1
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Yang C, Georgiou M, Atkinson R, Collin J, Al-Aama J, Nagaraja-Grellscheid S, Johnson C, Ali R, Armstrong L, Mozaffari-Jovin S, Lako M. Pre-mRNA Processing Factors and Retinitis Pigmentosa: RNA Splicing and Beyond. Front Cell Dev Biol 2021; 9:700276. [PMID: 34395430 PMCID: PMC8355544 DOI: 10.3389/fcell.2021.700276] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease characterized by progressive degeneration of photoreceptors and/or retinal pigment epithelium that eventually results in blindness. Mutations in pre-mRNA processing factors (PRPF3, 4, 6, 8, 31, SNRNP200, and RP9) have been linked to 15–20% of autosomal dominant RP (adRP) cases. Current evidence indicates that PRPF mutations cause retinal specific global spliceosome dysregulation, leading to mis-splicing of numerous genes that are involved in a variety of retina-specific functions and/or general biological processes, including phototransduction, retinol metabolism, photoreceptor disk morphogenesis, retinal cell polarity, ciliogenesis, cytoskeleton and tight junction organization, waste disposal, inflammation, and apoptosis. Importantly, additional PRPF functions beyond RNA splicing have been documented recently, suggesting a more complex mechanism underlying PRPF-RPs driven disease pathogenesis. The current review focuses on the key RP-PRPF genes, depicting the current understanding of their roles in RNA splicing, impact of their mutations on retinal cell’s transcriptome and phenome, discussed in the context of model species including yeast, zebrafish, and mice. Importantly, information on PRPF functions beyond RNA splicing are discussed, aiming at a holistic investigation of PRPF-RP pathogenesis. Finally, work performed in human patient-specific lab models and developing gene and cell-based replacement therapies for the treatment of PRPF-RPs are thoroughly discussed to allow the reader to get a deeper understanding of the disease mechanisms, which we believe will facilitate the establishment of novel and better therapeutic strategies for PRPF-RP patients.
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Affiliation(s)
- Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert Atkinson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jumana Al-Aama
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Colin Johnson
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Robin Ali
- King's College London, London, United Kingdom
| | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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2
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Lacadie SA, Rosbash M. Cotranscriptional spliceosome assembly dynamics and the role of U1 snRNA:5'ss base pairing in yeast. Mol Cell 2005; 19:65-75. [PMID: 15989965 DOI: 10.1016/j.molcel.2005.05.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 04/05/2005] [Accepted: 05/09/2005] [Indexed: 11/16/2022]
Abstract
To investigate the mechanism of spliceosome assembly in vivo, we performed chromatin immunoprecipitation (ChIP) analysis of U1, U2, and U5 small nuclear ribonucleoprotein particles (snRNPs) to intron-containing yeast (S. cerevisiae) genes. The snRNPs display patterns that indicate a cotranscriptional assembly model: U1 first, then U2, and the U4/U6*U5 tri-snRNP followed by U1 destabilization. cis-splicing mutations also support a role of U2 and/or the tri-snRNP in U1 destabilization. Moreover, they indicate that splicing efficiency has a major impact on cotranscriptional snRNP recruitment and suggest that cotranscriptional recruitment of U2 or the tri-snRNP is required to commit the pre-mRNA to splicing. Branchpoint (BP) mutations had a major effect on the U1 pattern, whereas 5' splice site (5'ss) mutations had a stronger effect on the U2 pattern. A 5'ss-U1 snRNA complementation experiment suggests that pairing between U1 and the 5'ss occurs after U1 recruitment and contributes to a specific U1:substrate conformation required for efficient U2 and tri-snRNP recruitment.
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Affiliation(s)
- Scott A Lacadie
- Howard Hughes Medical Institute, Biology Department MS008, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, USA
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3
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Abstract
Pre-messenger RNA (pre-mRNA) splicing is a central step in gene expression. Lying between transcription and protein synthesis, pre-mRNA splicing removes sequences (introns) that would otherwise disrupt the coding potential of intron-containing transcripts. This process takes place in the nucleus, catalyzed by a large RNA-protein complex called the spliceosome. Prp8p, one of the largest and most highly conserved of nuclear proteins, occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there. Recently, Prp8p has also come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa.Prp8 is unique, having no obvious homology to other proteins; however, using bioinformatical analysis we reveal the presence of a conserved RNA recognition motif (RRM), an MPN/JAB domain and a putative nuclear localization signal (NLS). Here, we review biochemical and genetical data, mostly related to the human and yeast proteins, that describe Prp8's central role within the spliceosome and its molecular interactions during spliceosome formation, as splicing proceeds, and in post-splicing complexes.
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Affiliation(s)
- Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
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4
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Ben-Yehuda S, Dix I, Russell CS, McGarvey M, Beggs JD, Kupiec M. Genetic and physical interactions between factors involved in both cell cycle progression and pre-mRNA splicing in Saccharomyces cerevisiae. Genetics 2000; 156:1503-17. [PMID: 11102353 PMCID: PMC1461362 DOI: 10.1093/genetics/156.4.1503] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The PRP17/CDC40 gene of Saccharomyces cerevisiae functions in two different cellular processes: pre-mRNA splicing and cell cycle progression. The Prp17/Cdc40 protein participates in the second step of the splicing reaction and, in addition, prp17/cdc40 mutant cells held at the restrictive temperature arrest in the G2 phase of the cell cycle. Here we describe the identification of nine genes that, when mutated, show synthetic lethality with the prp17/cdc40Delta allele. Six of these encode known splicing factors: Prp8p, Slu7p, Prp16p, Prp22p, Slt11p, and U2 snRNA. The other three, SYF1, SYF2, and SYF3, represent genes also involved in cell cycle progression and in pre-mRNA splicing. Syf1p and Syf3p are highly conserved proteins containing several copies of a repeated motif, which we term RTPR. This newly defined motif is shared by proteins involved in RNA processing and represents a subfamily of the known TPR (tetratricopeptide repeat) motif. Using two-hybrid interaction screens and biochemical analysis, we show that the SYF gene products interact with each other and with four other proteins: Isy1p, Cef1p, Prp22p, and Ntc20p. We discuss the role played by these proteins in splicing and cell cycle progression.
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Affiliation(s)
- S Ben-Yehuda
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
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5
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Käufer NF, Potashkin J. Analysis of the splicing machinery in fission yeast: a comparison with budding yeast and mammals. Nucleic Acids Res 2000; 28:3003-10. [PMID: 10931913 PMCID: PMC108416 DOI: 10.1093/nar/28.16.3003] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Based on genetic and bioinformatic analysis, 80 proteins from the newly sequenced Schizosaccharomyces pombe genome appear to be splicing factors. The fission yeast splicing factors were compared to those of Homo sapiens and Saccharomyces cerevisiae in order to determine the extent of conservation or divergence that has occurred over the billion years of evolution that separate these organisms. Our results indicate that many of the factors present in all three organisms have been well conserved throughout evolution. It is calculated that 38% of the fission yeast splicing factors are more similar to the human proteins than to the budding yeast proteins (>10% more similar or similar over a greater region). Many of the factors in this category are required for recognition of the 3' splice site. Ten fission yeast splicing factors, including putative regulatory factors, have human homologs, but no apparent budding yeast homologs based on sequence data alone. Many of the budding yeast factors that are absent in fission yeast are associated with the U1 and U4/U6.U5 snRNP. Collectively the data presented in this survey indicate that of the two yeasts, S.POMBE: contains a splicing machinery more closely reflecting the archetype of a spliceosome.
