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Molina-Sánchez MD, Toro N. DNA cleavage and reverse splicing of ribonucleoprotein particles reconstituted in vitro with linear RmInt1 RNA. RNA Biol 2019; 16:930-939. [PMID: 30943851 DOI: 10.1080/15476286.2019.1601379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
The RmInt1 group II intron is an efficient self-splicing mobile retroelement that catalyzes its own excision as lariat, linear and circular molecules. In vivo, the RmInt1 lariat and the reverse transcriptase (IEP) it encodes form a ribonucleoprotein particle (RNP) that recognizes the DNA target for site-specific full intron insertion via a two-step reverse splicing reaction. RNPs containing linear group II intron RNA are generally thought to be unable to complete the reverse splicing reaction. Here, we show that reconstituted in vitro RNPs containing linear RmInt1 ΔORF RNA can mediate the cleavage of single-stranded DNA substrates in a very precise manner with the attachment of the intron RNA to the 3´exon as the first step of a reverse splicing reaction. Notably, we also observe molecules in which the 5´exon is linked to the RmInt1 RNA, suggesting the completion of the reverse splicing reaction, albeit rather low and inefficiently. That process depends on DNA target recognition and can be successful completed by RmInt1 RNPs with linear RNA displaying 5´ modifications.
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Affiliation(s)
- María Dolores Molina-Sánchez
- a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain
| | - Nicolás Toro
- a Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems , Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas , Granada , Spain
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2
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Russell R, Jarmoskaite I, Lambowitz AM. Toward a molecular understanding of RNA remodeling by DEAD-box proteins. RNA Biol 2012; 10:44-55. [PMID: 22995827 PMCID: PMC3590237 DOI: 10.4161/rna.22210] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
DEAD-box proteins are superfamily 2 helicases that function in all aspects of RNA metabolism. They employ ATP binding and hydrolysis to generate tight, yet regulated RNA binding, which is used to unwind short RNA helices non-processively and promote structural transitions of RNA and RNA-protein substrates. In the last few years, substantial progress has been made toward a detailed, quantitative understanding of the structural and biochemical properties of DEAD-box proteins. Concurrently, progress has been made toward a physical understanding of the RNA rearrangements and folding steps that are accelerated by DEAD-box proteins in model systems. Here, we review the recent progress on both of these fronts, focusing on the mitochondrial DEAD-box proteins Mss116 and CYT-19 and their mechanisms in promoting the splicing of group I and group II introns.
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Affiliation(s)
- Rick Russell
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA.
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Abstract
DEAD-box proteins are vitally important to cellular processes and make up the largest class of helicases. Many DEAD-box proteins function as RNA chaperones by accelerating structural transitions of RNA, which can result in the resolution of misfolded conformers or conversion between functional structures. While the biological importance of chaperone proteins is clear, their mechanisms are incompletely understood. Here, we illustrate how the catalytic activity of certain RNAs can be used to measure RNA chaperone activity. By measuring the amount of substrate converted to product, the fraction of catalytically active molecules is measured over time, providing a quantitative measure of the formation or loss of native RNA. The assays are described with references to group I and group II introns and their ribozyme derivatives, and examples are included that illustrate potential complications and indicate how catalytic activity measurements can be combined with physical approaches to gain insights into the mechanisms of DEAD-box proteins as RNA chaperones.
