1
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Norppa AJ, Chowdhury I, van Rooijen LE, Ravantti JJ, Snel B, Varjosalo M, Frilander MJ. Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome. Nucleic Acids Res 2024; 52:4037-4052. [PMID: 38499487 DOI: 10.1093/nar/gkae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/19/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
Here, we identify RBM41 as a novel unique protein component of the minor spliceosome. RBM41 has no previously recognized cellular function but has been identified as a paralog of U11/U12-65K, a known unique component of the U11/U12 di-snRNP. Both proteins use their highly similar C-terminal RRMs to bind to 3'-terminal stem-loops in U12 and U6atac snRNAs with comparable affinity. Our BioID data indicate that the unique N-terminal domain of RBM41 is necessary for its association with complexes containing DHX8, an RNA helicase, which in the major spliceosome drives the release of mature mRNA from the spliceosome. Consistently, we show that RBM41 associates with excised U12-type intron lariats, is present in the U12 mono-snRNP, and is enriched in Cajal bodies, together suggesting that RBM41 functions in the post-splicing steps of the minor spliceosome assembly/disassembly cycle. This contrasts with U11/U12-65K, which uses its N-terminal region to interact with U11 snRNP during intron recognition. Finally, while RBM41 knockout cells are viable, they show alterations in U12-type 3' splice site usage. Together, our results highlight the role of the 3'-terminal stem-loop of U12 snRNA as a dynamic binding platform for the U11/U12-65K and RBM41 proteins, which function at distinct stages of the assembly/disassembly cycle.
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Affiliation(s)
- Antto J Norppa
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Iftekhar Chowdhury
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura E van Rooijen
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Janne J Ravantti
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Helsinki, Finland
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Markku Varjosalo
- Molecular Systems Biology Research Group and Proteomics Unit, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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2
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Bai R, Yuan M, Zhang P, Luo T, Shi Y, Wan R. Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Science 2024; 383:1245-1252. [PMID: 38484052 DOI: 10.1126/science.adn7272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/09/2024] [Indexed: 03/19/2024]
Abstract
The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly.
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Affiliation(s)
- Rui Bai
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Meng Yuan
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pu Zhang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ting Luo
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Yigong Shi
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
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3
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Fortuna TR, Kour S, Chimata AV, Muiños-Bühl A, Anderson EN, Nelson Iv CH, Ward C, Chauhan O, O'Brien C, Rajasundaram D, Rajan DS, Wirth B, Singh A, Pandey UB. SMN regulates GEMIN5 expression and acts as a modifier of GEMIN5-mediated neurodegeneration. Acta Neuropathol 2023; 146:477-498. [PMID: 37369805 DOI: 10.1007/s00401-023-02607-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023]
Abstract
GEMIN5 is essential for core assembly of small nuclear Ribonucleoproteins (snRNPs), the building blocks of spliceosome formation. Loss-of-function mutations in GEMIN5 lead to a neurodevelopmental syndrome among patients presenting with developmental delay, motor dysfunction, and cerebellar atrophy by perturbing SMN complex protein expression and assembly. Currently, molecular determinants of GEMIN5-mediated disease have yet to be explored. Here, we identified SMN as a genetic suppressor of GEMIN5-mediated neurodegeneration in vivo. We discovered that an increase in SMN expression by either SMN gene therapy replacement or the antisense oligonucleotide (ASO), Nusinersen, significantly upregulated the endogenous levels of GEMIN5 in mammalian cells and mutant GEMIN5-derived iPSC neurons. Further, we identified a strong functional association between the expression patterns of SMN and GEMIN5 in patient Spinal Muscular Atrophy (SMA)-derived motor neurons harboring loss-of-function mutations in the SMN gene. Interestingly, SMN binds to the C-terminus of GEMIN5 and requires the Tudor domain for GEMIN5 binding and expression regulation. Finally, we show that SMN upregulation ameliorates defective snRNP biogenesis and alternative splicing defects caused by loss of GEMIN5 in iPSC neurons and in vivo. Collectively, these studies indicate that SMN acts as a regulator of GEMIN5 expression and neuropathologies.
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Affiliation(s)
- Tyler R Fortuna
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Anixa Muiños-Bühl
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Charlie H Nelson Iv
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Caroline Ward
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Om Chauhan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Casey O'Brien
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Deepa S Rajan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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4
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Ciancone AM, Hosseinibarkooie S, Bai DL, Borne AL, Ferris HA, Hsu KL. Global profiling identifies a stress-responsive tyrosine site on EDC3 regulating biomolecular condensate formation. Cell Chem Biol 2022; 29:1709-1720.e7. [PMID: 36476517 PMCID: PMC9779741 DOI: 10.1016/j.chembiol.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
RNA granules are cytoplasmic condensates that organize biochemical and signaling complexes in response to cellular stress. Functional proteomic investigations under RNA-granule-inducing conditions are needed to identify protein sites involved in coupling stress response with ribonucleoprotein regulation. Here, we apply chemical proteomics using sulfonyl-triazole (SuTEx) probes to capture cellular responses to oxidative and nutrient stress. The stress-responsive tyrosine and lysine sites detected mapped to known proteins involved in processing body (PB) and stress granule (SG) pathways, including LSM14A, FUS, and Enhancer of mRNA-decapping protein 3 (EDC3). Notably, disruption of EDC3 tyrosine 475 (Y475) resulted in hypo-phosphorylation at S161 and S131 and altered protein-protein interactions (PPIs) with decapping complex components (DDX6, DCP1A/B) and 14-3-3 proteins. This resulting mutant form of EDC3 was capable of rescuing the PB-deficient phenotype of EDC3 knockout cells. Taken together, our findings identify Y475 as an arsenic-responsive site that regulates RNA granule formation by coupling EDC3 post-translational modification and PPI states.
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Affiliation(s)
- Anthony M Ciancone
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Adam L Borne
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Heather A Ferris
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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5
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Höfler S, Lukat P, Blankenfeldt W, Carlomagno T. High-resolution structure of eukaryotic Fibrillarin interacting with Nop56 amino-terminal domain. RNA 2021; 27:496-512. [PMID: 33483369 PMCID: PMC7962484 DOI: 10.1261/rna.077396.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Ribosomal RNA (rRNA) carries extensive 2'-O-methyl marks at functionally important sites. This simple chemical modification is thought to confer stability, promote RNA folding, and contribute to generate a heterogenous ribosome population with a yet-uncharacterized function. 2'-O-methylation occurs both in archaea and eukaryotes and is accomplished by the Box C/D RNP enzyme in an RNA-guided manner. Extensive and partially conflicting structural information exists for the archaeal enzyme, while no structural data is available for the eukaryotic enzyme. The yeast Box C/D RNP consists of a guide RNA, the RNA-primary binding protein Snu13, the two scaffold proteins Nop56 and Nop58, and the enzymatic module Nop1. Here we present the high-resolution structure of the eukaryotic Box C/D methyltransferase Nop1 from Saccharomyces cerevisiae bound to the amino-terminal domain of Nop56. We discuss similarities and differences between the interaction modes of the two proteins in archaea and eukaryotes and demonstrate that eukaryotic Nop56 recruits the methyltransferase to the Box C/D RNP through a protein-protein interface that differs substantially from the archaeal orthologs. This study represents a first achievement in understanding the evolution of the structure and function of these proteins from archaea to eukaryotes.
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MESH Headings
- Amino Acid Sequence
- Archaeal Proteins/chemistry
- Archaeal Proteins/genetics
- Archaeal Proteins/metabolism
- Binding Sites
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Crystallography, X-Ray
- Gene Expression
- Methylation
- Models, Molecular
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Pyrococcus furiosus/genetics
- Pyrococcus furiosus/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/genetics
- Ribonucleoproteins, Small Nucleolar/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Alignment
- Structural Homology, Protein
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Simone Höfler
- Leibniz University Hannover, Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ), D-30167 Hannover, Germany
| | - Peer Lukat
- Helmholtz Centre for Infection Research, Department of Structure and Function of Proteins, D-38124 Braunschweig, Germany
| | - Wulf Blankenfeldt
- Helmholtz Centre for Infection Research, Department of Structure and Function of Proteins, D-38124 Braunschweig, Germany
| | - Teresa Carlomagno
- Leibniz University Hannover, Institute for Organic Chemistry and Centre for Biomolecular Drug Research (BMWZ), D-30167 Hannover, Germany
- Helmholtz Centre for Infection Research, Group of NMR-based Structural Chemistry, D-38124 Braunschweig, Germany
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6
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Strittmatter LM, Capitanchik C, Newman AJ, Hallegger M, Norman CM, Fica SM, Oubridge C, Luscombe NM, Ule J, Nagai K. psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation. Nat Commun 2021; 12:1488. [PMID: 33674615 PMCID: PMC7935899 DOI: 10.1038/s41467-021-21745-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 02/05/2021] [Indexed: 11/09/2022] Open
Abstract
RNA helicases remodel the spliceosome to enable pre-mRNA splicing, but their binding and mechanism of action remain poorly understood. To define helicase-RNA contacts in specific spliceosomal states, we develop purified spliceosome iCLIP (psiCLIP), which reveals dynamic helicase-RNA contacts during splicing catalysis. The helicase Prp16 binds along the entire available single-stranded RNA region between the branchpoint and 3'-splice site, while Prp22 binds diffusely downstream of the branchpoint before exon ligation, but then switches to more narrow binding in the downstream exon after exon ligation, arguing against a mechanism of processive translocation. Depletion of the exon-ligation factor Prp18 destabilizes Prp22 binding to the pre-mRNA, suggesting that proofreading by Prp22 may sense the stability of the spliceosome during exon ligation. Thus, psiCLIP complements structural studies by providing key insights into the binding and proofreading activity of spliceosomal RNA helicases.
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Affiliation(s)
| | | | | | - Martina Hallegger
- The Francis Crick Institute, London, UK
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | | | | | | | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- UCL Genetics Institute, Department of Genetics, Environment and Evolution, University College London, London, UK
- Okinawa Institute of Science & Technology Graduate University, Okinawa, Japan
| | - Jernej Ule
- The Francis Crick Institute, London, UK.
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK.
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7
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Hu X, Kim JK, Yu C, Jun HI, Liu J, Sankaran B, Huang L, Qiao F. Quality-Control Mechanism for Telomerase RNA Folding in the Cell. Cell Rep 2020; 33:108568. [PMID: 33378677 DOI: 10.1016/j.celrep.2020.108568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/12/2020] [Accepted: 12/07/2020] [Indexed: 01/28/2023] Open
Abstract
Long non-coding RNAs can often fold into different conformations. Telomerase RNA, an essential component of the telomerase ribonucleoprotein (RNP) enzyme, must fold into a defined structure to fulfill its function with the protein catalytic subunit (TERT) and other accessory factors. However, the mechanism by which the correct folding of telomerase RNA is warranted in a cell is still unknown. Here we show that La-related protein Pof8 specifically recognizes the conserved pseudoknot region of telomerase RNA and instructs the binding of the Lsm2-8 complex to its mature 3' end, thus selectively protecting the correctly folded RNA from exonucleolytic degradation. In the absence of Pof8, TERT assembles with misfolded RNA and produces little telomerase activity. Therefore, Pof8 plays a key role in telomerase RNA folding quality control, ensuring that TERT only assembles with functional telomerase RNA to form active telomerase. Our finding reveals a mechanism for non-coding RNA folding quality control.
