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Pánek J, Roithová A, Radivojević N, Sýkora M, Prusty AB, Huston N, Wan H, Pyle AM, Fischer U, Staněk D. The SMN complex drives structural changes in human snRNAs to enable snRNP assembly. Nat Commun 2023; 14:6580. [PMID: 37852981 PMCID: PMC10584915 DOI: 10.1038/s41467-023-42324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Spliceosomal snRNPs are multicomponent particles that undergo a complex maturation pathway. Human Sm-class snRNAs are generated as 3'-end extended precursors, which are exported to the cytoplasm and assembled together with Sm proteins into core RNPs by the SMN complex. Here, we provide evidence that these pre-snRNA substrates contain compact, evolutionarily conserved secondary structures that overlap with the Sm binding site. These structural motifs in pre-snRNAs are predicted to interfere with Sm core assembly. We model structural rearrangements that lead to an open pre-snRNA conformation compatible with Sm protein interaction. The predicted rearrangement pathway is conserved in Metazoa and requires an external factor that initiates snRNA remodeling. We show that the essential helicase Gemin3, which is a component of the SMN complex, is crucial for snRNA structural rearrangements during snRNP maturation. The SMN complex thus facilitates ATP-driven structural changes in snRNAs that expose the Sm site and enable Sm protein binding.
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Affiliation(s)
- Josef Pánek
- Laboratory of Bioinformatics, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic.
| | - Adriana Roithová
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Regulation of Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Nenad Radivojević
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Sýkora
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | | | - Nicholas Huston
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, USA
| | - Han Wan
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, USA
- Department of Chemistry, Yale University, New Haven, USA
- Howard Hughes Medical Institute, Chevy Chase, USA
| | - Utz Fischer
- Department of Biochemistry, Theodor Boveri Institute, University of Würzburg, Würzburg, Germany
| | - David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic.
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2
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Rodrigues KS, Petroski LP, Utumi PH, Ferrasa A, Herai RH. IARA: a complete and curated atlas of the biogenesis of spliceosome machinery during RNA splicing. Life Sci Alliance 2023; 6:e202201593. [PMID: 36609432 PMCID: PMC9834665 DOI: 10.26508/lsa.202201593] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023] Open
Abstract
Splicing is one of the most important post-transcriptional processing systems and is responsible for the generation of transcriptome diversity in all living eukaryotes. Splicing is regulated by the spliceosome machinery, which is responsible for each step of primary RNA processing. However, current molecules and stages involved in RNA splicing are still spread over different studies. Thus, a curated atlas of spliceosome-related molecules and all involved stages during RNA processing can provide all researchers with a reliable resource to better investigate this important mechanism. Here, we present IARA (website access: https://pucpr-bioinformatics.github.io/atlas/), an extensively curated and constantly updated catalog of molecules involved in spliceosome machinery. IARA has a map of the steps involved in the human splicing mechanism, and it allows a detailed overview of the molecules involved throughout the distinct steps of splicing.
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Affiliation(s)
- Kelren S Rodrigues
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Luiz P Petroski
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Paulo H Utumi
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Adriano Ferrasa
- Informatics Department, Universidade Estadual de Ponta GrossaPonta Grossa, Brazil
| | - Roberto H Herai
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
- Research Division, Buko Kaesemodel Institute, Curitiba, Brazil
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3
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Artemyeva-Isman OV, Porter ACG. U5 snRNA Interactions With Exons Ensure Splicing Precision. Front Genet 2021; 12:676971. [PMID: 34276781 PMCID: PMC8283771 DOI: 10.3389/fgene.2021.676971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Imperfect conservation of human pre-mRNA splice sites is necessary to produce alternative isoforms. This flexibility is combined with the precision of the message reading frame. Apart from intron-termini GU_AG and the branchpoint A, the most conserved are the exon-end guanine and +5G of the intron start. Association between these guanines cannot be explained solely by base-pairing with U1 snRNA in the early spliceosome complex. U6 succeeds U1 and pairs +5G in the pre-catalytic spliceosome, while U5 binds the exon end. Current U5 snRNA reconstructions by CryoEM cannot explain the conservation of the exon-end G. Conversely, human mutation analyses show that guanines of both exon termini can suppress splicing mutations. Our U5 hypothesis explains the mechanism of splicing precision and the role of these conserved guanines in the pre-catalytic spliceosome. We propose: (1) optimal binding register for human exons and U5-the exon junction positioned at U5Loop1 C39|C38; (2) common mechanism for base-pairing of human U5 snRNA with diverse exons and bacterial Ll.LtrB intron with new loci in retrotransposition-guided by base pair geometry; and (3) U5 plays a significant role in specific exon recognition in the pre-catalytic spliceosome. Statistical analyses showed increased U5 Watson-Crick pairs with the 5'exon in the absence of +5G at the intron start. In 5'exon positions -3 and -5, this effect is specific to U5 snRNA rather than U1 snRNA of the early spliceosome. Increased U5 Watson-Crick pairs with 3'exon position +1 coincide with substitutions of the conserved -3C at the intron 3'end. Based on mutation and X-ray evidence, we propose that -3C pairs with U2 G31 juxtaposing the branchpoint and the 3'intron end. The intron-termini pair, formed in the pre-catalytic spliceosome to be ready for transition after branching, and the early involvement of the 3'intron end ensure that the 3'exon contacts U5 in the pre-catalytic complex. We suggest that splicing precision is safeguarded cooperatively by U5, U6, and U2 snRNAs that stabilize the pre-catalytic complex by Watson-Crick base pairing. In addition, our new U5 model explains the splicing effect of exon-start +1G mutations: U5 Watson-Crick pairs with exon +2C/+3G strongly promote exon inclusion. We discuss potential applications for snRNA therapeutics and gene repair by reverse splicing.
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Affiliation(s)
- Olga V Artemyeva-Isman
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
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4
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Ciavarella J, Perea W, Greenbaum NL. Topology of the U12-U6 atac snRNA Complex of the Minor Spliceosome and Binding by NTC-Related Protein RBM22. ACS OMEGA 2020; 5:23549-23558. [PMID: 32984674 PMCID: PMC7512442 DOI: 10.1021/acsomega.0c01674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/04/2020] [Indexed: 06/02/2023]
Abstract
Splicing of precursor messenger RNA is catalyzed by the spliceosome, a dynamic ribonucleoprotein assembly including five small nuclear (sn)RNAs and >100 proteins. RNA components catalyze the two transesterification reactions, but proteins perform critical roles in assembly and rearrangement. The catalytic core comprises a paired complex of U2 and U6 snRNAs for the major form of the spliceosome and U12 and U6atac snRNAs for the minor variant (∼0.3% of all spliceosomes in higher eukaryotes); the latter shares key catalytic sequence elements and performs identical chemistry. Here we use solution NMR techniques to show that the U12-U6atac snRNA complex of both human and Arabidopsis maintain base-pairing patterns similar to those in the three-helix model of the U2-U6 snRNA complex that position key elements to form the spliceosome's active site. However, in place of the stacked base pairs at the base of the U6 snRNA intramolecular stem loop and the central junction of the U2-U6 snRNA complex, we see altered geometry in the single-stranded hinge region opposing termini of the snRNAs to enable interaction between the key elements. We then use electrophoretic mobility shift assays and fluorescence assays to show that the protein RBM22, implicated in remodeling the human U2-U6 snRNA complex prior to catalysis, also binds the U12-U6atac snRNA complexes specifically and with similar affinity as to U2-U6 snRNA (a mean K d for the two methods = 3.4 and 8.0 μM for U2-U6 and U12-U6atac snRNA complexes, respectively), suggesting that RBM22 performs the same role in both spliceosomes.
