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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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2
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Abstract
Idiopathic inflammatory myopathies (IIM) are chronic inflammatory diseases of muscle characterized by proximal muscle weakness. There are three main groups of diseases, dermatomyositis, polymyositis and inclusion body myositis. The muscle tissue is invaded by the humoral autoantibody producing immune system (B-cells) and by the cellular immune system with autoaggressive and inflammation modulating cells (e.g. dendritic cells, monocytes/macrophages, CD4 + and CD8 + T-cells and natural killer cells). The presence of specific or associated autoantibodies and inflammatory cellular infiltrates with cytotoxic and immune autoreactive properties are characteristic for IIM diseases. The pathogenesis is still unknown; nevertheless, there are several hints that exogenic factors might be involved in initiation and disease progression and bacterial, fungal and viral infections are thought to be possible initiators. Up to now information on prognostic markers to help with decision-making for individual treatment are limited. In addition, there has been only limited therapeutic success including conventional or novel drugs and biologicals and comparative validation studies are needed using similar outcome measurements. Moreover, to facilitate the use and development of novel therapies, elaboration of intracellular and cell-specific regulation could be useful to understand the etiopathogenesis and allow a better diagnosis, prognosis and possibly also a prediction for individualized subgroup treatment.
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3
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Sato H, Maquat LE. Remodeling of the pioneer translation initiation complex involves translation and the karyopherin importin beta. Genes Dev 2009; 23:2537-50. [PMID: 19884259 DOI: 10.1101/gad.1817109] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Mammalian mRNAs lose and acquire proteins throughout their life span while undergoing processing, transport, translation, and decay. How translation affects messenger RNA (mRNA)-protein interactions is largely unknown. The pioneer round of translation uses newly synthesized mRNA that is bound by cap-binding protein 80 (CBP80)-CBP20 (also known as the cap-binding complex [CBC]) at the cap, poly(A)-binding protein N1 (PABPN1) and PABPC1 at the poly(A) tail, and, provided biogenesis involves pre-mRNA splicing, exon junction complexes (EJCs) at exon-exon junctions. Subsequent rounds of translation engage mRNA that is bound by eukaryotic translation initiation factor 4E (eIF4E) at the cap and PABPC1 at the poly(A) tail, but that lacks detectable EJCs and PABPN1. Using the level of intracellular iron to regulate the translation of specific mRNAs, we show that translation promotes not only removal of EJC constituents, including the eIF4AIII anchor, but also replacement of PABPN1 by PABPC1. Remarkably, translation does not affect replacement of CBC by eIF4E. Instead, replacement of CBC by eIF4E is promoted by importin beta (IMPbeta): Inhibiting the binding of IMPbeta to the complex of CBC-IMPalpha at an mRNA cap using the IMPalpha IBB (IMPbeta-binding) domain or a RAN variant increases the amount of CBC-bound mRNA and decreases the amount of eIF4E-bound mRNA. Our studies uncover a previously unappreciated role for IMPbeta and a novel paradigm for how newly synthesized messenger ribonucleoproteins (mRNPs) are matured.
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Affiliation(s)
- Hanae Sato
- Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
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4
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Kofler M, Schuemann M, Merz C, Kosslick D, Schlundt A, Tannert A, Schaefer M, Lührmann R, Krause E, Freund C. Proline-rich sequence recognition: I. Marking GYF and WW domain assembly sites in early spliceosomal complexes. Mol Cell Proteomics 2009; 8:2461-73. [PMID: 19483244 DOI: 10.1074/mcp.m900191-mcp200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proline-rich sequences (PRS) and their recognition domains have emerged as transposable protein interaction modules during eukaryotic evolution. They are especially abundant in proteins associated with pre-mRNA splicing and likely assist in the formation of the spliceosome by binding to GYF and WW domains. Here we profile PRS-mediated interactions of the CD2BP2/52K GYF domain by a site-specific peptide inhibitor and stable isotope labeling/mass spectrometry analysis. Several PRS hubs with multiple proline-rich motifs exist that can recruit GYF and/or WW domains. Saturating the PRS sites by an isolated GYF domain inhibited splicing at the level of A complex formation. The interactions mediated by PRS are therefore important to the early phases of spliceosomal assembly.
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Affiliation(s)
- Michael Kofler
- Protein Engineering Group, Leibniz Institute for Molecular Pharmacology and Freie Universität Berlin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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5
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Abstract
Studies of RNA-protein interactions often require assembly of the RNA-protein complex using in vitro synthesized RNA or recombinant protein. Here, we describe a protocol to assemble a functional spliceosome in yeast extracts using transcribed or synthetic RNAs. The in vitro assembled spliceosome is stable and can be isolated by sedimentation through glycerol gradients for subsequent analysis. The protocols describe two procedures to prepare RNA: using bacteriophage RNA polymerases or ligation of RNA oligos using T4 DNA ligase. We also describe the preparation of splicing competent yeast extracts, the assembly of the spliceosome, and the isolation of the spliceosome by glycerol gradient sedimentation. To allow exogenously added U6 RNA to be incorporated into the spliceosome, the endogenous U6 small nuclear RNA (snRNA) in the extract is eliminated by an antisense U6 DNA oligo and ribonuclease H; a "neutralizing" U6 DNA oligo was then added to protect the incoming U6 RNA. This protocol allows study of the role individual bases or the phosphate backbone of U6 plays in splicing and of the interaction between U6 snRNA and the spliceosomal proteins.
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6
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Abstract
In addition to standard MS-based protein identification, quantification of proteins by mass spectrometry (MS) is rapidly gaining acceptance in proteomic studies. MS-based quantification involves either the incorporation of stable isotopes or can be performed label-free. Recently, more attention has been devoted to label-free quantification; however, this approach has not been fully established among the proteomic community yet. More common is still the introduction of stable isotopes, which can be done by metabolic (e.g., SILAC) or by chemical (e.g., ICAT, iTRAQ, etc.) labeling. Here, we present an overall quantification strategy for chemical labeling of in-gel digested proteins using iTRAQ reagents. This includes (1) protein separation by gel electrophoresis, (2) excision of protein bands, (3) in-gel digestion and extraction of peptides, (4) labeling of peptides, (5) pooling the samples to be compared, (6) LC-MS/MS of labeled peptides, and (7) database search. The presented workflow is well suited for protein samples of moderate complexity (i.e., protein samples of 300-400 components), and it is exemplified by using different amounts of 25S [U4/U6.U5] tri-snRNPs.