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Affiliation(s)
- Xichan Hu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Jin-Kwang Kim
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697-4560, USA
| | - Hyun-Ik Jun
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Jinqiang Liu
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697-4560, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697-1700, USA.
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8
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Stoszko M, Al-Hatmi AMS, Skriba A, Roling M, Ne E, Crespo R, Mueller YM, Najafzadeh MJ, Kang J, Ptackova R, LeMasters E, Biswas P, Bertoldi A, Kan TW, de Crignis E, Sulc M, Lebbink JH, Rokx C, Verbon A, van Ijcken W, Katsikis PD, Palstra RJ, Havlicek V, de Hoog S, Mahmoudi T. Gliotoxin, identified from a screen of fungal metabolites, disrupts 7SK snRNP, releases P-TEFb, and reverses HIV-1 latency. Sci Adv 2020; 6:eaba6617. [PMID: 32851167 PMCID: PMC7423394 DOI: 10.1126/sciadv.aba6617] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 07/01/2020] [Indexed: 05/16/2023]
Abstract
A leading pharmacological strategy toward HIV cure requires "shock" or activation of HIV gene expression in latently infected cells with latency reversal agents (LRAs) followed by their subsequent clearance. In a screen for novel LRAs, we used fungal secondary metabolites as a source of bioactive molecules. Using orthogonal mass spectrometry (MS) coupled to latency reversal bioassays, we identified gliotoxin (GTX) as a novel LRA. GTX significantly induced HIV-1 gene expression in latent ex vivo infected primary cells and in CD4+ T cells from all aviremic HIV-1+ participants. RNA sequencing identified 7SK RNA, the scaffold of the positive transcription elongation factor b (P-TEFb) inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex, to be significantly reduced upon GTX treatment of CD4+ T cells. GTX directly disrupted 7SK snRNP by targeting La-related protein 7 (LARP7), releasing active P-TEFb, which phosphorylated RNA polymerase II (Pol II) C-terminal domain (CTD), inducing HIV transcription.
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Affiliation(s)
- Mateusz Stoszko
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Abdullah M. S. Al-Hatmi
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
- Center of Expertise in Mycology of Radboud UMC/CWZ, Nijmegen, Netherlands
- Ministry of Health, Directorate General of Health Services, Ibri, Oman
| | - Anton Skriba
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, CZ 14220 Prague 4, Czech Republic
| | - Michael Roling
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Enrico Ne
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Raquel Crespo
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Yvonne M. Mueller
- Department of Immunology, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Mohammad Javad Najafzadeh
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
- Department of Parasitology and Mycology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Joyce Kang
- Key Laboratory of Environmental Pollution Monitoring/Disease Control, Ministry of Education and Guizhou Talent Base of Microbes and Human Health, School of Basic Medicine, Guizhou Medical University, Guiyang 550025, P. R. China
| | - Renata Ptackova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, CZ 14220 Prague 4, Czech Republic
| | - Elizabeth LeMasters
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Pritha Biswas
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Alessia Bertoldi
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
- Microbiology Section, Department of Experimental, Diagnostic and Specialty Medicine, School of Medicine, University of Bologna, Bologna, Italy
| | - Tsung Wai Kan
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Elisa de Crignis
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Miroslav Sulc
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, CZ 14220 Prague 4, Czech Republic
| | - Joyce H.G. Lebbink
- Departments of Molecular Genetics and Radiation Oncology, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Casper Rokx
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, Netherlands
| | - Annelies Verbon
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, Netherlands
| | - Wilfred van Ijcken
- Erasmus MC Genomics Core Facility, Department of Cell Biology, Erasmus University Medical Center, PO Box 2040, 3000 CA, Rotterdam, Netherlands
| | - Peter D. Katsikis
- Department of Immunology, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Robert-Jan Palstra
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
| | - Vladimir Havlicek
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, CZ 14220 Prague 4, Czech Republic
| | - Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, Netherlands
- Center of Expertise in Mycology of Radboud UMC/CWZ, Nijmegen, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, Netherlands
- Corresponding author.
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9
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Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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10
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Abstract
BACKGROUND Recent advances in genetics and genomics present unique opportunities for enhancing our understanding of mammalian biology and evolution through detailed multi-species comparative analysis of gene organization and expression. Yet, of the more than 20,000 protein coding genes found in mammalian genomes, fewer than 10% have been examined in any detail. Here we elucidate the power of data available in publicly-accessible genomic and genetic resources by querying them to evaluate Zmat2, a minimally studied gene whose human ortholog has been implicated in spliceosome function and in keratinocyte differentiation. RESULTS We find extensive conservation in coding regions and overall structure of Zmat2 in 18 mammals representing 13 orders and spanning ~ 165 million years of evolutionary development, and in their encoded proteins. We identify a tandem duplication in the Zmat2 gene and locus in opossum, but not in other monotremes, marsupials, or other mammals, indicating that this event occurred subsequent to the divergence of these species from one another. We also define a collection of Zmat2 pseudogenes in half of the mammals studied, and suggest based on phylogenetic analysis that they each arose independently in the recent evolutionary past. CONCLUSIONS Mammalian Zmat2 genes and ZMAT2 proteins illustrate conservation of structure and sequence, along with the development and diversification of pseudogenes in a large fraction of species. Collectively, these observations also illustrate how the focused identification and interpretation of data found in public genomic and gene expression resources can be leveraged to reveal new insights of potentially high biological significance.
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Affiliation(s)
- Peter Rotwein
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech Health University Health Sciences Center, El Paso, TX, 79905, USA.
| | - Kabita Baral
- Graduate School, College of Science, University of Texas at El Paso, El Paso, TX, 79902, USA
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11
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Sun Y, Liu Z, Cao X, Lu Y, Mi Z, He C, Liu J, Zheng Z, Li MJ, Li T, Xu D, Wu M, Cao Y, Li Y, Yang B, Mei C, Zhang L, Chen Y. Activation of P-TEFb by cAMP-PKA signaling in autosomal dominant polycystic kidney disease. Sci Adv 2019; 5:eaaw3593. [PMID: 31183407 PMCID: PMC6551191 DOI: 10.1126/sciadv.aaw3593] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 05/02/2019] [Indexed: 05/06/2023]
Abstract
Positive transcription elongation factor b (P-TEFb) functions as a central regulator of transcription elongation. Activation of P-TEFb occurs through its dissociation from the transcriptionally inactive P-TEFb/HEXIM1/7SK snRNP complex. However, the mechanisms of signal-regulated P-TEFb activation and its roles in human diseases remain largely unknown. Here, we demonstrate that cAMP-PKA signaling disrupts the inactive P-TEFb/HEXIM1/7SK snRNP complex by PKA-mediated phosphorylation of HEXIM1 at serine-158. The cAMP pathway plays central roles in the development of autosomal dominant polycystic kidney disease (ADPKD), and we show that P-TEFb is hyperactivated in mouse and human ADPKD kidneys. Genetic activation of P-TEFb promotes cyst formation in a zebrafish ADPKD model, while pharmacological inhibition of P-TEFb attenuates cyst development by suppressing the pathological gene expression program in ADPKD mice. Our study therefore elucidates a mechanism by which P-TEFb activation by cAMP-PKA signaling promotes cystogenesis in ADPKD.
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Affiliation(s)
- Yongzhan Sun
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Zhiheng Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xinyi Cao
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yi Lu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Zeyun Mi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chaoran He
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jing Liu
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Zhanye Zheng
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Mulin Jun Li
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Tiegang Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Dechao Xu
- Kidney Institute, Department of Nephrology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Ming Wu
- Department of Nephrology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, TCM Institute of Kidney Disease of Shanghai University of Traditional Chinese Medicine, Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shanghai 201203, China
| | - Ying Cao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuhao Li
- Department of Pathology, Nankai University School of Medicine, 94 Weijin Road, Tianjin 300071, China
| | - Baoxue Yang
- Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing 100038, China
| | - Changlin Mei
- Kidney Institute, Department of Nephrology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
- Corresponding author. (C.M.); (L.Z.); (Y.C.)
| | - Lirong Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
- Corresponding author. (C.M.); (L.Z.); (Y.C.)
| | - Yupeng Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, Oncology Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin 300060, China
- Corresponding author. (C.M.); (L.Z.); (Y.C.)
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12
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Doggett K, Williams BB, Markmiller S, Geng FS, Coates J, Mieruszynski S, Ernst M, Thomas T, Heath JK. Early developmental arrest and impaired gastrointestinal homeostasis in U12-dependent splicing-defective Rnpc3-deficient mice. RNA 2018; 24:1856-1870. [PMID: 30254136 PMCID: PMC6239176 DOI: 10.1261/rna.068221.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/20/2018] [Indexed: 05/10/2023]
Abstract
Splicing is an essential step in eukaryotic gene expression. While the majority of introns is excised by the U2-dependent, or major class, spliceosome, the appropriate expression of a very small subset of genes depends on U12-dependent, or minor class, splicing. The U11/U12 65K protein (hereafter 65K), encoded by RNPC3, is one of seven proteins that are unique to the U12-dependent spliceosome, and previous studies including our own have established that it plays a role in plant and vertebrate development. To pinpoint the impact of 65K loss during mammalian development and in adulthood, we generated germline and conditional Rnpc3-deficient mice. Homozygous Rnpc3-/- embryos died prior to blastocyst implantation, whereas Rnpc3+/- mice were born at the expected frequency, achieved sexual maturity, and exhibited a completely normal lifespan. Systemic recombination of conditional Rnpc3 alleles in adult (Rnpc3lox/lox ) mice caused rapid weight loss, leukopenia, and degeneration of the epithelial lining of the entire gastrointestinal tract, the latter due to increased cell death and a reduction in cell proliferation. Accompanying this, we observed a loss of both 65K and the pro-proliferative phospho-ERK1/2 proteins from the stem/progenitor cells at the base of intestinal crypts. RT-PCR analysis of RNA extracted from purified preparations of intestinal epithelial cells with recombined Rnpc3lox alleles revealed increased frequency of U12-type intron retention in all transcripts tested. Our study, using a novel conditional mouse model of Rnpc3 deficiency, establishes that U12-dependent splicing is not only important during development but is indispensable throughout life.
