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Guidarelli Mattioli F, Saltalamacchia A, Magistrato A. Tracing Allostery in the Spliceosome Ski2-like RNA Helicase Brr2. J Phys Chem Lett 2024; 15:3502-3508. [PMID: 38517341 DOI: 10.1021/acs.jpclett.3c03538] [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] [Indexed: 03/23/2024]
Abstract
RNA ATPases/helicases remodel substrate RNA-protein complexes in distinct ways. The different RNA ATPases/helicases, taking part in the spliceosome complex, reshape the RNA/RNA-protein contacts to enable premature-mRNA splicing. Among them, the bad response to refrigeration 2 (Brr2) helicase promotes U4/U6 small nuclear (sn)RNA unwinding via ATP-driven translocation of the U4 snRNA strand, thus playing a pivotal role during the activation, catalytic, and disassembly phases of splicing. The plastic Brr2 architecture consists of an enzymatically active N-terminal cassette (N-cassette) and a structurally similar but inactive C-terminal cassette (C-cassette). The C-cassette, along with other allosteric effectors and regulators, tightly and timely controls Brr2's function via an elusive mechanism. Here, microsecond-long molecular dynamics simulations, dynamical network theory, and community network analysis are combined to elucidate how allosteric effectors/regulators modulate the Brr2 function. We unexpectedly reveal that U4 snRNA itself acts as an allosteric regulator, amplifying the cross-talk of distal Brr2 domains and triggering a conformational reorganization of the protein. Our findings offer fundamental understanding into Brr2's mechanism of action and broaden our knowledge on the sophisticated regulatory mechanisms by which spliceosome ATPases/helicases control gene expression. This includes their allosteric regulation exerted by client RNA strands, a mechanism that may be broadly applicable to other RNA-dependent ATPases/helicases.
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Affiliation(s)
| | - Andrea Saltalamacchia
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy, Institute of Material Foundry at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
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2
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Klimešová K, Petržílková H, Bařinka C, Staněk D. SART3 associates with a post-splicing complex. J Cell Sci 2023; 136:jcs260380. [PMID: 36620952 DOI: 10.1242/jcs.260380] [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: 06/27/2022] [Accepted: 12/10/2022] [Indexed: 01/10/2023] Open
Abstract
SART3 is a multifunctional protein that acts in several steps of gene expression, including assembly and recycling of the spliceosomal U4/U6 small nuclear ribonucleoprotein particle (snRNP). In this work, we provide evidence that SART3 associates via its N-terminal HAT domain with the 12S U2 snRNP. Further analysis showed that SART3 associates with the post-splicing complex containing U2 and U5 snRNP components. In addition, we observed an interaction between SART3 and the RNA helicase DHX15, which disassembles post-splicing complexes. Based on our data, we propose a model that SART3 associates via its N-terminal HAT domain with the post-splicing complex, where it interacts with U6 snRNA to protect it and to initiate U6 snRNA recycling before a next round of splicing.
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MESH Headings
- RNA Splicing/genetics
- Spliceosomes/genetics
- Spliceosomes/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U5 Small Nuclear/genetics
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
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Affiliation(s)
- Klára Klimešová
- Department of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Hana Petržílková
- Department of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Cyril Bařinka
- Laboratory of Structural Biology, Institute of Biotechnology, Czech Academy of Sciences, 252 50 Prague, Czech Republic
| | - David Staněk
- Department of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
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3
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Llinas RJ, Xiong JQ, Clark NM, Burkhart SE, Bartel B. An Arabidopsis pre-RNA processing8a (prp8a) missense allele restores splicing of a subset of mis-spliced mRNAs. Plant Physiol 2022; 189:2175-2192. [PMID: 35608297 PMCID: PMC9342983 DOI: 10.1093/plphys/kiac221] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Eukaryotic precursor mRNAs often harbor noncoding introns that must be removed prior to translation. Accurate splicing of precursor messenger RNA depends on placement and assembly of small nuclear ribonucleoprotein (snRNP) sub-complexes of the spliceosome. Yeast (Saccharomyces cerevisiae) studies established a role in splice-site selection for PRE-RNA PROCESSING8 (PRP8), a conserved spliceosome scaffolding protein of the U5 snRNP. However, analogous splice-site selection studies in multicellular eukaryotes are lacking. Such studies are crucial for a comprehensive understanding of alternative splicing, which is extensive in plants and animals but limited in yeast. In this work, we describe an Arabidopsis (Arabidopsis thaliana) prp8a mutant that modulates splice-site selection. We isolated prp8a-14 from a screen for suppressors of pex14-6, which carries a splice-site mutation in the PEROXIN14 (PEX14) peroxisome biogenesis gene. To elucidate Arabidopsis PRP8A function in spliceosome fidelity, we combined prp8a-14 with various pex14 splice-site mutations and monitored the double mutants for physiological and molecular consequences of dysfunctional and functional peroxisomes that correspond to impaired and recovered splicing, respectively. prp8a-14 restored splicing and PEX14 function to alleles with mutations in the exonic guanine of the 5'-splice site but did not restore splicing or function to alleles with mutations in the intronic guanine of 5'- or 3'-splice sites. We used RNA-seq to reveal the systemic impact of prp8a-14 and found hundreds of differentially spliced transcripts and thousands of transcripts with significantly altered levels. Among differentially spliced transcripts, prp8a-14 significantly altered 5'- and 3'-splice-site utilization to favor sites resulting in shorter introns. This study provides a genetic platform for probing splicing in plants and hints at a role for plant PRP8 in splice-site selection.
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Affiliation(s)
- Roxanna J Llinas
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
| | | | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Sarah E Burkhart
- Department of Biosciences, Rice University, Houston, Texas 77005, USA
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4
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Ahmed MB, Islam SU, Sonn JK, Lee YS. PRP4 Kinase Domain Loss Nullifies Drug Resistance and Epithelial-Mesenchymal Transition in Human Colorectal Carcinoma Cells. Mol Cells 2020; 43:662-670. [PMID: 32576716 PMCID: PMC7398799 DOI: 10.14348/molcells.2020.2263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/23/2020] [Accepted: 04/26/2020] [Indexed: 01/24/2023] Open
Abstract
We have investigated the involvement of the pre-mRNA processing factor 4B (PRP4) kinase domain in mediating drug resistance. HCT116 cells were treated with curcumin, and apoptosis was assessed based on flow cytometry and the generation of reactive oxygen species (ROS). Cells were then transfected with PRP4 or pre-mRNA-processing-splicing factor 8 (PRP8), and drug resistance was analyzed both in vitro and in vivo. Furthermore, we deleted the kinase domain in PRP4 using GatewayTM technology. Curcumin induced cell death through the production of ROS and decreased the activation of survival signals, but PRP4 overexpression reversed the curcumin-induced oxidative stress and apoptosis. PRP8 failed to reverse the curcumin-induced apoptosis in the HCT116 colon cancer cell line. In xenograft mouse model experiments, curcumin effectively reduced tumour size whereas PRP4 conferred resistance to curcumin, which was evident from increasing tumour size, while PRP8 failed to regulate the curcumin action. PRP4 overexpression altered the morphology, rearranged the actin cytoskeleton, triggered epithelial-mesenchymal transition (EMT), and decreased the invasiveness of HCT116 cells. The loss of E-cadherin, a hallmark of EMT, was observed in HCT116 cells overexpressing PRP4. Moreover, we observed that the EMT-inducing potential of PRP4 was aborted after the deletion of its kinase domain. Collectively, our investigations suggest that the PRP4 kinase domain is responsible for promoting drug resistance to curcumin by inducing EMT. Further evaluation of PRP4-induced inhibition of cell death and PRP4 kinase domain interactions with various other proteins might lead to the development of novel approaches for overcoming drug resistance in patients with colon cancer.
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Affiliation(s)
- Muhammad Bilal Ahmed
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 4566, Korea
| | - Salman Ul Islam
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 4566, Korea
| | - Jong Kyung Sonn
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea
| | - Young Sup Lee
- School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 4566, Korea
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Ren H, Fabbri C, Uher R, Rietschel M, Mors O, Henigsberg N, Hauser J, Zobel A, Maier W, Dernovsek MZ, Souery D, Cattaneo A, Breen G, Craig IW, Farmer AE, McGuffin P, Lewis CM, Aitchison KJ. Genes associated with anhedonia: a new analysis in a large clinical trial (GENDEP). Transl Psychiatry 2018; 8:150. [PMID: 30104601 PMCID: PMC6089928 DOI: 10.1038/s41398-018-0198-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 02/17/2018] [Accepted: 03/26/2018] [Indexed: 12/14/2022] Open
Abstract
A key feature of major depressive disorder (MDD) is anhedonia, which is a predictor of response to antidepressant treatment. In order to shed light on its genetic underpinnings, we conducted a genome-wide association study (GWAS) followed by investigation of biological pathway enrichment using an anhedonia dimension for 759 patients with MDD in the GENDEP study. The GWAS identified 18 SNPs associated at genome-wide significance with the top one being an intronic SNP (rs9392549) in PRPF4B (pre-mRNA processing factor 4B) located on chromosome 6 (P = 2.07 × 10-9) while gene-set enrichment analysis returned one gene ontology term, axon cargo transport (GO: 0008088) with a nominally significant P value (1.15 × 10-5). Furthermore, our exploratory analysis yielded some interesting, albeit not statistically significant genetic correlation with Parkinson's Disease and nucleus accumbens gray matter. In addition, polygenic risk scores (PRSs) generated from our association analysis were found to be able to predict treatment efficacy of the antidepressants in this study. In conclusion, we found some markers significantly associated with anhedonia, and some suggestive findings of related pathways and biological functions, which could be further investigated in other studies.
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Affiliation(s)
- Hongyan Ren
- Psychiatry and Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Chiara Fabbri
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Rudolf Uher
- Psychiatry Department, Dalhousie University, Halifax, NS, Canada
| | - Marcella Rietschel
- Division of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim, Germany
| | - Ole Mors
- Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Neven Henigsberg
- Croatian Institute for Brain Research, University of Zagreb, Zagreb, Croatia
| | - Joanna Hauser
- Psychiatry Department, University of Poznan, Poznan, Poland
| | - Astrid Zobel
- Psychiatry Department, University of Bonn, Bonn, Germany
| | - Wolfgang Maier
- Psychiatry Department, University of Bonn, Bonn, Germany
| | - Mojca Z Dernovsek
- University Psychiatric Clinic, University of Ljubliana, Ljubljana, Slovenia
| | - Daniel Souery
- Psychological Medicine, Free University of Brussels, Brussels, Belgium
| | | | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Ian W Craig
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Anne E Farmer
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Peter McGuffin
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Cathryn M Lewis
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Katherine J Aitchison
- Psychiatry and Medical Genetics, University of Alberta, Edmonton, AB, Canada.
- MRC Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK.
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MacRae AJ, Mayerle M, Hrabeta-Robinson E, Chalkley RJ, Guthrie C, Burlingame AL, Jurica MS. Prp8 positioning of U5 snRNA is linked to 5' splice site recognition. RNA 2018; 24:769-777. [PMID: 29487104 PMCID: PMC5959246 DOI: 10.1261/rna.065458.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 02/26/2018] [Indexed: 05/22/2023]
Abstract
Prp8 is an essential protein that regulates spliceosome assembly and conformation during pre-mRNA splicing. Recent cryo-EM structures of the spliceosome model Prp8 as a scaffold for the spliceosome's catalytic U snRNA components. Using a new amino acid probing strategy, we identified a dynamic region in human Prp8 that is positioned to stabilize the pre-mRNA in the spliceosome active site through interactions with U5 snRNA. Mutagenesis of the identified Prp8 residues in yeast indicates a role in 5' splice site recognition. Genetic interactions with spliceosome proteins Isy1, which buttresses the intron branch point, and Snu114, a regulatory GTPase that directly contacts Prp8, further corroborate a role for the same Prp8 residues in substrate positioning and activation. Together the data suggest that adjustments in interactions between Prp8 and U5 snRNA help establish proper positioning of the pre-mRNA into the active site to enhance 5' splice site fidelity.