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Affiliation(s)
- Carla Schmidt
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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7
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Yang J, Välineva T, Hong J, Bu T, Yao Z, Jensen ON, Frilander MJ, Silvennoinen O. Transcriptional co-activator protein p100 interacts with snRNP proteins and facilitates the assembly of the spliceosome. Nucleic Acids Res 2007; 35:4485-94. [PMID: 17576664 PMCID: PMC1935017 DOI: 10.1093/nar/gkm470] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcription and pre-mRNA splicing are the key nuclear processes in eukaryotic gene expression, and identification of factors common to both processes has suggested that they are functionally coordinated. p100 protein has been shown to function as a transcriptional co-activator for several transcription factors. p100 consists of staphylococcal nuclease (SN)-like and Tudor-SN (TSN) domains of which the SN-like domains have been shown to function in transcription, but the function of TSN domain has remained elusive. Here we identified interaction between p100 and small nuclear ribonucleoproteins (snRNP) that function in pre-mRNA splicing. The TSN domain of p100 specifically interacts with components of the U5 snRNP, but also with the other spliceosomal snRNPs. In vitro splicing assays revealed that the purified p100, and specifically the TSN domain of p100, accelerates the kinetics of the spliceosome assembly, particularly the formation of complex A, and the transition from complex A to B. Consistently, the p100 protein, as well as the separated TSN domain, enhanced the kinetics of the first step of splicing in an in vitro splicing assay in dose-dependent manner. Thus our results suggest that p100 protein is a novel dual function regulator of gene expression that participates via distinct domains in both transcription and splicing.
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Affiliation(s)
- Jie Yang
- Department of Immunology, Tianjin Medical University, Heping District Qixiangtai Road No.22, 300070 Tianjin, P.R. China, Institute of Medical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland, Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark, Institute of Biotechnology, Program on Development Biology, PL56, 00014 University of Helsinki and Department of Clinical Microbiology, Tampere University Hospital, 33520 Tampere, Finland
| | - Tuuli Välineva
- Department of Immunology, Tianjin Medical University, Heping District Qixiangtai Road No.22, 300070 Tianjin, P.R. China, Institute of Medical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland, Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark, Institute of Biotechnology, Program on Development Biology, PL56, 00014 University of Helsinki and Department of Clinical Microbiology, Tampere University Hospital, 33520 Tampere, Finland
| | - Jingxin Hong
- Department of Immunology, Tianjin Medical University, Heping District Qixiangtai Road No.22, 300070 Tianjin, P.R. China, Institute of Medical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland, Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark, Institute of Biotechnology, Program on Development Biology, PL56, 00014 University of Helsinki and Department of Clinical Microbiology, Tampere University Hospital, 33520 Tampere, Finland
| | - Tianxu Bu
- Department of Immunology, Tianjin Medical University, Heping District Qixiangtai Road No.22, 300070 Tianjin, P.R. China, Institute of Medical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland, Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark, Institute of Biotechnology, Program on Development Biology, PL56, 00014 University of Helsinki and Department of Clinical Microbiology, Tampere University Hospital, 33520 Tampere, Finland
| | - Zhi Yao
- Department of Immunology, Tianjin Medical University, Heping District Qixiangtai Road No.22, 300070 Tianjin, P.R. China, Institute of Medical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland, Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark, Institute of Biotechnology, Program on Development Biology, PL56, 00014 University of Helsinki and Department of Clinical Microbiology, Tampere University Hospital, 33520 Tampere, Finland
| | - Ole N. Jensen
- Department of Immunology, Tianjin Medical University, Heping District Qixiangtai Road No.22, 300070 Tianjin, P.R. China, Institute of Medical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland, Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark, Institute of Biotechnology, Program on Development Biology, PL56, 00014 University of Helsinki and Department of Clinical Microbiology, Tampere University Hospital, 33520 Tampere, Finland
| | - Mikko J. Frilander
- Department of Immunology, Tianjin Medical University, Heping District Qixiangtai Road No.22, 300070 Tianjin, P.R. China, Institute of Medical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland, Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark, Institute of Biotechnology, Program on Development Biology, PL56, 00014 University of Helsinki and Department of Clinical Microbiology, Tampere University Hospital, 33520 Tampere, Finland
| | - Olli Silvennoinen
- Department of Immunology, Tianjin Medical University, Heping District Qixiangtai Road No.22, 300070 Tianjin, P.R. China, Institute of Medical Technology, University of Tampere, Biokatu 8, 33520 Tampere, Finland, Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark, Institute of Biotechnology, Program on Development Biology, PL56, 00014 University of Helsinki and Department of Clinical Microbiology, Tampere University Hospital, 33520 Tampere, Finland
- *To whom correspondence should be addressed. Tel:+358 3 3551 7845; Fax:+358 3 3551 7332; Correspondence may also be addressed to Jie Yang. Tel:+86 22 23542520 +86 22 23542581
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8
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Yang WH, Bloch DB. Probing the mRNA processing body using protein macroarrays and "autoantigenomics". RNA (NEW YORK, N.Y.) 2007; 13:704-12. [PMID: 17339575 PMCID: PMC1852818 DOI: 10.1261/rna.411907] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Messenger RNA processing bodies (P-bodies) are cellular structures that have a direct role in mRNA degradation. P-bodies have also been implicated in RNAi-mediated post-transcriptional gene silencing. Despite the important roles of P-bodies in cellular biology, the constituents of P-bodies and their organization have been only partially defined. Approximately 5% of patients with the autoimmune disease primary biliary cirrhosis have antibodies directed against these structures. Recent advances in protein macroarray technology permit the simultaneous screening of thousands of proteins for reactivity with autoantibodies. We used serum from patients with anti-P-body autoantibodies to screen a protein macroarray and identified 67 potential autoantigens. Immunoreactive proteins included four known P-body components and three additional primary biliary cirrhosis autoantigens. Y-box protein 1 (YB-1), a 50-kDa RNA-binding protein that was not previously known to be a P-body component, was recognized by serum from four of seven patients. YB-1 colocalized with P-body components DCP1a and Ge-1. In cells subjected to arsenite-induced oxidative stress, YB-1 localized to TIA-containing stress granules. Both YB-1 and the previously identified P-body component RAP55 translocated from P-bodies to stress granules during oxidative stress. During recovery, however, the reappearance of YB-1 in P-bodies was delayed compared with that of RAP55, suggesting that YB-1 and RAP55 may have different functions. This study demonstrates that the combination of human autoantibodies and protein macroarray technology provides a novel method for identifying and characterizing components of mRNA P-bodies.
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Affiliation(s)
- Wei-Hong Yang
- Center for Immunology and Inflammatory Diseases of the General Medical Services, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02129, USA
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9
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Saveanu C, Fromont-Racine M, Jacquier A. 18 RNA Gene Analysis. METHODS IN MICROBIOLOGY 2007. [DOI: 10.1016/s0580-9517(06)36018-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Shi Y, Reddy B, Manley JL. PP1/PP2A phosphatases are required for the second step of Pre-mRNA splicing and target specific snRNP proteins. Mol Cell 2006; 23:819-29. [PMID: 16973434 DOI: 10.1016/j.molcel.2006.07.022] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 06/05/2006] [Accepted: 07/26/2006] [Indexed: 11/22/2022]
Abstract
Pre-mRNA splicing is a complex and dynamic process in which protein phosphorylation and dephosphorylation both play important roles. Although specific phosphatases, such as PP1 and PP2A, have been implicated in splicing, direct evidence for their involvement has been lacking, and their exact function(s) in this process remain unknown. In this study, we show that PP1 and certain PP2A family phosphatases play essential but redundant roles in splicing. Unexpectedly, we found that these phosphatases are required principally for the second step of the splicing reaction. Furthermore, we provide evidence that components of U2 and U5 snRNPs, specifically SAP155 and U5-116 kDa, are the key spliceosomal substrates for these phosphatases. Based on these data, we propose that dephosphorylation of U2 and U5 snRNP components by PP1/PP2A family phosphatases facilitates essential structural rearrangements in the spliceosome during the transition from the first to the second step.
