Scientific article
Open access

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

Published inScientific reports, vol. 7, no. 1, 9903
Publication date2017-08-29
First online date2017-08-29

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 Hfq 6 :A 18 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.

Affiliation Not a UNIGE publication
Citation (ISO format)
SCHULZ, Eike C. et al. Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. In: Scientific reports, 2017, vol. 7, n° 1, p. 9903. doi: 10.1038/s41598-017-10085-8
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Article (Published version)
ISSN of the journal2045-2322

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