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Affiliation(s)
- Andrew J MacRae
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Megan Mayerle
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
| | - Eva Hrabeta-Robinson
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
| | - Robert J Chalkley
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94122, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94122, USA
| | - Melissa S Jurica
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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7
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Abstract
Spliceosomal proteins have been revealed as SUMO conjugation targets. Moreover, we have reported that many of these are in a SUMO-conjugated form when bound to a pre-mRNA substrate during a splicing reaction. We demonstrated that SUMOylation of Prp3 (PRPF3), a component of the U4/U6 di-snRNP, is required for U4/U6•U5 tri-snRNP formation and/or recruitment to active spliceosomes. Expanding upon our previous results, we have shown that the splicing factor SRSF1 stimulates SUMO conjugation to several spliceosomal proteins. Given the relevance of the splicing process, as well as the complex and dynamic nature of its governing machinery, the spliceosome, the molecular mechanisms that modulate its function represent an attractive topic of research. We posit that SUMO conjugation could represent a way of modulating spliceosome assembly and thus, splicing efficiency. How cycles of SUMOylation/de-SUMOylation of spliceosomal proteins become integrated throughout the highly choreographed spliceosomal cycle awaits further investigation.
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Affiliation(s)
- Berta Pozzi
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Pablo Mammi
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Laureano Bragado
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Luciana E. Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
| | - Anabella Srebrow
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE, UBA- CONICET); Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Ciudad Universitaria, Buenos Aires, Argentina
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8
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Hsu J, Gore-Panter S, Tchou G, Castel L, Lovano B, Moravec CS, Pettersson GB, Roselli EE, Gillinov AM, McCurry KR, Smedira NG, Barnard J, Van Wagoner DR, Chung MK, Smith JD. Genetic Control of Left Atrial Gene Expression Yields Insights into the Genetic Susceptibility for Atrial Fibrillation. Circ Genom Precis Med 2018; 11:e002107. [PMID: 29545482 PMCID: PMC5858469 DOI: 10.1161/circgen.118.002107] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 03/07/2017] [Accepted: 01/23/2018] [Indexed: 02/01/2023]
Abstract
BACKGROUND Genome-wide association studies have identified 23 loci for atrial fibrillation (AF), but the mechanisms responsible for these associations, as well as the causal genes and genetic variants, remain undefined. METHODS To identify the effect of common genetic variants on gene expression that might explain the mechanisms linking genome-wide association loci with AF risk, we performed RNA sequencing of left atrial appendages from a biracial cohort of 265 subjects. RESULTS Combining gene expression data with genome-wide single nucleotide polymorphism data, we found that approximately two-thirds of the expressed genes were regulated in cis by common genetic variants at a false discovery rate of <0.05, defined as cis-expression quantitative trait loci. Twelve of 23 reported AF genome-wide association loci displayed genome-wide significant cis-expression quantitative trait loci, at PRRX1 (chromosome 1q24), SNRNP27 (1q24), CEP68 (2p14), FKBP7 (2q31), KCNN2 (5q22), FAM13B (5q31), CAV1 (7q31), ASAH1 (8p22), MYOZ1 (10q22), C11ORF45 (11q24), TBX5 (12q24), and SYNE2 (14q23), suggesting that altered expression of these genes plays a role in AF susceptibility. Allelic expression imbalance was used as an independent method to characterize the cis-control of gene expression. One thousand two hundred forty-eight of 5153 queried genes had cis-single nucleotide polymorphisms that significantly regulated allelic expression at a false discovery rate of <0.05. CONCLUSIONS We provide a genome-wide catalog of the genetic control of gene expression in human left atrial appendage. These data can be used to confirm the relevance of genome-wide association loci and to direct future functional studies to identify the genes and genetic variants responsible for complex diseases such as AF.
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Affiliation(s)
- Jeffrey Hsu
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Shamone Gore-Panter
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Gregory Tchou
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Laurie Castel
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Beth Lovano
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Christine S Moravec
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Gosta B Pettersson
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Eric E Roselli
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - A Marc Gillinov
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Kenneth R McCurry
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Nicholas G Smedira
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - John Barnard
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - David R Van Wagoner
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Mina K Chung
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH
| | - Jonathan D Smith
- From the Departments of Cellular and Molecular Medicine (J.H., G.T., J.D.S.), Quantitative Health Sciences (J.B.), Molecular Cardiology (S.G.-P., L.C., B.L., C.S.M., D.R.V.W., M.K.C.), Cardiovascular Medicine (C.S.M., D.R.V.W., M.K.C., J.D.S.), and Cardiothoracic Surgery (G.B.P., E.E.R., A.M.G., K.R.M., N.G.S.), Cleveland Clinic, Cleveland, OH.
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9
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Liu S, Li X, Zhang L, Jiang J, Hill RC, Cui Y, Hansen KC, Zhou ZH, Zhao R. Structure of the yeast spliceosomal postcatalytic P complex. Science 2017; 358:1278-1283. [PMID: 29146870 PMCID: PMC5828012 DOI: 10.1126/science.aar3462] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [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: 10/28/2017] [Accepted: 11/09/2017] [Indexed: 12/20/2022]
Abstract
The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, Bact, C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, and intron release, but lacked information on 3'-ss recognition, exon ligation, and exon release. Here we report a cryo-electron microscopy structure of the postcatalytic P complex at 3.3-angstrom resolution, revealing that the 3' ss is mainly recognized through non-Watson-Crick base pairing with the 5' ss and branch point. Furthermore, one or more unidentified proteins become stably associated with the P complex, securing the 3' exon and potentially regulating activity of the helicase Prp22. Prp22 binds nucleotides 15 to 21 in the 3' exon, enabling it to pull the intron-exon or ligated exons in a 3' to 5' direction to achieve 3'-ss proofreading or exon release, respectively.
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Affiliation(s)
- Shiheng Liu
- Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jiansen Jiang
- Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Yanxiang Cui
- Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Z Hong Zhou
- Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA.
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10
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Abstract
Major developments in cryo-electron microscopy in the past three or four years have led to the solution of a number of spliceosome structures at high resolution, e.g., the fully assembled but not yet active spliceosome (Bact), the spliceosome just after the first step of splicing (C), and the spliceosome activated for the second step (C*). Therefore 30 years of genetics and biochemistry of the spliceosome can now be interpreted at the structural level. I have closely examined the RNase H domain of Prp8 in each of the structures. Interestingly, the RNase H domain has different and unexpected roles in each of the catalytic steps of splicing.
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Affiliation(s)
- John Abelson
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
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11
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Gao X, Jin Q, Jiang C, Li Y, Li C, Liu H, Kang Z, Xu JR. FgPrp4 Kinase Is Important for Spliceosome B-Complex Activation and Splicing Efficiency in Fusarium graminearum. PLoS Genet 2016; 12:e1005973. [PMID: 27058959 PMCID: PMC4825928 DOI: 10.1371/journal.pgen.1005973] [Citation(s) in RCA: 22] [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: 12/11/2015] [Accepted: 03/11/2016] [Indexed: 12/23/2022] Open
Abstract
PRP4 encodes the only kinase among the spliceosome components. Although it is an essential gene in the fission yeast and other eukaryotic organisms, the Fgprp4 mutant was viable in the wheat scab fungus Fusarium graminearum. Deletion of FgPRP4 did not block intron splicing but affected intron splicing efficiency in over 60% of the F. graminearum genes. The Fgprp4 mutant had severe growth defects and produced spontaneous suppressors that were recovered in growth rate. Suppressor mutations were identified in the PRP6, PRP31, BRR2, and PRP8 orthologs in nine suppressor strains by sequencing analysis with candidate tri-snRNP component genes. The Q86K mutation in FgMSL1 was identified by whole genome sequencing in suppressor mutant S3. Whereas two of the suppressor mutations in FgBrr2 and FgPrp8 were similar to those characterized in their orthologs in yeasts, suppressor mutations in Prp6 and Prp31 orthologs or FgMSL1 have not been reported. Interestingly, four and two suppressor mutations identified in FgPrp6 and FgPrp31, respectively, all are near the conserved Prp4-phosphorylation sites, suggesting that these mutations may have similar effects with phosphorylation by Prp4 kinase. In FgPrp31, the non-sense mutation at R464 resulted in the truncation of the C-terminal 130 aa region that contains all the conserved Prp4-phosphorylation sites. Deletion analysis showed that the N-terminal 310-aa rich in SR residues plays a critical role in the localization and functions of FgPrp4. We also conducted phosphoproteomics analysis with FgPrp4 and identified S289 as the phosphorylation site that is essential for its functions. These results indicated that FgPrp4 is critical for splicing efficiency but not essential for intron splicing, and FgPrp4 may regulate pre-mRNA splicing by phosphorylation of other components of the tri-snRNP although itself may be activated by phosphorylation at S289.
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Affiliation(s)
- Xuli Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiaojun Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Yang Li
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Chaohui Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Dept. of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail:
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12
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Eckert D, Andrée N, Razanau A, Zock-Emmenthal S, Lützelberger M, Plath S, Schmidt H, Guerra-Moreno A, Cozzuto L, Ayté J, Käufer NF. Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation. PLoS Genet 2016; 12:e1005768. [PMID: 26730850 PMCID: PMC4701394 DOI: 10.1371/journal.pgen.1005768] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 07/03/2015] [Accepted: 12/03/2015] [Indexed: 12/02/2022] Open
Abstract
The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth. These include the cell-cycle regulator Cdc2, as well as several kinases that coordinate cell growth, polarity, and morphogenesis during the cell cycle. In this study, we further characterized another of these essential kinases, Prp4, and showed that the splicing of many introns is dependent on Prp4 kinase activity. For detailed characterization, we chose the genes res1 and ppk8, each of which contains one intron of typical size and position. Splicing of the res1 intron was dependent on Prp4 kinase activity, whereas splicing of the ppk8 intron was not. Extensive mutational analyses of the 5’ splice site of both genes revealed that proper transient interaction with the 5’ end of snRNA U1 governs the dependence of splicing on Prp4 kinase activity. Proper transient interaction between the branch sequence and snRNA U2 was also important. Therefore, the Prp4 kinase is required for recognition and efficient splicing of introns displaying weak exon1/5’ splice sites and weak branch sequences. Prp4 is an essential protein kinase that is involved in the splicing of some introns. Using a conditional mutant of Prp4, we showed that a subset of genes, including several cell cycle–regulatory genes, are dependent on Prp4 for splicing. Furthermore, we could convert genes between Prp4-dependent and -independent states by introducing single-nucleotide mutations in the exon1/5’ splice sites and branch sequence of introns. This work shows that Prp4 activity is required for splicing surveillance in a subset of mRNAs.