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Affiliation(s)
- N F Käufer
- Institut für Genetik-Biozentrum, Technische Universität Braunschweig, 38106 Braunschweig, Germany
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6
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Ben-Yehuda S, Russell CS, Dix I, Beggs JD, Kupiec M. Extensive genetic interactions between PRP8 and PRP17/CDC40, two yeast genes involved in pre-mRNA splicing and cell cycle progression. Genetics 2000; 154:61-71. [PMID: 10628969 PMCID: PMC1460917 DOI: 10.1093/genetics/154.1.61] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biochemical and genetic experiments have shown that the PRP17 gene of the yeast Saccharomyces cerevisiae encodes a protein that plays a role during the second catalytic step of the splicing reaction. It was found recently that PRP17 is identical to the cell division cycle CDC40 gene. cdc40 mutants arrest at the restrictive temperature after the completion of DNA replication. Although the PRP17/CDC40 gene product is essential only at elevated temperatures, splicing intermediates accumulate in prp17 mutants even at the permissive temperature. In this report we describe extensive genetic interactions between PRP17/CDC40 and the PRP8 gene. PRP8 encodes a highly conserved U5 snRNP protein required for spliceosome assembly and for both catalytic steps of the splicing reaction. We show that mutations in the PRP8 gene are able to suppress the temperature-sensitive growth phenotype and the splicing defect conferred by the absence of the Prp17 protein. In addition, these mutations are capable of suppressing certain alterations in the conserved PyAG trinucleotide at the 3' splice junction, as detected by an ACT1-CUP1 splicing reporter system. Moreover, other PRP8 alleles exhibit synthetic lethality with the absence of Prp17p and show a reduced ability to splice an intron bearing an altered 3' splice junction. On the basis of these findings, we propose a model for the mode of interaction between the Prp8 and Prp17 proteins during the second catalytic step of the splicing reaction.
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Affiliation(s)
- S Ben-Yehuda
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
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7
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McDonald WH, Ohi R, Smelkova N, Frendewey D, Gould KL. Myb-related fission yeast cdc5p is a component of a 40S snRNP-containing complex and is essential for pre-mRNA splicing. Mol Cell Biol 1999; 19:5352-62. [PMID: 10409726 PMCID: PMC84378 DOI: 10.1128/mcb.19.8.5352] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Myb-related cdc5p is required for G(2)/M progression in the yeast Schizosaccharomyces pombe. We report here that all detectable cdc5p is stably associated with a multiprotein 40S complex. Immunoaffinity purification has allowed the identification of 10 cwf (complexed with cdc5p) proteins. Two (cwf6p and cwf10p) are members of the U5 snRNP; one (cwf9p) is a core snRNP protein. cwf8p is the apparent ortholog of the Saccharomyces cerevisiae splicing factor Prp19p. cwf1(+) is allelic to the prp5(+) gene defined by the S. pombe splicing mutant, prp5-1, and there is a strong negative genetic interaction between cdc5-120 and prp5-1. Five cwfs have not been recognized previously as important for either pre-mRNA splicing or cell cycle control. Further characterization of cwf1p, cwf2p, cwf3p, and cwf4p demonstrates that they are encoded by essential genes, cosediment with cdc5p at 40S, and coimmunoprecipitate with cdc5p. We further show that cdc5p associates with the U2, U5, and U6 snRNAs and that cells lacking cdc5(+) function are defective in pre-mRNA splicing. These data raise the possibility that the cdc5p complex is an intermediate in the assembly or disassembly of an active S. pombe spliceosome.
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Affiliation(s)
- W H McDonald
- Department of Cell Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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8
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Siatecka M, Reyes JL, Konarska MM. Functional interactions of Prp8 with both splice sites at the spliceosomal catalytic center. Genes Dev 1999; 13:1983-93. [PMID: 10444596 PMCID: PMC316927 DOI: 10.1101/gad.13.15.1983] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/1999] [Accepted: 06/24/1999] [Indexed: 11/25/2022]
Abstract
A U5 snRNP protein, hPrp8, interacts closely with the GU dinucleotide at the 5' splice site (5'SS), forming a specific UV-inducible cross-link. To test if this physical contact between the 5'SS and the carboxy-terminal region of Prp8 reflects a functional recognition of the 5'SS during spliceosome assembly, we mutagenized the corresponding region of yeast Prp8 and screened the resulting mutants for suppression of 5'SS mutations in vivo. All of the isolated prp8 alleles not only suppress 5'SS but also 3'SS mutations, affecting the second catalytic step. Suppression of the 5'SS mutations by prp8 alleles was also tested in the presence of U1-7U snRNA, a predicted suppressor of the U+2A mutation. As expected, U1-7U efficiently suppresses prespliceosome formation, and the first, but not the second, step of U+2A pre-mRNA splicing. Independently, Prp8 functionally interacts with both splice sites at the later stage of splicing, affecting the efficiency of the second catalytic step. The striking proximity of two of the prp8 suppressor mutations to the site of the 5'SS:hPrp8 cross-link suggests that some protein:5'SS contacts made before the first step may be subsequently extended to accommodate the 3'SS for the second catalytic step. Together, these results strongly implicate Prp8 in specific interactions at the catalytic center of the spliceosome.
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MESH Headings
- Alleles
- Amino Acid Sequence
- Carrier Proteins
- Catalytic Domain
- Fungal Proteins/genetics
- Fungal Proteins/metabolism
- Genes, Suppressor/genetics
- Genomic Library
- Introns/genetics
- Metallothionein/genetics
- Models, Genetic
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation
- Phenotype
- RNA Splicing/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Nuclear/genetics
- Regulatory Sequences, Nucleic Acid/genetics
- Ribonucleoprotein, U4-U6 Small Nuclear
- Ribonucleoprotein, U5 Small Nuclear
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae Proteins
- Spliceosomes/genetics
- Spliceosomes/metabolism
- Suppression, Genetic
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Affiliation(s)
- M Siatecka
- The Rockefeller University, New York, New York 10021, USA
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9
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Stevens SW, Abelson J. Purification of the yeast U4/U6.U5 small nuclear ribonucleoprotein particle and identification of its proteins. Proc Natl Acad Sci U S A 1999; 96:7226-31. [PMID: 10377396 PMCID: PMC22060 DOI: 10.1073/pnas.96.13.7226] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The yeast U4/U6.U5 pre-mRNA splicing small nuclear ribonucleoprotein (snRNP) is a 25S small nuclear ribonucleoprotein particle similar in size, composition, and morphology to its counterpart in human cells. The yeast U4/U6.U5 snRNP complex has been purified to near homogeneity by affinity chromatography and preparative glycerol gradient sedimentation. We show that there are at least 24 proteins stably associated with this particle and performed mass spectrometry microsequencing to determine their identities. In addition to the seven canonical core Sm proteins, there are a set of U6 snRNP specific Sm proteins, eight previously described U4/U6.U5 snRNP proteins, and four novel proteins. Two of the novel proteins have likely RNA binding properties, one has been implicated in the cell cycle, and one has no identifiable sequence homologues or functional motifs. The purification of the low abundance U4/U6.U5 snRNP from yeast and the powerful sequencing methodologies using small amounts of protein make possible the rapid identification of novel and previously unidentified components of large, low-abundance macromolecular machines from any genetically manipulable organism.
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Affiliation(s)
- S W Stevens
- California Institute of Technology, Division of Biology, 1200 East California Boulevard 147-75, Pasadena, CA 91125, USA
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10
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Fast NM, Doolittle WF. Trichomonas vaginalis possesses a gene encoding the essential spliceosomal component, PRP8. Mol Biochem Parasitol 1999; 99:275-8. [PMID: 10340492 DOI: 10.1016/s0166-6851(99)00017-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N M Fast
- Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia, Canada.
