title: DEAD-box protein CYT-19 is activated by exposed helices in a group I intron RNA.
abstract: DEAD-box proteins are nonprocessive RNA helicases and can function as RNA chaperones, but the mechanisms of their chaperone activity remain incompletely understood. The Neurospora crassa DEAD-box protein CYT-19 is a mitochondrial RNA chaperone that promotes group I intron splicing and has been shown to resolve misfolded group I intron structures, allowing them to refold. Building on previous results, here we use a series of tertiary contact mutants of the Tetrahymena group I intron ribozyme to demonstrate that the efficiency of CYT-19-mediated unfolding of the ribozyme is tightly linked to global RNA tertiary stability. Efficient unfolding of destabilized ribozyme variants is accompanied by increased ATPase activity of CYT-19, suggesting that destabilized ribozymes provide more productive interaction opportunities. The strongest ATPase stimulation occurs with a ribozyme that lacks all five tertiary contacts and does not form a compact structure, and small-angle X-ray scattering indicates that ATPase activity tracks with ribozyme compactness. Further, deletion of three helices that are prominently exposed in the folded structure decreases the ATPase stimulation by the folded ribozyme. Together, these results lead to a model in which CYT-19, and likely related DEAD-box proteins, rearranges complex RNA structures by preferentially interacting with and unwinding exposed RNA secondary structure. Importantly, this mechanism could bias DEAD-box proteins to act on misfolded RNAs and ribonucleoproteins, which are likely to be less compact and more dynamic than their native counterparts.
authors.affiliation: Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712; and.
authors.forename: Inga
authors.initials: I
authors.lastname: Jarmoskaite
authors.affiliation: Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712; and.
authors.forename: Hari
authors.initials: H
authors.lastname: Bhaskaran
authors.affiliation: X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439.
authors.forename: Soenke
authors.initials: S
authors.lastname: Seifert
authors.affiliation: Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712; and rick_russell@cm.utexas.edu.
authors.forename: Rick
authors.initials: R
authors.lastname: Russell
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D053487:DEAD-box RNA Helicases / Q000378:metabolism*; D004789:Enzyme Activation / Q000187:drug effects; D005656:Fungal Proteins / Q000378:metabolism*; D006868:Hydrolysis / Q000187:drug effects; D007438:Introns / Q000235:genetics*; D008274:Magnesium / Q000494:pharmacology; D008958:Models, Molecular; D009492:Neurospora crassa / Q000201:enzymology; D009690:Nucleic Acid Conformation; D017510:Protein Folding / Q000187:drug effects; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism; D013768:Tetrahymena / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; C116167:GIR1 ribozyme; D016337:RNA, Catalytic; D012313:RNA; D000255:Adenosine Triphosphate; D000251:Adenosine Triphosphatases; D053487:DEAD-box RNA Helicases; D008274:Magnesium
keywords: RNA folding; RNA misfolding; RNA tertiary structure; RNA unwinding; superfamily 2 helicase