51
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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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52
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Mayerle M, Guthrie C. Genetics and biochemistry remain essential in the structural era of the spliceosome. Methods 2017; 125:3-9. [PMID: 28132896 DOI: 10.1016/j.ymeth.2017.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/23/2017] [Indexed: 12/31/2022] Open
Abstract
The spliceosome is not a single macromolecular machine. Rather it is a collection of dynamic heterogeneous subcomplexes that rapidly interconvert throughout the course of a typical splicing cycle. Because of this, for many years the only high resolution structures of the spliceosome available were of smaller, isolated protein or RNA components. Consequently much of our current understanding of the spliceosome derives from biochemical and genetic techniques. Now with the publication of multiple, high resolution structures of the spliceosome, some question the relevance of traditional biochemical and genetic techniques to the splicing field. We argue such techniques are not only relevant, but vital for an in depth mechanistic understanding of pre-mRNA splicing.
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Affiliation(s)
- Megan Mayerle
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA.
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53
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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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54
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Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K. Structure of a spliceosome remodelled for exon ligation. Nature 2017; 542:377-380. [PMID: 28076345 PMCID: PMC5321579 DOI: 10.1038/nature21078] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022]
Abstract
The spliceosome excises introns from pre-mRNAs in two sequential transesterifications – branching and exon ligation1 – catalysed at a single catalytic metal site in U6 snRNA2,3. The recent structures of the spliceosomal C complex4,5 with the cleaved 5’-exon and lariat—3’-exon bound to the catalytic centre revealed that branching-specific factors such as Cwc25 lock the branch helix into position for nucleophilic attack of the branch adenosine at the 5’-splice site. Furthermore, the ATPase Prp16 is positioned to bind and translocate the intron downstream of the branch point to destabilize branching-specific factors and release the branch helix from the active site4. Here we present the 3.8Å cryo-EM structure of a Saccharomyces cerevisiae spliceosome stalled after Prp16-mediated remodelling but prior to exon ligation. While the U6 snRNA catalytic core remains firmly held in the active site cavity of Prp8 by proteins common to both steps, the branch helix has rotated by 75 degrees compared to complex C and is stabilized into a new position by Prp17, Cef1, and the reoriented Prp8 RNaseH domain. This rotation of the branch helix removes the branch adenosine from the catalytic core, creates a space for 3’-exon docking, and restructures the pairing of the 5’-splice site with the U6 snRNA ACAGAGA region. Slu7 and Prp18, which promote exon ligation, bind together to the Prp8 RNaseH domain. The ATPase Prp22, bound to Prp8 in place of Prp16, could interact with the 3’-exon, suggesting a possible basis for mRNA release after exon ligation6,7. Together with the C complex structure4, our new C* complex structure reveals the two major conformations of the spliceosome during the catalytic stages of splicing.
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Affiliation(s)
- Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wojciech P Galej
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Max E Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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55
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Martin WJ, Reiter NJ. Structural Roles of Noncoding RNAs in the Heart of Enzymatic Complexes. Biochemistry 2016; 56:3-13. [PMID: 27935277 DOI: 10.1021/acs.biochem.6b01106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Over billions of years of evolution, nature has embraced proteins as the major workhorse molecules of the cell. However, nearly every aspect of metabolism is dependent upon how structured RNAs interact with proteins, ligands, and other nucleic acids. Key processes, including telomere maintenance, RNA processing, and protein synthesis, require large RNAs that assemble into elaborate three-dimensional shapes. These RNAs can (i) act as flexible scaffolds for protein subunits, (ii) participate directly in substrate recognition, and (iii) serve as catalytic components. Here, we juxtapose the near atomic level interactions of three ribonucleoprotein complexes: ribonuclease P (involved in 5' pre-tRNA processing), the spliceosome (responsible for pre-mRNA splicing), and telomerase (an RNA-directed DNA polymerase that extends the ends of chromosomes). The focus of this perspective is profiling the structural and dynamic roles of RNAs at the core of these enzymes, highlighting how large RNAs contribute to molecular recognition and catalysis.
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Affiliation(s)
- William J Martin
- Department of Biochemistry, Vanderbilt University , Nashville, Tennessee 37232, United States
| | - Nicholas J Reiter
- Department of Biochemistry, Vanderbilt University , Nashville, Tennessee 37232, United States
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56
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Agrawal RK, Wang HW, Belfort M. Forks in the tracks: Group II introns, spliceosomes, telomeres and beyond. RNA Biol 2016; 13:1218-1222. [PMID: 27726484 DOI: 10.1080/15476286.2016.1244595] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Group II introns are large catalytic RNAs that form a ribonucleoprotein (RNP) complex by binding to an intron-encoded protein (IEP). The IEP, which facilitates both RNA splicing and intron mobility, has multiple activities including reverse transcriptase. Recent structures of a group II intron RNP complex and of IEPs from diverse bacteria fuel arguments that group II introns are ancestrally related to eukaryotic spliceosomes as well as to telomerase and viruses. Furthermore, recent structural studies of various functional states of the spliceosome allow us to draw parallels between the group II intron RNP and the spliceosome. Here we present an overview of these studies, with an emphasis on the structure of the IEPs in their isolated and RNA-bound states and on their evolutionary relatedness. In addition, we address the conundrum of the free, albeit truncated IEPs forming dimers, whereas the IEP bound to the intron ribozyme is a monomer in the mature RNP. Future studies needed to resolve some of the outstanding issues related to group II intron RNP function and dynamics are also discussed.