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Potratz JP, Campo MD, Wolf RZ, Lambowitz AM, Russell R. ATP-dependent roles of the DEAD-box protein Mss116p in group II intron splicing in vitro and in vivo. J Mol Biol 2011; 411:661-79. [PMID: 21679717 PMCID: PMC3146569 DOI: 10.1016/j.jmb.2011.05.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/24/2011] [Accepted: 05/28/2011] [Indexed: 01/03/2023]
Abstract
The yeast DEAD-box protein Mss116p functions as a general RNA chaperone in splicing mitochondrial group I and group II introns. For most of its functions, Mss116p is thought to use ATP-dependent RNA unwinding to facilitate RNA structural transitions, but it has been suggested to assist in the folding of one group II intron (aI5γ) primarily by stabilizing a folding intermediate. Here we compare three aI5γ constructs: one with long exons, one with short exons, and a ribozyme construct lacking exons. The long exons result in slower splicing, suggesting that they misfold and/or stabilize nonnative intronic structures. Nevertheless, Mss116p acceleration of all three constructs depends on ATP and is inhibited by mutations that compromise RNA unwinding, suggesting similar mechanisms. Results of splicing assays and a new two-stage assay that separates ribozyme folding and catalysis indicate that maximal folding of all three constructs by Mss116p requires ATP-dependent RNA unwinding. ATP-independent activation is appreciable for only a subpopulation of the minimal ribozyme construct and not for constructs containing exons. As expected for a general RNA chaperone, Mss116p can also disrupt the native ribozyme, which can refold after Mss116p removal. Finally, using yeast strains with mitochondrial DNA containing only the single intron aI5γ, we show that Mss116p mutants promote splicing in vivo to degrees that correlate with their residual ATP-dependent RNA-unwinding activities. Together, our results indicate that, although DEAD-box proteins play multiple roles in RNA folding, the physiological function of Mss116p in aI5γ splicing includes a requirement for ATP-dependent local unfolding, allowing the conversion of nonfunctional RNA structure into functional RNA structure.
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Affiliation(s)
- Jeffrey P. Potratz
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Mark Del Campo
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Rachel Z. Wolf
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Alan M. Lambowitz
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
- Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Rick Russell
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
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Zingler N, Solem A, Pyle AM. Dual roles for the Mss116 cofactor during splicing of the ai5γ group II intron. Nucleic Acids Res 2010; 38:6602-9. [PMID: 20554854 PMCID: PMC2965245 DOI: 10.1093/nar/gkq530] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The autocatalytic group II intron ai5γ from Saccharomyces cerevisiae self-splices under high-salt conditions in vitro, but requires the assistance of the DEAD-box protein Mss116 in vivo and under near-physiological conditions in vitro. Here, we show that Mss116 influences the folding mechanism in several ways. By comparing intron precursor RNAs with long (∼300 nt) and short (∼20 nt) exons, we observe that long exon sequences are a major obstacle for self-splicing in vitro. Kinetic analysis indicates that Mss116 not only mitigates the inhibitory effects of long exons, but also assists folding of the intron core. Moreover, a mutation in conserved Motif III that impairs unwinding activity (SAT → AAA) only affects the construct with long exons, suggesting helicase unwinding during exon unfolding, but not in intron folding. Strong parallels between Mss116 and the related protein Cyt-19 from Neurospora crassa suggest that these proteins form a subclass of DEAD-box proteins that possess a versatile repertoire of diverse activities for resolving the folding problems of large RNAs.
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Affiliation(s)
- Nora Zingler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Del Campo M, Tijerina P, Bhaskaran H, Mohr S, Yang Q, Jankowsky E, Russell R, Lambowitz AM. Do DEAD-box proteins promote group II intron splicing without unwinding RNA? Mol Cell 2008; 28:159-66. [PMID: 17936712 DOI: 10.1016/j.molcel.2007.07.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 07/12/2007] [Accepted: 07/26/2007] [Indexed: 11/16/2022]
Abstract
The DEAD-box protein Mss116p promotes group II intron splicing in vivo and in vitro. Here we explore two hypotheses for how Mss116p promotes group II intron splicing: by using its RNA unwinding activity to act as an RNA chaperone or by stabilizing RNA folding intermediates. We show that an Mss116p mutant in helicase motif III (SAT/AAA), which was reported to stimulate splicing without unwinding RNA, retains ATP-dependent unwinding activity and promotes unfolding of a structured RNA. Its unwinding activity increases sharply with decreasing duplex length and correlates with group II intron splicing activity in quantitative assays. Additionally, we show that Mss116p can promote ATP-independent RNA unwinding, presumably via single-strand capture, also potentially contributing to DEAD-box protein RNA chaperone activity. Our findings favor the hypothesis that DEAD-box proteins function in group II intron splicing as in other processes by using their unwinding activity to act as RNA chaperones.
