1
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Meissner J, Eysmont K, Matylla-Kulińska K, Konarska MM. Characterization of Cwc2, U6 snRNA, and Prp8 interactions destabilized by Prp16 ATPase at the transition between the first and second steps of splicing. RNA (NEW YORK, N.Y.) 2024; 30:1199-1212. [PMID: 38876504 PMCID: PMC11331412 DOI: 10.1261/rna.079886.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
The spliceosome performs two consecutive transesterification reactions using one catalytic center, thus requiring its rearrangement between the two catalytic steps of splicing. The Prp16 ATPase facilitates exit from the first-step conformation of the catalytic center by destabilizing some interactions important for catalysis. To better understand rearrangements within the Saccharomyces cerevisiae catalytic center, we characterize factors that modulate the function of Prp16: Cwc2, N-terminal domain of Prp8, and U6-41AACAAU46 region. Alleles of these factors were identified through genetic screens for mutants that correct cs defects of prp16-302 alleles. Several of the identified U6, cwc2, and prp8 alleles are located in close proximity of each other in cryo-EM structures of the spliceosomal catalytic conformations. Cwc2 and U6 interact with the intron sequences in the first step, but they do not seem to contribute to the stability of the second-step catalytic center. On the other hand, the N-terminal segment of Prp8 not only affects intron positioning for the first step, but it also makes important contacts in the proximity of the active site for both the first and second steps of splicing. By identifying interactions important for the stability of catalytic conformations, our genetic analyses indirectly inform us about features of the transition-state conformation of the spliceosome.
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Affiliation(s)
- Jadwiga Meissner
- IMol, Polish Academy of Sciences, 02-247 Warsaw, Poland
- ReMedy-International Research Agenda Unit, 02-247 Warsaw, Poland
| | | | | | - Maria M Konarska
- IMol, Polish Academy of Sciences, 02-247 Warsaw, Poland
- ReMedy-International Research Agenda Unit, 02-247 Warsaw, Poland
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2
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Beusch I, Madhani HD. Understanding the dynamic design of the spliceosome. Trends Biochem Sci 2024; 49:583-595. [PMID: 38641465 DOI: 10.1016/j.tibs.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
The spliceosome catalyzes the splicing of pre-mRNAs. Although the spliceosome evolved from a prokaryotic self-splicing intron and an associated protein, it is a vastly more complex and dynamic ribonucleoprotein (RNP) whose function requires at least eight ATPases and multiple RNA rearrangements. These features afford stepwise opportunities for multiple inspections of the intron substrate, coupled with spliceosome disassembly for substrates that fail inspection. Early work using splicing-defective pre-mRNAs or small nuclear (sn)RNAs in Saccharomyces cerevisiae demonstrated that such checks could occur in catalytically active spliceosomes. We review recent results on pre-mRNA splicing in various systems, including humans, suggesting that earlier steps in spliceosome assembly are also subject to such quality control. The inspection-rejection framework helps explain the dynamic nature of the spliceosome.
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Affiliation(s)
- Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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3
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Senn KA, Lipinski KA, Zeps NJ, Griffin AF, Wilkinson ME, Hoskins AA. Control of 3' splice site selection by the yeast splicing factor Fyv6. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592262. [PMID: 38746449 PMCID: PMC11092753 DOI: 10.1101/2024.05.04.592262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Pre-mRNA splicing is catalyzed in two steps: 5' splice site (SS) cleavage and exon ligation. A number of proteins transiently associate with spliceosomes to specifically impact these steps (1st and 2nd step factors). We recently identified Fyv6 (FAM192A in humans) as a 2nd step factor in S. cerevisiae; however, we did not determine how widespread Fyv6's impact is on the transcriptome. To answer this question, we have used RNA-seq to analyze changes in splicing. These results show that loss of Fyv6 results in activation of non-consensus, branch point (BP) proximal 3' SS transcriptome-wide. To identify the molecular basis of these observations, we determined a high-resolution cryo-EM structure of a yeast product complex spliceosome containing Fyv6 at 2.3 Å. The structure reveals that Fyv6 is the only 2nd step factor that contacts the Prp22 ATPase and that Fyv6 binding is mutually exclusive with that of the 1st step factor Yju2. We then use this structure to dissect Fyv6 functional domains and interpret results of a genetic screen for fyv6Δ suppressor mutations. The combined transcriptomic, structural, and genetic studies allow us to propose a model in which Yju2/Fyv6 exchange facilitates exon ligation and Fyv6 promotes usage of consensus, BP distal 3' SS.