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Affiliation(s)
- Rajendra Kumar Agrawal
- a Laboratory of Cellular and Molecular Basis of Diseases, Division of Translational Medicine, Wadsworth Center , New York State Department of Health , Albany , NY , USA.,b Department of Biomedical Sciences, School of Public Health , University at Albany , Albany , NY , USA
| | - Hong-Wei Wang
- c Ministry of Education Key Laboratory of Protein Sciences , Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University , Beijing , China.,d Department of Molecular Biophysics and Biochemistry , Yale University , New Haven , CT , USA
| | - Marlene Belfort
- b Department of Biomedical Sciences, School of Public Health , University at Albany , Albany , NY , USA.,e Department of Biological Sciences and RNA Institute , University at Albany , Albany , NY , USA
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57
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Sun C, Rigo N, Fabrizio P, Kastner B, Lührmann R. A protein map of the yeast activated spliceosome as obtained by electron microscopy. RNA (NEW YORK, N.Y.) 2016; 22:1427-40. [PMID: 27368340 PMCID: PMC4986897 DOI: 10.1261/rna.057778.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 05/31/2016] [Indexed: 05/09/2023]
Abstract
We have elucidated the spatial arrangement of proteins and snRNP subunits within the purified spliceosomal B(act) complex from Saccharomyces cerevisiae, using negative-stain immunoelectron microscopy. The B(act) spliceosome exhibits a mushroom-like shape with a main body connected to a foot and a steep and a shallow slope. The U5 core components, including proteins Snu114 and Prp8, are located in the main body and foot, while Brr2 is on the shallow slope. U2 snRNP components and the RNA helicase Prp2 were predominantly located in the upper regions of both slopes. While several proteins of the "nineteen complex" are located on the steep slope, Prp19, Cef1, and the U6 snRNA-binding protein Cwc2 are on the main body. Our results also indicate that the catalytic core RNP of the spliceosome resides in its main body. We thus assign distinct domains of the B(act) complex to its snRNP and protein components, and we provide first structural insights into the remodeling events at the spliceosome during its transformation from the B to the B(act) complex.
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Affiliation(s)
- Chengfu Sun
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Norbert Rigo
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrizia Fabrizio
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Berthold Kastner
- 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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58
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Rauhut R, Fabrizio P, Dybkov O, Hartmuth K, Pena V, Chari A, Kumar V, Lee CT, Urlaub H, Kastner B, Stark H, Lührmann R. Molecular architecture of the Saccharomyces cerevisiae activated spliceosome. Science 2016; 353:1399-1405. [PMID: 27562955 DOI: 10.1126/science.aag1906] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/18/2016] [Indexed: 12/30/2022]
Abstract
The activated spliceosome (Bact) is in a catalytically inactive state and is remodeled into a catalytically active machine by the RNA helicase Prp2, but the mechanism is unclear. Here, we describe a 3D electron cryomicroscopy structure of the Saccharomyces cerevisiae Bact complex at 5.8-angstrom resolution. Our model reveals that in Bact, the catalytic U2/U6 RNA-Prp8 ribonucleoprotein core is already established, and the 5' splice site (ss) is oriented for step 1 catalysis but occluded by protein. The first-step nucleophile-the branchsite adenosine-is sequestered within the Hsh155 HEAT domain and is held 50 angstroms away from the 5'ss. Our structure suggests that Prp2 adenosine triphosphatase-mediated remodeling leads to conformational changes in Hsh155's HEAT domain that liberate the first-step reactants for catalysis.
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Affiliation(s)
- Reinhard Rauhut
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Patrizia Fabrizio
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Olexandr Dybkov
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Klaus Hartmuth
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Vladimir Pena
- Research Group Macromolecular Crystallography, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ashwin Chari
- 3D Electron Cryomicroscopy Group, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Vinay Kumar
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Chung-Tien Lee
- Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Robert-Koch-Straße 40, D-37075 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Robert-Koch-Straße 40, D-37075 Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
| | - Holger Stark
- 3D Electron Cryomicroscopy Group, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany. Department of 3D Electron Cryomicroscopy, Georg-August Universität, Göttingen, Justus von-Liebig-Weg 11, D-37077 Germany.