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11
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Bahia D, Font J, Khaouja A, Carreras N, Espuny R, Cicarelli RM, Ingelmo M, Bach-Elias M. Antibodies to yeast Sm motif 1 cross-react with human Sm core polypeptides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:371-8. [PMID: 10215846 DOI: 10.1046/j.1432-1327.1999.00287.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two regions common to all UsnRNP core polypeptides have been described: Sm motif 1 and Sm motif 2. Rabbits were immunized with a 22 amino-acid peptide containing one segment of Sm motif 1 (YRGTLVSTDNYFNLQLNEAEEF, corresponding to residues 11-32) from yeast F protein. After immunization, the rabbit sera contained antibodies that not only reacted specifically with the peptide from yeast F protein but also cross-reacted with Sm polypeptides from mammals; that is, with purified human U1snRNPs. The results suggest that the peptide used and human Sm polypeptides contain a common feature recognized by the polyclonal antibodies. A large collection of human systemic lupus erythematosus sera was assayed using the yeast peptide as an antigen source. Seventy per cent of systemic lupus erythematosus sera contain an antibody specificity that cross-reacts with the yeast peptide.
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12
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Ségault V, Will CL, Polycarpou-Schwarz M, Mattaj IW, Branlant C, Lührmann R. Conserved loop I of U5 small nuclear RNA is dispensable for both catalytic steps of pre-mRNA splicing in HeLa nuclear extracts. Mol Cell Biol 1999; 19:2782-90. [PMID: 10082544 PMCID: PMC84071 DOI: 10.1128/mcb.19.4.2782] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The function of conserved regions of the metazoan U5 snRNA was investigated by reconstituting U5 small nuclear ribonucleoprotein particles (snRNPs) from purified snRNP proteins and HeLa or Xenopus U5 snRNA mutants and testing their ability to restore splicing to U5-depleted nuclear extracts. Substitution of conserved nucleotides comprising internal loop 2 or deletion of internal loop 1 had no significant effect on the ability of reconstituted U5 snRNPs to complement splicing. However, deletion of internal loop 2 abolished U5 activity in splicing and spliceosome formation. Surprisingly, substitution of the invariant loop 1 nucleotides with a GAGA tetraloop had no effect on U5 activity. Furthermore, U5 snRNPs reconstituted from an RNA formed by annealing the 5' and 3' halves of the U5 snRNA, which lacked all loop 1 nucleotides, complemented both steps of splicing. Thus, in contrast to yeast, loop 1 of the human U5 snRNA is dispensable for both steps of splicing in HeLa nuclear extracts. This suggests that its function can be compensated for in vitro by other spliceosomal components: for example, by proteins associated with the U5 snRNP. Consistent with this idea, immunoprecipitation studies indicated that several functionally important U5 proteins associate stably with U5 snRNPs containing a GAGA loop 1 substitution.
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Affiliation(s)
- V Ségault
- UMR CNRS 7567 Maturation des ARN et Enzymologie Moleculaire Université H. Poincaré, 54506 Vandoeuvre-Les-Nancy Cédex, France
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13
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Wong CH, Hendrix M, Manning DD, Rosenbohm C, Greenberg WA. A Library Approach to the Discovery of Small Molecules That Recognize RNA: Use of a 1,3-Hydroxyamine Motif as Core. J Am Chem Soc 1998. [DOI: 10.1021/ja980826p] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chi-Huey Wong
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Martin Hendrix
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - David D. Manning
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Christoph Rosenbohm
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - William A. Greenberg
- Contribution from the Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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14
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Abstract
Proteins have been implicated in an expanding variety of functions during pre-mRNA splicing. Molecular cloning has identified genes encoding spliceosomal proteins that potentially act as novel RNA helicases, GTPases, or protein isomerases. Novel protein-protein and protein-RNA interactions that are required for functional spliceosome formation have also been described. Finally, growing evidence suggests that proteins may contribute directly to the spliceosome's active sites.
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Affiliation(s)
- C L Will
- Institut für Molekularbiologie und Tumorforschung, Philipps Universität Marburg, Emil Mannkopff Strasse 2, 35037, Marburg, Germany.
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15
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Hendrix M, Priestley ES, Joyce GF, Wong CH. Direct observation of aminoglycoside-RNA interactions by surface plasmon resonance. J Am Chem Soc 1997; 119:3641-8. [PMID: 11540136 DOI: 10.1021/ja964290o] [Citation(s) in RCA: 167] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The specificity of neomycin B and related aminoglycoside antibiotics in their interaction with the Rev responsive element (RRE) of HIV-1 mRNA has been studied by directly observing the aminoglycoside-RNA complexes using surface plasmon resonance. Several different RNA sequences, each with a biotin tag, have been prepared using T7 RNA polymerase-catalyzed transcription of synthetic DNA templates and have been immobilized on a streptavidin-coated surface for the binding study. The results indicate that neomycin B is not specific for the G-rich bubble region in RRE. Rather, it appears to interact with three different sites, each with a submicromolar dissociation constant, within the 67-nucleotide domain II of RRE. Further analysis of neomycin B binding with three short synthetic RNA hairpins showed binding with submicromolar affinity and 1:1 stoichiometry in each case. This suggests that neomycin B may generally bind with this affinity to regular A-form RNA or hairpin loops. The approach described here is generally useful for understanding the fundamental interactions involved in the specific recognition of nucleic acids by small molecules which is the basis of rational drug design.
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MESH Headings
- Anti-Bacterial Agents/chemistry
- Anti-Bacterial Agents/metabolism
- Antibody Affinity
- Base Sequence
- Binding Sites
- Biotinylation
- Chemistry, Pharmaceutical
- Framycetin/chemistry
- Framycetin/metabolism
- Gene Products, rev/chemistry
- Gene Products, rev/genetics
- Gene Products, rev/metabolism
- Genes, env
- HIV-1/chemistry
- HIV-1/genetics
- Paromomycin/chemistry
- Paromomycin/metabolism
- Protein Binding
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Structure-Activity Relationship
- rev Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- M Hendrix
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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16
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McBrien KD, Gao Q, Huang S, Klohr SE, Wang RR, Pirnik DM, Neddermann KM, Bursuker I, Kadow KF, Leet JE. Fusaricide, a new cytotoxic N-hydroxypyridone from Fusarium sp. JOURNAL OF NATURAL PRODUCTS 1996; 59:1151-1153. [PMID: 8988601 DOI: 10.1021/np960521t] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A new cytotoxic N-hydroxypyridone, fusaricide (1), was isolated from a Fusarium sp. Its structure was solved by X-ray diffraction and spectroscopic analyses.
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Affiliation(s)
- K D McBrien
- Bristol-Myers Squibb Company, Pharmaceutical Research Institute, Wallingford, Connecticut 06492, USA
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17
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Hinz M, Moore MJ, Bindereif A. Domain analysis of human U5 RNA. Cap trimethylation, protein binding, and spliceosome assembly. J Biol Chem 1996; 271:19001-7. [PMID: 8702566 DOI: 10.1074/jbc.271.31.19001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have analyzed the sequence requirements of the human U5 RNA during small nuclear ribonucleoprotein (snRNP) and spliceosome assembly. A collection of mutant derivatives of the human U5 RNA gene was constructed in a U1 expression vector and transiently transfected in mammalian cells. Using immunoprecipitation and affinity selection assays, the cap trimethylation, the binding of Sm proteins and of the U5 snRNP-specific protein p220, as well as the assembly of the U4/U5/U6 triple snRNP and of spliceosomes were determined. By mutational analysis we were able to assign distinct functions to several structural elements of the human U5 RNA. Efficient binding of the Sm proteins requires the 3' stem-loop. Both the Sm protein-binding site and the 3' stem-loop are necessary for the formation of the trimethyl guanosine cap, consistent with Sm protein binding being a prerequisite for cap trimethylation. Specific elements of the U5 RNA 5' stem-loop contribute to efficient p220 association, in particular stem Ib. Interestingly, the highly conserved loop I appears to be a multifunctional element; in addition to its function in splice-site selection the 5' loop is involved in binding of p220 and in the assembly of the U4/U5/U6 triple snRNP. In sum, this mutational analysis has identified four functional domains of the human U5 RNA.