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Affiliation(s)
- Katherine A. Senn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Karli A. Lipinski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Natalie J. Zeps
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Amory F. Griffin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Max E. Wilkinson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH UK
- Present Addresses: Broad Institute of MIT and Harvard, Cambridge MA 02142 USA and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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4
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Black CS, Whelan TA, Garside EL, MacMillan AM, Fast NM, Rader SD. Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes. RNA (NEW YORK, N.Y.) 2023; 29:531-550. [PMID: 36737103 PMCID: PMC10158995 DOI: 10.1261/rna.079273.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/06/2023] [Indexed: 05/06/2023]
Abstract
Premessenger RNA splicing is catalyzed by the spliceosome, a multimegadalton RNA-protein complex that assembles in a highly regulated process on each intronic substrate. Most studies of splicing and spliceosomes have been carried out in human or S. cerevisiae model systems. There exists, however, a large diversity of spliceosomes, particularly in organisms with reduced genomes, that suggests a means of analyzing the essential elements of spliceosome assembly and regulation. In this review, we characterize changes in spliceosome composition across phyla, describing those that are most frequently observed and highlighting an analysis of the reduced spliceosome of the red alga Cyanidioschyzon merolae We used homology modeling to predict what effect splicing protein loss would have on the spliceosome, based on currently available cryo-EM structures. We observe strongly correlated loss of proteins that function in the same process, for example, in interacting with the U1 snRNP (which is absent in C. merolae), regulation of Brr2, or coupling transcription and splicing. Based on our observations, we predict splicing in C. merolae to be inefficient, inaccurate, and post-transcriptional, consistent with the apparent trend toward its elimination in this lineage. This work highlights the striking flexibility of the splicing pathway and the spliceosome when viewed in the context of eukaryotic diversity.
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Affiliation(s)
- Corbin S Black
- Department of Chemistry and Biochemistry, University of Northern British Columbia, Prince George, British Columbia, Canada V2N 4Z9
- Department of Anatomy and Cell Biology, McGill University, Montréal, Quebec, Canada H3A 0C7
| | - Thomas A Whelan
- Biodiversity Research Center and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Erin L Garside
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Andrew M MacMillan
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Naomi M Fast
- Biodiversity Research Center and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Stephen D Rader
- Department of Chemistry and Biochemistry, University of Northern British Columbia, Prince George, British Columbia, Canada V2N 4Z9
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5
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Wilkinson ME, Fica SM, Galej WP, Nagai K. Structural basis for conformational equilibrium of the catalytic spliceosome. Mol Cell 2021; 81:1439-1452.e9. [PMID: 33705709 PMCID: PMC8022279 DOI: 10.1016/j.molcel.2021.02.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/14/2020] [Accepted: 02/11/2021] [Indexed: 12/21/2022]
Abstract
The ATPase Prp16 governs equilibrium between the branching (B∗/C) and exon ligation (C∗/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the Saccharomyces cerevisiae C-complex spliceosome at 2.8 Å resolution and identify a novel C-complex intermediate (Ci) that elucidates the molecular basis for this equilibrium. The exon-ligation factors Prp18 and Slu7 bind to Ci before ATP hydrolysis by Prp16 can destabilize the branching conformation. Biochemical assays suggest that these pre-bound factors prime the C complex for conversion to C∗ by Prp16. A complete model of the Prp19 complex (NTC) reveals how the branching factors Yju2 and Isy1 are recruited by the NTC before branching. Prp16 remodels Yju2 binding after branching, allowing Yju2 to remain tethered to the NTC in the C∗ complex to promote exon ligation. Our results explain how Prp16 action modulates the dynamic binding of step-specific factors to alternatively stabilize the C or C∗ conformation and establish equilibrium of the catalytic spliceosome. Cryo-EM reveals new Ci spliceosome intermediate between branching and exon ligation Binding of branching and exon-ligation factors to Ci governs spliceosome equilibrium Exon-ligation factors Slu7 and Prp18 bind Ci weakly before Prp16 action After Prp16 action, pre-bound Slu7 and Prp18 bind strongly to promote exon ligation