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute (MPI) for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
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59
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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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60
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Cryo-EM structure of the spliceosome immediately after branching. Nature 2016; 537:197-201. [PMID: 27459055 PMCID: PMC5156311 DOI: 10.1038/nature19316] [Citation(s) in RCA: 177] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/19/2016] [Indexed: 12/11/2022]
Abstract
Precursor mRNA (pre-mRNA) splicing proceeds by two consecutive transesterification reactions via a lariat-intron intermediate. Here we present the 3.8 Å cryo-electron microscopy structure of the spliceosome immediately after lariat formation. The 5'-splice site is cleaved but remains close to the catalytic Mg2+ site in the U2/U6 small nuclear RNA (snRNA) triplex, and the 5'-phosphate of the intron nucleotide G(+1) is linked to the branch adenosine 2'OH. The 5'-exon is held between the Prp8 amino-terminal and linker domains, and base-pairs with U5 snRNA loop 1. Non-Watson-Crick interactions between the branch helix and 5'-splice site dock the branch adenosine into the active site, while intron nucleotides +3 to +6 base-pair with the U6 snRNA ACAGAGA sequence. Isy1 and the step-one factors Yju2 and Cwc25 stabilize docking of the branch helix. The intron downstream of the branch site emerges between the Prp8 reverse transcriptase and linker domains and extends towards the Prp16 helicase, suggesting a plausible mechanism of remodelling before exon ligation.
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61
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Tremblay N, Baril M, Chatel-Chaix L, Es-Saad S, Park AY, Koenekoop RK, Lamarre D. Spliceosome SNRNP200 Promotes Viral RNA Sensing and IRF3 Activation of Antiviral Response. PLoS Pathog 2016; 12:e1005772. [PMID: 27454487 PMCID: PMC4959778 DOI: 10.1371/journal.ppat.1005772] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/27/2016] [Indexed: 12/18/2022] Open
Abstract
Spliceosomal SNRNP200 is a Ski2-like RNA helicase that is associated with retinitis pigmentosa 33 (RP33). Here we found that SNRNP200 promotes viral RNA sensing and IRF3 activation through the ability of its amino-terminal Sec63 domain (Sec63-1) to bind RNA and to interact with TBK1. We show that SNRNP200 relocalizes into TBK1-containing cytoplasmic structures upon infection, in contrast to the RP33-associated S1087L mutant, which is also unable to rescue antiviral response of SNRNP200 knockdown cells. This functional rescue correlates with the Sec63-1-mediated binding of viral RNA. The hindered IFN-β production of knockdown cells was further confirmed in peripheral blood cells of RP33 patients bearing missense mutation in SNRNP200 upon infection with Sendai virus (SeV). This work identifies a novel immunoregulatory role of the spliceosomal SNRNP200 helicase as an RNA sensor and TBK1 adaptor for the activation of IRF3-mediated antiviral innate response. The innate immune system is the first line of defense against pathogens and relies on the recognition of molecular structures specific to pathogens by sensor receptors. These receptors activate a signaling cascade and induce a protective cellular innate immune response. In this study, we provide evidence for a role of the spliceosomal SNRNP200 RNA helicase in promoting antiviral response that is clearly distinguishable of the one in pre-mRNA splicing. The depletion of SNRNP200 in human cells resulted in a reduced interferon-β (IFNB1) production and increased susceptibility to viral infection. We showed that SNRNP200 positively regulates activation of the key transcription factor IRF3 via interaction with TANK kinase 1 (TBK1). Upon infection, SNRNP200 binds viral RNA and relocalizes into TBK1-containing cytoplasmic structures to promote IRF3 activation and IFNB1 production. Of clinical relevance, we observed a significantly hindered antiviral response of PBMCs from patients carrying a dominant SNRNP200 mutation associated with retina pigmentosa type 33 (RP33), an inherited degenerative eye disease. We showed that the RP33-associated S1087L SNRNP200 mutant has lost the ability to bind RNA and that its expression fails to rescue antiviral response in SNRNP200 silenced cells. Our study provides new insights into a role within the antiviral response for spliceosome SNRNP200 helicase as an RNA sensor and TBK1 adaptor in IRF3 signaling.
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Affiliation(s)
- Nicolas Tremblay
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Martin Baril
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
| | | | - Salwa Es-Saad
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
| | - Alex Young Park
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Robert K. Koenekoop
- Departments of Pediatric Surgery, Human Genetics and Ophthalmology, McGill University, Montréal, Canada
| | - Daniel Lamarre
- Centre de Recherche du CHUM (CRCHUM), Montréal, Québec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Canada
- * E-mail:
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62
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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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63
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Taylor AI, Beuron F, Peak-Chew SY, Morris EP, Herdewijn P, Holliger P. Nanostructures from Synthetic Genetic Polymers. Chembiochem 2016; 17:1107-10. [PMID: 26992063 PMCID: PMC4973672 DOI: 10.1002/cbic.201600136] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Indexed: 12/22/2022]
Abstract
Nanoscale objects of increasing complexity can be constructed from DNA or RNA. However, the scope of potential applications could be enhanced by expanding beyond the moderate chemical diversity of natural nucleic acids. Here, we explore the construction of nano-objects made entirely from alternative building blocks: synthetic genetic polymers not found in nature, also called xeno nucleic acids (XNAs). Specifically, we describe assembly of 70 kDa tetrahedra elaborated in four different XNA chemistries (2'-fluro-2'-deoxy-ribofuranose nucleic acid (2'F-RNA), 2'-fluoroarabino nucleic acids (FANA), hexitol nucleic acids (HNA), and cyclohexene nucleic acids (CeNA)), as well as mixed designs, and a ∼600 kDa all-FANA octahedron, visualised by electron microscopy. Our results extend the chemical scope for programmable nanostructure assembly, with implications for the design of nano-objects and materials with an expanded range of structural and physicochemical properties, including enhanced biostability.
