title: DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture.
abstract: DEAD-box helicase proteins accelerate folding and rearrangements of highly structured RNAs and RNA-protein complexes (RNPs) in many essential cellular processes. Although DEAD-box proteins have been shown to use ATP to unwind short RNA helices, it is not known how they disrupt RNA tertiary structure. Here, we use single molecule fluorescence to show that the DEAD-box protein CYT-19 disrupts tertiary structure in a group I intron using a helix capture mechanism. CYT-19 binds to a helix within the structured RNA only after the helix spontaneously loses its tertiary contacts, and then CYT-19 uses ATP to unwind the helix, liberating the product strands. Ded1, a multifunctional yeast DEAD-box protein, gives analogous results with small but reproducible differences that may reflect its in vivo roles. The requirement for spontaneous dynamics likely targets DEAD-box proteins toward less stable RNA structures, which are likely to experience greater dynamic fluctuations, and provides a satisfying explanation for previous correlations between RNA stability and CYT-19 unfolding efficiency. Biologically, the ability to sense RNA stability probably biases DEAD-box proteins to act preferentially on less stable misfolded structures and thereby to promote native folding while minimizing spurious interactions with stable, natively folded RNAs. In addition, this straightforward mechanism for RNA remodeling does not require any specific structural environment of the helicase core and is likely to be relevant for DEAD-box proteins that promote RNA rearrangements of RNP complexes including the spliceosome and ribosome.
authors.affiliation: Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Pan
authors.affiliation: Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Potratz
authors.affiliation: Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Brian
authors.initials: B
authors.lastname: Cannon
authors.affiliation: Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Zachary B
authors.initials: ZB
authors.lastname: Simpson
authors.affiliation: Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Ziehr
authors.affiliation: Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Pilar
authors.initials: P
authors.lastname: Tijerina
authors.affiliation: Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America.
authors.forename: Rick
authors.initials: R
authors.lastname: Russell
mesh_terms: D053487:DEAD-box RNA Helicases / Q000378:metabolism*; D031541:Fluorescence Resonance Energy Transfer; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D016337:RNA, Catalytic / Q000378:metabolism; D016808:Tetrahymena thermophila / Q000378:metabolism*
chemical_list: D016337:RNA, Catalytic; D053487:DEAD-box RNA Helicases