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Affiliation(s)
- Karen Doggett
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ben B Williams
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Sebastian Markmiller
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Fan-Suo Geng
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Janine Coates
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Stephen Mieruszynski
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3050, Australia
| | - Tim Thomas
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Joan K Heath
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Iyer CC, Corlett KM, Massoni-Laporte A, Duque SI, Madabusi N, Tisdale S, McGovern VL, Le TT, Zaworski PG, Arnold WD, Pellizzoni L, Burghes AHM. Mild SMN missense alleles are only functional in the presence of SMN2 in mammals. Hum Mol Genet 2018; 27:3404-3416. [PMID: 29982416 PMCID: PMC6140769 DOI: 10.1093/hmg/ddy251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/19/2018] [Accepted: 07/02/2018] [Indexed: 12/17/2022] Open
Abstract
Spinal muscular atrophy (SMA) is caused by reduced levels of full-length SMN (FL-SMN). In SMA patients with one or two copies of the Survival Motor Neuron 2 (SMN2) gene there are a number of SMN missense mutations that result in milder-than-predicted SMA phenotypes. These mild SMN missense mutation alleles are often assumed to have partial function. However, it is important to consider the contribution of FL-SMN as these missense alleles never occur in the absence of SMN2. We propose that these patients contain a partially functional oligomeric SMN complex consisting of FL-SMN from SMN2 and mutant SMN protein produced from the missense allele. Here we show that mild SMN missense mutations SMND44V, SMNT74I or SMNQ282A alone do not rescue mice lacking wild-type FL-SMN. Thus, missense mutations are not functional in the absence of FL-SMN. In contrast, when the same mild SMN missense mutations are expressed in a mouse containing two SMN2 copies, functional SMN complexes are formed with the small amount of wild-type FL-SMN produced by SMN2 and the SMA phenotype is completely rescued. This contrasts with SMN missense alleles when studied in C. elegans, Drosophila and zebrafish. Here we demonstrate that the heteromeric SMN complex formed with FL-SMN is functional and sufficient to rescue small nuclear ribonucleoprotein assembly, motor neuron function and rescue the SMA mice. We conclude that mild SMN missense alleles are not partially functional but rather they are completely non-functional in the absence of wild-type SMN in mammals.
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Affiliation(s)
- Chitra C Iyer
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Kaitlyn M Corlett
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Aurélie Massoni-Laporte
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Sandra I Duque
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Narasimhan Madabusi
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Sarah Tisdale
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Vicki L McGovern
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Thanh T Le
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - W David Arnold
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Arthur H M Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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15
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Norppa AJ, Kauppala TM, Heikkinen HA, Verma B, Iwaï H, Frilander MJ. Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA. RNA 2018; 24:396-409. [PMID: 29255062 PMCID: PMC5824358 DOI: 10.1261/rna.062844.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/12/2017] [Indexed: 05/09/2023]
Abstract
Mutations in the components of the minor spliceosome underlie several human diseases. A subset of patients with isolated growth hormone deficiency (IGHD) harbors mutations in the RNPC3 gene, which encodes the minor spliceosome-specific U11/U12-65K protein. Although a previous study showed that IGHD patient cells have defects in U12-type intron recognition, the biochemical effects of these mutations on the 65K protein have not been characterized. Here, we show that a proline-to-threonine missense mutation (P474T) and a nonsense mutation (R502X) in the C-terminal RNA recognition motif (C-RRM) of the 65K protein impair the binding of 65K to U12 and U6atac snRNAs. We further show that the nonsense allele is targeted to the nonsense-mediated decay (NMD) pathway, but in an isoform-specific manner, with the nuclear-retained 65K long-3'UTR isoform escaping the NMD pathway. In contrast, the missense P474T mutation leads, in addition to the RNA-binding defect, to a partial defect in the folding of the C-RRM and reduced stability of the full-length protein, thus reducing the formation of U11/U12 di-snRNP complexes. We propose that both the C-RRM folding defect and NMD-mediated decrease in the levels of the U11/U12-65K protein reduce formation of the U12-type intron recognition complex and missplicing of a subset of minor introns leading to pituitary hypoplasia and a subsequent defect in growth hormone secretion.
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Affiliation(s)
- Antto J Norppa
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Tuuli M Kauppala
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Harri A Heikkinen
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Bhupendra Verma
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
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16
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Abstract
Intron removal requires assembly of the spliceosome on precursor mRNA (pre-mRNA) and extensive remodelling to form the spliceosome's catalytic centre. Here we report the cryo-electron microscopy structure of the yeast Saccharomyces cerevisiae pre-catalytic B complex spliceosome at near-atomic resolution. The mobile U2 small nuclear ribonucleoprotein particle (snRNP) associates with U4/U6.U5 tri-snRNP through the U2/U6 helix II and an interface between U4/U6 di-snRNP and the U2 snRNP SF3b-containing domain, which also transiently contacts the helicase Brr2. The 3' region of the U2 snRNP is flexibly attached to the SF3b-containing domain and protrudes over the concave surface of tri-snRNP, where the U1 snRNP may reside before its release from the pre-mRNA 5' splice site. The U6 ACAGAGA sequence forms a hairpin that weakly tethers the 5' splice site. The B complex proteins Prp38, Snu23 and Spp381 bind the Prp8 N-terminal domain and stabilize U6 ACAGAGA stem-pre-mRNA and Brr2-U4 small nuclear RNA interactions. These results provide important insights into the events leading to active site formation.
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MESH Headings
- Base Sequence
- Biocatalysis
- Catalytic Domain
- Cryoelectron Microscopy
- Introns/genetics
- Models, Biological
- Models, Molecular
- Nuclear Proteins/chemistry
- Nuclear Proteins/metabolism
- Protein Binding
- Protein Domains
- Protein Stability
- RNA Helicases/chemistry
- RNA Helicases/metabolism
- RNA Helicases/ultrastructure
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Precursors/ultrastructure
- RNA Splice Sites/genetics
- RNA Splicing
- RNA Splicing Factors/chemistry
- RNA Splicing Factors/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U2 Small Nuclear/chemistry
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U5 Small Nuclear/chemistry
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/chemistry
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/metabolism
- Saccharomyces cerevisiae Proteins/ultrastructure
- Spliceosomes/chemistry
- Spliceosomes/metabolism
- Spliceosomes/ultrastructure
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Affiliation(s)
- Clemens Plaschka
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Pei-Chun Lin
- 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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17
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Schwer B, Roth AJ, Shuman S. Will the circle be unbroken: specific mutations in the yeast Sm protein ring expose a requirement for assembly factor Brr1, a homolog of Gemin2. RNA 2017; 23:420-430. [PMID: 27974620 PMCID: PMC5311505 DOI: 10.1261/rna.059881.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/12/2016] [Indexed: 05/08/2023]
Abstract
A seven-subunit Sm protein ring assembles around specific U-rich RNA segments of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP crystal structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure-function relationships of the SmD1 and SmD2 subunits. Of 18 conserved amino acids comprising their RNA-binding sites or intersubunit interfaces, only Arg88 in SmD1 and Arg97 in SmD2 were essential for growth. Tests for genetic interactions with non-Sm splicing factors identified benign mutations of SmD1 (N37A, R88K, R93A) and SmD2 (R49A, N66A, R97K, D99A) that were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and/or Msl1. Tests of 264 pairwise combinations of SmD1 and SmD2 alleles with each other and with a collection of SmG, SmE, SmF, SmB, and SmD3 alleles revealed 92 instances of inter-Sm synthetic lethality. We leveraged the Sm mutant collection to illuminate the function of the yeast Sm assembly factor Brr1 and its relationship to the metazoan Sm assembly factor Gemin2. Mutations in the adjacent SmE (K83A), SmF (K32A, F33A, R74K), SmD2 (R49A, N66A, E74A, R97K, D99A), and SmD1 (E18A, N37A) subunits-but none in the SmG, SmD3, and SmB subunits-were synthetically lethal with brr1Δ. Using complementation of brr1Δ lethality in two Sm mutant backgrounds as an in vivo assay of Brr1 activity, we identified as essential an N-terminal segment of Brr1 (amino acids 24-47) corresponding to the Gemin2 α1 helix that interacts with SmF and a Brr1 C-terminal peptide (336QKDLIE341) that, in Gemin2, interacts with SmD2.
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MESH Headings
- Amino Acid Sequence
- Binding Sites
- Gene Expression
- Genes, Lethal
- Genetic Complementation Test
- Humans
- Mutation
- Nerve Tissue Proteins/chemistry
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Protein Subunits/chemistry
- Protein Subunits/genetics
- Protein Subunits/metabolism
- RNA Splicing
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Spliceosomes/genetics
- Spliceosomes/metabolism
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Affiliation(s)
- Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Allen J Roth
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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18
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Schwer B, Kruchten J, Shuman S. Structure-function analysis and genetic interactions of the SmG, SmE, and SmF subunits of the yeast Sm protein ring. RNA 2016; 22:1320-8. [PMID: 27417296 PMCID: PMC4986888 DOI: 10.1261/rna.057448.116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/14/2016] [Indexed: 05/08/2023]
Abstract
A seven-subunit Sm protein ring forms a core scaffold of the U1, U2, U4, and U5 snRNPs that direct pre-mRNA splicing. Using human snRNP structures to guide mutagenesis in Saccharomyces cerevisiae, we gained new insights into structure-function relationships of the SmG, SmE, and SmF subunits. An alanine scan of 19 conserved amino acids of these three proteins, comprising the Sm RNA binding sites or inter-subunit interfaces, revealed that, with the exception of Arg74 in SmF, none are essential for yeast growth. Yet, for SmG, SmE, and SmF, as for many components of the yeast spliceosome, the effects of perturbing protein-RNA and protein-protein interactions are masked by built-in functional redundancies of the splicing machine. For example, tests for genetic interactions with non-Sm splicing factors showed that many benign mutations of SmG, SmE, and SmF (and of SmB and SmD3) were synthetically lethal with null alleles of U2 snRNP subunits Lea1 and Msl1. Tests of pairwise combinations of SmG, SmE, SmF, SmB, and SmD3 alleles highlighted the inherent redundancies within the Sm ring, whereby simultaneous mutations of the RNA binding sites of any two of the Sm subunits are lethal. Our results suggest that six intact RNA binding sites in the Sm ring suffice for function but five sites may not.