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| | - Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
| | - Wojciech P Galej
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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6
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Wilkinson ME, Fica SM, Galej WP, Norman CM, Newman AJ, Nagai K. Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection. Science 2017; 358:1283-1288. [PMID: 29146871 DOI: 10.1126/science.aar3729] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/09/2017] [Indexed: 12/27/2022]
Abstract
Introns are removed from eukaryotic messenger RNA precursors by the spliceosome in two transesterification reactions-branching and exon ligation. The mechanism of 3'-splice site recognition during exon ligation has remained unclear. Here we present the 3.7-angstrom cryo-electron microscopy structure of the yeast P-complex spliceosome immediately after exon ligation. The 3'-splice site AG dinucleotide is recognized through non-Watson-Crick pairing with the 5' splice site and the branch-point adenosine. After the branching reaction, protein factors work together to remodel the spliceosome and stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation. The structure accounts for the strict conservation of the GU and AG dinucleotides at the 5' and 3' ends of introns and provides insight into the catalytic mechanism of exon ligation.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | | | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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7
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Kanno T, Lin WD, Fu JL, Matzke AJM, Matzke M. A genetic screen implicates a CWC16/Yju2/CCDC130 protein and SMU1 in alternative splicing in Arabidopsis thaliana. RNA (NEW YORK, N.Y.) 2017; 23:1068-1079. [PMID: 28373290 PMCID: PMC5473141 DOI: 10.1261/rna.060517.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/30/2017] [Indexed: 05/02/2023]
Abstract
To identify regulators of pre-mRNA splicing in plants, we developed a forward genetic screen based on an alternatively spliced GFP reporter gene in Arabidopsis thaliana In wild-type plants, three major splice variants issue from the GFP gene but only one represents a translatable GFP mRNA. Compared to wild-type seedlings, which exhibit an intermediate level of GFP expression, mutants identified in the screen feature either a "GFP-weak" or "Hyper-GFP" phenotype depending on the ratio of the three splice variants. GFP-weak mutants, including previously identified prp8 and rtf2, contain a higher proportion of unspliced transcript or canonically spliced transcript, neither of which is translatable into GFP protein. In contrast, the coilin-deficient hyper-gfp1 (hgf1) mutant displays a higher proportion of translatable GFP mRNA, which arises from enhanced splicing of a U2-type intron with noncanonical AT-AC splice sites. Here we report three new hgf mutants that are defective, respectively, in spliceosome-associated proteins SMU1, SmF, and CWC16, an Yju2/CCDC130-related protein that has not yet been described in plants. The smu1 and cwc16 mutants have substantially increased levels of translatable GFP transcript owing to preferential splicing of the U2-type AT-AC intron, suggesting that SMU1 and CWC16 influence splice site selection in GFP pre-mRNA. Genome-wide analyses of splicing in smu1 and cwc16 mutants revealed a number of introns that were variably spliced from endogenous pre-mRNAs. These results indicate that SMU1 and CWC16, which are predicted to act directly prior to and during the first catalytic step of splicing, respectively, function more generally to modulate splicing patterns in plants.
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Affiliation(s)
- Tatsuo Kanno
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jason L Fu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Antonius J M Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
| | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan
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8
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Abstract
Major developments in cryo-electron microscopy in the past three or four years have led to the solution of a number of spliceosome structures at high resolution, e.g., the fully assembled but not yet active spliceosome (Bact), the spliceosome just after the first step of splicing (C), and the spliceosome activated for the second step (C*). Therefore 30 years of genetics and biochemistry of the spliceosome can now be interpreted at the structural level. I have closely examined the RNase H domain of Prp8 in each of the structures. Interestingly, the RNase H domain has different and unexpected roles in each of the catalytic steps of splicing.
