Mechanism of maturase-promoted group II intron splicing

Matsuura, Manabu; Noah, James W.; Lambowitz, Alan M.

doi:10.1093/emboj/20.24.7259

Cited by 141 publications

(204 citation statements)

References 21 publications

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“…Reverse-branching reactions with the Ll.LtrB intron were done in 100 mM NH 4 Cl, 5 mM MgCl 2 , 40 mM Tris⅐HCl, pH 7.5 at 30°C. Similar results were obtained with 500 mM NH 4 Cl, which is optimal for maturase-promoted forward splicing (6,7). In some incubations, 20 mg͞ml protease K and 0.1% SDS were added to lariat RNA after preincubation with CYT-19 or LtrA.…”

Section: Methodssupporting

confidence: 68%

“…These differences suggest that the active structures of aI5␥ and bI1 at physiological KCl and Mg 2ϩ concentrations may differ in significant ways from those formed under self-splicing conditions. A similar conclusion was reached for the maturase-promoted and selfsplicing reactions of the Ll.LtrB intron based on chemical structure mapping and analysis of UV-induced RNA-RNA cross-links (7,8). We suggested previously that inactive structures stabilized by high Mg 2ϩ concentrations might contribute to the strongly decreased rate of self-splicing compared with maturase-dependent splicing of that intron (7,8).…”

Section: Discussionmentioning

confidence: 99%

“…Until now, a protein-dependent in vitro splicing system has been developed only for the RT͞maturase protein encoded by the mobile Lactococcus lactis Ll.LtrB intron (5, 6). Studies using this system showed that the maturase binds specifically to the intron RNA and promotes its splicing by stabilizing the catalytically active RNA structure (7,8).In addition to proteins that stabilize specific RNA structures, cellular RNAs may require RNA chaperones to disrupt stable inactive structure (''kinetic traps'') during RNA folding (9, 10). In the case of group I and II introns, this RNA chaperone function is thought to be fulfilled by specific DExH͞D-box proteins (11, 12).…”

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A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone

Mohr

Matsuura

Perlman

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Group II intron RNAs self-splice in vitro but only at high salt and͞or Mg 2؉ concentrations and have been thought to require proteins to stabilize their active structure for efficient splicing in vivo. Here, we show that a DEAD-box protein, CYT-19, can by itself promote the splicing and reverse splicing of the yeast aI5␥ and bI1 group II introns under near-physiological conditions by acting as an ATPdependent RNA chaperone, whose continued presence is not required after RNA folding. Our results suggest that the folding of some group II introns may be limited by kinetic traps and that their active structures, once formed, do not require proteins or high Mg 2؉ concentrations for structural stabilization. Thus, during evolution, group II introns could have spliced and transposed by reverse splicing by using ubiquitous RNA chaperones before acquiring more specific protein partners to promote their splicing and mobility. More generally, our results provide additional evidence for the widespread role of RNA chaperones in folding cellular RNAs.catalytic RNA ͉ ribozyme ͉ RNA helicase ͉ RNA structure G roup II introns are mobile catalytic RNAs that splice via a lariat intermediate and may be ancestors of eukaryotic spliceosomal introns (1-3). To catalyze splicing, the intron RNAs fold into a conserved three-dimensional structure, which aligns the splice sites and branch-point nucleotide residue and uses bound Mg 2ϩ ions to activate the appropriate bonds for catalysis. The conserved three-dimensional structure of group II introns consists of six double-helical domains (D1 to D6), which interact with each other via tertiary contacts (3). Some group II introns self-splice in vitro, but only under nonphysiological conditions, including high monovalent salt and Mg 2ϩ concentrations, which were thought essential for RNA folding and structural stabilization. Thus far, most of what is known about group II intron RNA structure, folding, and reactivity has come from studies under such conditions (1-3).The efficient splicing of group II introns in vivo requires proteins to help the intron RNA fold into the catalytically active structure (reviewed in refs. 2-4). Mobile group II introns encode proteins, which have reverse transcriptase (RT) activity and also promote the splicing of the intron in which they are encoded (''maturase'' activity). Other group II introns do not encode maturases and instead rely on host proteins, which appear to differ in different organisms (2-4). Until now, a protein-dependent in vitro splicing system has been developed only for the RT͞maturase protein encoded by the mobile Lactococcus lactis Ll.LtrB intron (5, 6). Studies using this system showed that the maturase binds specifically to the intron RNA and promotes its splicing by stabilizing the catalytically active RNA structure (7,8).In addition to proteins that stabilize specific RNA structures, cellular RNAs may require RNA chaperones to disrupt stable inactive structure (''kinetic traps'') during RNA folding (9, 10). In the case of group I and II int...

