Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq
Autor: | Vivian Pogenberg, Norbert Mücke, Markus Seiler, Vladimir Rybin, Eike C. Schulz, Orsolya Barabas, Toby J. Gibson, Franka Voigt, Matthias Wilmanns, Cecilia Zuliani |
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Rok vydání: | 2017 |
Předmět: |
0301 basic medicine
Models Molecular Amino Acid Motifs Regulator Stacking lcsh:Medicine Plasma protein binding Biology Host Factor 1 Protein Bioinformatics Article 03 medical and health sciences Structure-Activity Relationship Gene expression Structure–activity relationship ddc:610 RNA Messenger Binding site lcsh:Science Multidisciplinary Binding Sites Base Sequence Molecular Structure Escherichia coli Proteins lcsh:R RNA In vitro Solutions 030104 developmental biology Biophysics Nucleic Acid Conformation lcsh:Q Protein Binding |
Zdroj: | Scientific Reports 'Scientific Reports ', vol: 7, pages: 9903-1-9903-15 (2017) Scientific Reports, Vol 7, Iss 1, Pp 1-15 (2017) |
ISSN: | 2045-2322 |
Popis: | 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. |
Databáze: | OpenAIRE |
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