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Affiliation(s)
- Joanna Ciavarella
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, Hunter College of the City
University of New York, New York, New York 10065, United States
| | - William Perea
- Department
of Chemistry, Hunter College of the City
University of New York, New York, New York 10065, United States
| | - Nancy L. Greenbaum
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, Hunter College of the City
University of New York, New York, New York 10065, United States
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5
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Chu H, Perea W, Greenbaum NL. Role of the central junction in folding topology of the protein-free human U2-U6 snRNA complex. RNA (NEW YORK, N.Y.) 2020; 26:836-850. [PMID: 32220895 PMCID: PMC7297123 DOI: 10.1261/rna.073379.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/16/2020] [Indexed: 06/02/2023]
Abstract
U2 and U6 small nuclear (sn)RNAs are the only snRNAs directly implicated in catalyzing the splicing of pre-mRNA, but assembly and rearrangement steps prior to catalysis require numerous proteins. Previous studies have shown that the protein-free U2-U6 snRNA complex adopts two conformations in equilibrium, characterized by four and three helices surrounding a central junction. The four-helix conformer is strongly favored in the in vitro protein-free state, but the three-helix conformer predominates in spliceosomes. To analyze the role of the central junction in positioning elements forming the active site, we derived three-dimensional models of the two conformations from distances measured between fluorophores at selected locations in constructs representing the protein-free human U2-U6 snRNA complex by time-resolved fluorescence resonance energy transfer. Data describing four angles in the four-helix conformer suggest tetrahedral geometry; addition of Mg2+ results in shortening of the distances between neighboring helices, indicating compaction of the complex around the junction. In contrast, the three-helix conformer shows a closer approach between helices bearing critical elements, but the addition of Mg2+ widens the distance between them; thus in neither conformer are the critical helices positioned to favor the proposed triplex interaction. The presence of Mg2+ also enhances the fraction of the three-helix conformer, as does incubation with the Prp19-related protein RBM22, which has been implicated in the remodeling of the U2-U6 snRNA complex to render it catalytically active. These data suggest that although the central junction assumes a significant role in orienting helices, spliceosomal proteins and Mg2+ facilitate formation of the catalytically active conformer.
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Affiliation(s)
- Huong Chu
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
| | - William Perea
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10065, USA
| | - Nancy L Greenbaum
- Department of Chemistry, Hunter College of the City University of New York, New York, New York 10065, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
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6
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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7
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O'Connell AA, Hanson JA, McCaskill DC, Moore ET, Lewis DC, Grover N. Thermodynamic examination of pH and magnesium effect on U6 RNA internal loop. RNA (NEW YORK, N.Y.) 2019; 25:1779-1792. [PMID: 31548339 PMCID: PMC6859860 DOI: 10.1261/rna.070466.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
U6 RNA contains a 1 × 2-nt internal loop that folds and unfold during spliceosomal assembly and activation. The 1 × 2 loop consists of a C67•A79 base pair that forms an additional hydrogen bond upon protonation, C67•A+79, and uracil (U80) that coordinates the catalytically essential magnesium ions. We designed a series of RNA and DNA constructs with a 1 × 2 loop sequence contained in the ISL, and its modifications, to measure the thermodynamic effects of protonation and magnesium binding using UV-visible thermal denaturation experiments. We show that the wild-type RNA construct gains 0.43 kcal/mol in 1 M KCl upon lowering the pH from 7.5 to 5.5; the presence of magnesium ions increases its stability by 2.17 kcal/mol at pH 7.5 over 1 M KCl. Modifications of the helix closing base pairs from C-G to U•G causes a loss in protonation-dependent stability and a decrease in stability in the presence of magnesium ions, especially in the C68U construct. A79G single-nucleotide bulge loop construct showed the largest gain in stability in the presence of magnesium ions. The DNA wild-type construct shows a smaller effect on stability upon lowering the pH and in the presence of magnesium ions, highlighting differences in RNA and DNA structures. A U6 RNA 1 × 2 loop sequence is rare in the databases examined.
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Affiliation(s)
- Allison A O'Connell
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Jared A Hanson
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Darryl C McCaskill
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Ethan T Moore
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Daniel C Lewis
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Neena Grover
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
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8
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Kirsch R, Olzog VJ, Bonin S, Weinberg CE, Betat H, Stadler PF, Mörl M. A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking in vitro. Biotechniques 2019; 67:178-183. [PMID: 31462065 DOI: 10.2144/btn-2019-0047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Until recently, RNA-RNA interactions were mainly identified by crosslinking RNAs with interacting proteins, RNA proximity ligation and deep sequencing. Recently, AMT-based direct RNA crosslinking was established. Yet, several steps of these procedures are rather inefficient, reducing the output of identified interaction partners. To increase the local concentration of RNA ends, interacting RNAs are often fragmented. However, the resulting 2',3'-cyclic phosphate and 5'-OH ends are not accepted by T4 RNA ligase and have to be converted to 3'-OH and 5'-phosphate ends. Using an artificial mRNA/sRNA pair, we optimized the workflow downstream of the crosslinking reaction in vitro. The use of a tRNA ligase allows direct fusion of 2',3'-cyclic phosphate and 5'-OH RNA ends.
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Affiliation(s)
- Rebecca Kirsch
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany.,Center for Non-Coding RNA in Technology & Health, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
| | - V Janett Olzog
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | - Sonja Bonin
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | | | - Heike Betat
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
| | - Peter F Stadler
- Center for Non-Coding RNA in Technology & Health, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.,Bioinformatics Group, Department of Computer Science & Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Mario Mörl
- Institute for Biochemistry, Brüderstraße 34, 04103 Leipzig, Germany
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9
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Bao P, Boon KL, Will CL, Hartmuth K, Lührmann R. Multiple RNA-RNA tertiary interactions are dispensable for formation of a functional U2/U6 RNA catalytic core in the spliceosome. Nucleic Acids Res 2019; 46:12126-12138. [PMID: 30335160 PMCID: PMC6294511 DOI: 10.1093/nar/gky966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 01/24/2023] Open
Abstract
The active 3D conformation of the spliceosome's catalytic U2/U6 RNA core is stabilised by a network of secondary and tertiary RNA interactions, but also depends on spliceosomal proteins for its formation. To determine the contribution towards splicing of specific RNA secondary and tertiary interactions in the U2/U6 RNA core, we introduced mutations in critical U6 nucleotides and tested their effect on splicing using a yeast in vitro U6 depletion/complementation system. Elimination of selected RNA tertiary interactions involving the U6 catalytic triad, or deletions of the bases of U6-U80 or U6-A59, had moderate to no effect on splicing, showing that the affected secondary and tertiary interactions are not required for splicing catalysis. However, removal of the base of U6-G60 of the catalytic triad completely blocked splicing, without affecting assembly of the activated spliceosome or its subsequent conversion into a B*-like complex. Our data suggest that the catalytic configuration of the RNA core that allows catalytic metal M1 binding can be maintained by Protein–RNA contacts. However, RNA stacking interactions in the U2/U6 RNA core are required for productive coordination of metal M2. The functional conformation of the U2/U6 RNA core is thus highly buffered, with overlapping contributions from RNA–RNA and Protein–RNA interactions.
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Affiliation(s)
- Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Kum-Loong Boon
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Klaus Hartmuth
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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10
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Izumikawa K, Nobe Y, Ishikawa H, Yamauchi Y, Taoka M, Sato K, Nakayama H, Simpson RJ, Isobe T, Takahashi N. TDP-43 regulates site-specific 2'-O-methylation of U1 and U2 snRNAs via controlling the Cajal body localization of a subset of C/D scaRNAs. Nucleic Acids Res 2019; 47:2487-2505. [PMID: 30759234 PMCID: PMC6412121 DOI: 10.1093/nar/gkz086] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 12/12/2022] Open
Abstract
TDP-43 regulates cellular levels of Cajal bodies (CBs) that provide platforms for the assembly and RNA modifications of small nuclear ribonucleoproteins (snRNPs) involved in pre-mRNA splicing. Alterations in these snRNPs may be linked to pathogenesis of amyotrophic lateral sclerosis. However, specific roles for TDP-43 in CBs remain unknown. Here, we demonstrate that TDP-43 regulates the CB localization of four UG-rich motif-bearing C/D-box-containing small Cajal body-specific RNAs (C/D scaRNAs; i.e. scaRNA2, 7, 9 and 28) through the direct binding to these scaRNAs. TDP-43 enhances binding of a CB-localizing protein, WD40-repeat protein 79 (WDR79), to a subpopulation of scaRNA2 and scaRNA28; the remaining population of the four C/D scaRNAs was localized to CB-like structures even with WDR79 depletion. Depletion of TDP-43, in contrast, shifted the localization of these C/D scaRNAs, mainly into the nucleolus, as well as destabilizing scaRNA2, and reduced the site-specific 2'-O-methylation of U1 and U2 snRNAs, including at 70A in U1 snRNA and, 19G, 25G, 47U and 61C in U2 snRNA. Collectively, we suggest that TDP-43 and WDR79 have separate roles in determining CB localization of subsets of C/D and H/ACA scaRNAs.