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Affiliation(s)
- Daniela Eckert
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nicole Andrée
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Aleh Razanau
- Department of Physiology and Pathophysiology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada
| | | | - Martin Lützelberger
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Susann Plath
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Henning Schmidt
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Angel Guerra-Moreno
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Luca Cozzuto
- CRG Bioinformatics Core, Centre de Regulació Genòmica (CRG), and Universitat Pompeu Fabra, Barcelona, Spain
| | - José Ayté
- Oxidative Stress and Cell Cycle Group, Universitat Pompeu Fabra, Barcelona, Spain
- * E-mail: (JA); (NFK)
| | - Norbert F. Käufer
- Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail: (JA); (NFK)
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13
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Rubio-Peña K, Fontrodona L, Aristizábal-Corrales D, Torres S, Cornes E, García-Rodríguez FJ, Serrat X, González-Knowles D, Foissac S, Porta-De-La-Riva M, Cerón J. Modeling of autosomal-dominant retinitis pigmentosa in Caenorhabditis elegans uncovers a nexus between global impaired functioning of certain splicing factors and cell type-specific apoptosis. RNA 2015; 21:2119-31. [PMID: 26490224 PMCID: PMC4647465 DOI: 10.1261/rna.053397.115] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/19/2015] [Indexed: 06/05/2023]
Abstract
Retinitis pigmentosa (RP) is a rare genetic disease that causes gradual blindness through retinal degeneration. Intriguingly, seven of the 24 genes identified as responsible for the autosomal-dominant form (adRP) are ubiquitous spliceosome components whose impairment causes disease only in the retina. The fact that these proteins are essential in all organisms hampers genetic, genomic, and physiological studies, but we addressed these difficulties by using RNAi in Caenorhabditis elegans. Our study of worm phenotypes produced by RNAi of splicing-related adRP (s-adRP) genes functionally distinguishes between components of U4 and U5 snRNP complexes, because knockdown of U5 proteins produces a stronger phenotype. RNA-seq analyses of worms where s-adRP genes were partially inactivated by RNAi, revealed mild intron retention in developing animals but not in adults, suggesting a positive correlation between intron retention and transcriptional activity. Interestingly, RNAi of s-adRP genes produces an increase in the expression of atl-1 (homolog of human ATR), which is normally activated in response to replicative stress and certain DNA-damaging agents. The up-regulation of atl-1 correlates with the ectopic expression of the pro-apoptotic gene egl-1 and apoptosis in hypodermal cells, which produce the cuticle, but not in other cell types. Our model in C. elegans resembles s-adRP in two aspects: The phenotype caused by global knockdown of s-adRP genes is cell type-specific and associated with high transcriptional activity. Finally, along with a reduced production of mature transcripts, we propose a model in which the retina-specific cell death in s-adRP patients can be induced through genomic instability.
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Affiliation(s)
- Karinna Rubio-Peña
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Laura Fontrodona
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - David Aristizábal-Corrales
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Silvia Torres
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Eric Cornes
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Francisco J García-Rodríguez
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Xènia Serrat
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - David González-Knowles
- Integromics, Integromics SL, Parque Científico de Madrid, 28760, Tres Cantos, Madrid, Spain
| | | | - Montserrat Porta-De-La-Riva
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain C. elegans Core Facility, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Julián Cerón
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona 08908, Spain
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14
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Boesler C, Rigo N, Agafonov DE, Kastner B, Urlaub H, Will CL, Lührmann R. Stable tri-snRNP integration is accompanied by a major structural rearrangement of the spliceosome that is dependent on Prp8 interaction with the 5' splice site. RNA 2015; 21:1993-2005. [PMID: 26385511 PMCID: PMC4604437 DOI: 10.1261/rna.053991.115] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 08/21/2015] [Indexed: 05/22/2023]
Abstract
Exon definition is the predominant initial spliceosome assembly pathway in higher eukaryotes, but it remains much less well-characterized compared to the intron-defined assembly pathway. Addition in trans of an excess of 5'ss containing RNA to a splicing reaction converts a 37S exon-defined complex, formed on a single exon RNA substrate, into a 45S B-like spliceosomal complex with stably integrated U4/U6.U5 tri-snRNP. This 45S complex is compositonally and structurally highly similar to an intron-defined spliceosomal B complex. Stable tri-snRNP integration during B-like complex formation is accompanied by a major structural change as visualized by electron microscopy. The changes in structure and stability during transition from a 37S to 45S complex can be induced in affinity-purified cross-exon complexes by adding solely the 5'ss RNA oligonucleotide. This conformational change does not require the B-specific proteins, which are recruited during this stabilization process, or site-specific phosphorylation of hPrp31. Instead it is triggered by the interaction of U4/U6.U5 tri-snRNP components with the 5'ss sequence, most importantly between Prp8 and nucleotides at the exon-intron junction. These studies provide novel insights into the conversion of a cross-exon to cross-intron organized spliceosome and also shed light on the requirements for stable tri-snRNP integration during B complex formation.
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Affiliation(s)
- Carsten Boesler
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Norbert Rigo
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Dmitry E Agafonov
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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15
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Schneider C, Agafonov DE, Schmitzová J, Hartmuth K, Fabrizio P, Lührmann R. Dynamic Contacts of U2, RES, Cwc25, Prp8 and Prp45 Proteins with the Pre-mRNA Branch-Site and 3' Splice Site during Catalytic Activation and Step 1 Catalysis in Yeast Spliceosomes. PLoS Genet 2015; 11:e1005539. [PMID: 26393790 PMCID: PMC4579134 DOI: 10.1371/journal.pgen.1005539] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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: 05/13/2015] [Accepted: 08/27/2015] [Indexed: 01/10/2023] Open
Abstract
Little is known about contacts in the spliceosome between proteins and intron nucleotides surrounding the pre-mRNA branch-site and their dynamics during splicing. We investigated protein-pre-mRNA interactions by UV-induced crosslinking of purified yeast B(act) spliceosomes formed on site-specifically labeled pre-mRNA, and analyzed their changes after conversion to catalytically-activated B* and step 1 C complexes, using a purified splicing system. Contacts between nucleotides upstream and downstream of the branch-site and the U2 SF3a/b proteins Prp9, Prp11, Hsh49, Cus1 and Hsh155 were detected, demonstrating that these interactions are evolutionarily conserved. The RES proteins Pml1 and Bud13 were shown to contact the intron downstream of the branch-site. A comparison of the B(act) crosslinking pattern versus that of B* and C complexes revealed that U2 and RES protein interactions with the intron are dynamic. Upon step 1 catalysis, Cwc25 contacts with the branch-site region, and enhanced crosslinks of Prp8 and Prp45 with nucleotides surrounding the branch-site were observed. Cwc25's step 1 promoting activity was not dependent on its interaction with pre-mRNA, indicating it acts via protein-protein interactions. These studies provide important insights into the spliceosome's protein-pre-mRNA network and reveal novel RNP remodeling events during the catalytic activation of the spliceosome and step 1 of splicing.
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Affiliation(s)
- Cornelius Schneider
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Göttingen, Germany
| | - Dmitry E. Agafonov
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Göttingen, Germany
| | - Jana Schmitzová
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Göttingen, Germany
| | - Klaus Hartmuth
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Göttingen, Germany
| | - Patrizia Fabrizio
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Göttingen, Germany
| | - Reinhard Lührmann
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Göttingen, Germany
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16
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Abstract
The cycle of spliceosome assembly, intron excision, and spliceosome disassembly involves large-scale structural rearrangements of U6 snRNA that are functionally important. U6 enters the splicing pathway bound to the Prp24 protein, which chaperones annealing of U6 to U4 RNA to form a U4/U6 di-snRNP. During catalytic activation of the assembled spliceosome, U4 snRNP is released and U6 is paired to U2 snRNA. Here we show that point mutations in U4 and U6 that decrease U4/U6 base-pairing in vivo are lethal in combination. However, this synthetic phenotype is rescued by a mutation in U6 that alters a U6-Prp24 contact and stabilizes U2/U6. Remarkably, the resulting viable triple mutant strain lacks detectable U4/U6 base-pairing and U4/U6 di-snRNP. Instead, this strain accumulates free U4 snRNP, protein-free U6 RNA, and a novel complex containing U2/U6 di-snRNP. Further mutational analysis indicates that disruption of the U6-Prp24 interaction rather than stabilization of U2/U6 renders stable U4/U6 di-snRNP assembly nonessential. We propose that an essential function of U4/U6 pairing is to displace Prp24 from U6 RNA, and thus a destabilized U6-Prp24 complex renders stable U4/U6 pairing nonessential.
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MESH Headings
- Base Pairing
- Base Sequence
- Epistasis, Genetic
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Mutation
- Nucleic Acid Conformation
- Protein Multimerization
- RNA Splicing/genetics
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Spliceosomes/metabolism
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Affiliation(s)
- Jordan E Burke
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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17
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Gautam A, Grainger RJ, Vilardell J, Barrass JD, Beggs JD. Cwc21p promotes the second step conformation of the spliceosome and modulates 3' splice site selection. Nucleic Acids Res 2015; 43:3309-17. [PMID: 25740649 PMCID: PMC4381068 DOI: 10.1093/nar/gkv159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 01/14/2015] [Accepted: 02/18/2015] [Indexed: 12/20/2022] Open
Abstract
Pre-mRNA splicing involves two transesterification steps catalyzed by the spliceosome. How RNA substrates are positioned in each step and the molecular rearrangements involved, remain obscure. Here, we show that mutations in PRP16, PRP8, SNU114 and the U5 snRNA that affect this process interact genetically with CWC21, that encodes the yeast orthologue of the human SR protein, SRm300/SRRM2. Our microarray analysis shows changes in 3′ splice site selection at elevated temperature in a subset of introns in cwc21Δ cells. Considering all the available data, we propose a role for Cwc21p positioning the 3′ splice site at the transition to the second step conformation of the spliceosome, mediated through its interactions with the U5 snRNP. This suggests a mechanism whereby SRm300/SRRM2, might influence splice site selection in human cells.
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MESH Headings
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Alternative Splicing
- Amino Acid Sequence
- Carrier Proteins/chemistry
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Gene Deletion
- Genes, Fungal
- Humans
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Conformation
- RNA Helicases/chemistry
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splice Sites
- RNA Splicing
- RNA Splicing Factors
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U5 Small Nuclear/chemistry
- Ribonucleoprotein, U5 Small Nuclear/genetics
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Spliceosomes/chemistry
- Spliceosomes/genetics
- Spliceosomes/metabolism
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Affiliation(s)
- Amit Gautam
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, UK
| | - Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, UK
| | - J Vilardell
- Department of Molecular Genomics, Institute of Molecular Biology of Barcelona (IBMB), 08028 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - J David Barrass
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, UK
| | - Jean D Beggs
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3BF, UK
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18
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Linder B, Hirmer A, Gal A, Rüther K, Bolz HJ, Winkler C, Laggerbauer B, Fischer U. Identification of a PRPF4 loss-of-function variant that abrogates U4/U6.U5 tri-snRNP integration and is associated with retinitis pigmentosa. PLoS One 2014; 9:e111754. [PMID: 25383878 PMCID: PMC4226509 DOI: 10.1371/journal.pone.0111754] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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: 07/10/2014] [Accepted: 09/30/2014] [Indexed: 12/19/2022] Open
Abstract
Pre-mRNA splicing by the spliceosome is an essential step in the maturation of nearly all human mRNAs. Mutations in six spliceosomal proteins, PRPF3, PRPF4, PRPF6, PRPF8, PRPF31 and SNRNP200, cause retinitis pigmentosa (RP), a disease characterized by progressive photoreceptor degeneration. All splicing factors linked to RP are constituents of the U4/U6.U5 tri-snRNP subunit of the spliceosome, suggesting that the compromised function of this particle may lead to RP. Here, we report the identification of the p.R192H variant of the tri-snRNP factor PRPF4 in a patient with RP. The mutation affects a highly conserved arginine residue that is crucial for PRPF4 function. Introduction of a corresponding mutation into the zebrafish homolog of PRPF4 resulted in a complete loss of function in vivo. A series of biochemical experiments suggested that p.R192H disrupts the binding interface between PRPF4 and its interactor PRPF3. This interferes with the ability of PRPF4 to integrate into the tri-snRNP, as shown in a human cell line and in zebrafish embryos. These data suggest that the p.R192H variant of PRPF4 represents a functional null allele. The resulting haploinsufficiency of PRPF4 compromises the function of the tri-snRNP, reinforcing the notion that this spliceosomal particle is of crucial importance in the physiology of the retina.