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Affiliation(s)
- Alexander I Taylor
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Department of Biology/Centre for Applied Synthetic Biology, Concordia University, 7141 Rue Sherbrooke, Montreal, H4B 1R6, Canada.
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories), 237 Fulham Road, London, SW3 6JB, UK
| | - Sew-Yeu Peak-Chew
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, Chester Beatty Laboratories), 237 Fulham Road, London, SW3 6JB, UK
| | - Piet Herdewijn
- Rega Institute, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
- Institute of Systems and Synthetic Biology, Université Evry, 5 rue Henri Desbrueres, 91030, Evry Cedex, France
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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64
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Zhao C, Pyle AM. Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution. Nat Struct Mol Biol 2016; 23:558-65. [PMID: 27136328 PMCID: PMC4899126 DOI: 10.1038/nsmb.3224] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/06/2016] [Indexed: 12/17/2022]
Abstract
Group II introns are self-splicing ribozymes that are essential in many organisms, and they have been hypothesized to share a common evolutionary ancestor with the spliceosome. Although structural similarity of RNA components supports this connection, it is of interest to determine whether associated protein factors also share an evolutionary heritage. Here we present the crystal structures of reverse transcriptase (RT) domains from two group II intron-encoded proteins (maturases) from Roseburia intestinalis and Eubacterium rectale, obtained at 1.2-Å and 2.1-Å resolution, respectively. These domains are more similar in architecture to the spliceosomal Prp8 RT-like domain than to any other RTs, and they share substantial similarity with flaviviral RNA polymerases. The RT domain itself is sufficient for binding intron RNA with high affinity and specificity, and it is contained within an active RT enzyme. These studies provide a foundation for understanding structure-function relationships within group II intron-maturase complexes.
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Affiliation(s)
- Chen Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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65
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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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66
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Cornilescu G, Didychuk AL, Rodgers ML, Michael LA, Burke JE, Montemayor EJ, Hoskins AA, Butcher SE. Structural Analysis of Multi-Helical RNAs by NMR-SAXS/WAXS: Application to the U4/U6 di-snRNA. J Mol Biol 2016; 428:777-789. [PMID: 26655855 PMCID: PMC4790120 DOI: 10.1016/j.jmb.2015.11.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/25/2015] [Accepted: 11/30/2015] [Indexed: 01/17/2023]
Abstract
NMR and SAXS (small-angle X-ray scattering)/WAXS (wide-angle X-ray scattering) are highly complementary approaches for the analysis of RNA structure in solution. Here we describe an efficient NMR-SAXS/WAXS approach for structural investigation of multi-helical RNAs. We illustrate this approach by determining the overall fold of a 92-nt 3-helix junction from the U4/U6 di-snRNA. The U4/U6 di-snRNA is conserved in eukaryotes and is part of the U4/U6.U5 tri-snRNP, a large ribonucleoprotein complex that comprises a major subunit of the assembled spliceosome. Helical orientations can be determined by X-ray scattering data alone, but the addition of NMR RDC (residual dipolar coupling) restraints improves the structure models. RDCs were measured in two different external alignment media and also by magnetic susceptibility anisotropy. The resulting alignment tensors are collinear, which is a previously noted problem for nucleic acids. Including WAXS data in the calculations produces models with significantly better fits to the scattering data. In solution, the U4/U6 di-snRNA forms a 3-helix junction with a planar Y-shaped structure and has no detectable tertiary interactions. Single-molecule Förster resonance energy transfer data support the observed topology. A comparison with the recently determined cryo-electron microscopy structure of the U4/U6.U5 tri-snRNP illustrates how proteins scaffold the RNA and dramatically alter the geometry of the U4/U6 3-helix junction.