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Affiliation(s)
- Yongsheng Shi
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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11
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Cohen LS, Mikhli C, Jiao X, Kiledjian M, Kunkel G, Davis RE. Dcp2 Decaps m2,2,7GpppN-capped RNAs, and its activity is sequence and context dependent. Mol Cell Biol 2005; 25:8779-91. [PMID: 16199859 PMCID: PMC1265788 DOI: 10.1128/mcb.25.20.8779-8791.2005] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Hydrolysis of the mRNA cap plays a pivotal role in initiating and completing mRNA turnover. In nematodes, mRNA metabolism and cap-interacting proteins must deal with two populations of mRNAs, spliced leader trans-spliced mRNAs with a trimethylguanosine cap and non-trans-spliced mRNAs with a monomethylguanosine cap. We describe here the characterization of nematode Dcp1 and Dcp2 proteins. Dcp1 was inactive in vitro on both free cap and capped RNA and did not significantly enhance Dcp2 activity. Nematode Dcp2 is an RNA-decapping protein that does not bind cap and is not inhibited by cap analogs but is effectively inhibited by competing RNA irrespective of RNA sequence and cap. Nematode Dcp2 activity is influenced by both 5' end sequence and its context. The trans-spliced leader sequence on mRNAs reduces Dcp2 activity approximately 10-fold, suggesting that 5'-to-3' turnover of trans-spliced RNAs may be regulated. Nematode Dcp2 decaps both m(7)GpppG- and m(2,2,7)GpppG-capped RNAs. Surprisingly, both budding yeast and human Dcp2 are also active on m(2,2,7)GpppG-capped RNAs. Overall, the data suggest that Dcp2 activity can be influenced by both sequence and context and that Dcp2 may contribute to gene regulation in multiple RNA pathways, including monomethyl- and trimethylguanosine-capped RNAs.
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Affiliation(s)
- Leah S Cohen
- Department of Biology, City University of New York Graduate Center, CSI, Staten Island, 10314, USA
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12
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Abstract
The Tudor domain is an approximately 60-amino acid structure motif in search of a function. Herein we show that the Tudor domains of the spinal muscular atrophy gene product SMN, the splicing factor 30 kDa (SPF30), and the Tudor domain-containing 3 (TDRD3) proteins interacted with arginine-glycine-rich motifs in a methylarginine-dependent manner. The Tudor domains also associated with methylarginine-containing cellular proteins, providing evidence that methylated arginines represent physiological ligands for this protein module. In addition, we report that spliceosomal small nuclear ribonucleoprotein particles core Sm proteins accumulated in the cytoplasm when arginine methylation was inhibited with adenosine dialdehyde or in the presence of an excessive amount of unmethylated arginine-glycine-rich peptides. These data provide in vivo evidence in support of a role for arginine methylation in the proper assembly and localization of spliceosomal Sm proteins.
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Affiliation(s)
- Jocelyn Côté
- Terry Fox Molecular Oncology Group and the Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital and Department of Oncology, McGill University, Montréal, Québec H3T 1E2, Canada
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13
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Yong J, Wan L, Dreyfuss G. Why do cells need an assembly machine for RNA-protein complexes? Trends Cell Biol 2004; 14:226-32. [PMID: 15130578 DOI: 10.1016/j.tcb.2004.03.010] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Small nuclear ribonucleoproteins (snRNPs) are crucial for pre-mRNA processing to mRNAs. Each snRNP contains a small nuclear RNA (snRNA) and an extremely stable core of seven Sm proteins. The snRNP biogenesis pathway is complex, involving nuclear export of snRNA, Sm-core assembly in the cytoplasm and re-import of the mature snRNP. Although in vitro Sm cores assemble readily on uridine-rich RNAs, the assembly in cells is carried out by the survival of motor neurons (SMN) complex. The SMN complex stringently scrutinizes RNAs for specific features that define them as snRNAs and identifies the RNA-binding Sm proteins. We discuss how this surveillance capacity of the SMN complex might ensure assembly of Sm cores only on the correct RNAs and prevent illicit, potentially deleterious assembly of Sm cores on random RNAs.
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Affiliation(s)
- Jeongsik Yong
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6148, USA
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14
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Narayanan A, Eifert J, Marfatia KA, Macara IG, Corbett AH, Terns RM, Terns MP. Nuclear RanGTP is not required for targeting small nucleolar RNAs to the nucleolus. J Cell Sci 2003; 116:177-86. [PMID: 12456727 DOI: 10.1242/jcs.00176] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The small GTPase Ran is the central regulator of macromolecular transport between the cytoplasm and the nucleus. Recent work has suggested that RanGTP also plays an important role in regulating some intra-nuclear processes. In this study, we have investigated whether RanGTP is required for the intra-nuclear transport of RNAs. Specifically, we directly analyzed the nucleolar localization of Box C/D and Box H/ACA small nucleolar RNAs (snoRNAs) in mammalian (tsBN2) cells, Saccharomyces cerevisiae and Xenopus oocytes under conditions that deplete nuclear RanGTP and prevent RNA export to the cytoplasm. Our data suggest that depletion of nuclear RanGTP does not significantly alter the nucleolar localization of U3 snoRNA in tsBN2 cells. Complementary studies in the budding yeast S. cerevisiae using conditional Ran mutants as well as mutants in Ran regulatory proteins also indicate that disruption of the Ran gradient or of Ran itself does not detectably affect the nucleolar localization of snoRNAs. Finally, microinjection into Xenopus oocytes was used to clearly demonstrate that a specific pool of snoRNAs could still be efficiently targeted to the nucleolus even when the RanGTP gradient was disrupted by microinjection of mutant Ran proteins. Taken together, our data from three phylogenetically distinct experimental systems suggest that nuclear RanGTP, which is essential for trafficking of RNAs between the nuclear and cytoplasmic compartments, is not required for nuclear retention or nucleolar localization of snoRNAs.
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Affiliation(s)
- Aarthi Narayanan
- Department of Biochemistry and Molecular Biology, University of Georgia, Life Sciences Building, Athens, GA 30602, USA
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15
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Weik M, Modrof J, Klenk HD, Becker S, Mühlberger E. Ebola virus VP30-mediated transcription is regulated by RNA secondary structure formation. J Virol 2002; 76:8532-9. [PMID: 12163572 PMCID: PMC136988 DOI: 10.1128/jvi.76.17.8532-8539.2002] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The nucleocapsid protein VP30 of Ebola virus (EBOV), a member of the Filovirus family, is known to act as a transcription activator. By using a reconstituted minigenome system, the role of VP30 during transcription was investigated. We could show that VP30-mediated transcription activation is dependent on formation of a stem-loop structure at the first gene start site. Destruction of this secondary structure led to VP30-independent transcription. Analysis of the transcription products of bicistronic minigenomes with and without the ability to form the secondary structure at the first transcription start signal revealed that transcription initiation at the first gene start site is a prerequisite for transcription of the second gene, independent of the presence of VP30. When the transcription start signal of the second gene was exchanged with the transcription start signal of the first gene, transcription of the second gene also was regulated by VP30, indicating that the stem-loop structure of the first transcription start site acts autonomously and independently of its localization on the RNA genome. Our results suggest that VP30 regulates a very early step of EBOV transcription, most likely by inhibiting pausing of the transcription complex at the RNA structure of the first transcription start site.
