2002). Predicted structure and phyletic distribution of the RNA-binding protein Hfq.
  51. (2008). Prediction of disordered regions in proteins based on the meta approach.
  52. (2004). Preformed structural elements feature in partner recognition by intrinsically unstructured proteins.
  53. (2003). PRIMUS: a Windows PC-based system for small-angle scattering data analysis.
  54. (1990). Proton-proton correlation via carbon-carbon couplings: A three-dimensional NMR approach for the assignment of aliphatic resonances in proteins labeled with carbon-13.
  55. (2010). Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering.
  56. (2001). Recognition between flexible protein molecules: induced and assisted folding.
  57. (2009). Regulating the regulator: an RNA decoy acts as an OFF switch for the regulation of an sRNA.
  58. (2003). Regulatory roles for small RNAs in bacteria.
  59. (2005). Release of long-range tertiary interactions potentiates aggregation of natively unstructured alpha-synuclein.
  60. (2007). RNA chaperone activity and RNA-binding properties of the E. coli protein StpA.
  61. (2003). RNA chaperone activity of the Sm-like Hfq protein.
  62. (2003). Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli.
  63. (2003). Small non-coding RNAs, co-ordinators of adaptation processes in Escherichia coli: the RpoS paradigm.
  64. (2006). Small RNA regulators and the bacterial response to stress. Cold Spring Harb.
  65. (2008). Solution conformation and thermodynamic characteristics of RNA binding by the splicing factor U2AF65.
  66. (1995). Spectral density function mapping using 15 N relaxation data exclusively.
  67. (2000). Structural and thermodynamic strategies for site-specific DNA binding proteins.
  68. Structural polymorphism of 441-residue tau at single residue resolution.
  69. (2009). Structure of Escherichia coli Hfq bound to polyriboadenylate RNA.
  70. (2005). Structure of Pseudomonas aeruginosa Hfq protein. Acta Crystallogr.
  71. (2001). Structure, function, and dynamics of the dimerization and DNA-binding domain of oncogenic transcription factor v-Myc.
  72. (2010). Structure/function implications in a dynamic complex of the intrinsically disordered
  73. (2002). Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein.
  74. (2006). Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics.
  75. (2004). The C-terminal domain of Escherichia coli Hfq increases the stability of the hexamer.
  76. (2008). The C-terminal domain of Escherichia coli Hfq is required for regulation.
  77. (2008). The Jpred 3 secondary structure prediction server.
  78. (2009). The protein meta-structure: a novel concept for chemical and molecular biology.
  79. (2000). The PSIPRED protein structure prediction server.
  80. (1996). The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli.
  81. (2004). The role of structural disorder in the function of RNA and protein chaperones.
  82. (2008). The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA.
  83. (2002). The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs.
  84. (2004). The small RNA regulators of Escherichia coli: roles and mechanisms.
  85. (1996). The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli.
  86. (2010). The structures of mutant forms of Hfq from Pseudomonas aeruginosa reveal the importance of the conserved His57 for the protein hexamer organization.
  87. (1990). Three-dimensional triple-resonance NMR spectroscopy of isotopically enriched proteins.
  88. (2006). Translation initiation and the fate of bacterial mRNAs.
  89. (2005). Translational autocontrol of the Escherichia coli hfq RNA chaperone gene.
  90. (2008). Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation.
  91. (2007). Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory,
  92. (2007). X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.