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Affiliation(s)
- M Hinz
- Institut für Biochemie, Medizinische Fakultät der Humboldt-Universität/Charité, Monbijoustrasse 2 a, D-10117 Berlin, Federal Republic of Germany
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18
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Maddock JR, Roy J, Woolford JL. Six novel genes necessary for pre-mRNA splicing in Saccharomyces cerevisiae. Nucleic Acids Res 1996; 24:1037-44. [PMID: 8604335 PMCID: PMC145760 DOI: 10.1093/nar/24.6.1037] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have identified six new genes whose products are necessary for the splicing of nuclear pre-mRNA in the yeast Saccharomyces cerevisiae. A collection of 426 temperature-sensitive yeast strains was generated by EMS mutagenesis. These mutants were screened for pre-mRNA splicing defects by an RNA gel blot assay, using the intron- containing CRY1 and ACT1 genes as hybridization probes. We identified 20 temperature-sensitive mutants defective in pre-mRNA splicing. Twelve appear to be allelic to the previously identified prp2, prp3, prp6, prp16/prp23, prp18, prp19 or prp26 mutations that cause defects in spliceosome assembly or the first or second step of splicing. One is allelic to SNR14 encoding U4 snRNA. Six new complementation groups, prp29-prp34, were identified. Each of these mutants accumulates unspliced pre-mRNA at 37 degrees C and thus is blocked in spliceosome assembly or early steps of pre-mRNA splicing before the first cleavage and ligation reaction. The prp29 mutation is suppressed by multicopy PRP2 and displays incomplete patterns of complementation with prp2 alleles, suggesting that the PRP29 gene product may interact with that of PRP2. There are now at least 42 different gene products, including the five spliceosomal snRNAs and 37 different proteins that are necessary for pre-mRNA splicing in Saccharomyces cerevisiae. However, the number of yeast genes identifiable by this approach has not yet been exhausted.
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Affiliation(s)
- J R Maddock
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213 USA
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19
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Laggerbauer B, Lauber J, Lührmann R. Identification of an RNA-dependent ATPase activity in mammalian U5 snRNPs. Nucleic Acids Res 1996; 24:868-75. [PMID: 8600454 PMCID: PMC145735 DOI: 10.1093/nar/24.5.868] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Nuclear pre-mRNA splicing requires ATP at several steps from spliceosome assembly to product release. Here, we demonstrate that an integral component of the 20S U5 snRNP is an RNA-dependent ATPase. The ATPase activity of 20S U5 and 25S [U4/U6.U5] snRNPs purified by glycerol gradient centrifugation is strongly stimulated by homopolymeric RNA but not ssDNA. Purified 12S Ul and U2 snRNPs do not exhibit ATPase activity. Moreover, the U5-associated NTPase specifically hydrolyzes ATP and dATP. The additional purification of 20S U5 snRNPs by Mono Q chromatography does not affect the efficiency of ATP hydrolysis. Both U5 and tri-snRNPs bind ATP stoichiometrically in an RNA-independent manner. A candidate ATPase was identified by UV-irradiation of purified snRNPs with radiolabeled ATP. In the presence of homopolymeric RNA, the 200 kDa U5-specific protein is the major crosslinked protein, even in Mono Q-purified U5 snRNPs. The correlation between RNA-dependent ATPase activity in the U5 snRNP and the RNA-dependent onset of this crosslink strongly suggests that the 200 kDa protein is an RNA-dependent ATPase. Furthermore, both the formation of the crosslink and ATPase activity appear with a similar substrate specificity for ATP.
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Affiliation(s)
- B Laggerbauer
- Institut für Molekularbiologie und Tumorforschung, Marburg, Germany
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20
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Qian-Cutrone J, Huang S, Trimble J, Li H, Lin PF, Alam M, Klohr SE, Kadow KF. Niruriside, a new HIV REV/RRE binding inhibitor from Phyllanthus niruri. JOURNAL OF NATURAL PRODUCTS 1996; 59:196-199. [PMID: 8991954 DOI: 10.1021/np9600560] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
During the screening of natural products for their ability to inhibit the binding of HIV-REV protein to [33P]-labeled RRE RNA, one novel compound, niruriside (1), was isolated from the MeOH extract of the dried leaf of Phyllanthus niruri L. by bioassay-guided fractionation. The structure of niruriside was determined by spectroscopic methods. Niruriside showed specific inhibitory activity against the binding of REV protein to RRE RNA with an IC50 value of 3.3 microM; however, niruriside did not protect CEM-SS cells from acute HIV infection at concentrations up to 260 microM using an XTT dye reduction assay.
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Affiliation(s)
- J Qian-Cutrone
- Bristol-Myers Squibb Pharmaceutical Research Institute, Wallingford, Connecticut 06492, USA
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21
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Chabot B, Bisotto S, Vincent M. The nuclear matrix phosphoprotein p255 associates with splicing complexes as part of the [U4/U6.U5] tri-snRNP particle. Nucleic Acids Res 1995; 23:3206-13. [PMID: 7667097 PMCID: PMC307179 DOI: 10.1093/nar/23.16.3206] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The monoclonal antibody CC3 recognizes a phosphorylated epitope present on an interphase protein of 255 kDa. Previous work has shown that p255 is localized mainly to nuclear speckles and remains associated with the nuclear matrix scaffold following extraction with non-ionic detergents, nucleases and high salt. The association of p255 with splicing complexes is suggested by the finding that mAb CC3 can inhibit in vitro splicing and immunoprecipitate pre-messenger RNA and splicing products. Small nuclear RNA immunoprecipitation assays show that p255 is a component of the U5 small nuclear ribonucleoprotein (snRNP) and the [U4/U6.U5] tri-snRNP complex. In RNase protection assays, mAb CC3 immunoprecipitates fragments containing branch site and 3' splice site sequences. As predicted for a [U4/U6.U5]-associated component, the recovery of the branch site-protected fragment requires binding of U2 snRNP and is inhibited by EDTA. p255 may correspond to the previously identified p220 protein, the mammalian analogue of the yeast PRP8 protein. Our results suggest that changes in the phosphorylation of p255 may be part of control mechanisms that interface splicing activity with nuclear organization.
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Affiliation(s)
- B Chabot
- Département de Microbiologie, Faculté de Médecine, Université de Sherbrooke, Québec, Canada
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22
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Hodges PE, Jackson SP, Brown JD, Beggs JD. Extraordinary sequence conservation of the PRP8 splicing factor. Yeast 1995; 11:337-42. [PMID: 7785334 DOI: 10.1002/yea.320110406] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- P E Hodges
- Institute of Cell and Molecular Biology, University of Edinburgh, U.K
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23
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Abstract
The choice of a 3' splice site in Saccharomyces cerevisiae introns involves recognition of a uridine-rich tract upstream of the AG dinucleotide splice junction. By isolating mutants that eliminate the normal preference for uridine-containing 3' splice sites in a cis-competition, we identified a mutation that is an allele of PRP8, prp8-101. This was unexpected because previous analysis has demonstrated that the U5 snRNP protein encoded by PRP8 is required for spliceosome assembly prior to the first catalytic step of splicing. In contrast, the uridine recognition defect caused by the prp8-101 mutation selectively inhibits the second catalytic step of splicing. This defect is seen not only in 3' splice site cis-competitions but also in the splicing of an unusual intron in the TUB3 gene and in the ACT1 intron when utilization of its 3' splice site is rate limiting for splicing. Consistent with a direct role in 3' splice site selection, Prp8 can be cross-linked to the 3' splice site during the splicing reaction. These data demonstrate a novel function for Prp8 in 3' splice site recognition and utilization.
