Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-08-29

AUTHORS

Eike C. Schulz, Markus Seiler, Cecilia Zuliani, Franka Voigt, Vladimir Rybin, Vivian Pogenberg, Norbert Mücke, Matthias Wilmanns, Toby J. Gibson, Orsolya Barabas

ABSTRACT

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. More... »

PAGES

9903

References to SciGraph publications

  • 2011-11-24. ViennaRNA Package 2.0 in ALGORITHMS FOR MOLECULAR BIOLOGY
  • 1997-04-01. Improved R-factors for diffraction data analysis in macromolecular crystallography in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2016-12-22. GRIL-seq provides a method for identifying direct targets of bacterial small regulatory RNA by in vivo proximity ligation in NATURE MICROBIOLOGY
  • 2011-08-15. Hfq and its constellation of RNA in NATURE REVIEWS MICROBIOLOGY
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    http://scigraph.springernature.com/pub.10.1038/s41598-017-10085-8

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    http://dx.doi.org/10.1038/s41598-017-10085-8

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    https://app.dimensions.ai/details/publication/pub.1091331756

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28852099


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