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Affiliation(s)
- Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Joshua Kruchten
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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19
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Schwer B, Shuman S. Structure-function analysis and genetic interactions of the Yhc1, SmD3, SmB, and Snp1 subunits of yeast U1 snRNP and genetic interactions of SmD3 with U2 snRNP subunit Lea1. RNA 2015; 21:1173-86. [PMID: 25897024 PMCID: PMC4436669 DOI: 10.1261/rna.050583.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/04/2015] [Indexed: 05/08/2023]
Abstract
Yhc1 and U1-C are essential subunits of the yeast and human U1 snRNP, respectively, that stabilize the duplex formed by U1 snRNA at the pre-mRNA 5' splice site (5'SS). Mutational analysis of Yhc1, guided by the human U1 snRNP crystal structure, highlighted the importance of Val20 and Ser19 at the RNA interface. Though benign on its own, V20A was lethal in the absence of branchpoint-binding complex subunit Mud2 and caused a severe growth defect in the absence of U1 subunit Nam8. S19A caused a severe defect with mud2▵. Essential DEAD-box ATPase Prp28 was bypassed by mutations of Yhc1 Val20 and Ser19, consistent with destabilization of U1•5'SS interaction. We extended the genetic analysis to SmD3, which interacts with U1-C/Yhc1 in U1 snRNP, and to SmB, its neighbor in the Sm ring. Whereas mutations of the interface of SmD3, SmB, and U1-C/Yhc1 with U1-70K/Snp1, or deletion of the interacting Snp1 N-terminal peptide, had no growth effect, they elicited synthetic defects in the absence of U1 subunit Mud1. Mutagenesis of the RNA-binding triad of SmD3 (Ser-Asn-Arg) and SmB (His-Asn-Arg) provided insights to built-in redundancies of the Sm ring, whereby no individual side-chain was essential, but simultaneous mutations of Asn or Arg residues in SmD3 and SmB were lethal. Asn-to-Ala mutations SmB and SmD3 caused synthetic defects in the absence of Mud1 or Mud2. All three RNA site mutations of SmD3 were lethal in cells lacking the U2 snRNP subunit Lea1. Benign C-terminal truncations of SmD3 were dead in the absence of Mud2 or Lea1 and barely viable in the absence of Nam8 or Mud1. In contrast, SMD3-E35A uniquely suppressed the temperature-sensitivity of lea1▵.
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MESH Headings
- Autoantigens/chemistry
- Autoantigens/genetics
- Autoantigens/metabolism
- Binding Sites
- DNA Mutational Analysis
- Humans
- Models, Molecular
- Protein Structure, Tertiary
- Ribonucleoprotein, U1 Small Nuclear/chemistry
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Ribonucleoprotein, U2 Small Nuclear/chemistry
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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20
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Rodgers ML, Paulson J, Hoskins AA. Rapid isolation and single-molecule analysis of ribonucleoproteins from cell lysate by SNAP-SiMPull. RNA 2015; 21:1031-41. [PMID: 25805862 PMCID: PMC4408783 DOI: 10.1261/rna.047845.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/03/2015] [Indexed: 05/08/2023]
Abstract
Large macromolecular complexes such as the spliceosomal small nuclear ribonucleoproteins (snRNPs) play a variety of roles within the cell. Despite their biological importance, biochemical studies of snRNPs and other machines are often thwarted by practical difficulties in the isolation of sufficient amounts of material. Studies of the snRNPs as well as other macromolecular machines would be greatly facilitated by new approaches that enable their isolation and biochemical characterization. One such approach is single-molecule pull-down (SiMPull) that combines in situ immunopurification of complexes from cell lysates with subsequent single-molecule fluorescence microscopy experiments. We report the development of a new method, called SNAP-SiMPull, that can readily be applied to studies of splicing factors and snRNPs isolated from whole-cell lysates. SNAP-SiMPull overcomes many of the limitations imposed by conventional SiMPull strategies that rely on fluorescent proteins. We have used SNAP-SiMPull to study the yeast branchpoint bridging protein (BBP) as well as the U1 and U6 snRNPs. SNAP-SiMPull will likely find broad use for rapidly isolating complex cellular machines for single-molecule fluorescence colocalization experiments.
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Affiliation(s)
- Margaret L Rodgers
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Joshua Paulson
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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21
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Abstract
The mineralocorticoid receptor (MR) is a member of the nuclear receptor superfamily. Pathological activation of the MR causes cardiac fibrosis and heart failure, but clinical use of MR antagonists is limited by the renal side effect of hyperkalemia. Coregulator proteins are known to be critical for nuclear receptor-mediated gene expression. Identification of coregulators, which mediate MR activity in a tissue-specific manner, may allow for the development of novel tissue-selective MR modulators that confer cardiac protection without adverse renal effects. Our earlier studies identified a consensus motif among MR-interacting peptides, MPxLxxLL. Gem (nuclear organelle)-associated protein 4 (GEMIN4) is one of the proteins that contain this motif. Transient transfection experiments in HEK293 and H9c2 cells demonstrated that GEMIN4 repressed agonist-induced MR transactivation in a cell-specific manner. Furthermore, overexpression of GEMIN4 significantly decreased, while knockdown of GEMIN4 increased, the mRNA expression of specific endogenous MR target genes. A physical interaction between GEMIN4 and MR is suggested by their nuclear co-localization upon agonist treatment. These findings indicate that GEMIN4 functions as a novel coregulator of the MR.
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Affiliation(s)
- Jun Yang
- MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan
| | - Peter J Fuller
- MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan
| | - James Morgan
- MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan
| | - Hirotaka Shibata
- MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan
| | - Colin D Clyne
- MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan
| | - Morag J Young
- MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan MIMR-PHI InstitutePO Box 5152, Clayton, Victoria 3168, AustraliaDepartment of MedicineMonash University, Clayton, Victoria 3168, AustraliaDepartment of EndocrinologyMetabolism, Rheumatology and Nephrology, Oita University, Yufu 879-5593, Japan
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22
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Rothé B, Saliou JM, Quinternet M, Back R, Tiotiu D, Jacquemin C, Loegler C, Schlotter F, Peña V, Eckert K, Moréra S, Dorsselaer AV, Branlant C, Massenet S, Sanglier-Cianférani S, Manival X, Charpentier B. Protein Hit1, a novel box C/D snoRNP assembly factor, controls cellular concentration of the scaffolding protein Rsa1 by direct interaction. Nucleic Acids Res 2014; 42:10731-47. [PMID: 25170085 PMCID: PMC4176330 DOI: 10.1093/nar/gku612] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 01/09/2023] Open
Abstract
Biogenesis of eukaryotic box C/D small nucleolar ribonucleoprotein particles (C/D snoRNPs) involves conserved trans-acting factors, which are proposed to facilitate the assembly of the core proteins Snu13p/15.5K, Nop58p/NOP58, Nop56p/NOP56 and Nop1p/Fibrillarin on box C/D small nucleolar RNAs (C/D snoRNAs). In yeast, protein Rsa1 acts as a platform, interacting with both the RNA-binding core protein Snu13 and protein Pih1 of the Hsp82-R2TP chaperone complex. In this work, a proteomic approach coupled with functional and structural studies identifies protein Hit1 as a novel Rsa1p-interacting partner involved in C/D snoRNP assembly. Hit1p contributes to in vivo C/D snoRNA stability and pre-RNA maturation kinetics. It associates with U3 snoRNA precursors and influences its 3'-end processing. Remarkably, Hit1p is required to maintain steady-state levels of Rsa1p. This stabilizing activity is likely to be general across eukaryotic species, as the human protein ZNHIT3(TRIP3) showing sequence homology with Hit1p regulates the abundance of NUFIP1, the Rsa1p functional homolog. The nuclear magnetic resonance solution structure of the Rsa1p317-352-Hit1p70-164 complex reveals a novel mode of protein-protein association explaining the strong stability of the Rsa1p-Hit1p complex. Our biochemical data show that C/D snoRNAs and the core protein Nop58 can interact with the purified Snu13p-Rsa1p-Hit1p heterotrimer.
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Affiliation(s)
- Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Jean-Michel Saliou
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Marc Quinternet
- FR CNRS-3209 Bioingénierie Moléculaire, Cellulaire et Thérapeutique (BMCT), CNRS, Université de Lorraine, Biopôle, Campus Biologie Santé, CS 50184, 54505 Vandœuvre-lès-Nancy Cedex, France
| | - Régis Back
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Decebal Tiotiu
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Clémence Jacquemin
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Christine Loegler
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Florence Schlotter
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Vlad Peña
- Max-Planck-Institut für biophysikalische Chemie, Abtl. Röntgenkristallographie, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kelvin Eckert
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, 1 Avenue de Terrasse, 91198 Gif-sur Yvette, France
| | - Solange Moréra
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), CNRS, 1 Avenue de Terrasse, 91198 Gif-sur Yvette, France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Sarah Sanglier-Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg. CNRS, UMR 7178, 25 rue Becquerel, 67087 Strasbourg, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
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23
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Harbi D, Harrison PM. Interaction networks of prion, prionogenic and prion-like proteins in budding yeast, and their role in gene regulation. PLoS One 2014; 9:e100615. [PMID: 24972093 PMCID: PMC4074094 DOI: 10.1371/journal.pone.0100615] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/09/2014] [Indexed: 12/12/2022] Open
Abstract
Prions are transmissible, propagating alternative states of proteins. Prions in budding yeast propagate heritable phenotypes and can function in large-scale gene regulation, or in some cases occur as diseases of yeast. Other ‘prionogenic’ proteins are likely prions that have been determined experimentally to form amyloid in vivo, and to have prion-like domains that are able to propagate heritable states. Furthermore, there are over 300 additional ‘prion-like’ yeast proteins that have similar amino-acid composition to prions (primarily a bias for asparagines and glutamines). Here, we examine the protein functional and interaction networks that involve prion, prionogenic and prion-like proteins. Set against a marked overall preference for N/Q-rich prion-like proteins not to interact with each other, we observe a significant tendency of prion/prionogenic proteins to interact with other, N/Q-rich prion-like proteins. This tendency is mostly due to a small number of networks involving the proteins NUP100p, LSM4p and PUB1p. In general, different data analyses of functional and interaction networks converge to indicate a strong linkage of prionogenic and prion-like proteins, to stress-granule assembly and related biological processes. These results further elucidate how prions may impact gene regulation, and reveal a broader horizon for the functional relevance of N/Q-rich prion-like domains.
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Affiliation(s)
- Djamel Harbi
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Paul M. Harrison
- Department of Biology, McGill University, Montreal, Quebec, Canada
- * E-mail:
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24
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Abstract
RNA-protein complexes are critical for almost all aspects of gene expression. Analysis of RNA-protein interactions can be complicated by the disruption of native complexes and the formation of new, reassorted complexes upon cell lysis. Before concluding that a specific RNA and protein interact in vivo, cell-mixing experiments can be performed to ensure that observed RNA-protein complexes are not formed after lysis of cells.