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Affiliation(s)
- J G Umen
- Department of Biochemistry and Biophysics, University of California at San Francisco 94143, USA
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24
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Teigelkamp S, Whittaker E, Beggs JD. Interaction of the yeast splicing factor PRP8 with substrate RNA during both steps of splicing. Nucleic Acids Res 1995; 23:320-6. [PMID: 7885825 PMCID: PMC306678 DOI: 10.1093/nar/23.3.320] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
PRP8 protein of Saccharomyces cerevisiae interacts directly with pre-mRNA in spliceosomes, shown previously by UV-crosslinking. To analyse at which steps of splicing and with which precursor-derived RNA species the interaction(s) take place, UV-crosslinking was combined with PRP8-specific immunoprecipitation and the coprecipitated RNA species were analysed. Specific precipitation of intron-exon 2 and excised intron species was observed. PRP8 protein could be UV-crosslinked to pre-mRNA in PRP2-depleted spliceosomes stalled before initiation of the splicing reaction. Thus, the interaction of PRP8 protein with substrate RNA is established prior to the first transesterification reaction, is maintained during both steps of splicing and continues with the excised intron after completion of the splicing reaction. RNase T1 treatment of spliceosomes revealed that substrate RNA fragments of the 5' splice site region and the branchpoint-3' splice site region could be coimmunoprecipitated with PRP8 specific antibodies, indicating that these are potential sites of interaction for PRP8 protein with substrate RNA. Protection of the branch-point-3' splice site region was detected only after step 1 of splicing. The results allow a first glimpse at the pattern of PRP8 protein-RNA interactions during splicing and provide a fundamental basis for future analysis of these interactions.
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Affiliation(s)
- S Teigelkamp
- Institute of Cell and Molecular Biology, University of Edinburgh, UK
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25
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26
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27
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28
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MacMillan AM, Query CC, Allerson CR, Chen S, Verdine GL, Sharp PA. Dynamic association of proteins with the pre-mRNA branch region. Genes Dev 1994; 8:3008-20. [PMID: 8001820 DOI: 10.1101/gad.8.24.3008] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The association of proteins with the branch site region during pre-mRNA splicing was probed using a novel methodology to site-specifically modify the pre-mRNA with the photo-reagent benzophenone. Three sets of proteins were distinguished by the kinetics of their associations with pre-mRNAs, by their association with discrete splicing complexes, and by their differing factor requirements. An early U1 snRNP-dependent cross-link of the branch region to a p80 species was followed by cross-links to p14, p35, and p150 polypeptides associated with the U2 snRNP-pre-mRNA complex. Concomitant with formation of the spliceosome, a rearrangement of protein factors about the branch region occurred, in which the p35 and p150 cross-links were replaced by p220 and p70 species. These results establish that the branch region is recognized in a dynamic fashion by multiple distinct proteins during the course of spliceosomal assembly.
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Affiliation(s)
- A M MacMillan
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139-4307
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29
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Direct interactions between pre-mRNA and six U2 small nuclear ribonucleoproteins during spliceosome assembly. Mol Cell Biol 1994. [PMID: 8164655 DOI: 10.1128/mcb.14.5.2994] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Highly purified mammalian spliceosomal complex B contains more than 30 specific protein components. We have carried out UV cross-linking studies to determine which of these components directly contacts pre-mRNA in purified prespliceosomal and spliceosomal complexes. We show that heterogeneous nuclear ribonucleoproteins cross-link in the nonspecific complex H but not in the B complex. U2AF65, which binds to the 3' splice site, is the only splicing factor that cross-links in purified prespliceosomal complex E. U2AF65 and the U1 small nuclear ribonucleoprotein particle (snRNP) are subsequently destabilized, and a set of six spliceosome-associated proteins (SAPs) cross-links to the pre-mRNA in the prespliceosomal complex A. These proteins require the 3' splice site for binding and cross-link to an RNA containing only the branch site and 3' splice site. Significantly, all six of these SAPs are specifically associated with U2 snRNP. These proteins and a U5 snRNP component cross-link in the fully assembled B complex. Previous work detected an ATP-dependent, U2 snRNP-associated factor that protects a 30- to 40-nucleotide region surrounding the branchpoint sequence from RNase digestion. Our data indicate that the six U2 snRNP-associated SAPs correspond to this branchpoint protection factor. Four of the snRNP proteins that are in intimate contact with the pre-mRNA are conserved between Saccharomyces cerevisiae and humans, consistent with the possibility that these factors play key roles in mediating snRNA-pre-mRNA interactions during the splicing reaction.
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30
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Staknis D, Reed R. Direct interactions between pre-mRNA and six U2 small nuclear ribonucleoproteins during spliceosome assembly. Mol Cell Biol 1994; 14:2994-3005. [PMID: 8164655 PMCID: PMC358667 DOI: 10.1128/mcb.14.5.2994-3005.1994] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Highly purified mammalian spliceosomal complex B contains more than 30 specific protein components. We have carried out UV cross-linking studies to determine which of these components directly contacts pre-mRNA in purified prespliceosomal and spliceosomal complexes. We show that heterogeneous nuclear ribonucleoproteins cross-link in the nonspecific complex H but not in the B complex. U2AF65, which binds to the 3' splice site, is the only splicing factor that cross-links in purified prespliceosomal complex E. U2AF65 and the U1 small nuclear ribonucleoprotein particle (snRNP) are subsequently destabilized, and a set of six spliceosome-associated proteins (SAPs) cross-links to the pre-mRNA in the prespliceosomal complex A. These proteins require the 3' splice site for binding and cross-link to an RNA containing only the branch site and 3' splice site. Significantly, all six of these SAPs are specifically associated with U2 snRNP. These proteins and a U5 snRNP component cross-link in the fully assembled B complex. Previous work detected an ATP-dependent, U2 snRNP-associated factor that protects a 30- to 40-nucleotide region surrounding the branchpoint sequence from RNase digestion. Our data indicate that the six U2 snRNP-associated SAPs correspond to this branchpoint protection factor. Four of the snRNP proteins that are in intimate contact with the pre-mRNA are conserved between Saccharomyces cerevisiae and humans, consistent with the possibility that these factors play key roles in mediating snRNA-pre-mRNA interactions during the splicing reaction.
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Affiliation(s)
- D Staknis
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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31
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Maddock JR, Weidenhammer EM, Adams CC, Lunz RL, Woolford JL. Extragenic suppressors of Saccharomyces cerevisiae prp4 mutations identify a negative regulator of PRP genes. Genetics 1994; 136:833-47. [PMID: 8005438 PMCID: PMC1205889 DOI: 10.1093/genetics/136.3.833] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The PRP4 gene encodes a protein that is a component of the U4/U6 small nuclear ribonucleoprotein particle and is necessary for both spliceosome assembly and pre-mRNA splicing. To identify genes whose products interact with the PRP4 gene or gene product, we isolated second-site suppressors of temperature-sensitive prp4 mutations. We limited ourselves to suppressors with a distinct phenotype, cold sensitivity, to facilitate analysis of mutants. Ten independent recessive suppressors were obtained that identified four complementation groups, spp41, spp42, spp43 and spp44 (suppressor of prp4, numbers 1-4). spp41-spp44 suppress the pre-mRNA splicing defect as well as the temperature-sensitive phenotype of prp4 strains. Each of these spp mutations also suppresses prp3; spp41 and spp42 suppress prp11 as well. Neither spp41 nor spp42 suppressors null alleles of prp3 or prp4, indicating that the suppression does not occur via a bypass mechanism. The spp41 and spp42 mutations are neither allele- nor gene-specific in their pattern of suppression and do not result in a defect in pre-mRNA splicing. Thus the SPP41 and SPP42 gene products are unlikely to participate directly in mRNA splicing or interact directly with Prp3p or Prp4p. Expression of PRP3-lacZ and PRP4-lacZ gene fusions is increased in spp41 strains, suggesting that wild-type Spp41p represses expression of PRP3 and PRP4. SPP41 was cloned and sequenced and found to be essential. spp43 is allelic to the previously identified suppressor srn1, which encodes a negative regulator of gene expression.