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Affiliation(s)
- Gabriel Cornilescu
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Margaret L Rodgers
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Lauren A Michael
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Jordan E Burke
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric J Montemayor
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
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67
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Agafonov DE, Kastner B, Dybkov O, Hofele RV, Liu WT, Urlaub H, Lührmann R, Stark H. Molecular architecture of the human U4/U6.U5 tri-snRNP. Science 2016; 351:1416-20. [PMID: 26912367 DOI: 10.1126/science.aad2085] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/04/2016] [Indexed: 12/24/2022]
Abstract
The U4/U6.U5 triple small nuclear ribonucleoprotein (tri-snRNP) is a major spliceosome building block. We obtained a three-dimensional structure of the 1.8-megadalton human tri-snRNP at a resolution of 7 angstroms using single-particle cryo-electron microscopy (cryo-EM). We fit all known high-resolution structures of tri-snRNP components into the EM density map and validated them by protein cross-linking. Our model reveals how the spatial organization of Brr2 RNA helicase prevents premature U4/U6 RNA unwinding in isolated human tri-snRNPs and how the ubiquitin C-terminal hydrolase-like protein Sad1 likely tethers the helicase Brr2 to its preactivation position. Comparison of our model with cryo-EM three-dimensional structures of the Saccharomyces cerevisiae tri-snRNP and Schizosaccharomyces pombe spliceosome indicates that Brr2 undergoes a marked conformational change during spliceosome activation, and that the scaffolding protein Prp8 is also rearranged to accommodate the spliceosome's catalytic RNA network.
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Affiliation(s)
- Dmitry E Agafonov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Olexandr Dybkov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Romina V Hofele
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany. Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Wen-Ti Liu
- Department of 3D Electron Cryomicroscopy, Georg-August Universität Göttingen, D-37077 Göttingen, Germany. Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany. Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany.
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.
| | - Holger Stark
- Department of 3D Electron Cryomicroscopy, Georg-August Universität Göttingen, D-37077 Göttingen, Germany. Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.
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68
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McNeil BA, Semper C, Zimmerly S. Group II introns: versatile ribozymes and retroelements. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:341-55. [PMID: 26876278 DOI: 10.1002/wrna.1339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/10/2015] [Accepted: 12/22/2015] [Indexed: 01/10/2023]
Abstract
Group II introns are catalytic RNAs (ribozymes) and retroelements found in the genomes of bacteria, archaebacteria, and organelles of some eukaryotes. The prototypical retroelement form consists of a structurally conserved RNA and a multidomain reverse transcriptase protein, which interact with each other to mediate splicing and mobility reactions. A wealth of biochemical, cross-linking, and X-ray crystal structure studies have helped to reveal how the two components cooperate to carry out the splicing and mobility reactions. In addition to the standard retroelement form, group II introns have evolved into derivative forms by either losing specific splicing or mobility characteristics, or becoming functionally specialized. Of particular interest are the eukaryotic derivatives-the spliceosome, spliceosomal introns, and non-LTR retroelements-which together make up approximately half of the human genome. On a practical level, the properties of group II introns have been exploited to develop group II intron-based biotechnological tools. WIREs RNA 2016, 7:341-355. doi: 10.1002/wrna.1339 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Bonnie A McNeil
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Cameron Semper
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Steven Zimmerly
- Department of Biological Sciences, University of Calgary, Calgary, Canada
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69
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Nguyen THD, Galej WP, Bai XC, Oubridge C, Newman AJ, Scheres SHW, Nagai K. Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 Å resolution. Nature 2016; 530:298-302. [PMID: 26829225 PMCID: PMC4762201 DOI: 10.1038/nature16940] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
Abstract
U4/U6.U5 tri-snRNP represents a substantial part of the spliceosome before activation. A cryoEM structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP at 3.7Å resolution led to an essentially complete atomic model comprising 30 proteins plus U4/U6 and U5 snRNAs. The structure reveals striking interweaving interactions of the protein and RNA components including extended polypeptides penetrating into subunit interfaces. The invariant ACAGAGA sequence of U6 snRNA, which base-pairs with the 5′-splice site during catalytic activation, forms a hairpin stabilised by Dib1 and Prp8 while the adjacent nucleotides interact with the exon binding loop 1 of U5 snRNA. Snu114 harbours GTP but its putative catalytic histidine is held away from the γ-phosphate by hydrogen bonding to a tyrosine in Prp8’s N-terminal domain. Mutation of this histidine to alanine has no detectable effect on yeast growth. The structure provides important new insights into the spliceosome activation process leading to the formation of the catalytic centre.
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Affiliation(s)
| | - Wojciech P Galej
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Xiao-Chen Bai
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
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70
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CryoEM structures of two spliceosomal complexes: starter and dessert at the spliceosome feast. Curr Opin Struct Biol 2016; 36:48-57. [PMID: 26803803 PMCID: PMC4830896 DOI: 10.1016/j.sbi.2015.12.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/21/2015] [Indexed: 12/31/2022]
Abstract
Recent advances in cryoEM are revolutionizing our understanding of how molecular machines function. The structure of Saccharomyces cerevisiae U4/U6.U5 tri-snRNP has been revealed. The structure of Schizosaccharomyces pombe U2.U6.U5 spliceosomal complex has been revealed. These structures greatly advanced our understanding of the mechanism of pre-mRNA splicing.