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Section: Methodssupporting

confidence: 68%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone

Mohr

Matsuura

Perlman

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…The splicing of the group II intron aI2 depends on the intron-encoded p62 maturase, which by analogy to the Lactobacillus lactis Ll.LtrBencoded maturase (23,24) likely functions by stabilizing the catalytically active structure of the intron RNA. We were intrigued by the finding that expression of one copy of CYT-19 in mss116⌬ grown at 30°C restores wild-type levels of p62 (Fig.…”

Section: Mss116p Functions In Splicing Ai2mentioning

confidence: 99%

The splicing of yeast mitochondrial group I and group II introns requires a DEAD-box protein with RNA chaperone function

Huang

Rowe

Mohr

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

159

227

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Group I and II introns self-splice in vitro, but require proteins for efficient splicing in vivo, to stabilize the catalytically active RNA structure. Recent studies showed that the splicing of some Neurospora crassa mitochondrial group I introns additionally requires a DEAD-box protein, CYT-19, which acts as an RNA chaperone to resolve nonnative structures formed during RNA folding. Here we show that, in Saccharomyces cerevisiae mitochondria, a related DEAD-box protein, Mss116p, is required for the efficient splicing of all group I and II introns, some RNA end-processing reactions, and translation of a subset of mRNAs, and that all these defects can be partially or completely suppressed by the expression of CYT-19. Results for the aI2 group II intron indicate that Mss116p is needed after binding the intron-encoded maturase, likely for the disruption of stable but inactive RNA structures. Our results suggest that both group I and II introns are prone to kinetic traps in RNA folding in vivo and that the splicing of both types of introns may require DEAD-box proteins that function as RNA chaperones.bakers' yeast ͉ mitochondria ͉ splicing factor D ExH͞D-box proteins are a large, ubiquitous protein family, whose members use the energy of ATP hydrolysis to mediate RNA structural rearrangements in a variety of cellular processes (1, 2). These proteins have a core region containing nine conserved motifs flanked by unique N-and͞or C-terminal extensions, which in some cases target the proteins to their sites of action by specific RNA or protein interactions. The proteins are named for the amino acid sequence of motif II, which in different subfamilies is DEAD, DEAH, or some variant thereof. Experiments with model substrates show that DExH͞D-box proteins can act as RNA helicases (3) or can disrupt ribonucleoprotein (RNP) complexes independently of their helicase activity (4). However, how these proteins function on their natural substrates has remained largely unknown.Group I and II introns self-splice in vitro but require proteins for efficient splicing in vivo to help fold the intron RNA into the catalytically active structure (5). In the fungus Neurospora crassa, the splicing of a subset of mitochondrial (mt) group I introns depends on two proteins encoded by nuclear genes, the mt tyrosyl-tRNA synthetase (CYT-18 protein), which stabilizes the catalytically active RNA structure, and the DEAD-box protein 7). Recently, CYT-19 was shown to function as an ATP-dependent RNA chaperone to destabilize nonnative structures that constitute kinetic traps in the CYT-18-assisted RNA folding pathway (7). A mutation in the cyt-19 gene did not affect the splicing of non-CYT-18-dependent group I introns or a group II intron, but did inhibit some 5Ј and 3Ј end processing reactions and, possibly, mt translation (7,8).The Saccharomyces cerevisiae nuclear genome encodes three DExH͞D-box proteins (Suv3p, Mrh4p, and Mss116p) that function in mitochondria (9-11). Of these, Mss116p is the most closely related to CYT-19. The two proteins have 32...

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Rna Metabolism and Transcript Regulation

Zmudjak

Zer

2017

Annual Plant Reviews, Volume 50

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Mechanism of maturase-promoted group II intron splicing

Cited by 141 publications

References 21 publications

A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone

A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone

The splicing of yeast mitochondrial group I and group II introns requires a DEAD-box protein with RNA chaperone function

Rna Metabolism and Transcript Regulation

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