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Affiliation(s)
- J R Maddock
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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32
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Hodges D, Bernstein SI. Genetic and biochemical analysis of alternative RNA splicing. ADVANCES IN GENETICS 1994; 31:207-81. [PMID: 8036995 DOI: 10.1016/s0065-2660(08)60399-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- D Hodges
- Biology Department, San Diego State University, California 92182-0057
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33
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Bennett M, Reed R. Correspondence between a mammalian spliceosome component and an essential yeast splicing factor. Science 1993; 262:105-8. [PMID: 8211113 DOI: 10.1126/science.8211113] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
None of the mammalian splicing factors that have been cloned corresponds to the yeast pre-messenger RNA splicing factors, the PRP proteins. Here, a generalizable strategy was used to isolate a complementary DNA encoding the mammalian spliceosome-associated protein (SAP) SAP 62. It is demonstrated that SAP 62 is the likely functional homolog of the yeast PRP11 protein. Both PRP11 and SAP 62 associate stably with the spliceosome, contain a single zinc finger, and display significant amino acid sequence similarity. Unlike PRP11, SAP 62 contains 22 proline-rich heptapeptide repeats at the carboxyl-terminus.
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Affiliation(s)
- M Bennett
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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34
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Behrens SE, Galisson F, Legrain P, Lührmann R. Evidence that the 60-kDa protein of 17S U2 small nuclear ribonucleoprotein is immunologically and functionally related to the yeast PRP9 splicing factor and is required for the efficient formation of prespliceosomes. Proc Natl Acad Sci U S A 1993; 90:8229-33. [PMID: 8367487 PMCID: PMC47322 DOI: 10.1073/pnas.90.17.8229] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Small nuclear ribonucleoprotein (snRNP) U2 functions in the splicing of mRNA by recognizing the branch site of unspliced mRNA. The binding of U2 snRNP and other components to pre-mRNA leads to the formation of a stable prespliceosome. In HeLa nuclear extracts, U2 snRNP exists either as a 17S form (under low salt conditions) or a 12S form (at higher salt concentrations). We have recently shown that the purified 17S U2 snRNP contains nine proteins with apparent molecular masses of 35, 53, 60, 66, 92, 110, 120, 150, and 160 kDa in addition to the common snRNP proteins and the U2 proteins A' and B" that are found in the 12S U2 snRNP form. By using antibodies against the PRP9 protein from Saccharomyces cerevisiae (a protein required for the addition of U2 to prespliceosomes in yeast), we have shown that the 60-kDa protein specific to human U2 snRNP particles is structurally related to the yeast PRP9 protein. Interestingly, anti-PRP9 antibodies strongly inhibit prespliceosome formation in HeLa nuclear splicing extracts, resulting in a complete inhibition of the mRNA splicing reaction in vitro. This indicates that the U2 60-kDa protein may also be functionally related to its yeast counterpart PRP9. Most importantly, the addition of purified 17S U2 snRNPs, but not of 12S U2 snRNPs, to HeLa splicing extracts in which the endogeneous U2 snRNPs have been functionally neutralized with anti-PRP9 antibodies fully restores the mRNA-splicing activity of the extracts. These data suggest further that the 17S form is the functionally active form of U2 snRNP in the spliceosome.
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Affiliation(s)
- S E Behrens
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Germany
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35
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Dong B, Horowitz DS, Kobayashi R, Krainer AR. Purification and cDNA cloning of HeLa cell p54nrb, a nuclear protein with two RNA recognition motifs and extensive homology to human splicing factor PSF and Drosophila NONA/BJ6. Nucleic Acids Res 1993; 21:4085-92. [PMID: 8371983 PMCID: PMC310009 DOI: 10.1093/nar/21.17.4085] [Citation(s) in RCA: 131] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
While searching for a human homolog of the S.cerevisiae splicing factor PRP18, we found a polypeptide that reacted strongly with antibodies against PRP18. We purified this polypeptide from HeLa cells using a Western blot assay, and named it p54nrb (for nuclear RNA-binding protein, 54 kDa). cDNAs encoding p54nrb were cloned with probes derived from partial sequence of the purified protein. These cDNAs have identical coding sequences but differ as a result of alternative splicing in the 5' untranslated region. The cDNAs encode a 471 aa polypeptide that contains two RNA recognition motifs (RRMs). Human p54nrb has no homology to yeast PRP18, except for a common epitope, but is instead 71% identical to human splicing factor PSF within a 320 aa region that includes both RRMs. In addition, both p54nrb and PSF are rich in Pro and Gln residues outside the main homology region. The Drosophila puff-specific protein BJ6, one of three products encoded by the alternatively spliced no-on-transient A gene (nonA), which is required for normal vision and courtship song, is 42% identical to p54nrb in the same 320 aa region. The striking homology between p54nrb, PSF, and NONA/BJ6 defines a novel phylogenetically conserved protein segment, termed DBHS domain (for Drosophila behavior, human splicing), which may be involved in regulating diverse pathways at the level of pre-mRNA splicing.
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Affiliation(s)
- B Dong
- Cold Spring Harbor Laboratory, NY 11724-2208
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36
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Affiliation(s)
- J D Beggs
- Institute of Cell and Molecular Biology, University of Edinburgh, UK
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37
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Will CL, Behrens SE, Lührmann R. Protein composition of mammalian spliceosomal snRNPs. Mol Biol Rep 1993; 18:121-6. [PMID: 8232294 DOI: 10.1007/bf00986766] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- C L Will
- Institut für Molekularbiologie und Tumorforschung, Marburg, Germany
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38
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Rymond BC, Rokeach LA, Hoch SO. Human snRNP polypeptide D1 promotes pre-mRNA splicing in yeast and defines nonessential yeast Smd1p sequences. Nucleic Acids Res 1993; 21:3501-5. [PMID: 8346029 PMCID: PMC331451 DOI: 10.1093/nar/21.15.3501] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Parallel investigations of yeast and metazoan pre-mRNA splicing have documented enormous complexity in the nucleic acid and protein components of the cellular splicing apparatus, the spliceosome. The degree to which yeast and metazoan spliceosomal proteins differ in composition and structure is currently unknown. In this report we demonstrate that the human small nuclear ribonucleoprotein (snRNP) polypeptide D1 complements the cell lethality, splicing deficiency, and snRNA instability phenotypes associated with a yeast smd1 null allele. Mutational analysis of yeast SMD1, guided by a comparison of the predicted yeast and human proteins, reveals that a large, nonconserved portion of Smd1p is dispensable for biological activity. These observations firmly establish D1 as an essential component of the cellular splicing apparatus and suggest that yeast and metazoa are remarkably similar in the polypeptides guiding early snRNP assembly.
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Affiliation(s)
- B C Rymond
- T.H. Morgan School of Biological Sciences, University of Kentucky, Lexington 40506-0225
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39
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Arenas JE, Abelson JN. The Saccharomyces cerevisiae PRP21 gene product is an integral component of the prespliceosome. Proc Natl Acad Sci U S A 1993; 90:6771-5. [PMID: 8341697 PMCID: PMC47014 DOI: 10.1073/pnas.90.14.6771] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In Saccharomyces cerevisiae, the prp21 mutation causes accumulation of unspliced pre-mRNA at the nonpermissive temperature. We have cloned the PRP21 gene by complementation of its temperature-sensitive phenotype and found it to be the same as SPP91, an extragenic suppressor of the prp9 mutation previously studied in vivo by Chapon and Legrain [Chapon, C. & Legrain, P. (1992) EMBO J. 11, 3279-3288]. We have analyzed the effects of the prp21 mutation on splicing in vitro and have found that PRP21 is a splicing factor required for prespliceosome assembly. We also have analyzed the interaction of PRP21 with splicing complexes using anti-PRP21 antibodies and found that the RNA components of the prespliceosome--U1 and U2 small nuclear RNA (snRNA) particles and pre-mRNA--are specifically coimmunoprecipitated under splicing conditions in the presence of 0.2 M KCl. At higher KCl concentrations, U1 snRNP dissociates from splicing complexes; nevertheless, U2 snRNA and pre-mRNA are still efficiently immunoprecipitated. Immunoprecipitation of both U1 and U2 snRNA as well as pre-mRNA is ATP-dependent and requires a pre-mRNA capable of supporting prespliceosome assembly. Analysis of the unbound complexes in native gels confirmed that prespliceosomes are specifically immunoprecipitated by anti-PRP21 antibodies. These results demonstrate that PRP21 is an integral component of the prespliceosome and establishes a stable interaction with U2 snRNP and/or pre-mRNA in that complex.