The spliceosome is formed on pre-mRNA substrates from five small nuclear ribonucleoprotein particles (U1, U2, U4/U6 and U5 snRNPs), and numerous non-snRNP factors. Saccharomyces cerevisiae U4/U6.U5 tri-snRNP comprises U5 snRNA, U4/U6 snRNA duplex and approximately 30 proteins and represents a substantial part of the spliceosome before activation. Schizosaccharomyces pombe U2.U6.U5 spliceosomal complex is a post-catalytic intron lariat spliceosome containing U2 and U5 snRNPs, NTC (nineteen complex), NTC-related proteins (NTR), U6 snRNA, and an RNA intron lariat. Two recent papers describe near-complete atomic structures of these complexes based on cryoEM single-particle analysis. The U4/U6.U5 tri-snRNP structure provides crucial insight into the activation mechanism of the spliceosome. The U2.U6.U5 complex reveals the striking architecture of NTC and NTR and important features of the group II intron-like catalytic RNA core remaining after spliced mRNA is released. These two structures greatly advance our understanding of the mechanism of pre-mRNA splicing.
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71
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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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72
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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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73
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Hardin JW, Warnasooriya C, Kondo Y, Nagai K, Rueda D. Assembly and dynamics of the U4/U6 di-snRNP by single-molecule FRET. Nucleic Acids Res 2015; 43:10963-74. [PMID: 26503251 PMCID: PMC4678811 DOI: 10.1093/nar/gkv1011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/24/2015] [Indexed: 11/13/2022] Open
Abstract
In large ribonucleoprotein machines, such as ribosomes and spliceosomes, RNA functions as an assembly scaffold as well as a critical catalytic component. Protein binding to the RNA scaffold can induce structural changes, which in turn modulate subsequent binding of other components. The spliceosomal U4/U6 di-snRNP contains extensively base paired U4 and U6 snRNAs, Snu13, Prp31, Prp3 and Prp4, seven Sm and seven LSm proteins. We have studied successive binding of all protein components to the snRNA duplex during di-snRNP assembly by electrophoretic mobility shift assay and accompanying conformational changes in the U4/U6 RNA 3-way junction by single-molecule FRET. Stems I and II of the duplex were found to co-axially stack in free RNA and function as a rigid scaffold during the entire assembly, but the U4 snRNA 5' stem-loop adopts alternative orientations each stabilized by Prp31 and Prp3/4 binding accounting for altered Prp3/4 binding affinities in presence of Prp31.
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Affiliation(s)
- John W Hardin
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Chandani Warnasooriya
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Yasushi Kondo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Rueda
- Department of Medicine, Section of Virology, Imperial College London, London W12 0NN, UK Single Molecule Imaging Group, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
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74
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Hudson AJ, Stark MR, Fast NM, Russell AG, Rader SD. Splicing diversity revealed by reduced spliceosomes in C. merolae and other organisms. RNA Biol 2015; 12:1-8. [PMID: 26400738 PMCID: PMC4829280 DOI: 10.1080/15476286.2015.1094602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing has been considered one of the hallmarks of eukaryotes, yet its diversity is astonishing: the number of substrate introns for splicing ranges from hundreds of thousands in humans to a mere handful in certain parasites. The catalytic machinery that carries out splicing, the spliceosome, is similarly diverse, with over 300 associated proteins in humans to a few tens in other organisms. In this Point of View, we discuss recent work characterizing the reduced spliceosome of the acidophilic red alga Cyanidioschyzon merolae, which further highlights the diversity of splicing in that it does not possess the U1 snRNP that is characteristically responsible for 5′ splice site recognition. Comparisons to other organisms with reduced spliceosomes, such as microsporidia, trypanosomes, and Giardia, help to identify the most highly conserved splicing factors, pointing to the essential core of this complex machine. These observations argue for increased exploration of important biochemical processes through study of a wider ranger of organisms.