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Affiliation(s)
- Keiichi Izumikawa
- Department of Applied Biological Science and Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Hideaki Ishikawa
- Department of Applied Biological Science and Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Ko Sato
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Hiroshi Nakayama
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Richard J Simpson
- Department of Applied Biological Science and Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
- La Trobe Institute for Molecular Science (LIMS), LIMS Building 1, Room 412 La Trobe University, Melbourne Victoria 3086, Australia
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192–0397, Japan
| | - Nobuhiro Takahashi
- Department of Applied Biological Science and Global Innovation Research Organizations, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
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11
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Abstract
Pre-mRNA splicing must occur with extremely high fidelity. Spliceosomes assemble onto pre-mRNA guided by specific sequences (5' splice site, 3' splice site, and branchpoint). When splice sites are mutated, as in many hereditary diseases, the spliceosome can aberrantly select nearby pseudo- or "cryptic" splice sites, often resulting in nonfunctional protein. How the spliceosome distinguishes authentic splice sites from cryptic splice sites is poorly understood. We performed a Caenorhabditis elegans genetic screen to find cellular factors that affect the frequency with which the spliceosome uses cryptic splice sites and identified two alleles in core spliceosome component Prp8 that alter cryptic splicing frequency. Subsequent complementary genetic and structural analyses in yeast implicate these alleles in the stability of the spliceosome's catalytic core. However, despite a clear effect on cryptic splicing, high-throughput mRNA sequencing of these prp-8 mutant C. elegans reveals that overall alternative splicing patterns are relatively unchanged. Our data suggest the spliceosome evolved intrinsic mechanisms to reduce the occurrence of cryptic splicing and that these mechanisms are distinct from those that impact alternative splicing.
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12
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Zhan X, Yan C, Zhang X, Lei J, Shi Y. Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Cell Res 2018; 28:1129-1140. [PMID: 30315277 PMCID: PMC6274647 DOI: 10.1038/s41422-018-0094-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (Bact complex). The pre-B-to-B and B-to-Bact transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome.
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Affiliation(s)
- Xiechao Zhan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, 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 and School of Medicine, Tsinghua University, Beijing, 100084, China.
| | - Xiaofeng Zhang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, 100084, China
- Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein 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 and School of Medicine, Tsinghua University, Beijing, 100084, China.
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang, 310024, China.
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13
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Kappel K, Das R. Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking. Structure 2018; 27:140-151.e5. [PMID: 30416038 DOI: 10.1016/j.str.2018.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/27/2018] [Accepted: 10/05/2018] [Indexed: 10/27/2022]
Abstract
RNA-protein complexes underlie numerous cellular processes including translation, splicing, and posttranscriptional regulation of gene expression. The structures of these complexes are crucial to their functions but often elude high-resolution structure determination. Computational methods are needed that can integrate low-resolution data for RNA-protein complexes while modeling de novo the large conformational changes of RNA components upon complex formation. To address this challenge, we describe RNP-denovo, a Rosetta method to simultaneously fold-and-dock RNA to a protein surface. On a benchmark set of diverse RNA-protein complexes not solvable with prior strategies, RNP-denovo consistently sampled native-like structures with better than nucleotide resolution. We revisited three past blind modeling challenges involving the spliceosome, telomerase, and a methyltransferase-ribosomal RNA complex in which previous methods gave poor results. When coupled with the same sparse FRET, crosslinking, and functional data used previously, RNP-denovo gave models with significantly improved accuracy. These results open a route to modeling global folds of RNA-protein complexes from low-resolution data.
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Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Physics, Stanford University, Stanford, CA 94305, USA.
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14
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MacRae AJ, Mayerle M, Hrabeta-Robinson E, Chalkley RJ, Guthrie C, Burlingame AL, Jurica MS. Prp8 positioning of U5 snRNA is linked to 5' splice site recognition. RNA (NEW YORK, N.Y.) 2018; 24:769-777. [PMID: 29487104 PMCID: PMC5959246 DOI: 10.1261/rna.065458.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 02/26/2018] [Indexed: 05/22/2023]
Abstract
Prp8 is an essential protein that regulates spliceosome assembly and conformation during pre-mRNA splicing. Recent cryo-EM structures of the spliceosome model Prp8 as a scaffold for the spliceosome's catalytic U snRNA components. Using a new amino acid probing strategy, we identified a dynamic region in human Prp8 that is positioned to stabilize the pre-mRNA in the spliceosome active site through interactions with U5 snRNA. Mutagenesis of the identified Prp8 residues in yeast indicates a role in 5' splice site recognition. Genetic interactions with spliceosome proteins Isy1, which buttresses the intron branch point, and Snu114, a regulatory GTPase that directly contacts Prp8, further corroborate a role for the same Prp8 residues in substrate positioning and activation. Together the data suggest that adjustments in interactions between Prp8 and U5 snRNA help establish proper positioning of the pre-mRNA into the active site to enhance 5' splice site fidelity.
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Affiliation(s)
- Andrew J MacRae
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Megan Mayerle
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
| | - Eva Hrabeta-Robinson
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94122, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94122, USA
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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15
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Bao P, Höbartner C, Hartmuth K, Lührmann R. Yeast Prp2 liberates the 5' splice site and the branch site adenosine for catalysis of pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2017; 23:1770-1779. [PMID: 28864812 PMCID: PMC5688998 DOI: 10.1261/rna.063115.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/31/2017] [Indexed: 05/20/2023]
Abstract
The RNA helicase Prp2 facilitates the remodeling of the spliceosomal Bact complex to the catalytically activated B* complex just before step one of splicing. As a high-resolution cryo-EM structure of the B* complex is currently lacking, the precise spliceosome remodeling events mediated by Prp2 remain poorly understood. To investigate the latter, we used chemical structure probing to compare the RNA structure of purified yeast Bact and B* complexes. Our studies reveal deviations from conventional RNA helices in the functionally important U6 snRNA internal stem-loop and U2/U6 helix Ib in the activated Bact complex, and to a lesser extent in B*. Interestingly, the N7 of U6-G60 of the catalytic triad becomes accessible to DMS modification in the B* complex, suggesting that the Hoogsteen interaction with U6-A52 is destabilized in B*. Our data show that Prp2 action does not unwind double-stranded RNA, but enhances the flexibility of the first step reactants, the pre-mRNA's 5' splice site and branch site adenosine. Prp2 therefore appears to act primarily as an RNPase to achieve catalytic activation by liberating the first step reactants in preparation for catalysis of the first step of splicing.
