Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity.
The RNA-catalyzed splicing of group I and group II introns is facilitated by proteins that stabilize the active RNA structure or act as RNA chaperones to disrupt stable inactive structures that are kinetic traps in RNA folding. In Neurospora crassa and Saccharomyces cerevisiae, the latter function is fulfilled by specific DEAD-box proteins, denoted CYT-19 and Mss116p, respectively. Previous studies showed that purified CYT-19 stimulates the in vitro splicing of structurally diverse group I and group II introns, and uses the energy of ATP binding or hydrolysis to resolve kinetic traps. Here, we purified Mss116p and show that it has RNA-dependent ATPase activity, unwinds RNA duplexes in a non-polar fashion, and promotes ATP-independent strand-annealing. Further, we show that Mss116p binds RNA non-specifically and promotes in vitro splicing of both group I and group II intron RNAs, as well as RNA cleavage by the aI5gamma-derived D135 ribozyme. However, Mss116p also has ATP hydrolysis-independent effects on some of these reactions, which are not shared by CYT-19 and may reflect differences in its RNA-binding properties. We also show that a non-mitochondrial DEAD-box protein, yeast Ded1p, can function almost as efficiently as CYT-19 and Mss116p in splicing the yeast aI5gamma group II intron and less efficiently in splicing the bI1 group II intron. Together, our results show that Mss116p, like CYT-19, can act broadly as an RNA chaperone to stimulate the splicing of diverse group I and group II introns, and that Ded1p also has an RNA chaperone activity that can be assayed by its effect on splicing mitochondrial introns. Nevertheless, these DEAD-box protein RNA chaperones are not completely interchangeable and appear to function in somewhat different ways, using biochemical activities that have likely been tuned by coevolution to function optimally on specific RNA substrates.
Halls
Coralie
C
Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, School of Biological Sciences, University of Texas at Austin, Austin, TX 78712, USA.
Mohr
Sabine
S
Del Campo
Mark
M
Yang
Quansheng
Q
Jankowsky
Eckhard
E
Lambowitz
Alan M
AM
D000255:Adenosine Triphosphate / Q000378:metabolism*; D000818:Animals; D053487:DEAD-box RNA Helicases / Q000302:isolation & purification / Q000378:metabolism*; D006868:Hydrolysis / Q000187:drug effects; D007438:Introns / Q000187:drug effects / Q000235:genetics*; D008274:Magnesium / Q000494:pharmacology; D008928:Mitochondria / Q000187:drug effects / Q000378:metabolism; D018832:Molecular Chaperones / Q000378:metabolism*; D009492:Neurospora crassa; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D016366:Open Reading Frames / Q000187:drug effects / Q000235:genetics; D011485:Protein Binding / Q000187:drug effects; D012326:RNA Splicing / Q000187:drug effects / Q000235:genetics*; D016337:RNA, Catalytic / Q000378:metabolism; D012331:RNA, Fungal / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae; D029701:Saccharomyces cerevisiae Proteins / Q000302:isolation & purification / Q000378:metabolism*; D013379:Substrate Specificity / Q000187:drug effects; D016808:Tetrahymena thermophila
D018832:Molecular Chaperones; D016337:RNA, Catalytic; D012331:RNA, Fungal; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D000255:Adenosine Triphosphate; C492152:DED1 protein, S cerevisiae; C058150:MSS116 protein, S cerevisiae; D053487:DEAD-box RNA Helicases; D008274:Magnesium