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Affiliation(s)
- Andrew J Hudson
- a Alberta RNA Research and Training Institute and Department of Biological Sciences ; University of Lethbridge ; Lethbridge , Alberta , Canada
| | - Martha R Stark
- b Department of Chemistry ; University of Northern British Columbia ; Prince George , British Columbia , Canada
| | - Naomi M Fast
- c Biodiversity Research Center and Department of Botany ; University of British Columbia ; Vancouver , British Columbia , Canada
| | - Anthony G Russell
- a Alberta RNA Research and Training Institute and Department of Biological Sciences ; University of Lethbridge ; Lethbridge , Alberta , Canada
| | - Stephen D Rader
- b Department of Chemistry ; University of Northern British Columbia ; Prince George , British Columbia , Canada
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75
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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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76
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Truong DM, Hewitt FC, Hanson JH, Cui X, Lambowitz AM. Retrohoming of a Mobile Group II Intron in Human Cells Suggests How Eukaryotes Limit Group II Intron Proliferation. PLoS Genet 2015; 11:e1005422. [PMID: 26241656 PMCID: PMC4524724 DOI: 10.1371/journal.pgen.1005422] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/05/2015] [Indexed: 12/22/2022] Open
Abstract
Mobile bacterial group II introns are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of an autocatalytic intron RNA (a “ribozyme”) and an intron-encoded reverse transcriptase, which function together to promote intron integration into new DNA sites by a mechanism termed “retrohoming”. Although mobile group II introns splice and retrohome efficiently in bacteria, all examined thus far function inefficiently in eukaryotes, where their ribozyme activity is limited by low Mg2+ concentrations, and intron-containing transcripts are subject to nonsense-mediated decay (NMD) and translational repression. Here, by using RNA polymerase II to express a humanized group II intron reverse transcriptase and T7 RNA polymerase to express intron transcripts resistant to NMD, we find that simply supplementing culture medium with Mg2+ induces the Lactococcus lactis Ll.LtrB intron to retrohome into plasmid and chromosomal sites, the latter at frequencies up to ~0.1%, in viable HEK-293 cells. Surprisingly, under these conditions, the Ll.LtrB intron reverse transcriptase is required for retrohoming but not for RNA splicing as in bacteria. By using a genetic assay for in vivo selections combined with deep sequencing, we identified intron RNA mutations that enhance retrohoming in human cells, but <4-fold and not without added Mg2+. Further, the selected mutations lie outside the ribozyme catalytic core, which appears not readily modified to function efficiently at low Mg2+ concentrations. Our results reveal differences between group II intron retrohoming in human cells and bacteria and suggest constraints on critical nucleotide residues of the ribozyme core that limit how much group II intron retrohoming in eukaryotes can be enhanced. These findings have implications for group II intron use for gene targeting in eukaryotes and suggest how differences in intracellular Mg2+ concentrations between bacteria and eukarya may have impacted the evolution of introns and gene expression mechanisms. Mobile group II introns are bacterial retrotransposons that are evolutionary ancestors of spliceosomal introns and retroelements in eukaryotes. They consist of an autocatalytic intron RNA (a ribozyme) and an intron-encoded reverse transcriptase, which together promote intron mobility to new DNA sites by a mechanism called retrohoming. Although found in bacteria, archaea and eukaryotic organelles, group II introns are absent from eukaryotic nuclear genomes, where host defenses impede their expression and lower intracellular Mg2+ concentrations limit their ribozyme activity. Here, we developed a mobile group II intron expression system that bypasses expression barriers and show that simply adding Mg2+ to culture medium enables group II intron retrohoming into plasmid and chromosomal target sites in human cells at appreciable frequencies. Genetic selections and deep sequencing identified intron RNA mutations that moderately enhance retrohoming in human cells, but not without added Mg2+. Thus, low Mg2+ concentrations in human cells are a natural barrier to efficient retrohoming that is not readily overcome by mutational variation and selection. Our results have implications for group II intron use for gene targeting in higher organisms and highlight the impact of different intracellular environments on intron evolution and gene expression mechanisms in bacteria and eukarya.
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Affiliation(s)
- David M. Truong
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - F. Curtis Hewitt
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Joseph H. Hanson
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Xiaoxia Cui
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Alan M. Lambowitz
- Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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77
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Nguyen THD, Galej WP, Bai XC, Savva CG, Newman AJ, Scheres SHW, Nagai K. The architecture of the spliceosomal U4/U6.U5 tri-snRNP. Nature 2015; 523:47-52. [PMID: 26106855 PMCID: PMC4536768 DOI: 10.1038/nature14548] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/06/2015] [Indexed: 12/12/2022]
Abstract
U4/U6.U5 tri-snRNP is a 1.5-megadalton pre-assembled spliceosomal complex comprising U5 small nuclear RNA (snRNA), extensively base-paired U4/U6 snRNAs and more than 30 proteins, including the key components Prp8, Brr2 and Snu114. The tri-snRNP combines with a precursor messenger RNA substrate bound to U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), and transforms into a catalytically active spliceosome after extensive compositional and conformational changes triggered by unwinding of the U4 and U6 (U4/U6) snRNAs. Here we use cryo-electron microscopy single-particle reconstruction of Saccharomyces cerevisiae tri-snRNP at 5.9 Å resolution to reveal the essentially complete organization of its RNA and protein components. The single-stranded region of U4 snRNA between its 3' stem-loop and the U4/U6 snRNA stem I is loaded into the Brr2 helicase active site ready for unwinding. Snu114 and the amino-terminal domain of Prp8 position U5 snRNA to insert its loop I, which aligns the exons for splicing, into the Prp8 active site cavity. The structure provides crucial insights into the activation process and the active site of the spliceosome.