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Affiliation(s)
- Michael Weik
- Institut für Virologie der Philipps-Universität Marburg, 35037 Marburg, Germany
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16
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Lukowiak AA, Narayanan A, Li ZH, Terns RM, Terns MP. The snoRNA domain of vertebrate telomerase RNA functions to localize the RNA within the nucleus. RNA (NEW YORK, N.Y.) 2001; 7:1833-1844. [PMID: 11780638 PMCID: PMC1370221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Telomerase RNA is an essential component of the ribonucleoprotein enzyme involved in telomere length maintenance, a process implicated in cellular senescence and cancer. Vertebrate telomerase RNAs contain a box H/ACA snoRNA motif that is not required for telomerase activity in vitro but is essential in vivo. Using the Xenopus oocyte system, we have found that the box H/ACA motif functions in the subcellular localization of telomerase RNA. We have characterized the transport and biogenesis of telomerase RNA by injecting labeled wild-type and variant RNAs into Xenopus oocytes and assaying nucleocytoplasmic distribution, intranuclear localization, modification, and protein binding. Although yeast telomerase RNA shares characteristics of spliceosomal snRNAs, we show that human telomerase RNA is not associated with Sm proteins or efficiently imported into the nucleus. In contrast, the transport properties of vertebrate telomerase RNA resemble those of snoRNAs; telomerase RNA is retained in the nucleus and targeted to nucleoli. Furthermore, both nuclear retention and nucleolar localization depend on the box H/ACA motif. Our findings suggest that the H/ACA motif confers functional localization of vertebrate telomerase RNAs to the nucleus, the compartment where telomeres are synthesized. We have also found that telomerase RNA localizes to Cajal bodies, intranuclear structures where it is thought that assembly of various cellular RNPs takes place. Our results identify the Cajal body as a potential site of telomerase RNP biogenesis.
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Affiliation(s)
- A A Lukowiak
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens 30602, USA
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17
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Labourier E, Rio DC. Purification of Drosophila snRNPs and characterization of two populations of functional U1 particles. RNA (NEW YORK, N.Y.) 2001; 7:457-70. [PMID: 11333025 PMCID: PMC1370101 DOI: 10.1017/s1355838201001327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
U1 snRNP is required at an early stage during assembly of the spliceosome, the dynamic ribonucleoprotein (RNP) complex that performs nuclear pre-mRNA splicing. Here, we report the purification of U1 snRNP particles from Drosophila nuclear extracts and the characterization of their biochemical properties, polypeptide contents, and splicing activities. On the basis of their antigenicity, apparent molecular weight, and by peptide sequencing, the Drosophila 70K, SNF, B, U1-C, D1, D2, D3, E, F, and G proteins are shown to be integral components of these particles. Sequence database searches revealed that both the U1-specific and the Sm proteins are extensively conserved between human and Drosophila snRNPs. Furthermore, both species possess a conserved intrinsic U1-associated kinase activity with identical substrate specificity in vitro. Finally, our results demonstrate that a second type of functional U1 particle, completely lacking the U1/U2-specific protein SNF and the associated protein kinase activity, can be isolated from cultured Kc cell or Canton S embryonic nuclear extracts. This work describes the first characterization of a purified Drosophila snRNP particle and reinforces the view that their activity and composition, with the exception of the atypical bifunctional U1-A/U2-B" SNF protein, are highly conserved in metazoans.
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Affiliation(s)
- E Labourier
- Department of Molecular and Cell Biology, University of California, Berkeley 94720-3204, USA
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Dostie J, Lejbkowicz F, Sonenberg N. Nuclear eukaryotic initiation factor 4E (eIF4E) colocalizes with splicing factors in speckles. J Cell Biol 2000; 148:239-47. [PMID: 10648556 PMCID: PMC2174286 DOI: 10.1083/jcb.148.2.239] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The eukaryotic initiation factor 4E (eIF4E) plays a pivotal role in the control of protein synthesis. eIF4E binds to the mRNA 5' cap structure, m(7)GpppN (where N is any nucleotide) and promotes ribosome binding to the mRNA. It was previously shown that a fraction of eIF4E localizes to the nucleus (Lejbkowicz, F., C. Goyer, A. Darveau, S. Neron, R. Lemieux, and N. Sonenberg. 1992. Proc. Natl. Acad. Sci. USA. 89:9612-9616). Here, we show that the nuclear eIF4E is present throughout the nucleoplasm, but is concentrated in speckled regions. Double label immunofluorescence confocal microscopy shows that eIF4E colocalizes with Sm and U1snRNP. We also demonstrate that eIF4E is specifically released from the speckles by the cap analogue m(7)GpppG in a cell permeabilization assay. However, eIF4E is not released from the speckles by RNase A treatment, suggesting that retention of eIF4E in the speckles is not RNA-mediated. 5,6-dichloro-1-beta-d-ribofuranosylbenzimidazole (DRB) treatment of cells causes the condensation of eIF4E nuclear speckles. In addition, overexpression of the dual specificity kinase, Clk/Sty, but not of the catalytically inactive form, results in the dispersion of eIF4E nuclear speckles.
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Affiliation(s)
- Josée Dostie
- Department of Biochemistry and Cancer Centre, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Flavio Lejbkowicz
- Department of Biochemistry and Cancer Centre, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Cancer Centre, McGill University, Montréal, Québec H3G 1Y6, Canada
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Speckmann W, Narayanan A, Terns R, Terns MP. Nuclear retention elements of U3 small nucleolar RNA. Mol Cell Biol 1999; 19:8412-21. [PMID: 10567566 PMCID: PMC84939 DOI: 10.1128/mcb.19.12.8412] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The processing and methylation of precursor rRNA is mediated by the box C/D small nucleolar RNAs (snoRNAs). These snoRNAs differ from most cellular RNAs in that they are not exported to the cytoplasm. Instead, these RNAs are actively retained in the nucleus where they assemble with proteins into mature small nucleolar ribonucleoprotein particles and are targeted to their intranuclear site of action, the nucleolus. In this study, we have identified the cis-acting sequences responsible for the nuclear retention of U3 box C/D snoRNA by analyzing the nucleocytoplasmic distributions of an extensive panel of U3 RNA variants after injection of the RNAs into Xenopus oocyte nuclei. Our data indicate the importance of two conserved sequence motifs in retaining U3 RNA in the nucleus. The first motif is comprised of the conserved box C' and box D sequences that characterize the box C/D family. The second motif contains conserved box sequences B and C. Either motif is sufficient for nuclear retention, but disruption of both motifs leads to mislocalization of the RNAs to the cytoplasm. Variant RNAs that are not retained also lack 5' cap hypermethylation and fail to associate with fibrillarin. Furthermore, our results indicate that nuclear retention of U3 RNA does not simply reflect its nucleolar localization. A fragment of U3 containing the box B/C motif is not localized to nucleoli but retained in coiled bodies. Thus, nuclear retention and nucleolar localization are distinct processes with differing sequence requirements.