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Affiliation(s)
- Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Claudia Höbartner
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
| | - Klaus Hartmuth
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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16
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Pozzi B, Bragado L, Will CL, Mammi P, Risso G, Urlaub H, Lührmann R, Srebrow A. SUMO conjugation to spliceosomal proteins is required for efficient pre-mRNA splicing. Nucleic Acids Res 2017; 45:6729-6745. [PMID: 28379520 PMCID: PMC5499870 DOI: 10.1093/nar/gkx213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 03/24/2017] [Indexed: 12/26/2022] Open
Abstract
Pre-mRNA splicing is catalyzed by the spliceosome, a multi-megadalton ribonucleoprotein machine. Previous work from our laboratory revealed the splicing factor SRSF1 as a regulator of the SUMO pathway, leading us to explore a connection between this pathway and the splicing machinery. We show here that addition of a recombinant SUMO-protease decreases the efficiency of pre-mRNA splicing in vitro. By mass spectrometry analysis of anti-SUMO immunoprecipitated proteins obtained from purified splicing complexes formed along the splicing reaction, we identified spliceosome-associated SUMO substrates. After corroborating SUMOylation of Prp3 in cultured cells, we defined Lys 289 and Lys 559 as bona fide SUMO attachment sites within this spliceosomal protein. We further demonstrated that a Prp3 SUMOylation-deficient mutant while still capable of interacting with U4/U6 snRNP components, is unable to co-precipitate U2 and U5 snRNA and the spliceosomal proteins U2-SF3a120 and U5-Snu114. This SUMOylation-deficient mutant fails to restore the splicing of different pre-mRNAs to the levels achieved by the wild type protein, when transfected into Prp3-depleted cultured cells. This mutant also shows a diminished recruitment to active spliceosomes, compared to the wild type protein. These findings indicate that SUMO conjugation plays a role during the splicing process and suggest the involvement of Prp3 SUMOylation in U4/U6•U5 tri-snRNP formation and/or recruitment.
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Affiliation(s)
- Berta Pozzi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Laureano Bragado
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Pablo Mammi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Guillermo Risso
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, 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
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Anabella Srebrow
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
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17
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Mechanistic insights into precursor messenger RNA splicing by the spliceosome. Nat Rev Mol Cell Biol 2017; 18:655-670. [DOI: 10.1038/nrm.2017.86] [Citation(s) in RCA: 234] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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18
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Costa M, Walbott H, Monachello D, Westhof E, Michel F. Crystal structures of a group II intron lariat primed for reverse splicing. Science 2017; 354:354/6316/aaf9258. [PMID: 27934709 DOI: 10.1126/science.aaf9258] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 10/27/2016] [Indexed: 12/28/2022]
Abstract
The 2'-5' branch of nuclear premessenger introns is believed to have been inherited from self-splicing group II introns, which are retrotransposons of bacterial origin. Our crystal structures at 3.4 and 3.5 angstrom of an excised group II intron in branched ("lariat") form show that the 2'-5' branch organizes a network of active-site tertiary interactions that position the intron terminal 3'-hydroxyl group into a configuration poised to initiate reverse splicing, the first step in retrotransposition. Moreover, the branchpoint and flanking helices must undergo a base-pairing switch after branch formation. A group II-based model of the active site of the nuclear splicing machinery (the spliceosome) is proposed. The crucial role of the lariat conformation in active-site assembly and catalysis explains its prevalence in modern splicing.
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Affiliation(s)
- Maria Costa
- Group II introns as ribozymes and retrotransposons, Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), University Paris-Sud, University Paris-Saclay, 1 Avenue de la Terrasse, Bâtiment 26, 91198 Gif-sur-Yvette cedex, France.
| | - Hélène Walbott
- Structure and Dynamics of RNA, I2BC, UMR 9198 CNRS, CEA, University Paris-Sud, University Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Dario Monachello
- Group II introns as ribozymes and retrotransposons, Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), University Paris-Sud, University Paris-Saclay, 1 Avenue de la Terrasse, Bâtiment 26, 91198 Gif-sur-Yvette cedex, France
| | - Eric Westhof
- Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS, University of Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - François Michel
- Group II introns as ribozymes and retrotransposons, Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), University Paris-Sud, University Paris-Saclay, 1 Avenue de la Terrasse, Bâtiment 26, 91198 Gif-sur-Yvette cedex, France
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19
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Abstract
The discoveries of myriad non-coding RNA molecules, each transiting through multiple flexible states in cells or virions, present major challenges for structure determination. Advances in high-throughput chemical mapping give new routes for characterizing entire transcriptomes in vivo, but the resulting one-dimensional data generally remain too information-poor to allow accurate de novo structure determination. Multidimensional chemical mapping (MCM) methods seek to address this challenge. Mutate-and-map (M2), RNA interaction groups by mutational profiling (RING-MaP and MaP-2D analysis) and multiplexed •OH cleavage analysis (MOHCA) measure how the chemical reactivities of every nucleotide in an RNA molecule change in response to modifications at every other nucleotide. A growing body of in vitro blind tests and compensatory mutation/rescue experiments indicate that MCM methods give consistently accurate secondary structures and global tertiary structures for ribozymes, ribosomal domains and ligand-bound riboswitch aptamers up to 200 nucleotides in length. Importantly, MCM analyses provide detailed information on structurally heterogeneous RNA states, such as ligand-free riboswitches that are functionally important but difficult to resolve with other approaches. The sequencing requirements of currently available MCM protocols scale at least quadratically with RNA length, precluding general application to transcriptomes or viral genomes at present. We propose a modify-cross-link-map (MXM) expansion to overcome this and other current limitations to resolving the in vivo 'RNA structurome'.
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20
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Sidarovich A, Will CL, Anokhina MM, Ceballos J, Sievers S, Agafonov DE, Samatov T, Bao P, Kastner B, Urlaub H, Waldmann H, Lührmann R. Identification of a small molecule inhibitor that stalls splicing at an early step of spliceosome activation. eLife 2017; 6. [PMID: 28300534 PMCID: PMC5354520 DOI: 10.7554/elife.23533] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/26/2017] [Indexed: 11/13/2022] Open
Abstract
Small molecule inhibitors of pre-mRNA splicing are important tools for identifying new spliceosome assembly intermediates, allowing a finer dissection of spliceosome dynamics and function. Here, we identified a small molecule that inhibits human pre-mRNA splicing at an intermediate stage during conversion of pre-catalytic spliceosomal B complexes into activated Bact complexes. Characterization of the stalled complexes (designated B028) revealed that U4/U6 snRNP proteins are released during activation before the U6 Lsm and B-specific proteins, and before recruitment and/or stable incorporation of Prp19/CDC5L complex and other Bact complex proteins. The U2/U6 RNA network in B028 complexes differs from that of the Bact complex, consistent with the idea that the catalytic RNA core forms stepwise during the B to Bact transition and is likely stabilized by the Prp19/CDC5L complex and related proteins. Taken together, our data provide new insights into the RNP rearrangements and extensive exchange of proteins that occurs during spliceosome activation. DOI:http://dx.doi.org/10.7554/eLife.23533.001
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Affiliation(s)
- Anzhalika Sidarovich
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Maria M Anokhina
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Javier Ceballos
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sonja Sievers
- Compound Management and Screening Center, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dmitry E Agafonov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Timur Samatov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute for Clinical Chemistry Göttingen, University Medical Center, Göttingen, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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21
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Bertram K, Agafonov DE, Liu WT, Dybkov O, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Lührmann R. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Nature 2017; 542:318-323. [DOI: 10.1038/nature21079] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/04/2017] [Indexed: 12/18/2022]
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22
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Yan C, Wan R, Bai R, Huang G, Shi Y. Structure of a yeast step II catalytically activated spliceosome. Science 2016; 355:149-155. [PMID: 27980089 DOI: 10.1126/science.aak9979] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/05/2016] [Indexed: 12/30/2022]
Abstract
Each cycle of precursor messenger RNA (pre-mRNA) splicing comprises two sequential reactions, first freeing the 5' exon and generating an intron lariat-3' exon and then ligating the two exons and releasing the intron lariat. The second reaction is executed by the step II catalytically activated spliceosome (known as the C* complex). Here, we present the cryo-electron microscopy structure of a C* complex from Saccharomyces cerevisiae at an average resolution of 4.0 angstroms. Compared with the preceding spliceosomal complex (C complex), the lariat junction has been translocated by 15 to 20 angstroms to vacate space for the incoming 3'-exon sequences. The step I splicing factors Cwc25 and Yju2 have been dissociated from the active site. Two catalytic motifs from Prp8 (the 1585 loop and the β finger of the ribonuclease H-like domain), along with the step II splicing factors Prp17 and Prp18 and other surrounding proteins, are poised to assist the second transesterification. These structural features, together with those reported for other spliceosomal complexes, yield a near-complete mechanistic picture on the splicing cycle.