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Affiliation(s)
| | - Wojciech P Galej
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Xiao-chen Bai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christos G Savva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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78
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Burke JE, Butcher SE, Brow DA. Spliceosome assembly in the absence of stable U4/U6 RNA pairing. RNA (NEW YORK, N.Y.) 2015; 21:923-34. [PMID: 25762536 PMCID: PMC4408799 DOI: 10.1261/rna.048421.114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/10/2015] [Indexed: 05/08/2023]
Abstract
The cycle of spliceosome assembly, intron excision, and spliceosome disassembly involves large-scale structural rearrangements of U6 snRNA that are functionally important. U6 enters the splicing pathway bound to the Prp24 protein, which chaperones annealing of U6 to U4 RNA to form a U4/U6 di-snRNP. During catalytic activation of the assembled spliceosome, U4 snRNP is released and U6 is paired to U2 snRNA. Here we show that point mutations in U4 and U6 that decrease U4/U6 base-pairing in vivo are lethal in combination. However, this synthetic phenotype is rescued by a mutation in U6 that alters a U6-Prp24 contact and stabilizes U2/U6. Remarkably, the resulting viable triple mutant strain lacks detectable U4/U6 base-pairing and U4/U6 di-snRNP. Instead, this strain accumulates free U4 snRNP, protein-free U6 RNA, and a novel complex containing U2/U6 di-snRNP. Further mutational analysis indicates that disruption of the U6-Prp24 interaction rather than stabilization of U2/U6 renders stable U4/U6 di-snRNP assembly nonessential. We propose that an essential function of U4/U6 pairing is to displace Prp24 from U6 RNA, and thus a destabilized U6-Prp24 complex renders stable U4/U6 pairing nonessential.
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MESH Headings
- Base Pairing
- Base Sequence
- Epistasis, Genetic
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Mutation
- Nucleic Acid Conformation
- Protein Multimerization
- RNA Splicing/genetics
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Spliceosomes/metabolism
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Affiliation(s)
- Jordan E Burke
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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79
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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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80
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Abstract
Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA-protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA-RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions.
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Affiliation(s)
- Yeon Lee
- Center for RNA Systems Biology; Division of Biochemistry, Biophysics, and Structural Biology; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204;
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81
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Lee Y, Rio DC. Mechanisms and Regulation of Alternative Pre-mRNA Splicing. Annu Rev Biochem 2015. [PMID: 25784052 DOI: 10.1146/annurev-biochem-060614-034316.mechanisms] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA-protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA-RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions.
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Affiliation(s)
- Yeon Lee
- Center for RNA Systems Biology; Division of Biochemistry, Biophysics, and Structural Biology; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204;
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82
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Abstract
A diverse population of large RNA molecules controls every aspect of cellular function, and yet we know very little about their molecular structures. However, robust technologies developed for visualizing ribozymes and riboswitches, together with new approaches for mapping RNA inside cells, provide the foundation for visualizing the structures of long noncoding RNAs, mRNAs, and viral RNAs, thereby facilitating new mechanistic insights.
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Affiliation(s)
- Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology and Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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83
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Batey RT. Structural biology: Lariat lessons. Nature 2014; 514:173-4. [PMID: 25252981 DOI: 10.1038/nature13754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, USA
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84
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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: 99] [Impact Index Per Article: 9.9] [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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85
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Collier SE, Voehler M, Peng D, Ohi R, Gould KL, Reiter NJ, Ohi MD. Structural and functional insights into the N-terminus of Schizosaccharomyces pombe Cdc5. Biochemistry 2014; 53:6439-51. [PMID: 25263959 PMCID: PMC4204884 DOI: 10.1021/bi5008639] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
The
spliceosome is a dynamic macromolecular machine composed of
five small nuclear ribonucleoparticles (snRNPs), the NineTeen Complex
(NTC), and other proteins that catalyze the removal of introns mature
to form the mature message. The NTC, named after its founding member Saccharomyces cerevisiae Prp19, is a conserved spliceosome
subcomplex composed of at least nine proteins. During spliceosome
assembly, the transition to an active spliceosome correlates with
stable binding of the NTC, although the mechanism of NTC function
is not understood. Schizosaccharomyces pombe Cdc5, a core subunit of the NTC, is an essential protein required
for pre-mRNA splicing. The highly conserved Cdc5 N-terminus contains
two canonical Myb (myeloblastosis) repeats (R1 and R2) and a third
domain (D3) that was previously classified as a Myb-like repeat. Although
the N-terminus of Cdc5 is required for its function, how R1, R2, and
D3 each contribute to functionality is unclear. Using a combination
of yeast genetics, structural approaches, and RNA binding assays,
we show that R1, R2, and D3 are all required for the function of Cdc5
in cells. We also show that the N-terminus of Cdc5 binds RNA in vitro. Structural and functional analyses of Cdc5-D3
show that, while this domain does not adopt a Myb fold, Cdc5-D3 preferentially
binds double-stranded RNA. Our data suggest that the Cdc5 N-terminus
interacts with RNA structures proposed to be near the catalytic core
of the spliceosome.
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Affiliation(s)
- Scott E Collier
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center , Nashville, Tennessee 37232, United States
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86
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