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Affiliation(s)
- W Speckmann
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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Liang B, Gee RJ, Kashgarian MJ, Sharpe AH, Mamula MJ. B7 Costimulation in the Development of Lupus: Autoimmunity Arises Either in the Absence of B7.1/B7.2 or in the Presence of Anti-B7.1/B7.2 Blocking Antibodies. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.163.4.2322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Costimulatory molecules, termed B7.1 and B7.2, are present on the surfaces of APC and are important for the activation of T lymphocytes specific for both foreign Ags and autoantigens. We have examined the role of B7 costimulation in the MRL-lpr/lpr murine model of human systemic lupus erythematosus. MRL-lpr/lpr mice receiving both anti-B7.1 and anti-B7.2 Abs expressed significantly lower anti-small nuclear ribonucleoprotein particles (snRNP) and anti-dsDNA autoantibodies than did untreated mice. Anti-B7.2 Ab treatment alone inhibited anti-dsDNA autoantibody expression while having no effect on anti-snRNP autoantibody expression. Anti-B7.1 Ab treatment alone did not change the expression of either anti-snRNP or anti-dsDNA autoantibodies. Parallel studies performed in MRL-lpr/lpr mice genetically deficient in either B7.1 or B7.2 expressed autoantibody profiles comparable to those found in wild-type MRL-lpr/lpr mice. However, B7.1-deficient MRL-lpr/lpr mice exhibited distinct and more severe glomerulonephritis while B7.2-deficient MRL-lpr/lpr mice had significantly milder or absent kidney pathology as compared with age-matched wild-type mice. These studies indicate that each B7 costimulatory signal may control unique pathological events in murine systemic lupus erythematosus that may not always be apparent in autoantibody titers alone.
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Affiliation(s)
- Bailin Liang
- *Department of Internal Medicine, Section of Rheumatology, and
| | - Renelle J. Gee
- *Department of Internal Medicine, Section of Rheumatology, and
| | - Michael J. Kashgarian
- †Department of Pathology, Yale University School of Medicine, New Haven, CT 06510; and
| | - Arlene H. Sharpe
- ‡Immunology Research Division, Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115
| | - Mark J. Mamula
- *Department of Internal Medicine, Section of Rheumatology, and
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Mamula MJ, Gee RJ, Elliott JI, Sette A, Southwood S, Jones PJ, Blier PR. Isoaspartyl post-translational modification triggers autoimmune responses to self-proteins. J Biol Chem 1999; 274:22321-7. [PMID: 10428801 DOI: 10.1074/jbc.274.32.22321] [Citation(s) in RCA: 167] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The normal functioning immune system is programmed to attack foreign pathogens and other foreign proteins while maintaining tolerance to self-proteins. The mechanisms by which tolerance is broken in the initiation of autoimmunity are not completely understood. In the present study, mice immunized with the murine cytochrome c peptide 90-104 showed no response by the B or T cell compartments. However, immunization with the isoaspartyl form of this peptide, where the linkage of Asp(93) to Leu(94) occurs through the beta-carboxyl group, resulted in strong B and T cell autoimmune responses. Antibodies elicited by immunization with the isoaspartyl form of self-peptide were cross-reactive in binding to both isoforms of cytochrome c peptide and to native cytochrome c self-protein. In a similar manner, immunization of mice with the isoaspartyl form of a peptide autoantigen of human systemic lupus erythematosus (SLE) resulted in strong B and T cell responses while mice maintained tolerance to the normal aspartyl form of self-antigen. Isoaspartyl linkages within proteins are enhanced in aging and stressed cells and arise under physiological conditions. These post-translationally modified peptides may serve as an early immunologic stimulus in autoimmune disease.
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Affiliation(s)
- M J Mamula
- Section of Rheumatology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
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22
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Narayanan A, Speckmann W, Terns R, Terns MP. Role of the box C/D motif in localization of small nucleolar RNAs to coiled bodies and nucleoli. Mol Biol Cell 1999; 10:2131-47. [PMID: 10397754 PMCID: PMC25425 DOI: 10.1091/mbc.10.7.2131] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Small nucleolar RNAs (snoRNAs) are a large family of eukaryotic RNAs that function within the nucleolus in the biogenesis of ribosomes. One major class of snoRNAs is the box C/D snoRNAs named for their conserved box C and box D sequence elements. We have investigated the involvement of cis-acting sequences and intranuclear structures in the localization of box C/D snoRNAs to the nucleolus by assaying the intranuclear distribution of fluorescently labeled U3, U8, and U14 snoRNAs injected into Xenopus oocyte nuclei. Analysis of an extensive panel of U3 RNA variants showed that the box C/D motif, comprised of box C', box D, and the 3' terminal stem of U3, is necessary and sufficient for the nucleolar localization of U3 snoRNA. Disruption of the elements of the box C/D motif of U8 and U14 snoRNAs also prevented nucleolar localization, indicating that all box C/D snoRNAs use a common nucleolar-targeting mechanism. Finally, we found that wild-type box C/D snoRNAs transiently associate with coiled bodies before they localize to nucleoli and that variant RNAs that lack an intact box C/D motif are detained within coiled bodies. These results suggest that coiled bodies play a role in the biogenesis and/or intranuclear transport of box C/D snoRNAs.
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Affiliation(s)
- A Narayanan
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
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Kawahata K, Misaki Y, Komagata Y, Setoguchi K, Tsunekawa S, Yoshikawa Y, Miyazaki JI, Yamamoto K. Altered Expression Level of a Systemic Nuclear Autoantigen Determines the Fate of Immune Response to Self. THE JOURNAL OF IMMUNOLOGY 1999. [DOI: 10.4049/jimmunol.162.11.6482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
One of the hallmarks of systemic autoimmune diseases is immune responses to systemic nuclear autoantigens. We have examined the fate of the immune response against a nuclear autoantigen using human U1 small nuclear ribonucleoprotein-A protein (HuA) transgenic (Tg) mice by adoptive transfer of autoreactive lymphocytes. We obtained two Tg lines that have different expression levels of the transgene. After spleen cells from HuA-immunized wild-type mice were transferred to Tg mice and their non-Tg littermates, these recipients were injected with HuA/IFA to induce a recall memory response. HAB69, which expressed a lower amount of HuA, exhibited a vigorous increase in the autoantibody level and glomerulonephritis. Moreover, the autoreactivity spread to 70K autoantigen. Alternatively, in HAB64, which expressed a higher amount of HuA, the production of autoantibody was markedly suppressed. The immune response to HuA autoantigen was impaired as demonstrated in a both delayed-type hypersensitivity response and proliferation assay. This inhibition was Ag-specific and was mediated by T cells. These data suggest that the expression level of systemic autoantigens influences the outcome of the immune response to self.