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Affiliation(s)
- Sarah H Stubbs
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicholas K Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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25
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Lyons SM, Ricciardi AS, Guo AY, Kambach C, Marzluff WF. The C-terminal extension of Lsm4 interacts directly with the 3' end of the histone mRNP and is required for efficient histone mRNA degradation. RNA 2014; 20:88-102. [PMID: 24255165 PMCID: PMC3866647 DOI: 10.1261/rna.042531.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Metazoan replication-dependent histone mRNAs are the only known eukaryotic mRNAs that lack a poly(A) tail, ending instead in a conserved stem-loop sequence, which is bound to the stem-loop binding protein (SLBP) on the histone mRNP. Histone mRNAs are rapidly degraded when DNA synthesis is inhibited in S phase in mammalian cells. Rapid degradation of histone mRNAs is initiated by oligouridylation of the 3' end of histone mRNAs and requires the cytoplasmic Lsm1-7 complex, which can bind to the oligo(U) tail. An exonuclease, 3'hExo, forms a ternary complex with SLBP and the stem-loop and is required for the initiation of histone mRNA degradation. The Lsm1-7 complex is also involved in degradation of polyadenylated mRNAs. It binds to the oligo(A) tail remaining after deadenylation, inhibiting translation and recruiting the enzymes required for decapping. Whether the Lsm1-7 complex interacts directly with other components of the mRNP is not known. We report here that the C-terminal extension of Lsm4 interacts directly with the histone mRNP, contacting both SLBP and 3'hExo. Mutants in the C-terminal tail of Lsm4 that prevent SLBP and 3'hExo binding reduce the rate of histone mRNA degradation when DNA synthesis is inhibited.
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Affiliation(s)
- Shawn M. Lyons
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Adele S. Ricciardi
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Andrew Y. Guo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Christian Kambach
- Department of Biochemistry, Universität Bayreuth, Bayreuth, Germany 95447
| | - William F. Marzluff
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Corresponding authorE-mail
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26
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Fourmann JB, Tillault AS, Blaud M, Leclerc F, Branlant C, Charpentier B. Comparative study of two box H/ACA ribonucleoprotein pseudouridine-synthases: relation between conformational dynamics of the guide RNA, enzyme assembly and activity. PLoS One 2013; 8:e70313. [PMID: 23922977 PMCID: PMC3726423 DOI: 10.1371/journal.pone.0070313] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/18/2013] [Indexed: 11/22/2022] Open
Abstract
Multiple RNA-guided pseudouridine synthases, H/ACA ribonucleoprotein particles (RNPs) which contain a guide RNA and four proteins, catalyze site-specific post-transcriptional isomerization of uridines into pseudouridines in substrate RNAs. In archaeal particles, the guide small RNA (sRNA) is anchored by the pseudouridine synthase aCBF5 and the ribosomal protein L7Ae. Protein aNOP10 interacts with both aCBF5 and L7Ae. The fourth protein, aGAR1, interacts with aCBF5 and enhances catalytic efficiency. Here, we compared the features of two H/ACA sRNAs, Pab21 and Pab91, from Pyrococcus abyssi. We found that aCBF5 binds much more weakly to Pab91 than to Pab21. Surprisingly, the Pab91 sRNP exhibits a higher catalytic efficiency than the Pab21 sRNP. We thus investigated the molecular basis of the differential efficiencies observed for the assembly and catalytic activity of the two enzymes. For this, we compared profiles of the extent of lead-induced cleavages in these sRNAs during a stepwise reconstitution of the sRNPs, and analyzed the impact of the absence of the aNOP10–L7Ae interaction. Such probing experiments indicated that the sRNAs undergo a series of conformational changes upon RNP assembly. These changes were also evaluated directly by circular dichroism (CD) spectroscopy, a tool highly adapted to analyzing RNA conformational dynamics. In addition, our results reveal that the conformation of helix P1 formed at the base of the H/ACA sRNAs is optimized in Pab21 for efficient aCBF5 binding and RNP assembly. Moreover, P1 swapping improved the assembly of the Pab91 sRNP. Nonetheless, efficient aCBF5 binding probably also relies on the pseudouridylation pocket which is not optimized for high activity in the case of Pab21.
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Affiliation(s)
- Jean-Baptiste Fourmann
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Unité Mixte de Recherche Centre National de la Recherche Scientifique - Université de Lorraine, Biopôle de l’Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Anne-Sophie Tillault
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Unité Mixte de Recherche Centre National de la Recherche Scientifique - Université de Lorraine, Biopôle de l’Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Magali Blaud
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Unité Mixte de Recherche Centre National de la Recherche Scientifique - Université de Lorraine, Biopôle de l’Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Fabrice Leclerc
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Unité Mixte de Recherche Centre National de la Recherche Scientifique - Université de Lorraine, Biopôle de l’Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Christiane Branlant
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Unité Mixte de Recherche Centre National de la Recherche Scientifique - Université de Lorraine, Biopôle de l’Université de Lorraine, Vandœuvre-lès-Nancy, France
| | - Bruno Charpentier
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Unité Mixte de Recherche Centre National de la Recherche Scientifique - Université de Lorraine, Biopôle de l’Université de Lorraine, Vandœuvre-lès-Nancy, France
- * E-mail:
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27
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Abstract
The U1A/U2B″/SNF family of proteins found in the U1 and U2 spliceosomal small nuclear ribonucleoproteins is highly conserved. In spite of the high degree of sequence and structural conservation, modern members of this protein family have unique RNA binding properties. These differences have necessarily resulted from evolutionary processes, and therefore, we reconstructed the protein phylogeny in order to understand how and when divergence occurred and how protein function has been modulated. Contrary to the conventional understanding of an ancient human U1A/U2B″ gene duplication, we show that the last common ancestor of bilaterians contained a single ancestral protein (URB). The gene for URB was synthesized, the protein was overexpressed and purified, and we assessed RNA binding to modern snRNA sequences. We find that URB binds human and Drosophila U1 snRNA SLII and U2 snRNA SLIV with higher affinity than do modern homologs, suggesting that both Drosophila SNF and human U1A/U2B″ have evolved into weaker binders of one RNA or both RNAs.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Drosophila
- Drosophila Proteins/chemistry
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Evolution, Molecular
- Gene Duplication
- Humans
- Inverted Repeat Sequences
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phylogeny
- Protein Binding
- Protein Conformation
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U1 Small Nuclear/chemistry
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Sequence Alignment
- Spliceosomes/metabolism
- snRNP Core Proteins/chemistry
- snRNP Core Proteins/genetics
- snRNP Core Proteins/metabolism
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Affiliation(s)
- Sandra G Williams
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63108, USA
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28
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Mathioudakis N, Palencia A, Kadlec J, Round A, Tripsianes K, Sattler M, Pillai RS, Cusack S. The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors. RNA 2012; 18:2056-2072. [PMID: 22996915 PMCID: PMC3479395 DOI: 10.1261/rna.034181.112] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 07/31/2012] [Indexed: 06/01/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are small noncoding RNAs expressed in the germline of animals. They associate with Argonaute proteins of the Piwi subfamily, forming ribonucleoprotein complexes that are involved in maintaining genome integrity. The N-terminal region of some Piwi proteins contains symmetrically dimethylated arginines. This modification is thought to enable recruitment of Tudor domain-containing proteins (TDRDs), which might serve as platforms mediating interactions between various proteins in the piRNA pathway. We measured the binding affinity of the four individual extended Tudor domains (TDs) of murine TDRD1 protein for three different methylarginine-containing peptides from murine Piwi protein MILI. The results show a preference of TD2 and TD3 for consecutive MILI peptides, whereas TD4 and TD1 have, respectively, lower and very weak affinity for any peptide. The affinity of TD1 for methylarginine peptides can be restored by a single-point mutation back to the consensus aromatic cage sequence. These observations were confirmed by pull-down experiments with endogenous Piwi and Piwi-associated proteins. The crystal structure of TD3 bound to a methylated MILI peptide shows an unexpected orientation of the bound peptide, with additional contacts of nonmethylated residues being made outside of the aromatic cage, consistent with solution NMR titration experiments. Finally, the molecular envelope of the four tandem Tudor domains of TDRD1, derived from small angle scattering data, reveals a flexible, elongated shape for the protein. Overall, the results show that TDRD1 can accommodate different peptides from different proteins, and can therefore act as a scaffold protein for complex assembly in the piRNA pathway.
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Affiliation(s)
- Nikolas Mathioudakis
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, BP181, 38042 Grenoble Cedex 9, France
| | - Andres Palencia
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, BP181, 38042 Grenoble Cedex 9, France
| | - Jan Kadlec
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, BP181, 38042 Grenoble Cedex 9, France
| | - Adam Round
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, BP181, 38042 Grenoble Cedex 9, France
| | | | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Ramesh S. Pillai
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, BP181, 38042 Grenoble Cedex 9, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions, UJF-EMBL-CNRS, UMI 3265, BP181, 38042 Grenoble Cedex 9, France
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29
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Liu T, Jin X, Zhang X, Yuan H, Cheng J, Lee J, Zhang B, Zhang M, Wu J, Wang L, Tian G, Wang W. A novel missense SNRNP200 mutation associated with autosomal dominant retinitis pigmentosa in a Chinese family. PLoS One 2012; 7:e45464. [PMID: 23029027 PMCID: PMC3446876 DOI: 10.1371/journal.pone.0045464] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 08/22/2012] [Indexed: 11/18/2022] Open
Abstract
The SNRNP200 gene encodes hBrr2, a helicase essential for pre-mRNA splicing. Six mutations in SNRNP200 have recently been discovered to be associated with autosomal dominant retinitis pigmentosa (adRP). In this work, we analyzed a Chinese family with adRP and identified a novel missense mutation in SNRNP200. To identify the genetic defect in this family, exome of the proband was captured and sequencing analysis was performed to exclude known genetic defects and find possible pathogenic mutations. Subsequently, candidate mutations were validated in affected family members using Sanger sequencing. A novel missense mutation, c.2653C>G transition (p.Q885E), in exon 20 of SNRNP200 was identified. The mutation co-segregated with the disease phenotype over four generations and was absent in 100 normal unaffected individuals. This mutation occurs at highly conserved position in hBrr2 and is predicted to have a functional impact, suggesting that hBrr2-dependent small nuclear riboproteins (snRNPs) unwinding and spliceosome activation is important in the pathogenesis of some variants of RP.
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Affiliation(s)
- Tiecheng Liu
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
- Department of Ophthalmology, Hainan Branch of Chinese PLA General Hospital, Sanya, China
| | - Xin Jin
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
| | - Xuemin Zhang
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
| | - Huijun Yuan
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Jing Cheng
- Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
| | - Janet Lee
- Department of Ophthalmology and Shiley Eye Center, University of California San Diego, La Jolla, California, United States of America
| | - Baoquan Zhang
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
| | - Maonian Zhang
- Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China
| | - Jing Wu
- Department of Science and Technology, BGI-Tianjin, Tianjin, China
| | - Lijuan Wang
- Department of Reproductive Health, BGI-Shenzhen, Shenzhen, China
| | - Geng Tian
- Department of Science and Technology, BGI-Tianjin, Tianjin, China
| | - Weifeng Wang
- Department of Gastroenterology and Hepatology, Hainan Branch of Chinese PLA General Hospital, Sanya, China
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30
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Abstract
The integral telomerase RNA subunit templates the synthesis of telomeric repeats. The biological accumulation of human telomerase RNA (hTR) requires hTR H/ACA domain assembly with the same proteins that assemble on other human H/ACA RNAs. Despite this shared RNP composition, hTR accumulation is particularly sensitized to disruption by disease-linked H/ACA protein variants. We show that contrary to expectation, hTR-specific sequence requirements for biological accumulation do not act at an hTR-specific step of H/ACA RNP biogenesis; instead, they enhance hTR binding to the shared, chaperone-bound scaffold of H/ACA core proteins that mediates initial RNP assembly. We recapitulate physiological H/ACA RNP assembly with a preassembled NAF1/dyskerin/NOP10/NHP2 scaffold purified from cell extract and demonstrate that distributed sequence features of the hTR 3' hairpin synergize to improve scaffold binding. Our findings reveal that the hTR H/ACA domain is distinguished from other human H/ACA RNAs not by a distinct set of RNA-protein interactions but by an increased efficiency of RNP assembly. Our findings suggest a unifying mechanism for human telomerase deficiencies associated with H/ACA protein variants.
