Nucleic Acids Research Advance Access published online on January 26, 2007
Nucleic Acids Research, doi:10.1093/nar/gkl1124
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Spectroscopic observation of RNA chaperone activities of Hfq in post-transcriptional regulation by a small non-coding RNA
1Institut de Biologie Physico-Chimique, CNRS UPR 9073 conventionnée avec l’Université Paris 7, 13 rue P. et M. Curie, 75005 Paris, France, 2Department of Physics and Howard Hughes Medical Institute and 3Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois 61081, USA
*To whom correspondence should be addressed. Tel: (217) 265 0717; Fax: (217) 244 7187; Email: tjha{at}uiuc.edu
Received November 15, 2006. Revised December 8, 2006. Accepted December 8, 2006.
Hfq protein is vital for the function of many non-coding small (s)RNAs in bacteria but the mechanism by which Hfq facilitates the function of sRNA is still debated. We developed a fluorescence resonance energy transfer assay to probe how Hfq modulates the interaction between a sRNA, DsrA, and its regulatory target mRNA, rpoS. The relevant RNA fragments were labelled so that changes in intra- and intermolecular RNA structures can be monitored in real time. Our data show that Hfq promotes the strand exchange reaction in which the internal structure of rpoS is replaced by pairing with DsrA such that the Shine-Dalgarno sequence of the mRNA becomes exposed. Hfq appears to carry out strand exchange by inducing rapid association of DsrA and a premelted rpoS and by aiding in the slow disruption of the rpoS secondary structure. Unexpectedly, Hfq also disrupts a preformed complex between rpoS and DsrA. While it may not be a frequent event in vivo, this melting activity may have implications in the reversal of sRNA-based regulation. Overall, our data suggests that Hfq not only promotes strand exchange by binding rapidly to both DsrA and rpoS but also possesses RNA chaperoning properties that facilitates dynamic RNA–RNA interactions.
Present address: Sungchul Hohng, Department of Physics and Astronomy, Seoul National University, San 56-1 Sillim 9-dong, Gwanak-gu, Seoul 151-742, Korea
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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