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Affiliation(s)
- Kimito Kawahata
- *Department of Allergy and Rheumatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Yoshikata Misaki
- *Department of Allergy and Rheumatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Yoshinori Komagata
- *Department of Allergy and Rheumatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
- †Center for Neurologic Diseases, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02215
| | - Keigo Setoguchi
- *Department of Allergy and Rheumatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | | | - Yasuji Yoshikawa
- §Department of Clinical Laboratory, Medical Institute of Bioregulation, Kyushu University, Beppu, Japan; and
| | - Jun-ichi Miyazaki
- ¶Department of Nutrition and Physiological Chemistry, Osaka University Medical School, Suita, Japan
| | - Kazuhiko Yamamoto
- *Department of Allergy and Rheumatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
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24
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Brahms H, Raker VA, van Venrooij WJ, Lührmann R. A major, novel systemic lupus erythematosus autoantibody class recognizes the E, F, and G Sm snRNP proteins as an E-F-G complex but not in their denatured states. ARTHRITIS AND RHEUMATISM 1997; 40:672-82. [PMID: 9125249 DOI: 10.1002/art.1780400412] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To determine whether the E, F, and G Sm proteins present antigenic determinants recognized by systemic lupus erythematosus (SLE) patient sera, and if so, whether the antigenicity depends on the native conformations of the polypeptides and/or is E-F-G complex restricted. METHODS Radioimmunoprecipitation, epitope tagging, expression polymerase chain reaction, in vitro translation, in vitro reconstitution, and immunoblotting. RESULTS Most of the anti-Sm SLE patient sera tested reacted with one or more of the E, F, and G proteins in immunoprecipitation studies but not on immunoblots. All sera, however, highly efficiently immunoprecipitated the E-F-G complex. This complex recognition was detected exclusively in anti-Sm patient sera but not in patient sera with other serotypes. CONCLUSION We demonstrate the presence of a novel and abundant anti-Sm autoantibody class in SLE patient sera which exclusively or predominantly recognizes conformational Sm epitopes present on the E-F-G complex but not on the denatured proteins. This complex recognition is highly specific for sera of the anti-Sm serotype and may be relevant for clinical diagnosis as well as for understanding the etiology of anti-Sm autoantibody production.
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Affiliation(s)
- H Brahms
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg, Germany
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25
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Abstract
Immuno-detection by 'Midwestern' blotting provides a simple way to identify trimethylguanosine (TMG) capped RNAs. With this technique, over 20 bands are observed when total cellular RNA from Saccharomyces cerevisiae is transferred to a nylon membrane and probed with anti-TMG antibodies. Most, if not all, species known to contain a TMG cap are detected by this method. Only TMG-capped RNAs are detected on Midwestern blots unlike anti-TMG immunoprecipitates. Midwestern blotting is a useful alternative to immunoprecipitation and Northern analysis and may prove to be a better method for determining the relative abundance of capped RNAs. The blots can be reprobed multiple times with labeled antisense oligonucleotides to determine the identity of any TMG-capped species for which the primary sequence or a clone is available. This dual detection capability provides a powerful tool for the analysis of TMG-capped snRNAs and snoRNAs.
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Affiliation(s)
- T P Rasmussen
- Laboratories of Genetics and Molecular Biology, University of Wisconsin, Madison 53706, USA
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26
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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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Lauber J, Fabrizio P, Teigelkamp S, Lane WS, Hartmann E, Luhrmann R. The HeLa 200 kDa U5 snRNP-specific protein and its homologue in Saccharomyces cerevisiae are members of the DEXH-box protein family of putative RNA helicases. EMBO J 1996; 15:4001-15. [PMID: 8670905 PMCID: PMC452120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The primary structure of the 200 kDa protein of purified HeLa U5 snRNPs (U5-200kD) was characterized by cloning and sequencing of its cDNA. In order to confirm that U5-200kD is distinct from U5-220kD we demonstrate by protein sequencing that the human U5-specific 220 kDa protein is homologous to the yeast U5-specific protein Prp8p. A 246 kDa protein (Snu246p) homologous to U5-200kD was identified in Saccharomyces cerevisiae. Both proteins contain two conserved domains characteristic of the DEXH-box protein family of putative RNA helicases and RNA-stimulated ATPases. Antibodies raised against fusion proteins produced from fragments of the cloned mammalian cDNA interact specifically with the HeLa U5-200kD protein on Western blots and co-immunoprecipitate U5 snRNA and to a lesser extent U4 and U6 snRNAs from HeLa snRNPs. Similarly, U4, U5 and U6 snRNAs can be co-immunoprecipitated from yeast splicing extracts containing an HA-tagged derivative of Snu246p with HA-tag specific antibodies. U5-200kD and Snu246p are thus the first putative RNA helicases shown to be intrinsic components of snRNPs. Disruption of the SNU246 gene in yeast is lethal and leads to a splicing defect in vivo, indicating that the protein is essential for splicing. Anti-U5-200kD antibodies specifically block the second step of mammalian splicing in vitro, demonstrating for the first time that a DEXH-box protein is involved in mammalian splicing. We propose that U5-200kD and Snu246p promote one or more conformational changes in the dynamic network of RNA-RNA interactions in the spliceosome.
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Affiliation(s)
- J Lauber
- Institut fur Molekularbiologie und Tumorforschung, Philipps-Universitat Marburg, Emil Mannkopff-Strasse 2, D35037 Marburg, Germany
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Perl A, Colombo E, Dai H, Agarwal R, Mark KA, Banki K, Poiesz BJ, Phillips PE, Hoch SO, Reveille JD. Antibody reactivity to the HRES-1 endogenous retroviral element identifies a subset of patients with systemic lupus erythematosus and overlap syndromes. Correlation with antinuclear antibodies and HLA class II alleles. ARTHRITIS AND RHEUMATISM 1995; 38:1660-71. [PMID: 7488288 DOI: 10.1002/art.1780381119] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
OBJECTIVE To evaluate the correlation between the presence of antibodies to an endogenous retroviral element-encoded nuclear protein autoantigen, HRES-1, and the presence of other antinuclear antibodies and HLA class II alleles in patients with systemic lupus erythematosus (SLE) and overlap syndromes. METHODS Antibody reactivities to native and recombinant proteins and synthetic peptides were assessed by counterimmunoelectrophoresis, enzyme-linked immunosorbent assay, and Western blotting. HLA class II alleles were determined by oligonucleotide typing. RESULTS Forty-eight percent of the 153 patients with autoimmune disease, and 52% of the subgroup with SLE, had HRES-1 antibodies. In contrast, 3.6% of 111 normal donors, and none of 42 patients with the acquired immunodeficiency syndrome or 50 asymptomatic human immunodeficiency virus 1-infected patients, had HRES-1 antibodies. Chi-square analyses revealed a significant association between anti-HRES-1 and anti-RNP and an inverse correlation between HRES-1 and Ro/La autoantibodies in patients with SLE or overlap syndromes. Antigenic epitopes of HRES-1 and the retroviral gag-related region of the 70-kd protein component of U1 small nuclear RNP, which share 3 consecutive highly charged amino acids (Arg-Arg-Glu), an additional Arg, and functionally similar Arg/Lys residues, represent cross-reactive epitopes between the two proteins. Selective removal of HRES-1 antibodies from sera of HRES-1-seropositive/RNP-seropositive patients by absorption on recombinant HRES-1/glutathione-S-transferase-conjugated agarose beads had no effect on anti-RNP reactivities. A comparative multivariate analysis of HLA class II genes revealed a differential segregation of DQB1 alleles in HRES-1-seropositive versus HRES-1-seronegative patients (P = 0.04). While a relative increase of DQB1*0402 among HRES-1-seropositive patients was noted across ethnic groups (P = 0.02), a decrease of DQB1*0201 and DQB1*0301 was found in white HRES-1-seropositive patients (P = 0.04). CONCLUSION Autoantibodies to HRES-1 are detectable in a distinct subset of patients with autoimmune disease, primarily in those who do not have antibodies to Ro and La. Anti-HRES-1 and anti-RNP reactivities are mediated by cross-reactive but separate antibody molecules. HLA-DQB genes, rather than HLA-DRB or DQA genes, may have a more significant influence on generation of these antinuclear autoantibodies.