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Affiliation(s)
- John Abelson
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
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9
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Tseng CK, Chung CS, Chen HC, Cheng SC. A central role of Cwc25 in spliceosome dynamics during the catalytic phase of pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2017; 23:546-556. [PMID: 28057857 PMCID: PMC5340917 DOI: 10.1261/rna.059204.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/03/2017] [Indexed: 05/22/2023]
Abstract
Splicing of precursor mRNA occurs via two consecutive steps of transesterification reaction; both require ATP and several proteins. Despite the energy requirement in the catalytic phase, incubation of the purified spliceosome under proper ionic conditions can elicit competitive reversible transesterification, debranching, and spliced-exon-reopening reactions without the necessity for ATP or other factors, suggesting that small changes in the conformational state of the spliceosome can lead to disparate chemical consequences for the substrate. We show here that Cwc25 plays a central role in modulating the conformational state of the catalytic spliceosome during normal splicing reactions. Cwc25 binds tightly to the spliceosome after the reaction and is then removed from the spliceosome, which normally requires DExD/H-box protein Prp16 and ATP hydrolysis, to allow the occurrence of the second reaction. When deprived of Cwc25, the purified first-step spliceosome catalyzes both forward and reverse splicing reactions under normal splicing conditions without requiring energy. Both reactions are inhibited when Cwc25 is added back, presumably due to the stabilization of first-step conformation. Prp16 is dispensable for the second reaction when splicing is carried out under conditions that destabilize Cwc25. We also show that the purified precatalytic spliceosome can catalyze two steps of the reaction at a low efficiency without requiring Cwc25, Slu7, or Prp18 when incubated under proper conditions. Our study reveals conformational modulation of the spliceosome by Cwc25 and Prp16 in stabilization and destabilization of first-step conformation, respectively, to facilitate the splicing process.
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Affiliation(s)
- Chi-Kang Tseng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Che-Sheng Chung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Hsin-Chou Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
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10
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Role of Cwc24 in the First Catalytic Step of Splicing and Fidelity of 5' Splice Site Selection. Mol Cell Biol 2017; 37:MCB.00580-16. [PMID: 27994011 DOI: 10.1128/mcb.00580-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/11/2016] [Indexed: 12/17/2022] Open
Abstract
Cwc24 is an essential splicing factor but only transiently associates with the spliceosome, with an unknown function. The protein contains a RING finger and a zinc finger domain in the carboxyl terminus. The human ortholog of Cwc24, RNF113A, has been associated with the disorder trichothiodystrophy. Here, we show that the zinc finger domain is essential for Cwc24 function, while the RING finger domain is dispensable. Cwc24 binds to the spliceosome after the Prp19-associated complex and is released upon Prp2 action. Cwc24 is not required for Prp2-mediated remodeling of the spliceosome, but the spliceosome becomes inactive if remodeling occurs before the addition of Cwc24. Cwc24 binds directly to pre-mRNA at the 5' splice site, spanning the splice junction. In the absence of Cwc24, U5 and U6 modes of interaction with the 5' splice site are altered, and splicing is very inefficient, with aberrant cleavage at the 5' splice site. Our data suggest roles for Cwc24 in orchestrating organization of the spliceosome into an active configuration prior to Prp2-mediated spliceosome remodeling and in promoting specific interaction of U5 and U6 with the 5' splice site for fidelity of 5' splice site selection.
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11
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Rauhut R, Fabrizio P, Dybkov O, Hartmuth K, Pena V, Chari A, Kumar V, Lee CT, Urlaub H, Kastner B, Stark H, Lührmann R. Molecular architecture of the Saccharomyces cerevisiae activated spliceosome. Science 2016; 353:1399-1405. [PMID: 27562955 DOI: 10.1126/science.aag1906] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/18/2016] [Indexed: 12/30/2022]
Abstract
The activated spliceosome (Bact) is in a catalytically inactive state and is remodeled into a catalytically active machine by the RNA helicase Prp2, but the mechanism is unclear. Here, we describe a 3D electron cryomicroscopy structure of the Saccharomyces cerevisiae Bact complex at 5.8-angstrom resolution. Our model reveals that in Bact, the catalytic U2/U6 RNA-Prp8 ribonucleoprotein core is already established, and the 5' splice site (ss) is oriented for step 1 catalysis but occluded by protein. The first-step nucleophile-the branchsite adenosine-is sequestered within the Hsh155 HEAT domain and is held 50 angstroms away from the 5'ss. Our structure suggests that Prp2 adenosine triphosphatase-mediated remodeling leads to conformational changes in Hsh155's HEAT domain that liberate the first-step reactants for catalysis.
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Affiliation(s)
- Reinhard Rauhut
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Patrizia Fabrizio
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Olexandr Dybkov
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Klaus Hartmuth
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Vladimir Pena
- Research Group Macromolecular Crystallography, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ashwin Chari
- 3D Electron Cryomicroscopy Group, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Vinay Kumar
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Chung-Tien Lee
- Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Robert-Koch-Straße 40, D-37075 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Robert-Koch-Straße 40, D-37075 Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
| | - Holger Stark
- 3D Electron Cryomicroscopy Group, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. Department of 3D Electron Cryomicroscopy, Georg-August Universität, Göttingen, Justus von-Liebig-Weg 11, D-37077 Germany.