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Affiliation(s)
- Bastian Linder
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Anja Hirmer
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Andreas Gal
- Department of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Rüther
- Department of Ophthalmology, Sankt Gertrauden-Krankenhaus, Berlin, Germany
| | - Hanno Jörn Bolz
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
- Bioscientia Center for Human Genetics, Ingelheim, Germany
| | - Christoph Winkler
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | - Utz Fischer
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
- * E-mail:
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19
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Farkas MH, Lew DS, Sousa ME, Bujakowska K, Chatagnon J, Bhattacharya SS, Pierce EA, Nandrot EF. Mutations in pre-mRNA processing factors 3, 8, and 31 cause dysfunction of the retinal pigment epithelium. Am J Pathol 2014; 184:2641-52. [PMID: 25111227 PMCID: PMC4188860 DOI: 10.1016/j.ajpath.2014.06.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/11/2014] [Accepted: 06/13/2014] [Indexed: 10/24/2022]
Abstract
Mutations in the ubiquitously expressed pre-mRNA processing factors 3, 8, and 31 (PRPF3, PRPF8, and PRPF31) cause nonsyndromic dominant retinitis pigmentosa in humans, an inherited retinal degeneration. It is unclear what mechanisms, or which cell types of the retina, are affected. Transgenic mice with the human mutations in these genes display late-onset morphological changes in the retinal pigment epithelium (RPE). To determine whether the observed morphological changes are preceded by abnormal RPE function, we investigated its phagocytic function in Prpf3(T494M/T494M), Prpf8(H2309P/H2309P), and Prpf31(+/-) mice. We observe decreased phagocytosis in primary RPE cultures from mutant mice, and this is replicated by shRNA-mediated knockdown of PRPF31 in human ARPE-19 cells. The diurnal rhythmicity of phagocytosis is almost lost, indicated by the marked attenuation of the phagocytic burst 2 hours after light onset. The strength of adhesion between RPE apical microvilli and photoreceptor outer segments also declined during peak adhesion in all mutants. In all models, at least one of the receptors involved in binding and internalization of shed photoreceptor outer segments was subjected to changes in localization. Although the mechanism underlying these changes in RPE function is yet to be elucidated, these data are consistent with the mouse RPE being the primary cell affected by mutations in the RNA splicing factors, and these changes occur at an early age.
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Affiliation(s)
- Michael H Farkas
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Deborah S Lew
- Vision Institute, INSERM, U968, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, CNRS, UMR_7210, Paris, France
| | - Maria E Sousa
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | - Kinga Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts; Vision Institute, INSERM, U968, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, CNRS, UMR_7210, Paris, France
| | - Jonathan Chatagnon
- Vision Institute, INSERM, U968, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, CNRS, UMR_7210, Paris, France
| | - Shomi S Bhattacharya
- Vision Institute, INSERM, U968, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, CNRS, UMR_7210, Paris, France; Institute of Ophthalmology, University College London, London, United Kingdom; Andalusian Center of Molecular Biology and Regenerative Medicine, Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Sevilla, Spain
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, Massachusetts.
| | - Emeline F Nandrot
- Vision Institute, INSERM, U968, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, CNRS, UMR_7210, Paris, France.
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20
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Price AM, Görnemann J, Guthrie C, Brow DA. An unanticipated early function of DEAD-box ATPase Prp28 during commitment to splicing is modulated by U5 snRNP protein Prp8. RNA 2014; 20:46-60. [PMID: 24231520 PMCID: PMC3866644 DOI: 10.1261/rna.041970.113] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The stepwise assembly of the highly dynamic spliceosome is guided by RNA-dependent ATPases of the DEAD-box family, whose regulation is poorly understood. In the canonical assembly model, the U4/U6.U5 triple snRNP binds only after joining of the U1 and, subsequently, U2 snRNPs to the intron-containing pre-mRNA. Catalytic activation requires the exchange of U6 for U1 snRNA at the 5' splice site, which is promoted by the DEAD-box protein Prp28. Because Prp8, an integral U5 snRNP protein, is thought to be a central regulator of DEAD-box proteins, we conducted a targeted search in Prp8 for cold-insensitive suppressors of a cold-sensitive Prp28 mutant, prp28-1. We identified a cluster of suppressor mutations in an N-terminal bromodomain-like sequence of Prp8. To identify the precise defect in prp28-1 strains that is suppressed by the Prp8 alleles, we analyzed spliceosome assembly in vivo and in vitro. Surprisingly, in the prp28-1 strain, we observed a block not only to spliceosome activation but also to one of the earliest steps of assembly, formation of the ATP-independent commitment complex 2 (CC2). The Prp8 suppressor partially corrected both the early assembly and later activation defects of prp28-1, supporting a role for this U5 snRNP protein in both the ATP-independent and ATP-dependent functions of Prp28. We conclude that the U5 snRNP has a role in the earliest events of assembly, prior to its stable incorporation into the spliceosome.
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Affiliation(s)
- Argenta M. Price
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
| | - Janina Görnemann
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA
- Corresponding authorsE-mail E-mail
| | - David A. Brow
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
- Corresponding authorsE-mail E-mail
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Munding EM, Shiue L, Katzman S, Donohue JP, Ares M. Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Mol Cell 2013; 51:338-48. [PMID: 23891561 PMCID: PMC3771316 DOI: 10.1016/j.molcel.2013.06.012] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [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: 02/24/2013] [Revised: 05/18/2013] [Accepted: 06/18/2013] [Indexed: 01/08/2023]
Abstract
During meiosis in yeast, global splicing efficiency increases and then decreases. Here we provide evidence that splicing improves due to reduced competition for the splicing machinery. The timing of this regulation corresponds to repression and reactivation of ribosomal protein genes (RPGs) during meiosis. In vegetative cells, RPG repression by rapamycin treatment also increases splicing efficiency. Downregulation of the RPG-dedicated transcription factor gene IFH1 genetically suppresses two spliceosome mutations, prp11-1 and prp4-1, and globally restores splicing efficiency in prp4-1 cells. We conclude that the splicing apparatus is limiting and that pre-messenger RNAs compete. Splicing efficiency of a pre-mRNA therefore depends not just on its own concentration and affinity for limiting splicing factor(s), but also on those of competing pre-mRNAs. Competition between RNAs for limiting processing factors appears to be a general condition in eukaryotes for a variety of posttranscriptional control mechanisms including microRNA (miRNA) repression, polyadenylation, and splicing.
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Affiliation(s)
- Elizabeth M. Munding
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Lily Shiue
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Sol Katzman
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - John Paul Donohue
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Manuel Ares
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
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22
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Shehzad A, Lee J, Huh TL, Lee YS. Curcumin induces apoptosis in human colorectal carcinoma (HCT-15) cells by regulating expression of Prp4 and p53. Mol Cells 2013; 35:526-32. [PMID: 23686430 PMCID: PMC3887881 DOI: 10.1007/s10059-013-0038-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/13/2013] [Accepted: 03/28/2013] [Indexed: 12/30/2022] Open
Abstract
Curcumin (diferuloylmethane), the yellow pigment of turmeric, is one of the most commonly used and extensively studied phytochemicals due to its pleiotropic effects in several human cancers. In the current study, the therapeutic efficacy of curcumin was investigated in human colorectal carcinoma HCT-15 cells. Curcumin inhibited HCT-15 cells proliferation and induced apoptosis in a dose- and time-dependent manner. Hoechst 33342 and DCFHDA staining revealed morphological and biochemical features of apoptosis as well as ROS generation in HCT-15 cells treated with 30 and 50 μM curcumin. Over-expression of pre-mRNA processing factor 4B (Prp4B) and p53 mutations have been reported as hallmarks of cancer cells. Western blot analysis revealed that curcumin treatment activated caspase-3 and decreased expression of p53 and Prp4B in a time-dependent manner. Transfection of HCT-15 cells with Prp4B clone perturbed the growth inhibition induced by 30 μM curcumin. Fractionation of cells revealed increased accumulation of Prp4B in the nucleus, following its translocation from the cytoplasm. To further evaluate the underlying mechanism and survival effect of Prp4B, we generated siRNA-Prp4B HCT15 clones. Knockdown of Prp4B with siRNA diminished the protective effects of Prp4B against curcumin-induced apoptosis. These results suggest a possible underlying molecular mechanism in which Prp4B over-expression and activity are closely associated with the survival and regulation of apoptotic events in human colon cancer HCT-15 cells.
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Affiliation(s)
- Adeeb Shehzad
- School of Life Sciences, College of Natural Sciences, Kyungpook National University
| | | | - Tae-Lin Huh
- School of Life Sciences, College of Natural Sciences, Kyungpook National University
| | - Young Sup Lee
- School of Life Sciences, College of Natural Sciences, Kyungpook National University
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23
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Pozgajova M, Cipak L, Trakovicka A. Prp4 kinase is required for proper segregation of chromosomes during meiosis in Schizosaccharomyces pombe. Acta Biochim Pol 2013; 60:871-873. [PMID: 24432349] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/03/2013] [Accepted: 12/18/2013] [Indexed: 06/03/2023]
Abstract
Chromosome segregation during meiosis is a complex process, which leads to production of four haploid gametes from two precursor cells. Reversible phosphorylation of proteins plays a crucial role in this process. The Schizosaccharomyces pombe Prp4 is an essential serine/threonine protein kinase, which belongs to the Clk/Sty family. To study the role of Prp4 in meiosis, we analysed chromosome segregation in a strain carrying conditional analog-sensitive allele of Prp4 protein kinase (prp4-as2). Our data show, that Prp4 protein kinase plays important role in chromosome segregation during meiosis, as revealed by enhanced missegregation of chromosomes in prp4-as2 mutant cells.
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Affiliation(s)
- Miroslava Pozgajova
- Slovak University of Agriculture, Department of Genetics and Breeding Biology, Nitra, Slovakia
| | - Lubos Cipak
- Cancer Research Institute, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Anna Trakovicka
- Slovak University of Agriculture, Department of Genetics and Breeding Biology, Nitra, Slovakia
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24
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Klucevsek KM, Braun MA, Arndt KM. The Paf1 complex subunit Rtf1 buffers cells against the toxic effects of [PSI+] and defects in Rkr1-dependent protein quality control in Saccharomyces cerevisiae. Genetics 2012; 191:1107-18. [PMID: 22595241 PMCID: PMC3415995 DOI: 10.1534/genetics.112.141713] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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: 01/27/2012] [Accepted: 05/10/2012] [Indexed: 12/20/2022] Open
Abstract
The Rtf1 subunit of the Paf1 complex is required for specific histone modifications, including histone H2B lysine 123 monoubiquitylation. In Saccharomyces cerevisiae, deletion of RTF1 is lethal in the absence of Rkr1, a ubiquitin-protein ligase involved in the destruction of nonstop proteins, which arise from mRNAs lacking stop codons or translational readthrough into the poly(A) tail. We performed a transposon-based mutagenesis screen to identify suppressors of rtf1Δ rkr1Δ lethality and found that a mutation in the gene encoding the protein chaperone Hsp104 rescued viability. Hsp104 plays a role in prion propagation, including the maintenance of [PSI+], which contributes to the synthesis of nonstop proteins. We demonstrate that rtf1Δ and rkr1Δ are synthetically lethal only in the presence of [PSI+]. The deletion, inactivation, and overexpression of HSP104 or the overexpression of prion-encoding genes URE2 and LSM4 clear [PSI+] and rescue rtf1Δ rkr1Δ lethality. In addition, the presence of [PSI+] decreases the fitness of rkr1Δ strains. We investigated whether the loss of RTF1 exacerbates an overload in nonstop proteins in rkr1Δ [PSI+] strains but, using reporter plasmids, found that rtf1Δ decreases nonstop protein levels, indicating that excess nonstop proteins may not be the cause of synthetic lethality. Instead, our data suggest that the loss of Rtf1-dependent histone modifications increases the burden on quality control pathways in cells lacking Rkr1 and containing [PSI+].