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Affiliation(s)
- 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
| | - 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
| | - 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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23
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Sperling R. The nuts and bolts of the endogenous spliceosome. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27465259 DOI: 10.1002/wrna.1377] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 01/09/2023]
Abstract
The complex life of pre-mRNA from transcription to the production of mRNA that can be exported from the nucleus to the cytoplasm to encode for proteins entails intricate coordination and regulation of a network of processing events. Coordination is required between transcription and splicing and between several processing events including 5' and 3' end processing, splicing, alternative splicing and editing that are major contributors to the diversity of the human proteome, and occur within a huge and dynamic macromolecular machine-the endogenous spliceosome. Detailed mechanistic insight of the splicing reaction was gained from studies of the in vitro spliceosome assembled on a single intron. Because most pre-mRNAs are multiintronic that undergo alternative splicing, the in vivo splicing machine requires additional elements to those of the in vitro machine, to account for all these diverse functions. Information about the endogenous spliceosome is emerging from imaging studies in intact and live cells that support the cotranscriptional commitment to splicing model and provide information about splicing kinetics in vivo. Another source comes from studies of the in vivo assembled spliceosome, isolated from cell nuclei under native conditions-the supraspliceosome-that individually package pre-mRNA transcripts of different sizes and number of introns into complexes of a unique structure, indicating their universal nature. Recent years have portrayed new players affecting alternative splicing and novel connections between splicing, transcription and chromatin. The challenge ahead is to elucidate the structure and function of the endogenous spliceosome and decipher the regulation and coordination of its network of processing activities. WIREs RNA 2017, 8:e1377. doi: 10.1002/wrna.1377 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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24
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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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25
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Abstract
Group II introns are self-splicing catalytic RNAs found in bacteria and the organelles of fungi and plants. They are thought to share a common ancestor with the spliceosome, which catalyzes the removal of nuclear introns from pre-mRNAs in eukaryotes. Recent structural and biochemical evidence supports the hypothesis that the spliceosome has a catalytic RNA core homologous to that found in group II introns. The crystal structure of a eukaryotic group IIB intron was recently determined and reveals the architecture of a branched lariat RNA that is also formed by the spliceosome. Here we describe the active site components of this intron and propose a model for RNA splicing involving dynamic base triples in the catalytic triad. Based on this structure, we draw analogies to the U2/U6 snRNA pairing and RNA-protein interactions that form in the active site of the spliceosome.
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Affiliation(s)
- Jessica K Peters
- a Department of Chemistry and Biochemistry ; University of California, San Diego ; La Jolla , CA USA
| | - Navtej Toor
- a Department of Chemistry and Biochemistry ; University of California, San Diego ; La Jolla , CA USA
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26
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Boesler C, Rigo N, Anokhina MM, Tauchert MJ, Agafonov DE, Kastner B, Urlaub H, Ficner R, Will CL, Lührmann R. A spliceosome intermediate with loosely associated tri-snRNP accumulates in the absence of Prp28 ATPase activity. Nat Commun 2016; 7:11997. [PMID: 27377154 PMCID: PMC4935976 DOI: 10.1038/ncomms11997] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 05/20/2016] [Indexed: 11/17/2022] Open
Abstract
The precise role of the spliceosomal DEAD-box protein Prp28 in higher eukaryotes remains unclear. We show that stable tri-snRNP association during pre-catalytic spliceosomal B complex formation is blocked by a dominant-negative hPrp28 mutant lacking ATPase activity. Complexes formed in the presence of ATPase-deficient hPrp28 represent a novel assembly intermediate, the pre-B complex, that contains U1, U2 and loosely associated tri-snRNP and is stalled before disruption of the U1/5′ss base pairing interaction, consistent with a role for hPrp28 in the latter. Pre-B and B complexes differ structurally, indicating that stable tri-snRNP integration is accompanied by substantial rearrangements in the spliceosome. Disruption of the U1/5′ss interaction alone is not sufficient to bypass the block by ATPase-deficient hPrp28, suggesting hPrp28 has an additional function at this stage of splicing. Our data provide new insights into the function of Prp28 in higher eukaryotes, and the requirements for stable tri-snRNP binding during B complex formation. The assembly of the splicesome involves several distinct stages that require the sequential action of DExD/H-box RNA helicases. Here, the authors uncover a new intermediate, the pre-B complex, that accumulates in the presence of an inactive form of the DEAD-box protein Prp28.
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Affiliation(s)
- Carsten Boesler
- Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Norbert Rigo
- Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Maria M Anokhina
- Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Marcel J Tauchert
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Dmitry E Agafonov
- Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, 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
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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27
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Abstract
A majority of human genes contain non-coding intervening sequences – introns that must be precisely excised from the pre-mRNA molecule. This event requires the coordinated action of five major small nuclear ribonucleoprotein particles (snRNPs) along with additional non-snRNP splicing proteins. Introns must be removed with nucleotidal precision, since even a single nucleotide mistake would result in a reading frame shift and production of a non-functional protein. Numerous human inherited diseases are caused by mutations that affect splicing, including mutations in proteins which are directly involved in splicing catalysis. One of the most common hereditary diseases associated with mutations in core splicing proteins is retinitis pigmentosa (RP). So far, mutations in more than 70 genes have been connected to RP. While the majority of mutated genes are expressed specifically in the retina, eight target genes encode for ubiquitous core snRNP proteins (Prpf3, Prpf4, Prpf6, Prpf8, Prpf31, and SNRNP200/Brr2) and splicing factors (RP9 and DHX38). Why mutations in spliceosomal proteins, which are essential in nearly every cell in the body, causes a disease that displays such a tissue-specific phenotype is currently a mystery. In this review, we recapitulate snRNP functions, summarize the missense mutations which are found in spliceosomal proteins as well as their impact on protein functions and discuss specific models which may explain why the retina is sensitive to these mutations.
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Affiliation(s)
- Šárka Růžičková
- a Department of RNA Biology , Institute of Molecular Genetics AS CR , Prague , Czech Republic
| | - David Staněk
- a Department of RNA Biology , Institute of Molecular Genetics AS CR , Prague , Czech Republic
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28
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Abstract
This review focuses on recent developments in our understanding of group II intron function, the relationships of these introns to retrotransposons and spliceosomes, and how their common features have informed thinking about bacterial group II introns as key elements in eukaryotic evolution. Reverse transcriptase-mediated and host factor-aided intron retrohoming pathways are considered along with retrotransposition mechanisms to novel sites in bacteria, where group II introns are thought to have originated. DNA target recognition and movement by target-primed reverse transcription infer an evolutionary relationship among group II introns, non-LTR retrotransposons, such as LINE elements, and telomerase. Additionally, group II introns are almost certainly the progenitors of spliceosomal introns. Their profound similarities include splicing chemistry extending to RNA catalysis, reaction stereochemistry, and the position of two divalent metals that perform catalysis at the RNA active site. There are also sequence and structural similarities between group II introns and the spliceosome's small nuclear RNAs (snRNAs) and between a highly conserved core spliceosomal protein Prp8 and a group II intron-like reverse transcriptase. It has been proposed that group II introns entered eukaryotes during bacterial endosymbiosis or bacterial-archaeal fusion, proliferated within the nuclear genome, necessitating evolution of the nuclear envelope, and fragmented giving rise to spliceosomal introns. Thus, these bacterial self-splicing mobile elements have fundamentally impacted the composition of extant eukaryotic genomes, including the human genome, most of which is derived from close relatives of mobile group II introns.