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
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12
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Wan R, Yan C, Bai R, Huang G, Shi Y. Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution. Science 2016; 353:895-904. [PMID: 27445308 DOI: 10.1126/science.aag2235] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/14/2016] [Indexed: 12/30/2022]
Abstract
Each cycle of pre-messenger RNA splicing, carried out by the spliceosome, comprises two sequential transesterification reactions, which result in the removal of an intron and the joining of two exons. Here we report an atomic structure of a catalytic step I spliceosome (known as the C complex) from Saccharomyces cerevisiae, as determined by cryo-electron microscopy at an average resolution of 3.4 angstroms. In the structure, the 2'-OH of the invariant adenine nucleotide in the branch point sequence (BPS) is covalently joined to the phosphate at the 5' end of the 5' splice site (5'SS), forming an intron lariat. The freed 5' exon remains anchored to loop I of U5 small nuclear RNA (snRNA), and the 5'SS and BPS of the intron form duplexes with conserved U6 and U2 snRNA sequences, respectively. Specific placement of these RNA elements at the catalytic cavity of Prp8 is stabilized by 15 protein components, including Snu114 and the splicing factors Cwc21, Cwc22, Cwc25, and Yju2. These features, representing the conformation of the spliceosome after the first-step reaction, predict structural changes that are needed for the execution of the second-step transesterification reaction.
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Affiliation(s)
- Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Rui Bai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaoxingyu Huang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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13
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Abstract
The human spliceosome is a large ribonucleoprotein complex that catalyzes pre-mRNA splicing. It consists of five snRNAs and more than 200 proteins. Because of this complexity, much work has focused on the Saccharomyces cerevisiae spliceosome, viewed as a highly simplified system with fewer than half as many splicing factors as humans. Nevertheless, it has been difficult to ascribe a mechanistic function to individual splicing factors or even to discern which are critical for catalyzing the splicing reaction. We have identified and characterized the splicing machinery from the red alga Cyanidioschyzon merolae, which has been reported to harbor only 26 intron-containing genes. The U2, U4, U5, and U6 snRNAs contain expected conserved sequences and have the ability to adopt secondary structures and form intermolecular base-pairing interactions, as in other organisms. C. merolae has a highly reduced set of 43 identifiable core splicing proteins, compared with ∼90 in budding yeast and ∼140 in humans. Strikingly, we have been unable to find a U1 snRNA candidate or any predicted U1-associated proteins, suggesting that splicing in C. merolae may occur without the U1 small nuclear ribonucleoprotein particle. In addition, based on mapping the identified proteins onto the known splicing cycle, we propose that there is far less compositional variability during splicing in C. merolae than in other organisms. The observed reduction in splicing factors is consistent with the elimination of spliceosomal components that play a peripheral or modulatory role in splicing, presumably retaining those with a more central role in organization and catalysis.
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14
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Liang WW, Cheng SC. A novel mechanism for Prp5 function in prespliceosome formation and proofreading the branch site sequence. Genes Dev 2015; 29:81-93. [PMID: 25561497 PMCID: PMC4281567 DOI: 10.1101/gad.253708.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The DEAD-box RNA helicase Prp5 is required for the formation of the prespliceosome through an ATP-dependent function to remodel U2 snRNPs and an ATP-independent function of unknown mechanism. Liang and Cheng show that Prp5 binds to the spliceosome in association with U2 by interacting with the branchpoint-interacting stem–loop and is released upon base-pairing of U2 with the branch site to allow the recruitment of the tri-snRNP. The DEAD-box RNA helicase Prp5 is required for the formation of the prespliceosome through an ATP-dependent function to remodel U2 small nuclear ribonucleoprotein particles (snRNPs) and an ATP-independent function of unknown mechanism. Prp5 has also been implicated in proofreading the branch site sequence, but the molecular mechanism has not been well characterized. Using actin precursor mRNA (pre-mRNA) carrying branch site mutations, we identified a Prp5-containing prespliceosome with Prp5 directly bound to U2 small nuclear RNA (snRNA). Prp5 is in contact with U2 in regions on and near the branchpoint-interacting stem–loop (BSL), suggesting that Prp5 may function in stabilizing the BSL. Regardless of its ATPase activity, Prp5 mutants that suppress branch site mutations associate with the spliceosome less tightly and allow more tri-snRNP binding for the reaction to proceed. Our results suggest a novel mechanism for how Prp5 functions in prespliceosome formation and proofreading of the branch site sequence. Prp5 binds to the spliceosome in association with U2 by interacting with the BSL and is released upon the base-pairing of U2 with the branch site to allow the recruitment of the tri-snRNP. Mutations impairing U2–branch site base-pairing retard Prp5 release and impede tri-snRNP association. Prp5 mutations that destabilize the Prp5–U2 interaction suppress branch site mutations by allowing progression of the pathway.