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Affiliation(s)
- Kristin M. Klucevsek
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | | | - Karen M. Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
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25
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Abstract
Conformational change within the spliceosome is required between the first and second catalytic steps of pre-mRNA splicing. A prior genetic screen for suppressors of an intron mutant that stalls between the two steps yielded both prp8 and non-prp8 alleles that suppressed second-step splicing defects. We have now identified the strongest non-prp8 suppressors as alleles of the NTC (Prp19 complex) component, CEF1. These cef1 alleles generally suppress second-step defects caused by a variety of intron mutations, mutations in U6 snRNA, or deletion of the second-step protein factor Prp17, and they can activate alternative 3' splice sites. Genetic and functional interactions between cef1 and prp8 alleles suggest that they modulate the same event(s) in the first-to-second-step transition, most likely by stabilization of the second-step spliceosome; in contrast, alleles of U6 snRNA that also alter this transition modulate a distinct event, most likely by stabilization of the first-step spliceosome. These results implicate a myb-like domain of Cef1/CDC5 in interactions that modulate conformational states of the spliceosome and suggest that alteration of these events affects splice site use, resulting in alternative splicing-like patterns in yeast.
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Affiliation(s)
- Charles C. Query
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Corresponding authors.E-mail .E-mail .
| | - Maria M. Konarska
- The Rockefeller University, New York, New York 10065, USA
- Corresponding authors.E-mail .E-mail .
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26
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Liu S, Ghalei H, Lührmann R, Wahl MC. Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31. RNA 2011; 17:1655-63. [PMID: 21784869 PMCID: PMC3162331 DOI: 10.1261/rna.2690611] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [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: 02/22/2011] [Accepted: 06/24/2011] [Indexed: 05/23/2023]
Abstract
Human proteins 15.5K and hPrp31 are components of the major spliceosomal U4 snRNP and of the minor spliceosomal U4atac snRNP. The two proteins bind to related 5'-stem loops (5'SLs) of the U4 and U4atac snRNAs in a strictly sequential fashion. The primary binding 15.5K protein binds at K-turns that exhibit identical sequences in the two snRNAs. However, RNA sequences contacted by the secondary binding hPrp31 differ in U4 and U4atac snRNAs, and the mechanism by which hPrp31 achieves its dual specificity is presently unknown. We show by crystal structure analysis that the capping pentaloops of the U4 and U4atac 5'SLs adopt different structures in the ternary hPrp31-15.5K-snRNA complexes. In U4atac snRNA, a noncanonical base pair forms across the pentaloop, based on which the RNA establishes more intimate interactions with hPrp31 compared with U4 snRNA. Stacking of hPrp31-His270 on the noncanonical base pair at the base of the U4atac pentaloop recapitulates intramolecular stabilizing principles known from the UUCG and GNRA families of RNA tetraloops. Rational mutagenesis corroborated the importance of the noncanonical base pair and the U4atac-specific hPrp31-RNA interactions for complex stability. The more extensive hPrp31-U4atac snRNA interactions are in line with a higher stability of the U4atac compared with the U4-based ternary complex seen in gel-shift assays, which may explain how U4atac snRNA can compete with the more abundant U4 snRNA for the same protein partners in vivo.
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Affiliation(s)
- Sunbin Liu
- Freie Universität Berlin, Fachbereich Biologie/Chemie/Pharmazie, Abteilung Strukturbiochemie, Takustraße 6, D-14195 Berlin, Germany
| | - Homa Ghalei
- Freie Universität Berlin, Fachbereich Biologie/Chemie/Pharmazie, Abteilung Strukturbiochemie, Takustraße 6, D-14195 Berlin, Germany
- Max-Planck-Institut für Biophysikalische Chemie, Abteilung Zelluläre Biochemie, Am Faßberg 11, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Max-Planck-Institut für Biophysikalische Chemie, Abteilung Zelluläre Biochemie, Am Faßberg 11, D-37077 Göttingen, Germany
| | - Markus C. Wahl
- Freie Universität Berlin, Fachbereich Biologie/Chemie/Pharmazie, Abteilung Strukturbiochemie, Takustraße 6, D-14195 Berlin, Germany
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27
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Tanackovic G, Ransijn A, Thibault P, Abou Elela S, Klinck R, Berson EL, Chabot B, Rivolta C. PRPF mutations are associated with generalized defects in spliceosome formation and pre-mRNA splicing in patients with retinitis pigmentosa. Hum Mol Genet 2011; 20:2116-30. [PMID: 21378395 PMCID: PMC3090192 DOI: 10.1093/hmg/ddr094] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [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: 01/10/2011] [Revised: 02/08/2011] [Accepted: 03/01/2011] [Indexed: 01/22/2023] Open
Abstract
Proteins PRPF31, PRPF3 and PRPF8 (RP-PRPFs) are ubiquitously expressed components of the spliceosome, a macromolecular complex that processes nearly all pre-mRNAs. Although these spliceosomal proteins are conserved in eukaryotes and are essential for survival, heterozygous mutations in human RP-PRPF genes lead to retinitis pigmentosa, a hereditary disease restricted to the eye. Using cells from patients with 10 different mutations, we show that all clinically relevant RP-PRPF defects affect the stoichiometry of spliceosomal small nuclear RNAs (snRNAs), the protein composition of tri-small nuclear ribonucleoproteins and the kinetics of spliceosome assembly. These mutations cause inefficient splicing in vitro and affect constitutive splicing ex-vivo by impairing the removal of at least 9% of endogenously expressed introns. Alternative splicing choices are also affected when RP-PRPF defects are present. Furthermore, we show that the steady-state levels of snRNAs and processed pre-mRNAs are highest in the retina, indicating a particularly elevated splicing activity. Our results suggest a role for PRPFs defects in the etiology of PRPF-linked retinitis pigmentosa, which appears to be a truly systemic splicing disease. Although these mutations cause widespread and important splicing defects, they are likely tolerated by the majority of human tissues but are critical for retinal cell survival.
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Affiliation(s)
- Goranka Tanackovic
- Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
| | - Adriana Ransijn
- Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
| | - Philippe Thibault
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Canada
| | - Sherif Abou Elela
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Canada
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, CanadaJ1H 5N4 and
| | - Roscoe Klinck
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Canada
| | - Eliot L. Berson
- The Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Benoit Chabot
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Sherbrooke, Canada
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, CanadaJ1H 5N4 and
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne 1005, Switzerland
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28
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Abstract
Prp8 is the largest and most highly conserved protein of the spliceosome, encoded by all sequenced eukaryotic genomes but missing from prokaryotes and viruses. Despite all evidence that Prp8 is an integral part of the spliceosomal catalytic center, much remains to be learned about its molecular functions and evolutionary origin. By analyzing sequence and structure similarities between Prp8 and other protein domains, we show that its N-terminal region contains a putative bromodomain. The central conserved domain of Prp8 is related to the catalytic domain of reverse transcriptases (RTs) and is most similar to homologous enzymes encoded by prokaryotic retroelements. However, putative catalytic residues in this RT domain are only partially conserved and may not be sufficient for the nucleotidyltransferase activity. The RT domain is followed by an uncharacterized sequence region with relatives found in fungal RT-like proteins. This part of Prp8 is predicted to adopt an α-helical structure and may be functionally equivalent to diverse maturase/X domains of retroelements and to the thumb domain of retroviral RTs. Together with a previously identified C-terminal domain that has an RNaseH-like fold, our results suggest evolutionary connections between Prp8 and ancient mobile elements. Prp8 may have evolved by acquiring nucleic acid-binding domains from inactivated retroelements, and their present-day role may be in maintaining proper conformation of the bound RNA cofactors and substrates of the splicing reaction. This is only the second example-the other one being telomerase-of the RT recruitment from a genomic parasite to serve an essential cellular function.
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Affiliation(s)
- Mensur Dlakić
- Department of Microbiology, Montana State University, Bozeman, Montana 59717, USA.
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29
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Novotný I, Blažíková M, Staneˇk D, Herman P, Malinsky J. In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies. Mol Biol Cell 2011; 22:513-23. [PMID: 21177826 PMCID: PMC3038649 DOI: 10.1091/mbc.e10-07-0560] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [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: 07/02/2010] [Revised: 12/08/2010] [Accepted: 12/15/2010] [Indexed: 01/09/2023] Open
Abstract
The U4/U6·U5 tri-small nuclear ribonucleoprotein particle (tri-snRNP) is an essential pre-mRNA splicing factor, which is assembled in a stepwise manner before each round of splicing. It was previously shown that the tri-snRNP is formed in Cajal bodies (CBs), but little is known about the dynamics of this process. Here we created a mathematical model of tri-snRNP assembly in CBs and used it to fit kinetics of individual snRNPs monitored by fluorescence recovery after photobleaching. A global fitting of all kinetic data determined key reaction constants of tri-snRNP assembly. Our model predicts that the rates of di-snRNP and tri-snRNP assemblies are similar and that ∼230 tri-snRNPs are assembled in one CB per minute. Our analysis further indicates that tri-snRNP assembly is approximately 10-fold faster in CBs than in the surrounding nucleoplasm, which is fully consistent with the importance of CBs for snRNP formation in rapidly developing biological systems. Finally, the model predicted binding between SART3 and a CB component. We tested this prediction by Förster resonance energy transfer and revealed an interaction between SART3 and coilin in CBs.
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MESH Headings
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Cell Line, Tumor
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Coiled Bodies/genetics
- Coiled Bodies/metabolism
- HeLa Cells
- Humans
- Kinetics
- Models, Molecular
- Nuclear Proteins/metabolism
- Protein Binding/genetics
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splicing/genetics
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U5 Small Nuclear/genetics
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Spliceosomes/genetics
- Spliceosomes/metabolism
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Affiliation(s)
- Ivan Novotný
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Michaela Blažíková
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
- Faculty of Mathematics and Physics, Charles University, 121 16 Prague 2, Czech Republic
| | - David Staneˇk
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
| | - Petr Herman
- Faculty of Mathematics and Physics, Charles University, 121 16 Prague 2, Czech Republic
| | - Jan Malinsky
- Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, 142 20 Prague 4, Czech Republic
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30
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Abstract
In this work we report that carnitines, in particular acetyl-l-carnitine (ALC), are able to prolong the chronological aging of yeast cells during the stationary phase. Lifespan extension is significantly reduced in yca1 mutants as well in rho(0) strains, suggesting that the protective effects pass through the Yca1 caspase and mitochondrial functions. ALC can also prevent apoptosis in pro-apoptotic mutants, pointing to the importance of mitochondrial functions in regulating yeast apoptosis and aging. We also demonstrate that ALC attenuates mitochondrial fission in aged yeast cells, indicating a correlation between its protective effect and this process. Our findings suggest that ALC, used as therapeutic for stroke, myocardial infarction and neurodegenerative diseases, besides the well-known anti-oxidant effects, might exert protective effects also acting on mitochondrial morphology.
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Affiliation(s)
- Vanessa Palermo
- Department of Cell and Developmental Biology, University of Rome, Rome, Italy
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31
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Tonevitsky EA, Trushkin EV, Shkurnikov MU, Akimov EB, Sakharov DA. Changed profile of splicing regulator genes expression in response to exercise. Bull Exp Biol Med 2010; 147:733-6. [PMID: 19902070 DOI: 10.1007/s10517-009-0593-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Intensive exercise triggers the cascade processes of body adaptation, including modulation of splisosome functioning, and can lead to modification of its activity and choice of alternative exons. We studied the effect of exercise of the maximum aerobic power on activation of transcription of genes involved in the splicing process. Short-term exercise resulted in a significant increase of mRNA expression of genes encoding proteins involved in the formation of precatalytic splisosome: DDX17, DDX46, HNRNPR, PRPF4B, and SRPK2. The role of the detected regulators in initiation of splisosome assembly under conditions of maximally intensive exercise is discussed.