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Affiliation(s)
- Mark Del Campo
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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Costa M, Michel F, Toro N. Potential for alternative intron-exon pairings in group II intron RmInt1 from Sinorhizobium meliloti and its relatives. RNA (NEW YORK, N.Y.) 2006; 12:338-41. [PMID: 16431983 PMCID: PMC1383573 DOI: 10.1261/rna.2240906] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Ribozyme constructs derived from group II intron RmInt1 of Sinorhizobium meliloti self-splice in vitro when incubated under permissive conditions, but exon ligation is unusually inefficient when the 5' exon is truncated close to the IBS2 intron-binding site. One plausible explanation for this observation is the presence of an alternative intron-exon pairing between an intron segment that overlaps with the EBS2 exon-binding site and a 5' exon site located just distal of IBS2 relative to the splice junction. Strikingly, the existence of this pairing is supported by comparative sequence analysis of introns related to RmInt1.
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Mohr S, Matsuura M, Perlman PS, Lambowitz AM. A DEAD-box protein alone promotes group II intron splicing and reverse splicing by acting as an RNA chaperone. Proc Natl Acad Sci U S A 2006; 103:3569-74. [PMID: 16505350 PMCID: PMC1450124 DOI: 10.1073/pnas.0600332103] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Group II intron RNAs self-splice in vitro but only at high salt and/or Mg2+ 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 aI5gamma and bI1 group II introns under near-physiological conditions by acting as an ATP-dependent 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 Mg2+ 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.
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Affiliation(s)
- Sabine Mohr
- *Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas, Austin, TX 78712; and
| | - Manabu Matsuura
- *Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas, Austin, TX 78712; and
| | - Philip S. Perlman
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815
| | - Alan M. Lambowitz
- *Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas, Austin, TX 78712; and
- To whom correspondence should be addressed. E-mail:
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Abstract
We describe a general and efficient two-step strategy for lariat RNA synthesis. In the first step, a deoxyribozyme synthesizes 2',5'-branched RNA. In the second step, T4 RNA ligase closes the loop that completes the lariat. The loop-closure reaction can form either a natural or unnatural lariat isomer, depending on which of the two 3'-termini of the branched RNA reacts with the lone 5'-end. We demonstrate two approaches to control formation of either lariat isomer. In conjunction with other routes for lariat RNA synthesis, the two-step strategy described here will facilitate biochemical studies that require lariat RNAs of varying nucleotide sequence.
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Affiliation(s)
- Yangming Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
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Costa M, Michel F, Molina-Sánchez MD, Martinez-Abarca F, Toro N. An alternative intron-exon pairing scheme implied by unexpected in vitro activities of group II intron RmInt1 from Sinorhizobium meliloti. Biochimie 2006; 88:711-7. [PMID: 16460862 DOI: 10.1016/j.biochi.2005.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Accepted: 12/27/2005] [Indexed: 11/16/2022]
Abstract
RmInt1 is a mobile group II intron which interrupts ISRm2011-2, another mobile element from the bacterium Sinorhizobium meliloti. Ribozyme constructs derived from intron RmInt1 self-splice in vitro when incubated under permissive conditions, but the excised intron and ligated exons are largely replaced by unconventional products. These include a slightly shorter, 5'-end truncated 3' exon, truncated variants of the linear and lariat forms of the intron-3' exon reaction intermediate, as well as presumably circular molecules derived from the latter. Two factors explain the abundance of these products: (i) nucleotides 5-11 of the 3' exon (IBS1*) provide a better match to the EBS1 5'-exon-binding site than the authentic IBS1 sequence in the 5' exon; (ii) exon ligation is unusually inefficient, and especially so when the 5' exon is truncated close to the second (IBS2) intron-binding site. We propose that reactions at the IBS1* site play a part in the regulation of the intron ISRm2011-2 host in vivo.