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Affiliation(s)
- Emily D Egan
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, USA
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31
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Tan YW, Hong W, Liu DX. Binding of the 5'-untranslated region of coronavirus RNA to zinc finger CCHC-type and RNA-binding motif 1 enhances viral replication and transcription. Nucleic Acids Res 2012; 40:5065-77. [PMID: 22362731 PMCID: PMC3367200 DOI: 10.1093/nar/gks165] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 01/31/2012] [Accepted: 01/31/2012] [Indexed: 01/14/2023] Open
Abstract
Coronaviruses RNA synthesis occurs in the cytoplasm and is regulated by host cell proteins. In a screen based on a yeast three-hybrid system using the 5'-untranslated region (5'-UTR) of SARS coronavirus (SARS-CoV) RNA as bait against a human cDNA library derived from HeLa cells, we found a positive candidate cellular protein, zinc finger CCHC-type and RNA-binding motif 1 (MADP1), to be able to interact with this region of the SARS-CoV genome. This interaction was subsequently confirmed in coronavirus infectious bronchitis virus (IBV). The specificity of the interaction between MADP1 and the 5'-UTR of IBV was investigated and confirmed by using an RNA pull-down assay. The RNA-binding domain was mapped to the N-terminal region of MADP1 and the protein binding sequence to stem-loop I of IBV 5'-UTR. MADP1 was found to be translocated to the cytoplasm and partially co-localized with the viral replicase/transcriptase complexes (RTCs) in IBV-infected cells, deviating from its usual nuclear localization in a normal cell using indirect immunofluorescence. Using small interfering RNA (siRNA) against MADP1, defective viral RNA synthesis was observed in the knockdown cells, therefore indicating the importance of the protein in coronaviral RNA synthesis.
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Affiliation(s)
- Yong Wah Tan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673
| | - Wanjin Hong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673
| | - Ding Xiang Liu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673
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32
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Hoskins AA, Gelles J, Moore MJ. New insights into the spliceosome by single molecule fluorescence microscopy. Curr Opin Chem Biol 2011; 15:864-70. [PMID: 22057211 DOI: 10.1016/j.cbpa.2011.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/10/2011] [Accepted: 10/17/2011] [Indexed: 11/17/2022]
Abstract
Splicing is an essential eukaryotic process in which introns are excised from precursors to messenger RNAs and exons ligated together. This reaction is catalyzed by a multi-MegaDalton machine called the spliceosome, composed of 5 small nuclear RNAs (snRNAs) and a core set of ∼100 proteins minimally required for activity. Because of the spliceosome's size, its low abundance in cellular extracts, and its highly dynamic assembly pathway, analysis of the kinetics of splicing and the conformational rearrangements occurring during spliceosome assembly and disassembly has proven extraordinarily challenging. Here, we review recent progress in combining chemical biology methodologies with single molecule fluorescence techniques to provide a window into splicing in real time. These methods complement ensemble measurements of splicing in vivo and in vitro to facilitate kinetic dissection of pre-mRNA splicing.
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MESH Headings
- Biotin/chemistry
- Biotin/metabolism
- Exons
- Fluorescence Resonance Energy Transfer
- Fluorescent Dyes/analysis
- Fluorescent Dyes/chemistry
- Introns
- Microscopy, Fluorescence/methods
- RNA Precursors/analysis
- RNA Precursors/chemistry
- RNA Precursors/metabolism
- RNA Splicing/genetics
- RNA, Fungal/analysis
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Small Nuclear/analysis
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/analysis
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Spliceosomes/chemistry
- Spliceosomes/genetics
- Spliceosomes/metabolism
- Staining and Labeling/methods
- Streptavidin/chemistry
- Streptavidin/metabolism
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Affiliation(s)
- Aaron A Hoskins
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA.
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33
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Burch BD, Godfrey AC, Gasdaska PY, Salzler HR, Duronio RJ, Marzluff WF, Dominski Z. Interaction between FLASH and Lsm11 is essential for histone pre-mRNA processing in vivo in Drosophila. RNA 2011; 17:1132-47. [PMID: 21525146 PMCID: PMC3096045 DOI: 10.1261/rna.2566811] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Metazoan replication-dependent histone mRNAs are the only nonpolyadenylated cellular mRNAs. Formation of the histone mRNA 3' end requires the U7 snRNP, which contains Lsm10 and Lsm11, and FLASH, a processing factor that binds Lsm11. Here, we identify sequences in Drosophila FLASH (dFLASH) that bind Drosophila Lsm11 (dLsm11), allow localization of dFLASH to the nucleus and histone locus body (HLB), and participate in histone pre-mRNA processing in vivo. Amino acids 105-154 of dFLASH bind to amino acids 1-78 of dLsm11. A two-amino acid mutation of dLsm11 that prevents dFLASH binding but does not affect localization of U7 snRNP to the HLB cannot rescue the lethality or histone pre-mRNA processing defects resulting from an Lsm11 null mutation. The last 45 amino acids of FLASH are required for efficient localization to the HLB in Drosophila cultured cells. Removing the first 64 amino acids of FLASH has no effect on processing in vivo. Removal of 13 additional amino acids of dFLASH results in a dominant negative protein that binds Lsm11 but inhibits processing of histone pre-mRNA in vivo. Inhibition requires the Lsm11 binding site, suggesting that the mutant dFLASH protein sequesters the U7 snRNP in an inactive complex and that residues between 64 and 77 of dFLASH interact with a factor required for processing. Together, these studies demonstrate that direct interaction between dFLASH and dLsm11 is essential for histone pre-mRNA processing in vivo and for proper development and viability in flies.
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MESH Headings
- Animals
- Binding Sites
- Carrier Proteins/chemistry
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cells, Cultured
- Drosophila/genetics
- Drosophila/metabolism
- Drosophila Proteins/chemistry
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Histones/genetics
- Histones/metabolism
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Heterogeneous Nuclear/genetics
- RNA, Heterogeneous Nuclear/metabolism
- RNA, Messenger/metabolism
- Ribonucleoprotein, U7 Small Nuclear/genetics
- Ribonucleoprotein, U7 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
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Affiliation(s)
- Brandon D Burch
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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34
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Fuentes JL, Strayer MS, Matera AG. Molecular determinants of survival motor neuron (SMN) protein cleavage by the calcium-activated protease, calpain. PLoS One 2010; 5:e15769. [PMID: 21209906 PMCID: PMC3012718 DOI: 10.1371/journal.pone.0015769] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 11/28/2010] [Indexed: 01/13/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a leading genetic cause of childhood mortality, caused by reduced levels of survival motor neuron (SMN) protein. SMN functions as part of a large complex in the biogenesis of small nuclear ribonucleoproteins (snRNPs). It is not clear if defects in snRNP biogenesis cause SMA or if loss of some tissue-specific function causes disease. We recently demonstrated that the SMN complex localizes to the Z-discs of skeletal and cardiac muscle sarcomeres, and that SMN is a proteolytic target of calpain. Calpains are implicated in muscle and neurodegenerative disorders, although their relationship to SMA is unclear. Using mass spectrometry, we identified two adjacent calpain cleavage sites in SMN, S192 and F193. Deletion of small motifs in the region surrounding these sites inhibited cleavage. Patient-derived SMA mutations within SMN reduced calpain cleavage. SMN(D44V), reported to impair Gemin2 binding and amino-terminal SMN association, drastically inhibited cleavage, suggesting a role for these interactions in regulating calpain cleavage. Deletion of A188, a residue mutated in SMA type I (A188S), abrogated calpain cleavage, highlighting the importance of this region. Conversely, SMA mutations that interfere with self-oligomerization of SMN, Y272C and SMNΔ7, had no effect on cleavage. Removal of the recently-identified SMN degron (Δ268-294) resulted in increased calpain sensitivity, suggesting that the C-terminus of SMN is important in dictating availability of the cleavage site. Investigation into the spatial determinants of SMN cleavage revealed that endogenous calpains can cleave cytosolic, but not nuclear, SMN. Collectively, the results provide insight into a novel aspect of the post-translation regulation of SMN.
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Affiliation(s)
- Jennifer L. Fuentes
- Program in Molecular Biology and Biotechnology, Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Molly S. Strayer
- Program in Molecular Biology and Biotechnology, Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - A. Gregory Matera
- Program in Molecular Biology and Biotechnology, Departments of Biology and Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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35
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Martin-Tumasz S, Reiter NJ, Brow DA, Butcher SE. Structure and functional implications of a complex containing a segment of U6 RNA bound by a domain of Prp24. RNA 2010; 16:792-804. [PMID: 20181740 PMCID: PMC2844626 DOI: 10.1261/rna.1913310] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
U6 RNA plays a critical role in pre-mRNA splicing. Assembly of U6 into the spliceosome requires a significant structural rearrangement and base-pairing with U4 RNA. In the yeast Saccharomyces cerevisiae, this process requires the essential splicing factor Prp24. We present the characterization and structure of a complex containing one of Prp24's four RNA recognition motif (RRM) domains, RRM2, and a fragment of U6 RNA. NMR methods were used to identify the preferred U6 binding sequence of RRM2 (5'-GAGA-3'), measure the affinity of the interaction, and solve the structure of RRM2 bound to the hexaribonucleotide AGAGAU. Interdomain contacts observed between RRM2 and RRM3 in a crystal structure of the free protein are not detectable in solution. A structural model of RRM1 and RRM2 bound to a longer segment of U6 RNA is presented, and a partial mechanism for Prp24's annealing activity is proposed.
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Affiliation(s)
- Stephen Martin-Tumasz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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36
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Abstract
Repression of transposable elements is crucial for the survival of germ cells. In this issue of Developmental Cell, Shoji et al. provide evidence that a Tudor domain protein TDRD9 partners with MIWI2 to specifically silence LINE-1 transposons in the fetal germline of male mice.