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Affiliation(s)
- E A Tonevitsky
- All-Russian Institute of Physical Culture and Athletics, Moscow, Russia
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32
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Grainger RJ, Barrass JD, Jacquier A, Rain JC, Beggs JD. Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome. RNA 2009; 15:2161-73. [PMID: 19854871 PMCID: PMC2779682 DOI: 10.1261/rna.1908309] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [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: 08/31/2009] [Accepted: 09/15/2009] [Indexed: 05/20/2023]
Abstract
In Saccharomyces cerevisiae, Cwc21p is a protein of unknown function that is associated with the NineTeen Complex (NTC), a group of proteins involved in activating the spliceosome to promote the pre-mRNA splicing reaction. Here, we show that Cwc21p binds directly to two key splicing factors-namely, Prp8p and Snu114p-and becomes the first NTC-related protein known to dock directly to U5 snRNP proteins. Using a combination of proteomic techniques we show that the N-terminus of Prp8p contains an intramolecular fold that is a Snu114p and Cwc21p interacting domain (SCwid). Cwc21p also binds directly to the C-terminus of Snu114p. Complementary chemical cross-linking experiments reveal reciprocal protein footprints between the interacting Prp8 and Cwc21 proteins, identifying the conserved cwf21 domain in Cwc21p as a Prp8p binding site. Genetic and functional interactions between Cwc21p and Isy1p indicate that they have related functions at or prior to the first catalytic step of splicing, and suggest that Cwc21p functions at the catalytic center of the spliceosome, possibly in response to environmental or metabolic changes. We demonstrate that SRm300, the only SR-related protein known to be at the core of human catalytic spliceosomes, is a functional ortholog of Cwc21p, also interacting directly with Prp8p and Snu114p. Thus, the function of Cwc21p is likely conserved from yeast to humans.
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Affiliation(s)
- Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
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33
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Kershaw CJ, Barrass JD, Beggs JD, O'Keefe RT. Mutations in the U5 snRNA result in altered splicing of subsets of pre-mRNAs and reduced stability of Prp8. RNA 2009; 15:1292-304. [PMID: 19447917 PMCID: PMC2704078 DOI: 10.1261/rna.1347409] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [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: 05/04/2023]
Abstract
The U5 snRNA loop 1 aligns the 5' and 3' exons for ligation during the second step of pre-mRNA splicing. U5 is intimately associated with Prp8, which mediates pre-mRNA repositioning within the catalytic core of the spliceosome and interacts directly with U5 loop 1. The genome-wide effect of three U5 loop 1 mutants has been assessed by microarray analysis. These mutants exhibited impaired and improved splicing of subsets of pre-mRNAs compared to wild-type U5. Analysis of pre-mRNAs that accumulate revealed a change in base prevalence at specific positions near the splice sites. Analysis of processed pre-mRNAs exhibiting mRNA accumulation revealed a bias in base prevalence at one position within the 5' exon. While U5 loop 1 can interact with some of these positions the base bias is not directly related to sequence changes in loop 1. All positions that display a bias in base prevalence are at or next to positions known to interact with Prp8. Analysis of Prp8 in the presence of the three U5 loop 1 mutants revealed that the most severe mutant displayed reduced Prp8 stability. Depletion of U5 snRNA in vivo also resulted in reduced Prp8 stability. Our data suggest that certain mutations in U5 loop 1 perturb the stability of Prp8 and may affect interactions of Prp8 with a subset of pre-mRNAs influencing their splicing. Therefore, the integrity of U5 is important for the stability of Prp8 during splicing and provides one possible explanation for why U5 loop 1 and Prp8 are so highly conserved.
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Affiliation(s)
- Christopher J Kershaw
- Faculty of Life Sciences, The University of Manchester, Manchester M139PT, United Kingdom
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34
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Karaduman R, Dube P, Stark H, Fabrizio P, Kastner B, Lührmann R. Structure of yeast U6 snRNPs: arrangement of Prp24p and the LSm complex as revealed by electron microscopy. RNA 2008; 14:2528-37. [PMID: 18971323 PMCID: PMC2590955 DOI: 10.1261/rna.1369808] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Protein components of the U6 snRNP (Prp24p and LSm2-8) are thought to act cooperatively in facilitating the annealing of U6 and U4 snRNAs during U4/U6 di-snRNP formation. To learn more about the spatial arrangement of these proteins in S. cerevisiae U6 snRNPs, we investigated the structure of this particle by electron microscopy. U6 snRNPs, purified by affinity chromatography and gradient centrifugation, and then immediately adsorbed to the carbon film support, revealed an open form in which the Prp24 protein and the ring formed by the LSm proteins were visible as two separate morphological domains, while particles stabilized by chemical cross-linking in solution under mild conditions before binding to the carbon film exhibited a compact form, with the two domains in close proximity to one another. In the open form, individual LSm proteins were located by a novel approach employing C-terminal genetic tagging of the LSm proteins with yECitrine. These studies show the Prp24 protein at defined distances from each subunit of the LSm ring, which in turn suggests that the LSm ring is positioned in a consistent manner on the U6 RNA. Furthermore, in agreement with the EM observations, UV cross-linking revealed U6 RNA in contact with the LSm2 protein at the interface between Prp24p and the LSm ring. Further, LSmp-Prp24p interactions may be restricted to the closed form, which appears to represent the solution structure of the U6 snRNP particle.
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Affiliation(s)
- Ramazan Karaduman
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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35
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Abstract
In amphibian oocytes, most lateral loops of the lampbrush chromosomes correspond to active transcriptional sites for RNA polymerase II. We show that newly assembled small nuclear ribonucleoprotein (RNP [snRNP]) particles, which are formed upon cytoplasmic injection of fluorescently labeled spliceosomal small nuclear RNAs (snRNAs), target the nascent transcripts of the chromosomal loops. With this new targeting assay, we demonstrate that nonfunctional forms of U1 and U2 snRNAs still associate with the active transcriptional units. In particular, we find that their association with nascent RNP fibrils is independent of their base pairing with pre–messenger RNAs. Additionally, stem loop I of the U1 snRNA is identified as a discrete domain that is both necessary and sufficient for association with nascent transcripts. Finally, in oocytes deficient in splicing, the recruitment of U1, U4, and U5 snRNPs to transcriptional units is not affected. Collectively, these data indicate that the recruitment of snRNPs to nascent transcripts and the assembly of the spliceosome are uncoupled events.
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MESH Headings
- Animals
- Female
- Nucleic Acid Conformation
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splicing
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U1 Small Nuclear/genetics
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Ribonucleoprotein, U2 Small Nuclear/genetics
- Ribonucleoprotein, U2 Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U5 Small Nuclear/genetics
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Ribonucleoprotein, U7 Small Nuclear/genetics
- Ribonucleoprotein, U7 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Spliceosomes/genetics
- Spliceosomes/physiology
- Xenopus
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Affiliation(s)
- Snehal Bhikhu Patel
- Department of Biochemistry, College of Medicine, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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36
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Abstract
Activation of resting T lymphocytes initiates differentiation into mature effector cells over 3-7 days. The chemokine CCL5 (RANTES) and its major transcriptional regulator, Krüppel-like factor 13 (KLF13), are expressed late (3-5 days) after activation in T lymphocytes. Using yeast two-hybrid screening of a human thymus cDNA library, PRP4, a serine/threonine protein kinase, was identified as a KLF13-binding protein. Specific interaction of KLF13 and PRP4 was confirmed by reciprocal coimmunoprecipitation. PRP4 is expressed in PHA-stimulated human T lymphocytes from days 1 and 7 with a peak at day 3. Using an in vitro kinase assay, it was found that PRP4 phosphorylates KLF13. Furthermore, although phosphorylation of KLF13 by PRP4 results in lower binding affinity to the A/B site of the CCL5 promoter, coexpression of PRP4 and KLF13 increases nuclear localization of KLF13 and CCL5 transcription. Finally, knock-down of PRP4 by small interfering RNA markedly decreases CCL5 expression in T lymphocytes. Thus, PRP4-mediated phosphorylation of KLF13 plays a role in the regulation of CCL5 expression in T lymphocytes.
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MESH Headings
- Active Transport, Cell Nucleus/genetics
- Active Transport, Cell Nucleus/immunology
- Amino Acid Sequence
- Animals
- COS Cells
- Cell Cycle Proteins/biosynthesis
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/physiology
- Cells, Cultured
- Chemokine CCL5/biosynthesis
- Chemokine CCL5/genetics
- Chemokine CCL5/metabolism
- Chemokines, CC/biosynthesis
- Chemokines, CC/genetics
- Chemokines, CC/metabolism
- Chlorocebus aethiops
- Gene Expression Regulation/immunology
- Humans
- Kruppel-Like Transcription Factors/biosynthesis
- Kruppel-Like Transcription Factors/genetics
- Kruppel-Like Transcription Factors/physiology
- Mitogen-Activated Protein Kinases/metabolism
- Mitogen-Activated Protein Kinases/physiology
- Molecular Sequence Data
- Phosphorylation
- Protein Binding/genetics
- Protein Binding/immunology
- Protein Serine-Threonine Kinases/biosynthesis
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Repressor Proteins/biosynthesis
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Ribonucleoprotein, U4-U6 Small Nuclear/biosynthesis
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/physiology
- T-Lymphocyte Subsets/enzymology
- T-Lymphocyte Subsets/immunology
- Thymus Gland/cytology
- Thymus Gland/enzymology
- Thymus Gland/immunology
- Transcription, Genetic
- Two-Hybrid System Techniques
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Affiliation(s)
| | | | | | | | - Alan M. Krensky
- Address correspondence and reprint requests to Dr. Alan M. Krensky, Division of Immunology and Transplantation Biology, Stanford University, 300 Pasteur Drive, Stanford, CA 94305. E-mail address:
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37
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Comitato A, Spampanato C, Chakarova C, Sanges D, Bhattacharya SS, Marigo V. Mutations in splicing factor PRPF3, causing retinal degeneration, form detrimental aggregates in photoreceptor cells. Hum Mol Genet 2007; 16:1699-707. [PMID: 17517693 DOI: 10.1093/hmg/ddm118] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [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] [Indexed: 11/13/2022] Open
Abstract
PRPF3 is an element of the splicing machinery ubiquitously expressed, yet mutations in this gene are associated with a tissue-specific phenotype: autosomal dominant retinitis pigmentosa (RP). Here, we studied the subcellular localization of endogenous- and mutant-transfected PRPF3. We found that (i) subcellular distribution of the endogenous wild-type protein co-localizes with small nuclear ribonucleoproteins, partially with a nucleolar marker and accumulates in speckles labeled by SC35; (ii) in human retinas, PRPF3 does not show a distinctive abundance in photoreceptors, the cells affected in RP and (iii) the RP causing mutant PRPF3, differently from the wild-type protein, forms abnormally big aggregates in transfected photoreceptor cells. Aggregation of T494M mutant PRPF3 inside the nucleus triggers apoptosis only in photoreceptor cells. On the basis of the observation that mutant PRPF3 accumulates in the nucleolus and that transcriptional, translational and proteasome inhibition can induce this phenomenon in non-photoreceptor cells, we hypothesize that mutation affects splicing factor recycling. Noteworthy, accumulation of the mutant protein in big aggregates also affects distribution of some other splicing factors. Our data suggest that the mutant protein has a cell-specific dominant effect in rod photoreceptors while appears not to be harmful to epithelial and fibroblast cells.