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Affiliation(s)
- María Costa
- Centre de Genétique Moléculaire du CNRS, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
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Abstract
Recent reports have demonstrated that the group I ribozyme from Tetrahymena thermophila can perform trans-splicing reactions to repair mutant RNAs. For therapeutic use, such ribozymes must function efficiently when transcribed from genes delivered to human cells, yet it is unclear how group I splicing reactions are influenced by intracellular expression of the ribozyme. Here we evaluate the self-splicing efficiency of group I introns from transcripts expressed by RNA polymerase II in human cells to directly measure ribozyme catalysis in a therapeutically relevant setting. Intron-containing expression cassettes were transfected into a human cell line, and RNA transcripts were analyzed for intron removal. The percentage of transcripts that underwent self-splicing ranged from 0 to 50%, depending on the construct being tested. Thus, self-splicing activity is supported in the mammalian cellular environment. However, we find that the extent of self-splicing is greatly influenced by sequences flanking the intron and presumably reflects differences in the intron's ability to fold into an active conformation inside the cell. In support of this hypothesis, we show that the ability of the intron to fold and self-splice from cellular transcripts in vitro correlates well with the catalytic efficiency observed from the same transcripts expressed inside cells. These results underscore the importance of evaluating the impact of sequence context on the activity of therapeutic group I ribozymes. The self-splicing system that we describe should facilitate these efforts as well as aid in efforts at enhancing in vivo ribozyme activity for various applications of RNA repair.
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Affiliation(s)
- M B Long
- Departments of Genetics and Surgery, Center for Genetic and Cellular Therapies, Duke University Medical Center, Durham, North Carolina 27710, USA
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Costa M, Michel F. Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. EMBO J 1999; 18:1025-37. [PMID: 10022844 PMCID: PMC1171194 DOI: 10.1093/emboj/18.4.1025] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed.
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Affiliation(s)
- M Costa
- Centre de Génétique Moléculaire du CNRS, 91190 Gif-sur-Yvette, France.
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Boudvillain M, Pyle AM. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. EMBO J 1998; 17:7091-104. [PMID: 9843513 PMCID: PMC1171056 DOI: 10.1093/emboj/17.23.7091] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Group II introns are self-splicing RNA molecules that are of considerable interest as ribozymes, mobile genetic elements and examples of folded RNA. Although these introns are among the most common ribozymes, little is known about the chemical and structural determinants for their reactivity. By using nucleotide analog interference mapping (NAIM), it has been possible to identify the nucleotide functional groups (Rp phosphoryls, 2'-hydroxyls, guanosine exocyclic amines, adenosine N7 and N6) that are most important for composing the catalytic core of the intron. The majority of interference effects occur in clusters located within the two catalytically essential Domains 1 and 5 (D1 and D5). Collectively, the NAIM results indicate that key tetraloop-receptor interactions display a specific chemical signature, that the epsilon-epsilon' interaction includes an elaborate array of additional features and that one of the most important core structures is an uncharacterized three-way junction in D1. By combining NAIM with site-directed mutagenesis, a new tertiary interaction, kappa-kappa', was identified between this region and the most catalytically important section of D5, adjacent to the AGC triad in stem 1. Together with the known zeta-zeta' interaction, kappa-kappa' anchors D5 firmly into the D1 scaffold, thereby presenting chemically essential D5 functionalities for participation in catalysis.
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Affiliation(s)
- M Boudvillain
- The Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biophysics, 701 W. 168th Street, Room 616, Hammer Health Sciences Center, Columbia University, New York, NY 10032, USA
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