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Sm-like protein Hfq: Location of the ATP-binding site and the effect of ATP on Hfq–RNA complexes

¹ Institut de Biologie Physico-Chimique, CNRS UPR 9073 conventionnee avec l'université Paris 7, 75005 Paris, France
² Department of Chemistry, Lamar University, Beaumont, Texas 77710, USA
³ Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0365, USA
⁴ INSERM U759, Imagerie Integrative, Institut Curie, Centre de Recherche, Laboratoire Raymond Latarjet, Centre Universitaire d'Orsay, 91405 Orsay, France

(RECEIVED March 15, 2007; FINAL REVISION May 25, 2007; ACCEPTED May 29, 2007)

Sm-like proteins are ubiquitous ring-shaped oligomers that exhibit a variety of nucleic acid-binding activities. They have been linked functionally to various cellular events involving RNA, and it is generally believed that their activity is exerted via the passive binding of nucleic acids. Our earlier studies of the Sm-like Escherichia coli protein Hfq provided the first evidence indicating that Hfq is an ATP-binding protein. Using a combination of biochemical and genetic techniques, we have now determined a plausible ATP-binding site in Hfq and tested Hfq's ATP-binding affinity and stoichiometry. The results of RNA footprinting and binding analyses suggest that ATP binding by the Hfq–RNA complex results in its significant destabilization. RNA footprinting indicates deprotection of Hfq-bound RNA tracts in the presence of ATP, suggestive of their release by the protein. The results reported herein broaden the scope of potential in vivo roles for Hfq and other Sm-like proteins.

Keywords: Hfq; Sm; Sm-like; translation; conformational change; electrophoresis

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