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Affiliation(s)
- Antonella Comitato
- Department of Biomedical Sciences, University of Modena and Reggio Emilia, Modena, Italy
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38
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Trede NS, Medenbach J, Damianov A, Hung LH, Weber GJ, Paw BH, Zhou Y, Hersey C, Zapata A, Keefe M, Barut BA, Stuart AB, Katz T, Amemiya CT, Zon LI, Bindereif A. Network of coregulated spliceosome components revealed by zebrafish mutant in recycling factor p110. Proc Natl Acad Sci U S A 2007; 104:6608-13. [PMID: 17416673 PMCID: PMC1871833 DOI: 10.1073/pnas.0701919104] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [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] [Indexed: 11/18/2022] Open
Abstract
The spliceosome cycle consists of assembly, catalysis, and recycling phases. Recycling of postspliceosomal U4 and U6 small nuclear ribonucleoproteins (snRNPs) requires p110/SART3, a general splicing factor. In this article, we report that the zebrafish earl grey (egy) mutation maps in the p110 gene and results in a phenotype characterized by thymus hypoplasia, other organ-specific defects, and death by 7 to 8 days postfertilization. U4/U6 snRNPs were disrupted in egy mutant embryos, demonstrating the importance of p110 for U4/U6 snRNP recycling in vivo. Surprisingly, expression profiling of the egy mutant revealed an extensive network of coordinately up-regulated components of the spliceosome cycle, providing a mechanism compensating for the recycling defect. Together, our data demonstrate that a mutation in a general splicing factor can lead to distinct defects in organ development and cause disease.
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Affiliation(s)
- Nikolaus S. Trede
- *Department of Pediatrics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Jan Medenbach
- Institute of Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
| | - Andrey Damianov
- Institute of Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
| | - Lee-Hsueh Hung
- Institute of Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
| | - Gerhard J. Weber
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Barry H. Paw
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Yi Zhou
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Candace Hersey
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Agustin Zapata
- Department of Cell Biology, Faculty of Biology, Complutense University, 28040 Madrid, Spain; and
| | - Matthew Keefe
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Bruce A. Barut
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
| | - Andrew B. Stuart
- Benaroya Research Institute at Virginia Mason, Department of Biology, University of Washington, Seattle, WA 98101
| | - Tammisty Katz
- *Department of Pediatrics, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Chris T. Amemiya
- Benaroya Research Institute at Virginia Mason, Department of Biology, University of Washington, Seattle, WA 98101
| | - Leonard I. Zon
- Howard Hughes Medical Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA 02115
- **To whom correspondence may be addressed at:
Howard Hughes Medical Institute, Department of Hematology/Oncology, Children's Hospital, Harvard Medical School, Karp Family Research Laboratories, 300 Longwood Avenue, Boston, MA 02115. E-mail:
| | - Albrecht Bindereif
- Institute of Biochemistry, Justus-Liebig-University, D-35392 Giessen, Germany
- To whom correspondence may be addressed at:
Institute of Biochemistry, Justus-Liebig-University, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany. E-mail:
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39
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Singh S, Yang HYO, Chen MY, Yu SL. A kinetic-dynamic model for regulatory RNA processing. J Biotechnol 2006; 127:488-95. [PMID: 16978727 DOI: 10.1016/j.jbiotec.2006.07.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 05/25/2005] [Revised: 11/07/2005] [Accepted: 07/24/2006] [Indexed: 11/24/2022]
Abstract
A kinetic-dynamic model was proposed to simulate RNA processing by determining four essential reaction rates, including the rates of transcription, pre-mRNA turnover, pre-mRNA splicing, and mRNA decay. A family competition evolutionary algorithm (FCEA) was adapted herein to approximate these rates. Several artificial datasets were used to verify the correctness and robustness of the FCEA. The model was finally applied on time series data of yeast prp4-l mutant cells for determination of rates of RNA processing. Based on the FCEA, the model indicated that the pre-mRNA splicing was decreased in the mutant cells as well as the possible effects on transcription, pre-mRNA turnover, and mRNA decay, which was consistent with surveyed literature.
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Affiliation(s)
- Sher Singh
- National Taiwan University Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
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40
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Abstract
The human 25S U4/U6.U5 tri-snRNP is a major building block of the U2-type spliceosome and contains, in addition to the U4, U6, and U5 snRNAs, at least 30 distinct proteins. To learn more about the molecular architecture of the tri-snRNP, we have investigated interactions between tri-snRNP proteins using the yeast two-hybrid assay and in vitro binding assays, and, in addition, have identified distinct protein domains that are critical for the connectivity of this protein network in the human tri-snRNP. These studies revealed multiple interactions between distinct domains of the U5 proteins hPrp8, hBrr2 (a DExH/D-box helicase), and hSnu114 (a putative GTPase), which are key players in the catalytic activation of the spliceosome, during which the U4/U6 base-pairing interaction is disrupted and U4 is released from the spliceosome. Both the U5-specific, TPR/HAT-repeat-containing hPrp6 protein and the tri-snRNP-specific hSnu66 protein interact with several U5- and U4/U6-associated proteins, including hBrr2 and hPrp3, which contacts the U6 snRNA. Thus, both proteins are located at the interface between U5 and U4/U6 in the tri-snRNP complex, and likely play an important role in transmitting the activity of hBrr2 and hSnu114 in the U5 snRNP to the U4/U6 duplex during spliceosome activation. A more detailed analysis of these protein interactions revealed that different HAT repeats mediate interactions with specific hPrp6 partners. Taken together, data presented here provide a detailed picture of the network of protein interactions within the human tri-snRNP.
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Affiliation(s)
- Sunbin Liu
- Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany
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41
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Chen CH, Kao DI, Chan SP, Kao TC, Lin JY, Cheng SC. Functional links between the Prp19-associated complex, U4/U6 biogenesis, and spliceosome recycling. RNA 2006; 12:765-74. [PMID: 16540691 PMCID: PMC1440898 DOI: 10.1261/rna.2292106] [Citation(s) in RCA: 23] [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] [Indexed: 05/04/2023]
Abstract
The Prp19-associated complex, consisting of at least eight protein components, is involved in spliceosome activation by specifying the interaction of U5 and U6 with pre-mRNA for their stable association with the spliceosome after U4 dissociation. We show here that yeast cells depleted of one or two of the Prp19-associated components, accumulate the free form of U4. In NTC25-deleted cells, the level of U6 was also reduced. Extracts prepared from NTC25-deleted cells contained neither free U4 nor U6 and were ineffective in spliceosome recycling in the in vitro splicing reaction. Overexpression of U6 partially rescued the temperature-sensitive growth defect and decreased the relative amount of free U4 in NTC25-deleted cells, indicating that the accumulation of free U4 was a consequence of insufficient amounts of U6 snRNA. Extracts prepared from U6-overproducing NTC25-deleted cells containing free-form U6 were capable of spliceosome recycling, suggesting a role of free U6 RNP in spliceosome recycling. Our results demonstrate that in addition to direct participation in spliceosome activation, the Prp19-associated complex has an indirect role in spliceosome recycling through affecting the biogenesis of U4/U6 snRNP in the in vivo splicing reaction.
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Affiliation(s)
- Chun-Hong Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taiwan, Republic of China
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42
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Mazzoni C, Palermo V, Torella M, Falcone C. , the co-repressor of histone gene transcription of , acts as a multicopy suppressor of the apoptotic phenotypes of the mRNA degradation mutant. FEMS Yeast Res 2005; 5:1229-35. [PMID: 16169287 DOI: 10.1016/j.femsyr.2005.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [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: 05/17/2005] [Revised: 07/22/2005] [Accepted: 07/28/2005] [Indexed: 11/16/2022] Open
Abstract
We previously have reported that Saccharomyces cerevisiae mutants expressing Kllsm4Delta1, a truncated form of the KlLSM4 gene, as well as mutants in genes of the mRNA-decapping pathway, show phenotypic markers of apoptosis, increased temperature sensitivity and reduced growth in the presence of different drugs and oxidative stressing agents, such as acetic acid and H(2)O(2). To isolate multicopy extra-genic suppressors of these defects, we transformed the Kllsm4Delta1 mutant with a yeast DNA library and we selected a series of clones showing resistance to acetic acid. One of these clones carried a DNA fragment containing the HIR1 gene that encodes a transcriptional co-repressor of histone genes. The over-expression of HIR1 in the Kllsm4Delta1 mutant prevented rapid cell death during chronological aging, reduced nuclei fragmentation and increased resistance to H(2)O(2). Transcription analysis revealed that the expression of histone genes was lowered in the mutant over-expressing HIR1, indicating a relationship between the latter gene and apoptosis.
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Affiliation(s)
- Cristina Mazzoni
- Pasteur Institute-Cenci Bolognetti Foundation, Department of Cell and Developmental Biology, University of Rome La Sapienza, Piazzale Aldo Moro 5, Italy.
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43
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Abstract
Our progress in understanding mammalian gene function has lagged behind that of gene identification. New methods for mammalian gene functional analysis are needed to accelerate the process. In yeast, the powerful genetic shuffle system allows deletion of any chromosomal gene by homologous recombination and episomal expression of a mutant allele in the same cell. Here, we report a method for mammalian cells, which employs a helper-dependent adenoviral (HD-Ad) vector to synthesize small hairpin (sh) RNAs to knock-down the expression of an endogenous gene by targeting untranslated regions (UTRs). The vector simultaneously expresses an exogenous version of the same gene (wild-type or mutant allele) lacking the UTRs for functional analysis. We demonstrated the utility of the method by using PRPF3, which encodes the human RNA splicing factor Hprp3p. Recently, missense mutations in PRPF3 were found to cause autosomal-dominant Retinitis Pigmentosa, a form of genetic eye diseases affecting the retina. We knocked-down endogenous PRPF3 in multiple cell lines and rescued the phenotype (cell death) with exogenous PRPF3 cDNA, thereby creating a genetic complementation method. Because Ad vectors can efficiently transduce a wide variety of cell types, and many tissues in vivo, this method could have a wide application for gene function studies.
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Affiliation(s)
- Juana Maria Gonzalez-Santos
- Programme in Lung Biology Research and the Canadian Institutes of Health Research Group in Lung Development, Hospital for Sick ChildrenToronto, Canada M5G 1X8 and
- Laboratory Medicine and Pathobiology, University of TorontoToronto, Canada M5S 1A1
| | - Huibi Cao
- Programme in Lung Biology Research and the Canadian Institutes of Health Research Group in Lung Development, Hospital for Sick ChildrenToronto, Canada M5G 1X8 and
- Laboratory Medicine and Pathobiology, University of TorontoToronto, Canada M5S 1A1
| | - Anan Wang
- Programme in Lung Biology Research and the Canadian Institutes of Health Research Group in Lung Development, Hospital for Sick ChildrenToronto, Canada M5G 1X8 and
| | - David R. Koehler
- Programme in Lung Biology Research and the Canadian Institutes of Health Research Group in Lung Development, Hospital for Sick ChildrenToronto, Canada M5G 1X8 and
- Laboratory Medicine and Pathobiology, University of TorontoToronto, Canada M5S 1A1
| | - Bernard Martin
- Programme in Lung Biology Research and the Canadian Institutes of Health Research Group in Lung Development, Hospital for Sick ChildrenToronto, Canada M5G 1X8 and
| | - Roya Navab
- Programme in Lung Biology Research and the Canadian Institutes of Health Research Group in Lung Development, Hospital for Sick ChildrenToronto, Canada M5G 1X8 and
- Laboratory Medicine and Pathobiology, University of TorontoToronto, Canada M5S 1A1
| | - Jim Hu
- Programme in Lung Biology Research and the Canadian Institutes of Health Research Group in Lung Development, Hospital for Sick ChildrenToronto, Canada M5G 1X8 and
- Department of Paediatrics, University of TorontoToronto, Canada M5S 1A1
- Laboratory Medicine and Pathobiology, University of TorontoToronto, Canada M5S 1A1
- To whom correspondence should be addressed. Tel: +1 416 813 6412; Fax: +1 416 813 5771;
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Cojocaru V, Nottrott S, Klement R, Jovin TM. The snRNP 15.5K protein folds its cognate K-turn RNA: a combined theoretical and biochemical study. RNA 2005; 11:197-209. [PMID: 15659359 PMCID: PMC1370708 DOI: 10.1261/rna.7149605] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [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: 08/09/2004] [Accepted: 11/05/2004] [Indexed: 05/19/2023]
Abstract
The human 15.5K protein binds to the 5' stem-loop of U4 snRNA, promotes the assembly of the spliceosomal U4/U6 snRNP, and is required for the recruitment of the 61K protein and the 20/60/90K protein complex to the U4 snRNA. In the crystallographic structure of the 15.5K-U4 snRNA complex, the conformation of the RNA corresponds to the family of kink-turn (K-turn) structural motifs. We simulated the complex and the free RNA, showing how the protein binding and the intrinsic flexibility contribute to the RNA folding process. We found that the RNA is significantly more flexible in the absence of the 15.5K protein. Conformational transitions such as the interconversion between alternative purine stacking schemes, the loss of G-A base pairs, and the opening of the K-turn occur only in the free RNA. Furthermore, the stability of one canonical G-C base pair is influenced both by the binding of the 15.5K protein and the nature of the adjacent structural element in the RNA. We performed chemical RNA modification experiments and observed that the free RNA lacks secondary structure elements, a result in excellent agreement with the simulations. Based on these observations, we propose a protein-assisted RNA folding mechanism in which the RNA intrinsic flexibility functions as a catalyst.