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37
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Martin-Tumasz S, Butcher SE. (1)H, (13)C and (15)N resonance assignments of a ribonucleoprotein complex consisting of Prp24-RRM2 bound to a fragment of U6 RNA. Biomol NMR Assign 2009; 3:227-30. [PMID: 19693704 PMCID: PMC2972308 DOI: 10.1007/s12104-009-9181-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 08/09/2009] [Indexed: 05/19/2023]
Abstract
Saccharomyces cerevisiae Prp24 is an essential RNA binding protein involved in pre-mRNA splicing. Nearly complete backbone and side chain resonance assignments have been obtained for the second RNA recognition motif (RRM) of Prp24 (RRM2, residues M114-E197) both in isolation and bound to a six nucleotide fragment of U6 RNA (AGAGAU). In addition, nearly complete backbone assignments have been made for a Prp24 construct spanning the second and third RRMs (RRM23, residues M114-K290), both free and bound to AGAGAU.
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38
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Abstract
Among anti-nuclear antibodies, anti-Sm and anti-RNP antibodies are of the utmost importance in clinical practice. Anti-Sm antibodies are directed against 7 proteins (B/B', D1, D2, D3, E, F, G) that constitute the common core of U1, U2, U4 and U5 small nuclear ribonucleoprotein (snRNP) particles; B/B', D1 and D3 are more frequently targeted. Anti-RNP antibodies react with proteins (70 Kd, A, C) that are associated with U1 RNA and form U1snRNP. Anti-Sm and anti-RNP antibodies are directed towards both discontinuous and linear epitopes which are either contained in the protein sequence or are post-translationally modified. The assays to detect anti-Sm and anti-RNP antibodies are counterimmunoelectrophoresis (CIE), immunoblot, and ELISA, based on purified or recombinant proteins or synthetic peptides. Anti-Sm antibodies are detectable in a percentage of SLE patients comprised between 5 and 30%; they are more prevalent in blacks and because of their high specificity for SLE have been included in the serological criteria for diagnosing the disease.Anti-RNP are detectable in 25-47% of SLE patients; high titers of anti-RNP antibodies are diagnostic of mixed connective tissue disorder (MCTD). The measurement of anti-Sm and anti-RNP antibodies is more important in the diagnosis of SLE than in the follow-up of patients. However, anti-RNP antibodies are more prevalent in patients with Raynaud's phenomenon and are associated with milder renal involvement. On the contrary, anti-Sm antibodies are associated with the severity and the activity of renal involvement. The specificity of anti-Sm antibodies, together with epidemiological data, suggest that Epstein-Barr virus infection has the potential to induce anti-Sm antibodies by molecular mimicry.Anti-nuclear antibodies, a hallmark of the systemic autoimmune diseases, include several populations of antibodies with different specificities. Among them, anti-Sm and anti-RNP antibodies are of the utmost importance in clinical practice; in research, the study of the mechanisms inducing their production has opened up new perspectives and helped to elucidate the pathogenesis of autoimmune disorders.
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Affiliation(s)
- P Migliorini
- Clinical Immunology Unit, Department of Internal Medicine, University of Pisa, Italy
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39
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Abstract
RNA recognition motifs (RRMs) constitute versatile macromolecular interaction platforms. They are found in many components of spliceosomes, in which they mediate RNA and protein interactions by diverse molecular strategies. The human U11/U12-65K protein of the minor spliceosome employs a C-terminal RRM to bind hairpin III of the U12 small nuclear RNA (snRNA). This interaction comprises one side of a molecular bridge between the U11 and U12 small nuclear ribonucleoprotein particles (snRNPs) and is reminiscent of the binding of the N-terminal RRMs in the major spliceosomal U1A and U2B'' proteins to hairpins in their cognate snRNAs. Here we show by mutagenesis and electrophoretic mobility shift assays that the beta-sheet surface and a neighboring loop of 65K C-terminal RRM are involved in RNA binding, as previously seen in canonical RRMs like the N-terminal RRMs of the U1A and U2B'' proteins. However, unlike U1A and U2B'', some 30 residues N-terminal of the 65K C-terminal RRM core are additionally required for stable U12 snRNA binding. The crystal structure of the expanded 65K C-terminal RRM revealed that the N-terminal tail adopts an alpha-helical conformation and wraps around the protein toward the face opposite the RNA-binding platform. Point mutations in this part of the protein had only minor effects on RNA affinity. Removal of the N-terminal extension significantly decreased the thermal stability of the 65K C-terminal RRM. These results demonstrate that the 65K C-terminal RRM is augmented by an N-terminal element that confers stability to the domain, and thereby facilitates stable RNA binding.
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MESH Headings
- Crystallography, X-Ray
- Electrophoretic Mobility Shift Assay
- Humans
- Models, Molecular
- Protein Conformation
- Protein Structure, Secondary
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Spliceosomes
- snRNP Core Proteins/genetics
- snRNP Core Proteins/metabolism
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Affiliation(s)
- Catharina Netter
- Max-Planck-Institut für Biophysikalische Chemie, D-37077 Göttingen, Germany
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40
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Hardin JW, Reyes FE, Batey RT. Analysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex. J Biol Chem 2009; 284:15317-24. [PMID: 19336398 PMCID: PMC2685712 DOI: 10.1074/jbc.m901368200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Indexed: 11/06/2022] Open
Abstract
In archaea and eukarya, box C/D ribonucleoprotein (RNP) complexes are responsible for 2'-O-methylation of tRNAs and rRNAs. The archaeal box C/D small RNP complex requires a small RNA component (sRNA) possessing Watson-Crick complementarity to the target RNA along with three proteins: L7Ae, Nop5p, and fibrillarin. Transfer of a methyl group from S-adenosylmethionine to the target RNA is performed by fibrillarin, which by itself has no affinity for the sRNA-target duplex. Instead, it is targeted to the site of methylation through association with Nop5p, which in turn binds to the L7Ae-sRNA complex. To understand how Nop5p serves as a bridge between the targeting and catalytic functions of the box C/D small RNP complex, we have employed alanine scanning to evaluate the interaction between the Pyrococcus horikoshii Nop5p domain and an L7Ae box C/D RNA complex. From these data, we were able to construct an isolated RNA-binding domain (Nop-RBD) that folds correctly as demonstrated by x-ray crystallography and binds to the L7Ae box C/D RNA complex with near wild type affinity. These data demonstrate that the Nop-RBD is an autonomously folding and functional module important for protein assembly in a number of complexes centered on the L7Ae-kinkturn RNP.
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Affiliation(s)
- John W Hardin
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA
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41
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Ogawa C, Usui K, Ito F, Itoh M, Hayashizaki Y, Suzuki H. Role of survival motor neuron complex components in small nuclear ribonucleoprotein assembly. J Biol Chem 2009; 284:14609-17. [PMID: 19321448 PMCID: PMC2682908 DOI: 10.1074/jbc.m809031200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 03/19/2009] [Indexed: 11/06/2022] Open
Abstract
Survival motor neuron (SMN) complex is essential for the biogenesis of the small nuclear ribonucleoprotein (snRNP) complex, although the complete role of each SMN complex component for the snRNP synthesis is largely unclear. We have identified an interaction between the two components Gemin2-Gemin7 using the mammalian two-hybrid system. In vitro stability assay revealed that the known SMN-Gemin7 interaction becomes stable in the presence of Gemin2 possibly via the identified Gemin2-Gemin7 interaction. Gemin7 knockdown revealed a decrease in snRNP assembly activity and a decrease in SmE protein, a component of snRNP, in the SMN complex, which was consistent with a previous discussion that the Gemin6-Gemin7 heterodimer may serve as a surrogate for the SmD3-SmB particle in forming a subcore, the intermediate complex for snRNP. Interestingly, we found that Unrip, but not Gemin8, can remove Gemin7 from the stable SMN-Gemin2-Gemin7 ternary complex. In an in vitro snRNP assembly assay using the Unrip knockdown and the untreated cell lysates, we revealed that there was a decrease in Gemin7 and increase in SmB/B' in the SMN complex observed in untreated cells during the assay, suggesting that the Gemin6-Gemin7 heterodimer in the subcore is exchanged by the SmD3-SmB particle to form snRNP. Surprisingly, these changes were not observed in the assay using the Unrip knockdown cell extracts, indicating the importance of Unrip in the formation of snRNP likely via removal of the Gemin6-Gemin7 from the SMN complex. Taken together, these results indicate that snRNP is synthesized by harmonization of the SMN complex components.
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Affiliation(s)
- Chihiro Ogawa
- RIKEN Omics Sciences Center, RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Japan
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Singh SK, Gurha P, Gupta R. Dynamic guide-target interactions contribute to sequential 2'-O-methylation by a unique archaeal dual guide box C/D sRNP. RNA 2008; 14:1411-23. [PMID: 18515549 PMCID: PMC2441990 DOI: 10.1261/rna.1003308] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 04/16/2008] [Indexed: 05/05/2023]
Abstract
Assembly and guide-target interaction of an archaeal box C/D-guide sRNP was investigated under various conditions by analyzing the lead (II)-induced cleavage of the guide RNA. Guide and target RNAs derived from Haloferax volcanii pre-tRNA(Trp) were used with recombinant Methanocaldococcus jannaschii core proteins in the reactions. Core protein L7Ae binds differentially to C/D and C'/D' motifs of the guide RNA, and interchanging the two motifs relative to the termini of the guide RNA did not affect L7Ae binding or sRNA function. L7Ae binding to the guide RNA exposes its D'-guide sequence first followed by the D guide. These exposures are reduced when aNop5p and aFib proteins are added. The exposed guide sequences did not pair with the target sequences in the presence of L7Ae alone. The D-guide sequence could pair with the target in the presence of L7Ae and aNop5p, suggesting a role of aNop5p in target recruitment and rearrangement of sRNA structure. aFib binding further stabilizes this pairing. After box C/D-guided modification, target-guide pairing at the D-guide sequence is disrupted, suggesting that each round of methylation may require some conformational change or reassembly of the RNP. Asymmetric RNPs containing only one L7Ae at either of the two box motifs can be assembled, but a functional RNP requires L7Ae at the box C/D motif. This arrangement resembles the asymmetric eukaryal snoRNP. Observations of initial D-guide-target pairing and the functional requirement for L7Ae at the box C/D motif are consistent with our previous report of the sequential 2'-O-methylations of the target RNA.
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Affiliation(s)
- Sanjay K Singh
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA
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Workman H, Skalicky JJ, Flynn PF. Assignment of 1H, 13C, and 15N resonances of the RNA binding protein Snu13p from Saccharomyces cerevisiae. Biomol NMR Assign 2008; 2:1-3. [PMID: 19636910 DOI: 10.1007/s12104-007-9069-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 11/14/2007] [Indexed: 05/28/2023]
Abstract
Snu13p is a highly conserved RNA binding protein from Saccharomyces cerevisiae required for both eukaryotic pre-mRNA splicing and pre-rRNA processing. The 1H, 13C, and 15N assignments were determined from multidimensional, multinuclear NMR experiments conducted at 25 degrees C.
