title: DEAD-box helicases form nucleotide-dependent, long-lived complexes with RNA.
abstract: DEAD-box RNA helicases bind and remodel RNA and RNA-protein complexes in an ATP-dependent fashion. Several lines of evidence suggest that DEAD-box RNA helicases can also form stable, persistent complexes with RNA in a process referred to as RNA clamping. The molecular basis of RNA clamping is not well understood. Here we show that the yeast DEAD-box helicase Ded1p forms exceptionally long-lived complexes with RNA and the nonhydrolyzable ATP ground-state analogue ADP-BeFx or the nonhydrolyzable ATP transition state analogue ADP-AlFx. The complexes have lifetimes of several hours, and neither nucleotide nor Mg(2+) is released during this period. Mutation of arginine 489, which stabilizes the transition state, prevents formation of long-lived complexes with the ATP transition state analogue, but not with the ground state analogue. We also show that two other yeast DEAD-box helicases, Mss116p and Sub2p, form comparably long-lived complexes with RNA and ADP-BeFx. Like Ded1p, Mss116p forms long-lived complexes with ADP-AlFx, but Sub2p does not. These data suggest that the ATP transition state might vary for distinct DEAD-box helicases, or that the transition state triggers differing RNA binding properties in these proteins. In the ATP ground state, however, all tested DEAD-box helicases establish a persistent grip on RNA, revealing an inherent capacity of the enzymes to function as potent, ATP-dependent RNA clamps.
authors.affiliation: College of Veterinary Medicine, Nanjing Agricultural University , Nanjing, Jiangsu, 210095, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Liu
authors.forename: Andrea A
authors.initials: AA
authors.lastname: Putnam
authors.forename: Eckhard
authors.initials: E
authors.lastname: Jankowsky
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D053487:DEAD-box RNA Helicases / Q000737:chemistry* / Q000378:metabolism*; D006868:Hydrolysis; D009711:Nucleotides / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000201:enzymology; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D009711:Nucleotides; D029701:Saccharomyces cerevisiae Proteins; D012313:RNA; D000255:Adenosine Triphosphate; C492152:DED1 protein, S cerevisiae; D053487:DEAD-box RNA Helicases