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29
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Madan B, Kasprzak JM, Tuszynska I, Magnus M, Szczepaniak K, Dawson WK, Bujnicki JM. Modeling of Protein-RNA Complex Structures Using Computational Docking Methods. Methods Mol Biol 2016; 1414:353-372. [PMID: 27094302 DOI: 10.1007/978-1-4939-3569-7_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A significant part of biology involves the formation of RNA-protein complexes. X-ray crystallography has added a few solved RNA-protein complexes to the repertoire; however, it remains challenging to capture these complexes and often only the unbound structures are available. This has inspired a growing interest in finding ways to predict these RNA-protein complexes. In this study, we show ways to approach this problem by computational docking methods, either with a fully automated NPDock server or with a workflow of methods for generation of many alternative structures followed by selection of the most likely solution. We show that by introducing experimental information, the structure of the bound complex is rendered far more likely to be within reach. This study is meant to help the user of docking software understand how to grapple with a typical realistic problem in RNA-protein docking, understand what to expect in the way of difficulties, and recognize the current limitations.
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Affiliation(s)
- Bharat Madan
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Joanna M Kasprzak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
| | - Irina Tuszynska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
- Institute of Informatics, University of Warsaw, ul. Banacha 2, 02-097, Warsaw, Poland
| | - Marcin Magnus
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Krzysztof Szczepaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Wayne K Dawson
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109, Warsaw, Poland.
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
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30
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Abstract
Since the first description of the canonical B-form DNA double helix, it has been suggested that alternative DNA, DNA–RNA, and RNA structures exist and act as functional genomic elements. Indeed, over the past few years it has become clear that, in addition to serving as a repository for genetic information, genomic DNA elicits biological responses by adopting conformations that differ from the canonical right-handed double helix, and by interacting with RNA molecules to form complex secondary structures. This review focuses on recent advances on three-stranded (triplex) nucleic acids, with an emphasis on DNA–RNA and RNA–RNA interactions. Emerging work reveals that triplex interactions between noncoding RNAs and duplex DNA serve as platforms for delivering site-specific epigenetic marks critical for the regulation of gene expression. Additionally, an increasing body of genetic and structural studies demonstrates that triplex RNA–RNA interactions are essential for performing catalytic and regulatory functions in cellular nucleoprotein complexes, including spliceosomes and telomerases, and for enabling protein recoding during programmed ribosomal frameshifting. Thus, evidence is mounting that DNA and RNA triplex interactions are implemented to perform a range of diverse biological activities in the cell, some of which will be discussed in this review.
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Affiliation(s)
- Albino Bacolla
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, Texas, United States of America
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, Texas, United States of America
| | - Karen M. Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, Texas, United States of America
- * E-mail:
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31
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Papasaikas P, Valcárcel J. The Spliceosome: The Ultimate RNA Chaperone and Sculptor. Trends Biochem Sci 2015; 41:33-45. [PMID: 26682498 DOI: 10.1016/j.tibs.2015.11.003] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/02/2015] [Accepted: 11/06/2015] [Indexed: 01/08/2023]
Abstract
The spliceosome, one of the most complex machineries of eukaryotic cells, removes intronic sequences from primary transcripts to generate functional messenger and long noncoding RNAs (lncRNA). Genetic, biochemical, and structural data reveal that the spliceosome is an RNA-based enzyme. Striking mechanistic and structural similarities strongly argue that pre-mRNA introns originated from self-catalytic group II ribozymes. However, in the spliceosome, protein components organize and activate the catalytic-site RNAs, and recognize and pair together splice sites at intron boundaries. The spliceosome is a dynamic, reversible, and flexible machine that chaperones small nuclear (sn) RNAs and a variety of pre-mRNA sequences into conformations that enable intron removal. This malleability likely contributes to the regulation of alternative splicing, a prevalent process contributing to cell differentiation, homeostasis, and disease.
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Affiliation(s)
- Panagiotis Papasaikas
- Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu-Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu-Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Passeig Lluis Companys 23, 08010 Barcelona, Spain.
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32
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Hang J, Wan R, Yan C, Shi Y. Structural basis of pre-mRNA splicing. Science 2015; 349:1191-8. [PMID: 26292705 DOI: 10.1126/science.aac8159] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/10/2015] [Indexed: 01/27/2023]
Abstract
Splicing of precursor messenger RNA is performed by the spliceosome. In the cryogenic electron microscopy structure of the yeast spliceosome, U5 small nuclear ribonucleoprotein acts as a central scaffold onto which U6 and U2 small nuclear RNAs (snRNAs) are intertwined to form a catalytic center next to Loop I of U5 snRNA. Magnesium ions are coordinated by conserved nucleotides in U6 snRNA. The intron lariat is held in place through base-pairing interactions with both U2 and U6 snRNAs, leaving the variable-length middle portion on the solvent-accessible surface of the catalytic center. The protein components of the spliceosome anchor both 5' and 3' ends of the U2 and U6 snRNAs away from the active site, direct the RNA sequences, and allow sufficient flexibility between the ends and the catalytic center. Thus, the spliceosome is in essence a protein-directed ribozyme, with the protein components essential for the delivery of critical RNA molecules into close proximity of one another at the right time for the splicing reaction.
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Affiliation(s)
- Jing Hang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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33
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Abstract
Present in the genomes of bacteria and eukaryotic organelles, group II introns are an ancient class of ribozymes and retroelements that are believed to have been the ancestors of nuclear pre-mRNA introns. Despite long-standing speculation, there is limited understanding about the actual pathway by which group II introns evolved into eukaryotic introns. In this review, we focus on the evolution of group II introns themselves. We describe the different forms of group II introns known to exist in nature and then address how these forms may have evolved to give rise to spliceosomal introns and other genetic elements. Finally, we summarize the structural and biochemical parallels between group II introns and the spliceosome, including recent data that strongly support their hypothesized evolutionary relationship.
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Affiliation(s)
- Steven Zimmerly
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4 Canada
| | - Cameron Semper
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N 1N4 Canada
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34
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Sharma S, Wongpalee SP, Vashisht A, Wohlschlegel JA, Black DL. Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly. Genes Dev 2015; 28:2518-31. [PMID: 25403181 PMCID: PMC4233244 DOI: 10.1101/gad.248625.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The pairing of 5′ and 3′ splice sites across an intron is a critical step in spliceosome formation and its regulation. Sharma et al. report a new interaction between stem–loop 4 (SL4) of the U1 snRNA, which recognizes the 5′ splice, and a component of the U2 snRNP complex, which assembles across the intron at the 3′ splice site. U1-SL4 interacts with the SF3A1 protein of the U2 snRNP, and this interaction occurs within prespliceosomal complexes assembled on the pre-mRNA. The pairing of 5′ and 3′ splice sites across an intron is a critical step in spliceosome formation and its regulation. Interactions that bring the two splice sites together during spliceosome assembly must occur with a high degree of specificity and fidelity to allow expression of functional mRNAs and make particular alternative splicing choices. Here, we report a new interaction between stem–loop 4 (SL4) of the U1 snRNA, which recognizes the 5′ splice site, and a component of the U2 small nuclear ribonucleoprotein particle (snRNP) complex, which assembles across the intron at the 3′ splice site. Using a U1 snRNP complementation assay, we found that SL4 is essential for splicing in vivo. The addition of free U1-SL4 to a splicing reaction in vitro inhibits splicing and blocks complex assembly prior to formation of the prespliceosomal A complex, indicating a requirement for a SL4 contact in spliceosome assembly. To characterize the interactions of this RNA structure, we used a combination of stable isotope labeling by amino acids in cell culture (SILAC), biotin/Neutravidin affinity pull-down, and mass spectrometry. We show that U1-SL4 interacts with the SF3A1 protein of the U2 snRNP. We found that this interaction between the U1 snRNA and SF3A1 occurs within prespliceosomal complexes assembled on the pre-mRNA. Thus, SL4 of the U1 snRNA is important for splicing, and its interaction with SF3A1 mediates contact between the 5′ and 3′ splice site complexes within the assembling spliceosome.