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Affiliation(s)
- Hillary Workman
- Department of Chemistry, University of Utah, 315 S. 1400 E. Room 2020, Salt Lake City, UT 84112, USA
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Gonsalvez GB, Praveen K, Hicks AJ, Tian L, Matera AG. Sm protein methylation is dispensable for snRNP assembly in Drosophila melanogaster. RNA 2008; 14:878-887. [PMID: 18369183 PMCID: PMC2327358 DOI: 10.1261/rna.940708] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 01/30/2008] [Indexed: 05/26/2023]
Abstract
Sm proteins form stable ribonucleoprotein (RNP) complexes with small nuclear (sn)RNAs and are core components of the eukaryotic spliceosome. In vivo, the assembly of Sm proteins onto snRNAs requires the survival motor neurons (SMN) complex. Several reports have shown that SMN protein binds with high affinity to symmetric dimethylarginine (sDMA) residues present on the C-terminal tails of SmB, SmD1, and SmD3. This post-translational modification is thought to play a crucial role in snRNP assembly. In human cells, two distinct protein arginine methyltransferases (PRMT5 and PRMT7) are required for snRNP biogenesis. However, in Drosophila, loss of Dart5 (the fruit fly PRMT5 ortholog) has little effect on snRNP assembly, and homozygous mutants are completely viable. To resolve these apparent differences, we examined this topic in detail and found that Drosophila Sm proteins are also methylated by two methyltransferases, Dart5/PRMT5 and Dart7/PRMT7. Unlike dart5, we found that dart7 is an essential gene. However, the lethality associated with loss of Dart7 protein is apparently unrelated to defects in snRNP assembly. To conclusively test the requirement for sDMA modification of Sm proteins in Drosophila snRNP assembly, we constructed a fly strain that exclusively expresses an isoform of SmD1 that cannot be sDMA modified. Interestingly, these flies were viable, and snRNP assays revealed no defects in comparison to wild type. In contrast, dart5 mutants displayed a strong synthetic lethal phenotype in the presence of a hypomorphic Smn mutation. We therefore conclude that dart5 is required for viability when SMN is limiting.
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Affiliation(s)
- Graydon B Gonsalvez
- Department of Biology, Program in Molecular Biology and Biotechnology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
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Ali GS, Prasad KVSK, Hanumappa M, Reddy ASN. Analyses of in vivo interaction and mobility of two spliceosomal proteins using FRAP and BiFC. PLoS One 2008; 3:e1953. [PMID: 18414657 PMCID: PMC2278372 DOI: 10.1371/journal.pone.0001953] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Accepted: 03/05/2008] [Indexed: 12/22/2022] Open
Abstract
U1-70K, a U1 snRNP-specific protein, and serine/arginine-rich (SR) proteins are components of the spliceosome and play critical roles in both constitutive and alternative pre-mRNA splicing. However, the mobility properties of U1-70K, its in vivo interaction with SR proteins, and the mobility of the U1-70K-SR protein complex have not been studied in any system. Here, we studied the in vivo interaction of U1-70K with an SR protein (SR45) and the mobility of the U1-70K/SR protein complex using bimolecular fluorescence complementation (BiFC) and fluorescence recovery after photobleaching (FRAP). Our results show that U1-70K exchanges between speckles and the nucleoplasmic pool very rapidly and that this exchange is sensitive to ongoing transcription and phosphorylation. BiFC analyses showed that U1-70K and SR45 interacted primarily in speckles and that this interaction is mediated by the RS1 or RS2 domain of SR45. FRAP analyses showed considerably slower recovery of the SR45/U1-70K complex than either protein alone indicating that SR45/U1-70K complexes remain in the speckles for a longer duration. Furthermore, FRAP analyses with SR45/U1-70K complex in the presence of inhibitors of phosphorylation did not reveal any significant change compared to control cells, suggesting that the mobility of the complex is not affected by the status of protein phosphorylation. These results indicate that U1-70K, like SR splicing factors, moves rapidly in the nucleus ensuring its availability at various sites of splicing. Furthermore, although it appears that U1-70K moves by diffusion its mobility is regulated by phosphorylation and transcription.
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Affiliation(s)
- Gul Shad Ali
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, United States of America
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Affiliation(s)
- Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR 5535-IFR 122, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
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Abstract
Mass spectrometry is a powerful tool for the analysis of biomolecules, proteins, nucleic acids, carbohydrates, lipids. In combination with genome sequences that are available in the databases, it has proven to be the most straightforward and sensitive technique for the sequence analysis and hence the identification of protein components in the cells, their (post)translational modifications, and their relative and absolute abundance. In addition, mass spectrometric methods are successfully applied for the structural analysis of biomolecules (i.e., deciphering molecule-ligand interactions and spatial quartenary arrangements of molecule complexes). We describe a methodology for the mass spectrometric analysis of protein-RNA contact sites in purified ribonucleoprotein (RNP) particles. The method comprises ultraviolet (UV) crosslinking of proteins to RNA, hydrolysis of the protein and RNA moieties, isolation of cross-linked peptide-RNA oligonucleotides, MALDI (matrix-assisted laser desorption/ionization) mass spectrometry of the isolated conjugates to determine the sequence of the crosslinked peptide and RNA part. The utility of this methodology is demonstrated on crosslinks isolated from UV-irradiated spliceosomal particles; these were [15.5 K-61 K-U4atac] small nuclear ribonucleoprotein (snRNP) particles prepared by reconstitution in vitro and U1 snRNP particles purified from HeLa cells.
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Affiliation(s)
- Henning Urlaub
- Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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48
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Nielsen JS, Bøggild A, Andersen CBF, Nielsen G, Boysen A, Brodersen DE, Valentin-Hansen P. An Hfq-like protein in archaea: crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii. RNA 2007; 13:2213-2223. [PMID: 17959927 PMCID: PMC2080587 DOI: 10.1261/rna.689007] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Accepted: 09/11/2007] [Indexed: 05/25/2023]
Abstract
The Sm and Sm-like proteins are conserved in all three domains of life and have emerged as important players in many different RNA-processing reactions. Their proposed role is to mediate RNA-RNA and/or RNA-protein interactions. In marked contrast to eukaryotes, bacteria appear to contain only one distinct Sm-like protein belonging to the Hfq family of proteins. Similarly, there are generally only one or two subtypes of Sm-related proteins in archaea, but at least one archaeon, Methanococcus jannaschii, encodes a protein that is related to Hfq. This archaeon does not contain any gene encoding a conventional archaeal Sm-type protein, suggesting that Hfq proteins and archaeal Sm-homologs can complement each other functionally. Here, we report the functional characterization of M. jannaschii Hfq and its crystal structure at 2.5 A resolution. The protein forms a hexameric ring. The monomer fold, as well as the overall structure of the complex is similar to that found for the bacterial Hfq proteins. However, clear differences are seen in the charge distribution on the distal face of the ring, which is unusually negative in M. jannaschii Hfq. Moreover, owing to a very short N-terminal alpha-helix, the overall diameter of the archaeal Hfq hexamer is significantly smaller than its bacterial counterparts. Functional analysis reveals that Escherichia coli and M. jannaschii Hfqs display very similar biochemical and biological properties. It thus appears that the archaeal and bacterial Hfq proteins are largely functionally interchangeable.
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Affiliation(s)
- Jesper S Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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49
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Dobbyn HC, McEwan PA, Krause A, Novak-Frazer L, Bella J, O'Keefe RT. Analysis of pre-mRNA and pre-rRNA processing factor Snu13p structure and mutants. Biochem Biophys Res Commun 2007; 360:857-62. [PMID: 17631273 DOI: 10.1016/j.bbrc.2007.06.163] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 06/28/2007] [Indexed: 11/18/2022]
Abstract
Snu13p is a Saccharomyces cerevisiae protein essential for pre-messenger RNA splicing and pre-ribosomal RNA processing. Snu13p binds U4 snRNA of the spliceosome and box C/D snoRNAs of the pre-ribosomal RNA processing machinery to induce assembly of each ribonucleoprotein complex. Here, we present structural and biochemical analysis of Snu13p. The crystal structure of Snu13p reveals a region of the protein which could be important for protein interaction during ribonucleoprotein assembly. Using the structure of Snu13p we have designed the first temperature-sensitive mutants in Snu13p, L67W and I102A. Wild-type and mutant Snu13p proteins were assayed for binding to U4 snRNA and U3 snoRNA. Both temperature-sensitive mutants displayed significantly reduced RNA binding compared to wild-type protein. As the temperature-sensitive mutations are not in the known RNA binding region of Snu13p this indicates that these mutants indirectly influence the RNA binding properties of Snu13p. This work provides insight into Snu13p function during ribonucleoprotein assembly.
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Affiliation(s)
- Helen C Dobbyn
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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50
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Jeronimo C, Forget D, Bouchard A, Li Q, Chua G, Poitras C, Thérien C, Bergeron D, Bourassa S, Greenblatt J, Chabot B, Poirier GG, Hughes TR, Blanchette M, Price DH, Coulombe B. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Mol Cell 2007; 27:262-274. [PMID: 17643375 PMCID: PMC4498903 DOI: 10.1016/j.molcel.2007.06.027] [Citation(s) in RCA: 341] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 05/16/2007] [Accepted: 06/22/2007] [Indexed: 01/20/2023]
Abstract
We have performed a survey of soluble human protein complexes containing components of the transcription and RNA processing machineries using protein affinity purification coupled to mass spectrometry. Thirty-two tagged polypeptides yielded a network of 805 high-confidence interactions. Remarkably, the network is significantly enriched in proteins that regulate the formation of protein complexes, including a number of previously uncharacterized proteins for which we have inferred functions. The RNA polymerase II (RNAP II)-associated proteins (RPAPs) are physically and functionally associated with RNAP II, forming an interface between the enzyme and chaperone/scaffolding proteins. BCDIN3 is the 7SK snRNA methylphosphate capping enzyme (MePCE) present in an snRNP complex containing both RNA processing and transcription factors, including the elongation factor P-TEFb. Our results define a high-density protein interaction network for the mammalian transcription machinery and uncover multiple regulatory factors that target the transcription machinery.
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Affiliation(s)
- Célia Jeronimo
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Diane Forget
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Annie Bouchard
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Qintong Li
- Biochemistry Department, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Gordon Chua
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Christian Poitras
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Cynthia Thérien
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Dominique Bergeron
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Sylvie Bourassa
- Centre hospitalier universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada
| | - Jack Greenblatt
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Benoit Chabot
- Département de microbiologie et infectiologie, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Guy G Poirier
- Centre hospitalier universitaire de Québec, Université Laval, Québec, QC G1V 4G2, Canada
| | - Timothy R Hughes
- Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5G 1L6, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics, McGill University, Montréal, QC H3A 2B4, Canada
| | - David H Price
- Biochemistry Department, University of Iowa, Iowa City, IA 52242-1109, USA
| | - Benoit Coulombe
- Laboratory of Gene Transcription and Proteomics Discovery Platform, Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada.
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