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Affiliation(s)
- J E Arenas
- Division of Biology, California Institute of Technology, Pasadena 91125
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40
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A U5 small nuclear ribonucleoprotein particle protein involved only in the second step of pre-mRNA splicing in Saccharomyces cerevisiae. Mol Cell Biol 1993. [PMID: 8474454 DOI: 10.1128/mcb.13.5.2959] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The PRP18 gene, which had been identified in a screen for pre-mRNA splicing mutants in Saccharomyces cerevisiae, has been cloned and sequenced. Yeast strains bearing only a disrupted copy of PRP18 are temperature sensitive for growth; even at a low temperature, they grow extremely slowly and do not splice pre-mRNA efficiently. This unusual temperature sensitivity can be reproduced in vitro; extracts immunodepleted of PRP18 are temperature sensitive for the second step of splicing. The PRP18 protein has been overexpressed in active form in Escherichia coli and has been purified to near homogeneity. Antibodies directed against PRP18 precipitate the U4/U5/U6 small nuclear ribonucleoprotein particle (snRNP) from yeast extracts. From extracts depleted of the U6 small nuclear RNA (snRNA), the U4 and U5 snRNAs can be immunoprecipitated, while no snRNAs can be precipitated from extracts depleted of the U5 snRNA. PRP18 therefore appears to be primarily associated with the U5 snRNP. The antibodies against PRP18 inhibit the second step of pre-mRNA splicing in vitro. Together, these results imply that the U5 snRNP plays a role in the second step of splicing and suggest a model for the action of PRP18.
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41
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Horowitz DS, Abelson J. A U5 small nuclear ribonucleoprotein particle protein involved only in the second step of pre-mRNA splicing in Saccharomyces cerevisiae. Mol Cell Biol 1993; 13:2959-70. [PMID: 8474454 PMCID: PMC359689 DOI: 10.1128/mcb.13.5.2959-2970.1993] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The PRP18 gene, which had been identified in a screen for pre-mRNA splicing mutants in Saccharomyces cerevisiae, has been cloned and sequenced. Yeast strains bearing only a disrupted copy of PRP18 are temperature sensitive for growth; even at a low temperature, they grow extremely slowly and do not splice pre-mRNA efficiently. This unusual temperature sensitivity can be reproduced in vitro; extracts immunodepleted of PRP18 are temperature sensitive for the second step of splicing. The PRP18 protein has been overexpressed in active form in Escherichia coli and has been purified to near homogeneity. Antibodies directed against PRP18 precipitate the U4/U5/U6 small nuclear ribonucleoprotein particle (snRNP) from yeast extracts. From extracts depleted of the U6 small nuclear RNA (snRNA), the U4 and U5 snRNAs can be immunoprecipitated, while no snRNAs can be precipitated from extracts depleted of the U5 snRNA. PRP18 therefore appears to be primarily associated with the U5 snRNP. The antibodies against PRP18 inhibit the second step of pre-mRNA splicing in vitro. Together, these results imply that the U5 snRNP plays a role in the second step of splicing and suggest a model for the action of PRP18.
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Affiliation(s)
- D S Horowitz
- Division of Biology, California Institute of Technology, Pasadena 91125
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42
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Galisson F, Legrain P. The biochemical defects of prp4-1 and prp6-1 yeast splicing mutants reveal that the PRP6 protein is required for the accumulation of the [U4/U6.U5] tri-snRNP. Nucleic Acids Res 1993; 21:1555-62. [PMID: 8479905 PMCID: PMC309362 DOI: 10.1093/nar/21.7.1555] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have raised specific antibodies against the PRP6 protein and shown that the U4, U5 and U6 snRNAs are co-precipitated with this protein. Using splicing extracts prepared from in vivo heat-inactivated cells, we have characterized the prp4-1 and prp6-1 biochemical defects. In inactivated prp4-1 cell extracts, the U6 snRNA content as well as the U6, U4/U6 snRNPs and the [U4/U6.U5] tri-snRNP particles amounts are severely reduced. In inactivated prp6-1 cell extracts, the PRP6 mutant protein is barely detectable. Glycerol gradient analyses indicate that, in these extracts, the [U4/U6.U5] tri-snRNPs are present in very low amounts, but U4/U6 snRNP particles are normally represented. These results establish that the PRP6 protein is required for the accumulation of the [U4/U6.U5] tri-snRNP. We found no evidence for the presence of the PRP6 protein in the U4/U6 particle.
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Affiliation(s)
- F Galisson
- Département de Biologie Moléculaire, Institut Pasteur, Paris, France
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43
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Kulesza H, Simpson GG, Waugh R, Beggs JD, Brown JW. Detection of a plant protein analogous to the yeast spliceosomal protein, PRP8. FEBS Lett 1993; 318:4-6. [PMID: 8436222 DOI: 10.1016/0014-5793(93)81315-q] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have investigated whether a spliceosomal protein analogous to the yeast protein, PRP8, was present in higher plants. A protein with a molecular weight > 200 kDa was detected in Western blots of tobacco (Nicotiana tabacum L.) nuclear extracts with affinity-purified antibodies, raised against four different beta-galactosidase-PRP8 fusion proteins. The < 200 kDa protein was also immunoprecipitated by antibodies against the snRNA-specific trimethylguanosine cap structure and was, therefore, snRNP-associated. The presence of this protein in plants, in addition to yeast, Drosophila and humans, and the conservation of large size and epitopes highlights the importance of PRP8 in pre-mRNA splicing.
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Affiliation(s)
- H Kulesza
- Cellular and Molecular Genetics Department, Scottish Crop Research Institute, Invergowrie, Dundee, UK
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44
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Small nuclear ribonucleoprotein (RNP) U2 contains numerous additional proteins and has a bipartite RNP structure under splicing conditions. Mol Cell Biol 1993. [PMID: 8380223 DOI: 10.1128/mcb.13.1.307] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small nuclear (sn) ribonucleoprotein (RNP) U2 functions in the splicing of mRNA by recognizing the branch site of the unspliced pre-mRNA. When HeLa nuclear splicing extracts are centrifuged on glycerol gradients, U2 snRNPs sediment at either 12S (under high salt concentration conditions) or 17S (under low salt concentration conditions). We isolated the 17S U2 snRNPs from splicing extracts under nondenaturing conditions by using centrifugation and immunoaffinity chromatography and examined their structure by electron microscope. In addition to common proteins B', B, D1, D2, D3, E, F, and G and U2-specific proteins A' and B", which are present in the 12S U2 snRNP, at least nine previously unidentified proteins with apparent molecular masses of 35, 53, 60, 66, 92, 110, 120, 150, and 160 kDa bound to the 17S U2 snRNP. The latter proteins dissociate from the U2 snRNP at salt concentrations above 200 mM, yielding the 12S U2 snRNP particle. Under the electron microscope, the 17S U2 snRNPs exhibited a bipartite appearance, with two main globular domains connected by a short filamentous structure that is sensitive to RNase. These findings suggest that the additional globular domain, which is absent from 12S U2 snRNPs, contains some of the 17S U2-specific proteins. The 5' end of the RNA in the U2 snRNP is more exposed for reaction with RNase H and with chemical probes when the U2 snRNP is in the 17S form than when it is in the 12S form. Removal of the 5' end of this RNA reduces the snRNP's Svedberg value from 17S to 12S. Along with the peculiar morphology of the 17S snRNP, these data indicate that most of the 17S U2-specific proteins are bound to the 5' half of the U2 snRNA.