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Affiliation(s)
- A Perl
- SUNY Health Science Center, College of Medicine, Syracuse 13210, USA
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29
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Cheng Y, Dahlberg JE, Lund E. Diverse effects of the guanine nucleotide exchange factor RCC1 on RNA transport. Science 1995; 267:1807-10. [PMID: 7534442 DOI: 10.1126/science.7534442] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transport of RNAs within nuclei and through nuclear pore complexes (NPCs) are essential, but poorly understood, steps in gene expression. In experiments with mammalian cells, RCC1, the abundant nuclear guanine nucleotide exchange factor for the guanosine triphosphatase Ran/TC4, was shown to be required for nucleocytoplasmic transport of precursors of spliceosomal small nuclear RNAs (snRNAs), intranuclear transport of U3 snRNA, and processing of ribosomal RNAs, but not for export of transfer RNAs. It is proposed that guanosine triphosphate (GTP)-bound Ran/TC4 associates with ribonucleoprotein particles (RNPs) during intranuclear movement, and that GTP hydrolysis promotes deposition of RNPs at targeted sites such as NPCs or nucleoli.
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Affiliation(s)
- Y Cheng
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine, Madison 53706
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30
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Abstract
It is shown here that maturation of the m7G-capped precursors of U3 small nuclear RNA (snRNA) occurs by a previously unknown pathway. In contrast to the 5' m7G-capped precursors of other snRNAs, this RNA is not exported to the cytoplasm but is retained in the nuclei of Xenopus laevis oocytes, where it undergoes trimethylation of its 5' cap. The m7G caps of most snRNA precursors are trimethylated only after transport of the RNAs to the cytoplasm. The nuclear retention and maturation of this nucleolar RNA raises the possibility that other m7G-capped RNAs are also retained and modified in the nucleus.
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Affiliation(s)
- M P Terns
- Department of Biomolecular Chemistry, University of Wisconsin, Madison 53706
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31
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Wolff-Vorbeck G, Hackl W, Fenning S, Krawinkel U, Lührmann R, Peter HH, Schlesier M. Characterization of an HLA-DR4-restricted T cell clone recognizing a protein moiety of small nuclear ribonucleoproteins (UsnRNP). Clin Exp Immunol 1994; 95:378-84. [PMID: 8137535 PMCID: PMC1535078 DOI: 10.1111/j.1365-2249.1994.tb07007.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In sera of patients with mixed connective tissue disease (MCTD, Sharp Syndrome) high titres of IgG autoantibodies to U1snRNP-specific proteins are found. The isolated occurrence of these autoantibodies is highly associated with the HLA-DR4 haplotype. snRNP-specific T cells are supposed to be involved in this autoantibody production. To address this question we cultured mononuclear cells from MCTD patients and healthy donors with a highly purified UsnRNP preparation from HeLa cells using bulk or limiting dilution cultures. Secondary responses to snRNP were detected only rarely with T cell lines from two patients and two controls, and turned out to be unstable during further expansion. One T cell line derived from a healthy individual retained its snRNP reactivity upon limiting dilution cloning and could be characterized in detail. The CD4+ T cell clone recognized native snRNP particles presented by monocytes in an HLA-DR4 (B1*0401)-restricted manner. Separation of the protein and RNA moieties of snRNP particles revealed that the T cell clone responded specifically to the protein fraction, but not to RNA and diverse control antigens. Sequencing of the T cell receptor alpha and beta chain cDNAs revealed that the clone used the V alpha 14.2 and V beta 14 elements. Upon antigen-specific and mitogenic stimulation the T cell clone showed a Th1-specific cytokine pattern, and did not provide helper activity for in vitro immunoglobulin production. This study demonstrate the presence of self-reactive snRNP-specific T cells in a healthy donor. The T cell clone may not represent a helper T cell for the formation of U1snRNP-specific autoantibodies.
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Affiliation(s)
- G Wolff-Vorbeck
- Abt. Rheumatologie und Klinische Immunologie, Medizinische Klinik, Freiburg, Germany
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32
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Terns MP, Dahlberg JE, Lund E. Multiple cis-acting signals for export of pre-U1 snRNA from the nucleus. Genes Dev 1993; 7:1898-908. [PMID: 8405997 DOI: 10.1101/gad.7.10.1898] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have identified cis-acting sequences that promote nuclear export of pre-U1 RNA injected into Xenopus oocyte nuclei. At least three elements, the 5' m7G cap, the 3'-terminal stem-loop structure, and sequences in the 5'-terminal 124 nucleotides, contribute to efficient export of this RNA. Both the 5' and 3' export signals can function separately and do so independently of the cap structure. Experiments using hybrid RNAs indicate that the 5' and 3' export sequences of U1 RNA are sufficient to direct export of the heterologous, otherwise nonexportable, U6 RNA. The absence of comparable export signals in U6 RNA appears to be responsible for its retention in the nucleus. Stability of the pre-snRNAs in the nucleus depends on the presence of both a 5' cap structure and a 3' base-paired stem. The 5' m7G cap is neither sufficient nor necessary for nuclear export. The m7G cap by itself did not promote export of U6 RNA or nonspecific small RNAs. Moreover, substitution of this cap with either an AppG cap or gamma-mppG cap did not eliminate export of either full-length or a "minimal" U1 RNA (lacking most of the internal U1 RNA sequences), but it reduced the rate of export by about two to threefold. However, in the absence of the 3' stem-loop, substitution of the m7G cap led to a greater decrease in export rate, underscoring the cooperative action of the three different export elements of pre-U1 RNA. The m7G cap analog, m7GpppG, selectively destabilized pre-U1 RNA within the nucleus. Thus, nuclear components that recognize the 5' m7G cap may be important for both the stability and the export of pre-U1 RNA.