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Affiliation(s)
- Shalini Sharma
- Department of Basic Medical Sciences, University of Arizona, College of Medicine-Phoenix, Phoenix, Arizona 85004, USA; Department of Microbiology, Immunology, and Molecular Genetics
| | | | | | | | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
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35
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Robart AR, Chan RT, Peters JK, Rajashankar KR, Toor N. Crystal structure of a eukaryotic group II intron lariat. Nature 2014; 514:193-7. [PMID: 25252982 PMCID: PMC4197185 DOI: 10.1038/nature13790] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 08/22/2014] [Indexed: 11/12/2022]
Abstract
The formation of branched lariat RNA is an evolutionarily conserved feature of splicing reactions for both group II and spliceosomal introns. The lariat is important for the fidelity of 5' splice-site selection and consists of a 2'-5' phosphodiester bond between a bulged adenosine and the 5' end of the intron. To gain insight into this ubiquitous intramolecular linkage, we determined the crystal structure of a eukaryotic group IIB intron in the lariat form at 3.7 Å. This revealed that two tandem tetraloop-receptor interactions, η-η' and π-π', place domain VI in the core to position the lariat bond in the post-catalytic state. On the basis of structural and biochemical data, we propose that π-π' is a dynamic interaction that mediates the transition between the two steps of splicing, with η-η' serving an ancillary role. The structure also reveals a four-magnesium-ion cluster involved in both catalysis and positioning of the 5' end. Given the evolutionary relationship between group II and nuclear introns, it is likely that this active site configuration exists in the spliceosome as well.
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Affiliation(s)
- Aaron R. Robart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Russell T. Chan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Jessica K. Peters
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA
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36
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Lozano G, Fernandez N, Martinez-Salas E. Magnesium-dependent folding of a picornavirus IRES element modulates RNA conformation and eIF4G interaction. FEBS J 2014; 281:3685-700. [PMID: 24961997 PMCID: PMC4163634 DOI: 10.1111/febs.12890] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/12/2014] [Accepted: 06/20/2014] [Indexed: 12/24/2022]
Abstract
Internal ribosome entry site (IRES) elements are high-order RNA structures that promote internal initiation of translation to allow protein synthesis under situations that compromise the general cap-dependent translation mechanism. Picornavirus IRES elements are highly efficient elements with a modular RNA structure organization. Here we investigated the effect of Mg(2+) concentration on the local flexibility and solvent accessibility of the foot-and-mouth disease virus (FMDV) IRES element measured on the basis of selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reactivity and hydroxyl radical cleavage. We have found that Mg(2+) concentration affects the organization of discrete IRES regions, mainly the apical region of domain 3, the 10 nt loop of domain 4, and the pyrimidine tract of domain 5. In support of the effect of RNA structure on IRES activity, substitution or deletion mutants of the 10 nt loop of domain 4 impair internal initiation. In addition, divalent cations affect the binding of eIF4G, a eukaryotic initiation factor that is essential for IRES-dependent translation that interacts with domain 4. Binding of eIF4G is favored by the local RNA flexibility adopted at low Mg(2+) concentration, while eIF4B interacts with the IRES independently of the compactness of the RNA structure. Our study shows that the IRES element adopts a near-native structure in the absence of proteins, shedding light on the influence of Mg(2+) ions on the local flexibility and binding of eIF4G in a model IRES element.
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Affiliation(s)
- Gloria Lozano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco, Spain
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37
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Abstract
The lariat-capping (LC) ribozyme is a natural ribozyme isolated from eukaryotic microorganisms. Despite apparent structural similarity to group I introns, the LC ribozyme catalyzes cleavage by a 2',5' branching reaction, leaving the 3' product with a 3-nt lariat cap that functionally substitutes for a conventional mRNA cap in the downstream pre-mRNA encoding a homing endonuclease. We describe the crystal structures of the precleavage and postcleavage LC ribozymes, which suggest that structural features inherited from group I ribozymes have undergone speciation due to profound changes in molecular selection pressure, ultimately giving rise to an original branching ribozyme family. The structures elucidate the role of key elements that regulate the activity of the LC ribozyme by conformational switching and suggest a mechanism by which the signal for branching is transmitted to the catalytic core. The structures also show how conserved interactions twist residues, forming the lariat to join chemical groups involved in branching.
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38
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Fica SM, Mefford MA, Piccirilli JA, Staley JP. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat Struct Mol Biol 2014; 21:464-471. [PMID: 24747940 PMCID: PMC4257784 DOI: 10.1038/nsmb.2815] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/27/2014] [Indexed: 01/04/2023]
Abstract
To catalyze pre-mRNA splicing, U6 small nuclear RNA positions two metals that interact directly with the scissile phosphates. U6 metal ligands correspond stereospecifically to metal ligands within the catalytic domain V of a group II self-splicing intron. Domain V ligands are organized by base-triple interactions, which also juxtapose the 3' splice site with the catalytic metals. However, in the spliceosome, the mechanism for organizing catalytic metals and recruiting the substrate has remained unclear. Here we show by genetics, cross-linking and biochemistry in yeast that analogous triples form in U6 and promote catalytic-metal binding and both chemical steps of splicing. Because the triples include an element that defines the 5' splice site, they also provide a mechanism for juxtaposing the pre-mRNA substrate with the catalytic metals. Our data indicate that U6 adopts a group II intron-like tertiary conformation to catalyze splicing.
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Affiliation(s)
- Sebastian M Fica
- Graduate Program in Cell and Molecular Biology, The University of Chicago, Chicago IL.,Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago IL
| | - Melissa A Mefford
- Committee on Genetics Genomics and Systems Biology, The University of Chicago, Chicago, IL
| | - Joseph A Piccirilli
- Department of Chemistry, The University of Chicago, Chicago IL.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago IL
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39
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Mozaffari-Jovin S, Wandersleben T, Santos KF, Will CL, Lührmann R, Wahl MC. Novel regulatory principles of the spliceosomal Brr2 RNA helicase and links to retinal disease in humans. RNA Biol 2014; 11:298-312. [PMID: 24643059 DOI: 10.4161/rna.28353] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
For each round of pre-mRNA splicing, a spliceosome is assembled anew on its substrate. RNA-protein remodeling events required for spliceosome assembly, splicing catalysis, and spliceosome disassembly are driven and controlled by a conserved group of ATPases/RNA helicases. The activities of most of these enzymes are timed by their recruitment to the spliceosome. The Brr2 enzyme, however, which mediates spliceosome catalytic activation, is a stable subunit of the spliceosome, and thus, requires special regulation. Recent structural and functional studies have revealed diverse mechanisms whereby an RNaseH-like and a Jab1/MPN-like domain of the Prp8 protein regulate Brr2 activity during splicing both positively and negatively. Reversible Brr2 inhibition might in part be achieved via an intrinsically unstructured element of the Prp8 Jab1/MPN domain, a concept widespread in biological systems. Mutations leading to changes in the Prp8 Jab1/MPN domain, which are linked to a severe form of retinitis pigmentosa, disrupt Jab1/MPN-mediated regulation of Brr2.