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Affiliation(s)
- Wen-Wei Liang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan; Institute of Microbiology and Immunology, National Yang-Ming University, Taipei 112, Taiwan
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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Chen HC, Chang KJ, Su YL, Huang YH, Cheng SC. Structural requirement of Ntc77 for spliceosome activation and first catalytic step. Nucleic Acids Res 2014; 42:12261-71. [PMID: 25294830 PMCID: PMC4231770 DOI: 10.1093/nar/gku914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Prp19-associated complex is required for spliceosome activation by stabilizing the binding of U5 and U6 on the spliceosome after the release of U4. The complex comprises at least eight proteins, among which Ntc90 and Ntc77 contain multiple tetratricopeptide repeat (TPR) elements. We have previously shown that Ntc90 is not involved in spliceosome activation, but is required for the recruitment of essential first-step factor Yju2 to the spliceosome. We demonstrate here that Ntc77 has dual functions in both spliceosome activation and the first catalytic step in recruiting Yju2. We have identified an amino-terminal region of Ntc77, which encompasses the N-terminal domain and the first three TPR motifs, dispensable for spliceosome activation but required for stable interaction of Yju2 with the spliceosome. Deletion of this region had no severe effect on the integrity of the NTC, binding of NTC to the spliceosome or spliceosome activation, but impaired splicing and exhibited a dominant-negative growth phenotype. Our data reveal functional roles of Ntc77 in both spliceosome activation and the first catalytic step, and distinct structural domains of Ntc77 required for these two steps.
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Affiliation(s)
- Hsin-Chou Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China Institute of Microbiology and Immunology, National Yang-Ming University, Shih-Pai, Taipei, Taiwan 112, Republic of China
| | - Kae-Jiun Chang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Yu-Lun Su
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Yu-Hsin Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
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Livesay SB, Collier SE, Bitton DA, Bähler J, Ohi MD. Structural and functional characterization of the N terminus of Schizosaccharomyces pombe Cwf10. EUKARYOTIC CELL 2013; 12:1472-89. [PMID: 24014766 PMCID: PMC3837936 DOI: 10.1128/ec.00140-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 09/03/2013] [Indexed: 01/10/2023]
Abstract
The spliceosome is a dynamic macromolecular machine that catalyzes the removal of introns from pre-mRNA, yielding mature message. Schizosaccharomyces pombe Cwf10 (homolog of Saccharomyces cerevisiae Snu114 and human U5-116K), an integral member of the U5 snRNP, is a GTPase that has multiple roles within the splicing cycle. Cwf10/Snu114 family members are highly homologous to eukaryotic translation elongation factor EF2, and they contain a conserved N-terminal extension (NTE) to the EF2-like portion, predicted to be an intrinsically unfolded domain. Using S. pombe as a model system, we show that the NTE is not essential, but cells lacking this domain are defective in pre-mRNA splicing. Genetic interactions between cwf10-ΔNTE and other pre-mRNA splicing mutants are consistent with a role for the NTE in spliceosome activation and second-step catalysis. Characterization of Cwf10-NTE by various biophysical techniques shows that in solution the NTE contains regions of both structure and disorder. The first 23 highly conserved amino acids of the NTE are essential for its role in splicing but when overexpressed are not sufficient to restore pre-mRNA splicing to wild-type levels in cwf10-ΔNTE cells. When the entire NTE is overexpressed in the cwf10-ΔNTE background, it can complement the truncated Cwf10 protein in trans, and it immunoprecipitates a complex similar in composition to the late-stage U5.U2/U6 spliceosome. These data show that the structurally flexible NTE is capable of independently incorporating into the spliceosome and improving splicing function, possibly indicating a role for the NTE in stabilizing conformational rearrangements during a splice cycle.
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Affiliation(s)
- S. Brent Livesay
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Scott E. Collier
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Danny A. Bitton
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Jürg Bähler
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Melanie D. Ohi
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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