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45
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Behrens SE, Tyc K, Kastner B, Reichelt J, Lührmann R. Small nuclear ribonucleoprotein (RNP) U2 contains numerous additional proteins and has a bipartite RNP structure under splicing conditions. Mol Cell Biol 1993; 13:307-19. [PMID: 8380223 PMCID: PMC358910 DOI: 10.1128/mcb.13.1.307-319.1993] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Small nuclear (sn) ribonucleoprotein (RNP) U2 functions in the splicing of mRNA by recognizing the branch site of the unspliced pre-mRNA. When HeLa nuclear splicing extracts are centrifuged on glycerol gradients, U2 snRNPs sediment at either 12S (under high salt concentration conditions) or 17S (under low salt concentration conditions). We isolated the 17S U2 snRNPs from splicing extracts under nondenaturing conditions by using centrifugation and immunoaffinity chromatography and examined their structure by electron microscope. In addition to common proteins B', B, D1, D2, D3, E, F, and G and U2-specific proteins A' and B", which are present in the 12S U2 snRNP, at least nine previously unidentified proteins with apparent molecular masses of 35, 53, 60, 66, 92, 110, 120, 150, and 160 kDa bound to the 17S U2 snRNP. The latter proteins dissociate from the U2 snRNP at salt concentrations above 200 mM, yielding the 12S U2 snRNP particle. Under the electron microscope, the 17S U2 snRNPs exhibited a bipartite appearance, with two main globular domains connected by a short filamentous structure that is sensitive to RNase. These findings suggest that the additional globular domain, which is absent from 12S U2 snRNPs, contains some of the 17S U2-specific proteins. The 5' end of the RNA in the U2 snRNP is more exposed for reaction with RNase H and with chemical probes when the U2 snRNP is in the 17S form than when it is in the 12S form. Removal of the 5' end of this RNA reduces the snRNP's Svedberg value from 17S to 12S. Along with the peculiar morphology of the 17S snRNP, these data indicate that most of the 17S U2-specific proteins are bound to the 5' half of the U2 snRNA.
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Affiliation(s)
- S E Behrens
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Germany
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46
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Abstract
Recently, cis-acting elements and trans-acting RNA and protein factors necessary for splicing nuclear pre-mRNAs, group II introns or group III introns, have been discovered, and new roles for the splicing factors have been elucidated. Parallels among the pathways for splicing these different classes of introns have been identified.
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Affiliation(s)
- J L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
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47
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Bennett M, Michaud S, Kingston J, Reed R. Protein components specifically associated with prespliceosome and spliceosome complexes. Genes Dev 1992; 6:1986-2000. [PMID: 1398075 DOI: 10.1101/gad.6.10.1986] [Citation(s) in RCA: 180] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have carried out a systematic analysis of the protein composition of highly purified mammalian spliceosomes. We show that > 30 distinct proteins, including 20 previously unidentified components [designated spliceosome-associated proteins (SAPs)], are specifically associated with the spliceosome in a salt-resistant complex. In contrast to these spliceosome-specific proteins, we show that hnRNP proteins are not tightly associated with purified prespliceosome and spliceosome complexes. The splicing factor U2AF65, U1 snRNP-specific proteins, and several SAPs are present in the earliest prespliceosome complex (E). A set of 10 proteins is then added to the first ATP-dependent prespliceosome complex (A), and concomitantly, a significant decrease in the level of U2AF65 is observed. The fully assembled spliceosome is formed by the addition of 12 proteins in a reaction that requires ATP and both the 5' and 3' splice sites.
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Affiliation(s)
- M Bennett
- Department of Cellular and Molecular Physiology, Harvard Medical School, Boston, Massachusetts 02115
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48
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Jamison SF, Garcia-Blanco MA. An ATP-independent U2 small nuclear ribonucleoprotein particle/precursor mRNA complex requires both splice sites and the polypyrimidine tract. Proc Natl Acad Sci U S A 1992; 89:5482-6. [PMID: 1535158 PMCID: PMC49316 DOI: 10.1073/pnas.89.12.5482] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A complex is formed upon incubation of a precursor mRNA (pre-mRNA) with HeLA cell nuclear extract in the absence of added ATP (-ATP complex). Pre-mRNAs with mutations in the 5' splice site, the 3' splice site, or the polypyrimidine tract did not form this complex. Once formed, the -ATP complex was stable to competition by excess pre-mRNA. The complex was shown to contain the U2 small nuclear ribonucleoprotein particle (snRNP) and was distinct from the previously described U2 snRNP/pre-mRNA complex, the prespliceosome. These complexes have different electrophoretic mobilities, ATP requirements, and sensitivities to mutations of the 5' splice site. Although U1 snRNP was not found in the -ATP complex, a requirement for the U1 snRNP was suggested by immunodepletion experiments. The possible implications for the study of spliceosome formation are discussed.
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Affiliation(s)
- S F Jamison
- Section of Cell Growth, Regulation and Oncogenesis, Duke University Medical Center, Durham, NC 27710
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49
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Abstract
We have identified and characterized three new variants of U5 small nuclear RNA (snRNA) from HeLa cells, called U5D, U5E, and U5F. Each variant has a 2,2,7-trimethylguanosine cap and is packaged into an Sm-precipitable small nuclear ribonucleoprotein (snRNP) particle. All retain the evolutionarily invariant 9-base loop at the top of stem 1; however, numerous base changes relative to the abundant forms of U5 snRNA are present in other regions of the RNAs, including a loop that is part of the yeast U5 minimal domain required for viability and has been shown to bind a protein in HeLa extracts. U5E and U5F each constitute 7% of the total U5 population in HeLa cells and are slightly longer than the previously characterized human U5 (A, B, and C) species. U5D, which composes 5% of HeLa cell U5 snRNAs, is present in two forms: a full-length species, U5DL, and a shorter species, U5DS, which is truncated by 15 nucleotides at its 3' end and therefore resembles the short form of U5 (snR7S) in Saccharomyces cerevisiae. We have established conditions that allow specific detection of the individual U5 variants by either Northern blotting (RNA blotting) or primer extension; likewise, U5E and U5F can be specifically and completely degraded in splicing extracts by oligonucleotide-directed RNase H cleavage. All variant U5 snRNAs are assembled into functional particles, as indicated by their immunoprecipitability with anti-(U5) RNP antibodies, their incorporation into the U4/U5/U6 tri-snRNP complex, and their presence in affinity-purified spliceosomes. The higher abundance of these U5 variants in 293 cells compared with that in HeLa cells suggests possible roles in alternative splicing.
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50
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Abstract
U5 snRNA is an essential pre-mRNA splicing factor whose function remains enigmatic. Specific mutations in a conserved single-stranded loop sequence in yeast U5 snRNA can activate cleavage of G1----A mutant pre-mRNAs at aberrant 5' splice sites and facilitate processing of dead-end lariat intermediates to mRNA. Activation of aberrant 5' cleavage sites involves base pairing between U5 snRNA and nucleotides upstream of the cleavage site. Processing of dead-end lariat intermediates to mRNA correlates with base pairing between U5 and the first two bases in exon 2. The loop sequence in U5 snRNA may therefore by intimately involved in the transesterification reactions at 5' and 3' splice sites. This pattern of interactions is strikingly reminiscent of exon recognition events in group II self-splicing introns and is consistent with the notion that U5 snRNA may be related to a specific functional domain from a group II-like self-splicing ancestral intron.
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Affiliation(s)
- A J Newman
- MRC Laboratory of Molecular Biology, Cambridge, England
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