5new

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RNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimerRNA-RNA base stacking in the crystal structure of an Hfq6:RNA dimer

Structural highlights

5new is a 4 chain structure with sequence from Escherichia coli and Escherichia coli S88. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.511Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HFQ_ECOLI RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Involved in the regulation of stress responses mediated by the sigma factors RpoS, sigma-E and sigma-32. Binds with high specificity to tRNAs. In vitro, stimulates synthesis of long tails by poly(A) polymerase I. Required for RNA phage Qbeta replication.[1] [2] [3] [4] [5] Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation.[6] [7] [8] [9] [10]

Publication Abstract from PubMed

The RNA-chaperone Hfq catalyses the annealing of bacterial small RNAs (sRNAs) with target mRNAs to regulate gene expression in response to environmental stimuli. Hfq acts on a diverse set of sRNA-mRNA pairs using a variety of different molecular mechanisms. Here, we present an unusual crystal structure showing two Hfq-RNA complexes interacting via their bound RNA molecules. The structure contains two Hfq6:A18 RNA assemblies positioned face-to-face, with the RNA molecules turned towards each other and connected via interdigitating base stacking interactions at the center. Biochemical data further confirm the observed interaction, and indicate that RNA-mediated contacts occur between Hfq-RNA complexes with various (ARN)X motif containing RNA sequences in vitro, including the stress response regulator OxyS and its target, fhlA. A systematic computational survey also shows that phylogenetically conserved (ARN)X motifs are present in a subset of sRNAs, some of which share similar modular architectures. We hypothesise that Hfq can co-opt RNA-RNA base stacking, an unanticipated structural trick, to promote the interaction of (ARN)X motif containing sRNAs with target mRNAs on a "speed-dating" fashion, thereby supporting their regulatory function.

Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq.,Schulz EC, Seiler M, Zuliani C, Voigt F, Rybin V, Pogenberg V, Mucke N, Wilmanns M, Gibson TJ, Barabas O Sci Rep. 2017 Aug 29;7(1):9903. doi: 10.1038/s41598-017-10085-8. PMID:28852099[11]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Carmichael GG, Weber K, Niveleau A, Wahba AJ. The host factor required for RNA phage Qbeta RNA replication in vitro. Intracellular location, quantitation, and purification by polyadenylate-cellulose chromatography. J Biol Chem. 1975 May 25;250(10):3607-612. PMID:805130
  2. ↑ Hajnsdorf E, Regnier P. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1501-5. PMID:10677490 doi:10.1073/pnas.040549897
  3. ↑ Sledjeski DD, Whitman C, Zhang A. Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol. 2001 Mar;183(6):1997-2005. PMID:11222598 doi:10.1128/JB.183.6.1997-2005.2001
  4. ↑ Guisbert E, Rhodius VA, Ahuja N, Witkin E, Gross CA. Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli. J Bacteriol. 2007 Mar;189(5):1963-73. Epub 2006 Dec 8. PMID:17158661 doi:10.1128/JB.01243-06
  5. ↑ Kim Y, Wood TK. Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem Biophys Res Commun. 2010 Jan 1;391(1):209-13. doi:, 10.1016/j.bbrc.2009.11.033. Epub 2009 Nov 10. PMID:19909729 doi:10.1016/j.bbrc.2009.11.033
  6. ↑ Carmichael GG, Weber K, Niveleau A, Wahba AJ. The host factor required for RNA phage Qbeta RNA replication in vitro. Intracellular location, quantitation, and purification by polyadenylate-cellulose chromatography. J Biol Chem. 1975 May 25;250(10):3607-612. PMID:805130
  7. ↑ Hajnsdorf E, Regnier P. Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I. Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1501-5. PMID:10677490 doi:10.1073/pnas.040549897
  8. ↑ Sledjeski DD, Whitman C, Zhang A. Hfq is necessary for regulation by the untranslated RNA DsrA. J Bacteriol. 2001 Mar;183(6):1997-2005. PMID:11222598 doi:10.1128/JB.183.6.1997-2005.2001
  9. ↑ Guisbert E, Rhodius VA, Ahuja N, Witkin E, Gross CA. Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli. J Bacteriol. 2007 Mar;189(5):1963-73. Epub 2006 Dec 8. PMID:17158661 doi:10.1128/JB.01243-06
  10. ↑ Kim Y, Wood TK. Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli. Biochem Biophys Res Commun. 2010 Jan 1;391(1):209-13. doi:, 10.1016/j.bbrc.2009.11.033. Epub 2009 Nov 10. PMID:19909729 doi:10.1016/j.bbrc.2009.11.033
  11. ↑ Schulz EC, Seiler M, Zuliani C, Voigt F, Rybin V, Pogenberg V, Mucke N, Wilmanns M, Gibson TJ, Barabas O. Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. Sci Rep. 2017 Aug 29;7(1):9903. doi: 10.1038/s41598-017-10085-8. PMID:28852099 doi:http://dx.doi.org/10.1038/s41598-017-10085-8

5new, resolution 2.51Å

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