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MESH Headings
- Base Sequence
- Humans
- In Vitro Techniques
- Macromolecular Substances
- Models, Molecular
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Thermodynamics
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Affiliation(s)
- Vlad Cojocaru
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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Maita H, Kitaura H, Ariga H, Iguchi-Ariga SMM. Association of PAP-1 and Prp3p, the products of causative genes of dominant retinitis pigmentosa, in the tri-snRNP complex. Exp Cell Res 2005; 302:61-8. [PMID: 15541726 DOI: 10.1016/j.yexcr.2004.08.022] [Citation(s) in RCA: 29] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Revised: 08/02/2004] [Indexed: 11/16/2022]
Abstract
PAP-1 has been identified by us as a Pim-1-binding protein and has recently been implicated as the defective gene in RP9, one type of autosomal dominant retinitis pigmentosa (adRP). We have then shown that PAP-1 plays a role in pre-mRNA splicing. Because four causative genes for adRP, including PAP-1, Prp31, Prp8, and Prp3, encode proteins that function as splicing factors or splicing-modulating factors, we investigated the interaction of PAP-1 with Prp3p and Prp31p in this study. The results showed that PAP-1 interacted with Prp3p but not Prp31p in human cells and yeast, and that the basic region of PAP-1 and the C-terminal region of Prp3p, regions beside spots found in adRP mutations, were needed for binding. Furthermore, both Prp3p and a part of PAP-1 were found to be components of the U4/U6.U5-tri-snRNP complex, one form of the spliceosome, in Ba/F3 and K562 cells by analysis of sucrose density gradients, suggesting that PAP-1 is weakly associated with the spliceosome. These results also suggest that splicing factors implicated in adRP contribute alone or mutually to proper splicing in the retina and that loss of their functions leads to onset of adRP.
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Affiliation(s)
- Hiroshi Maita
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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Medenbach J, Schreiner S, Liu S, Lührmann R, Bindereif A. Human U4/U6 snRNP recycling factor p110: mutational analysis reveals the function of the tetratricopeptide repeat domain in recycling. Mol Cell Biol 2004; 24:7392-401. [PMID: 15314151 PMCID: PMC506986 DOI: 10.1128/mcb.24.17.7392-7401.2004] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
After each spliceosome cycle, the U4 and U6 snRNAs are released separately and are recycled to the functional U4/U6 snRNP, requiring in the mammalian system the U6-specific RNA binding protein p110 (SART3). Its domain structure is made up of an extensive N-terminal domain with at least seven tetratricopeptide repeat (TPR) motifs, followed by two RNA recognition motifs (RRMs) and a highly conserved C-terminal sequence of 10 amino acids. Here we demonstrate under in vitro recycling conditions that U6-p110 is an essential splicing factor. Recycling activity requires both the RRMs and the TPR domain but not the highly conserved C-terminal sequence. For U6-specific RNA binding, the two RRMs with some flanking regions are sufficient. Yeast two-hybrid assays reveal that p110 interacts through its TPR domain with the U4/U6-specific 90K protein, indicating a specific role of the TPR domain in spliceosome recycling. On the 90K protein, a short internal region (amino acids 416 to 550) suffices for the interaction with p110. Together, these data suggest a model whereby p110 brings together U4 and U6 snRNAs through both RNA-protein and protein-protein interactions.
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Affiliation(s)
- Jan Medenbach
- Institut für Biochemie, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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Wada Y, Itabashi T, Sato H, Tamai M. Clinical features of a Japanese family with autosomal dominant retinitis pigmentosa associated with a Thr494Met mutation in the HPRP3 gene. Graefes Arch Clin Exp Ophthalmol 2004; 242:956-61. [PMID: 15085354 DOI: 10.1007/s00417-004-0923-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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: 10/07/2003] [Revised: 03/01/2004] [Accepted: 03/01/2004] [Indexed: 11/25/2022] Open
Abstract
PURPOSE To determine the clinical features of a Japanese family with autosomal dominant retinitis pigmentosa (ADRP) associated with a Thr494Met mutation in the HPRP3 gene. METHODS Mutational screening by direct sequencing was performed on 96 unrelated patients with ADRP. The clinical features were determined by visual acuity, slit-lamp biomicroscopy, electroretinography, fluorescein angiography, and kinetic visual field testing. RESULTS A Thr494Met mutation in the HPRP3 gene was found in one family and it cosegregated with ADRP in the three affected members. The ophthalmic findings were those of typical retinitis pigmentosa with rapid progression after 40-years-of-age. One patient also had retinoblastoma as a child. CONCLUSION We conclude that the Thr494Met mutation in the HPRP3 gene causes ADRP in Japanese patients. This mutation was found in 1% of patients with ADRP in Japan.
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Affiliation(s)
- Yuko Wada
- Department of Ophthalmology, Tohoku University School of Medicine, 1-1, Seiryo-machi, Aoba-ku, 980-77, Sendai, Japan.
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Abstract
U12-dependent introns are spliced by the so-called minor spliceosome, requiring the U11, U12, and U4atac/U6atac snRNPs in addition to the U5 snRNP. We have recently identified U6-p110 (SART3) as a novel human recycling factor that is related to the yeast splicing factor Prp24. U6-p110 transiently associates with the U6 and U4/U6 snRNPs during the spliceosome cycle, regenerating functional U4/U6 snRNPs from singular U4 and U6 snRNPs. Here we investigated the involvement of U6-p110 in recycling of the U4atac/U6atac snRNP. In contrast to the major U6 and U4/U6 snRNPs, p110 is primarily associated with the U6atac snRNP but is almost undetectable in the U4atac/U6atac snRNP. Since p110 does not occur in U5 snRNA-containing complexes, it appears to be transiently associated with U6atac during the cycle of the minor spliceosome. The p110 binding site was mapped to U6 nucleotides 38 to 57 and U6atac nucleotides 10 to 30, which are highly conserved between these two functionally related snRNAs. With a U12-dependent in vitro splicing system, we demonstrate that p110 is required for recycling of the U4atac/U6atac snRNP.
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MESH Headings
- Antigens, Neoplasm/metabolism
- Base Sequence
- Binding Sites
- HeLa Cells
- Humans
- Models, Biological
- Molecular Sequence Data
- Protein Binding
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA-Binding Proteins/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/chemistry
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Spliceosomes/chemistry
- Spliceosomes/genetics
- Spliceosomes/metabolism
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Affiliation(s)
- Andrey Damianov
- Institut für Biochemie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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Liu Q, Liang XH, Uliel S, Belahcen M, Unger R, Michaeli S. Identification and functional characterization of lsm proteins in Trypanosoma brucei. J Biol Chem 2004; 279:18210-9. [PMID: 14990572 DOI: 10.1074/jbc.m400678200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA interference of Sm proteins in Trypanosoma brucei demonstrated that the stability of the small nuclear RNAs (U1, U2, U4, U5) and the spliced leader RNA, but not U6 RNA, were affected upon Sm depletion (Mandelboim, M., Barth, S., Biton, M., Liang, X. H., and Michaeli, S. (2003) J. Biol. Chem. 278, 51469-51478), suggesting that Lsm proteins that bind and stabilize U6 RNA in other eukaryotes should exist in trypanosomes. In this study, we identified seven Lsm proteins (Lsm2p to Lsm8p) and examined the function of Lsm3p and Lsm8p by RNA interference silencing. Both Lsm proteins were found to be essential for U6 stability and mRNA decay. Silencing was lethal, and cis- and trans-splicing were inhibited. Importantly, silencing also affected the level of U4.U6 and the U4.U6/U5 tri-small nuclear ribonucleoprotein complexes. The presence of Lsm proteins in trypanosomes that diverged early in the eukaryotic lineage suggests that these proteins are highly conserved in both structure and function among eukaryotes. Interestingly, however, Lsm1p that is specific to the mRNA decay complex was not identified in the genome data base of any kinetoplastidae, and the Lsm8p that in other eukaryotes exclusively functions in U6 stability was found to function in trypanosomes also in mRNA decay. These data therefore suggest that in trypanosomes only a single Lsm complex may exist.
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MESH Headings
- Amino Acid Sequence
- Animals
- Databases, Genetic
- Gene Silencing
- Protozoan Proteins/metabolism
- Protozoan Proteins/physiology
- RNA Splicing
- RNA Stability
- RNA, Small Interfering/pharmacology
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/physiology
- Ribonucleoprotein, U5 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear/physiology
- Sequence Alignment
- Trypanosoma brucei brucei/chemistry
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Affiliation(s)
- Qing Liu
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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50
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Zhu H, Hasman RA, Young KM, Kedersha NL, Lou H. U1 snRNP-dependent function of TIAR in the regulation of alternative RNA processing of the human calcitonin/CGRP pre-mRNA. Mol Cell Biol 2003; 23:5959-71. [PMID: 12917321 PMCID: PMC180986 DOI: 10.1128/mcb.23.17.5959-5971.2003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [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: 12/16/2002] [Revised: 03/06/2003] [Accepted: 06/10/2003] [Indexed: 12/24/2022] Open
Abstract
Alternative RNA processing of human calcitonin/CGRP pre-mRNA is regulated by an intronic enhancer element. Previous studies have demonstrated that multiple sequence motifs within the enhancer and a number of trans-acting factors play critical roles in the regulation. Here, we report the identification of TIAR as a novel player in the regulation of human calcitonin/CGRP alternative RNA processing. TIAR binds to the U tract sequence motif downstream of a pseudo 5' splice site within the previously characterized intron enhancer element. Binding of TIAR promotes inclusion of the alternative 3'-terminal exon located more than 200 nucleotides upstream from the U tract. In cells that preferentially include this exon, overexpression of a mutant TIAR that lacks the RNA binding domains suppressed inclusion of this exon. In this report, we also demonstrate an unusual novel interaction between U6 snRNA and the pseudo 5' splice site, which was shown previously to bind U1 snRNA. Interestingly, TIAR binding to the U tract sequence depends on the interaction of not only U1 but also U6 snRNA with the pseudo 5' splice site. Conversely, TIAR binding promotes U6 snRNA binding to its target. The synergistic relationship between TIAR and U6 snRNA strongly suggests a novel role of U6 snRNP in regulated alternative RNA processing.
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Affiliation(s)
- Hui Zhu
- Department of Genetics, School of Medicine, Case Western Reserve University, Ireland Cancer Center, University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
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