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Affiliation(s)
- Sina Mozaffari-Jovin
- Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Göttingen, Germany
| | - Traudy Wandersleben
- Laboratory of Structural Biochemistry; Freie Universität Berlin; Takustr. 6; Berlin, Germany
| | - Karine F Santos
- Laboratory of Structural Biochemistry; Freie Universität Berlin; Takustr. 6; Berlin, Germany
| | - Cindy L Will
- Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Göttingen, Germany
| | - Reinhard Lührmann
- Dept. of Cellular Biochemistry; Max Planck Institute for Biophysical Chemistry; Am Fassberg 11; Göttingen, Germany
| | - Markus C Wahl
- Laboratory of Structural Biochemistry; Freie Universität Berlin; Takustr. 6; Berlin, Germany
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40
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Wlodaver AM, Staley JP. The DExD/H-box ATPase Prp2p destabilizes and proofreads the catalytic RNA core of the spliceosome. RNA (NEW YORK, N.Y.) 2014; 20:282-94. [PMID: 24442613 PMCID: PMC3923124 DOI: 10.1261/rna.042598.113] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 10/30/2013] [Indexed: 05/25/2023]
Abstract
After undergoing massive RNA and protein rearrangements during assembly, the spliceosome undergoes a final, more subtle, ATP-dependent rearrangement that is essential for catalysis. This rearrangement requires the DEAH-box protein Prp2p, an RNA-dependent ATPase. Prp2p has been implicated in destabilizing interactions between the spliceosome and the protein complexes SF3 and RES, but a role for Prp2p in destabilizing RNA-RNA interactions has not been explored. Using directed molecular genetics in budding yeast, we have found that a cold-sensitive prp2 mutation is suppressed not only by mutations in SF3 and RES components but also by a range of mutations that disrupt the spliceosomal catalytic core element U2/U6 helix I, which is implicated in juxtaposing the 5' splice site and branch site and in positioning metal ions for catalysis within the context of a putative catalytic triplex; indeed, mutations in this putative catalytic triplex also suppressed a prp2 mutation. Remarkably, we also found that prp2 mutations rescue lethal mutations in U2/U6 helix I. These data provide evidence that RNA elements that comprise the catalytic core are already formed at the Prp2p stage and that Prp2p destabilizes these elements, directly or indirectly, both to proofread spliceosome activation and to promote reconfiguration of the spliceosome to a fully competent, catalytic conformation.
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Chen W, Shulha HP, Ashar-Patel A, Yan J, Green KM, Query CC, Rhind N, Weng Z, Moore MJ. Endogenous U2·U5·U6 snRNA complexes in S. pombe are intron lariat spliceosomes. RNA (NEW YORK, N.Y.) 2014; 20:308-20. [PMID: 24442611 PMCID: PMC3923126 DOI: 10.1261/rna.040980.113] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Excision of introns from pre-mRNAs is mediated by the spliceosome, a multi-megadalton complex consisting of U1, U2, U4/U6, and U5 snRNPs plus scores of associated proteins. Spliceosome assembly and disassembly are highly dynamic processes involving multiple stable intermediates. In this study, we utilized a split TAP-tag approach for large-scale purification of an abundant endogenous U2·U5·U6 complex from Schizosaccharomyces pombe. RNAseq revealed this complex to largely contain excised introns, indicating that it is primarily ILS (intron lariat spliceosome) complexes. These endogenous ILS complexes are remarkably resistant to both high-salt and nuclease digestion. Mass spectrometry analysis identified 68, 45, and 43 proteins in low-salt-, high-salt-, and micrococcal nuclease-treated preps, respectively. The protein content of a S. pombe ILS complex strongly resembles that previously reported for human spliced product (P) and Saccharomyces cerevisiae ILS complexes assembled on single pre-mRNAs in vitro. However, the ATP-dependent RNA helicase Brr2 was either substoichiometric in low-salt preps or completely absent from high-salt and MNase preps. Because Brr2 facilitates spliceosome disassembly, its relative absence may explain why the ILS complex accumulates logarithmically growing cultures and the inability of S. pombe extracts to support in vitro splicing.
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Affiliation(s)
- Weijun Chen
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Hennady P. Shulha
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Ami Ashar-Patel
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Jing Yan
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Karin M. Green
- UMMS Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | | | - Nick Rhind
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Zhiping Weng
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Melissa J. Moore
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
- Corresponding authorE-mail
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42
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Abstract
The spliceosome, an assembly of snRNAs and proteins, catalyzes the removal of introns from premessenger RNAs. A new study identifies specific phosphates in the U2-U6 snRNA complex that position two catalytic metals. Remarkably, these correspond precisely to metal-binding phosphates in a homologous structure of Group II self-splicing introns, long proposed to be the ribozyme progenitor of spliceosome.
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Affiliation(s)
- Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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43
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Chen W, Moore MJ. The spliceosome: disorder and dynamics defined. Curr Opin Struct Biol 2014; 24:141-9. [PMID: 24530854 DOI: 10.1016/j.sbi.2014.01.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/07/2014] [Accepted: 01/14/2014] [Indexed: 01/02/2023]
Abstract
Among the many macromolecular machines involved in eukaryotic gene expression, the spliceosome remains one of the most challenging for structural biologists. Defining features of this highly complex apparatus are its excessive number of individual parts, many of which have been evolutionarily selected for regions of structural disorder, and the remarkable compositional and conformation dynamics it must undertake to complete each round of splicing. Here we review recent advances in our understanding of spliceosome structural dynamics stemming from bioinformatics, deep sequencing, high throughput methods for determining protein-protein, protein-RNA and RNA-RNA interaction dynamics, single molecule microscopy and more traditional structural analyses. Together, these tools are rapidly changing our structural appreciation of this remarkably dynamic machine.
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Affiliation(s)
- Weijun Chen
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, RNA and Neuro Therapeutics Institutes, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Melissa J Moore
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, RNA and Neuro Therapeutics Institutes, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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44
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Galej WP, Nguyen THD, Newman AJ, Nagai K. Structural studies of the spliceosome: zooming into the heart of the machine. Curr Opin Struct Biol 2014; 25:57-66. [PMID: 24480332 PMCID: PMC4045393 DOI: 10.1016/j.sbi.2013.12.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/09/2013] [Accepted: 12/11/2013] [Indexed: 11/30/2022]
Abstract
Spliceosomes are large, dynamic ribonucleoprotein complexes that catalyse the removal of introns from messenger RNA precursors via a two-step splicing reaction. The recent crystal structure of Prp8 has revealed Reverse Transcriptase-like, Linker and Endonuclease-like domains. The intron branch-point cross-link with the Linker domain of Prp8 in active spliceosomes and together with suppressors of 5' and 3' splice site mutations this unambiguously locates the active site cavity. Structural and mechanistic similarities with group II self-splicing introns have encouraged the notion that the spliceosome is at heart a ribozyme, and recently the ligands for two catalytic magnesium ions were identified within U6 snRNA. They position catalytic divalent metal ions in the same way as Domain V of group II intron RNA, suggesting that the spliceosome and group II intron use the same catalytic mechanisms.
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Affiliation(s)
- Wojciech P Galej
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
| | - Thi Hoang Duong Nguyen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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45
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Fica SM, Tuttle N, Novak T, Li NS, Lu J, Koodathingal P, Dai Q, Staley JP, Piccirilli JA. RNA catalyses nuclear pre-mRNA splicing. Nature 2013; 503:229-34. [PMID: 24196718 PMCID: PMC4666680 DOI: 10.1038/nature12734] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/03/2013] [Indexed: 12/24/2022]
Abstract
In nuclear pre-messenger RNA splicing, introns are excised by the spliceosome, a multi-megadalton machine composed of both proteins and small nuclear RNAs (snRNAs). Over thirty years ago, following the discovery of self-splicing group II intron RNAs, the snRNAs were hypothesized to catalyze splicing. However, no definitive evidence for a role of either RNA or protein in catalysis by the spliceosome has been reported to date. By using metal rescue strategies, here we show that the U6 snRNA catalyzes both splicing reactions by positioning divalent metals that stabilize the leaving groups during each reaction. Strikingly, all of the U6 catalytic metal ligands we identified correspond to the ligands observed to position catalytic, divalent metals in crystal structures of a group II intron RNA. These findings indicate that group II introns and the spliceosome share common catalytic mechanisms, and likely common evolutionary origins. Our results demonstrate that RNA mediates catalysis within the spliceosome.
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Affiliation(s)
- Sebastian M Fica
- 1] Graduate Program in Cell and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA [2] Department of Molecular Genetics and Cell Biology, Cummings Life Sciences Center, 920 East 58th Street, The University of Chicago, Chicago, Illinois 60637, USA [3]
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46
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Affiliation(s)
- Sophie Bonnal
- 1] Centre de Regulació Genòmica, Barcelona, Spain [2] Universitat Pompeu Fabra, Barcelona, Spain
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