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Affiliation(s)
- M P Terns
- Department of Biomolecular Chemistry, University of Wisconsin, Madison 53706
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33
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Abstract
We describe the isolation and biochemical characterization of [U4/U6.U5] tri-snRNP complexes from HeLa cells under nondenaturing conditions using a monoclonal antibody reacting with the U5-specific 100-kD protein. We show that the [U4/U6.U5] complex contains five previously unobserved proteins with molecular masses of 90, 60, 27, 20, and 15.5 kD, in addition to the core proteins, common to the U4/U6, U5, U1, and U2 snRNPs, and the U5-specific proteins, as found in 20S U5 snRNPs. With approximately 20 distinct snRNP proteins the complexity of the [U4/U6.U5] tri-snRNP is surprising. One or more of the five proteins found exclusively in the 25S [U4/U6.U5] tri-snRNP appears to be involved in the assembly of the tri-snRNP complex, as, in an in vitro reconstitution assay, purified 20S U5 and 10S U4/U6 snRNPs formed stable 25S [U4/U6.U5] complexes only in the presence of the free tri-snRNP-specific proteins. The formation of the [U4/U6.U5] complex in vitro does not require ATP, and the stability of the purified tri-snRNP complex is not affected by ATP to a measurable extent. However, the native [U4/U6.U5] displays a kinase activity that is absent in isolated U5: A 52-kD protein present in both U5 and [U4/U6.U5] is phosphorylated only in the latter. The function of this phosphorylation is unclear thus far; it may be involved in the activation of [U4/U6.U5] in the spliceosome.
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Affiliation(s)
- S E Behrens
- Institut für Molekularbiologie und Tumorforschung, Marburg, Germany
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34
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Lührmann R, Kastner B, Bach M. Structure of spliceosomal snRNPs and their role in pre-mRNA splicing. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1087:265-92. [PMID: 2147394 DOI: 10.1016/0167-4781(90)90001-i] [Citation(s) in RCA: 323] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- R Lührmann
- Institut für Molekularbiologie und Tumorforschung, Philipps-Universität Marburg F.R.G
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35
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Hiepe F, Yamamoto K, Takeuchi A, Apostoloff E, Miyamoto T. Heterogeneity of RNP and Sm autoantigens in relation to the cell sources and the activated state of the cells. Rheumatol Int 1990; 10:121-6. [PMID: 2203134 DOI: 10.1007/bf02274826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The extracts of rabbit thymus (RTE), HeLa cells, human histiocytic lymphoma cell line U-937, human promyelocytic cell line HL-60, Ehrlich ascites tumor cells (EACs), and peripheral white blood cells (WBCs) were tested for their composition, molecular weight, and amount of Sm and RNP autoantigens on immunoblotting. The molecular weight of the so-called 68 kDa U1 RNP antigen, which is associated with mixed connective tissue disease (MCTD), was 64.5 kDa in RTE, 62.5 kDa in HeLa cells and HL-60 cells, and 59 kDa in WBCs. Surprisingly, in both WBCs and U-937 cells, the main protein band bearing the 68 kDa U1 RNP antigenic determinants was 30.5 kDa in molecular weight, which was confirmed using antibodies purified by affinity chromatography. After stimulation with phytohemagglutinin (PHA), there was in the human lymphocytes a diminished amount of the 30.5 kDa protein and simultaneously an increased synthesis of several proteins of higher molecular weight, especially the 57 kDa protein bearing the 68 kDa antigenic determinants. The concentrations of the A, B/B', C, D, and E proteins also increased with PHA stimulation. Our results indicate that the expression of Sm and RNP autoantigens may depend on the cell source as well as the activated state of cells. These differences should be taken into consideration in the detection of anti-RNP and anti-Sm antibodies by immunoblotting.
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MESH Headings
- Animals
- Autoantigens/immunology
- Carcinoma, Ehrlich Tumor/immunology
- Carcinoma, Ehrlich Tumor/pathology
- Cell Line
- HeLa Cells
- Humans
- Immunoblotting
- Leukemia, Promyelocytic, Acute/immunology
- Leukemia, Promyelocytic, Acute/pathology
- Leukocytes/cytology
- Leukocytes/immunology
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Ribonucleoproteins, Small Nuclear
- snRNP Core Proteins
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Affiliation(s)
- F Hiepe
- Department of Medicine and Physical Therapy, Faculty of Medicine, University of Tokyo, Japan
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36
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Myslinski E, Ségault V, Branlant C. An intron in the genes for U3 small nucleolar RNAs of the yeast Saccharomyces cerevisiae. Science 1990; 247:1213-6. [PMID: 1690452 DOI: 10.1126/science.1690452] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The origin of the intervening sequences (introns), which are removed during RNA maturation, is currently unknown. They are found in most genes encoding messenger RNAs, but are lacking in almost all small nuclear (sn)RNAs. One exceptional snRNA (U6) is part of the spliceosomal machinery that is involved in messenger RNA maturation. It has been suggested that its intron arose as a result of incorrect splicing of a messenger RNA precursor. This study revealed the presence of an intron, with the characteristic features of nuclear introns from precursors to messenger RNA, in the two genes coding for Saccharomyces cerevisiae U3 snRNA. The branch point was GACTAAC instead of the TACTAAC sequence found in all yeast introns examined so far. As U3 is a nucleolar snRNA required for maturation of ribosomal RNA, its intron could not have been acquired from aberrant messenger RNA processing in a spliceosome.
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Affiliation(s)
- E Myslinski
- Laboratoire d'Enzymologie et de Génie Génétique, Université de Nancy, France
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37
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Reuter R, Rothe S, Habets W, Van Venrooij WJ, Lührmann R. Autoantibody production against the U small nuclear ribonucleoprotein particle proteins E, F and G in patients with connective tissue diseases. Eur J Immunol 1990; 20:437-40. [PMID: 2138085 DOI: 10.1002/eji.1830200231] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The nucleoplasmic U small nuclear ribonucleoprotein particles (snRNP) have a set of seven proteins in common which are designated B', B, D, D', E, F and G. Patients suffering from rheumatoid autoimmune diseases such as systemic lupus erythematosus often develop autoantibodies against the proteins B', B, and D. Here we describe a sensitive immunoassay which allows the specific detection of autoantibodies reacting with the E, F or G snRNP proteins. We were able to identify several patient sera containing autoantibodies against one or more of these proteins. This demonstrates that all snRNP proteins described so far are potentially antigenic in systemic rheumatoid diseases. The characterization of the antibodies showed an immunological cross-reactivity between the snRNP protein G and the 70-kDa protein of U1 snRNP. Several sera contained autoantibodies which were specific for the F snRNP protein.
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Affiliation(s)
- R Reuter
- Max-Planck-Institut für molekulare Genetik, Otto-Warburg-Laboratorium, Berlin, FRG
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38
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Krämer A. Purification of small nuclear ribonucleoprotein particles active in RNA processing. Methods Enzymol 1990; 181:215-32. [PMID: 2143250 DOI: 10.1016/0076-6879(90)81124-d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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39
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Brunel C, Cathala G. Purification and characterization of U small nuclear ribonucleoproteins in cesium chloride gradients. Methods Enzymol 1990; 181:264-73. [PMID: 2143253 DOI: 10.1016/0076-6879(90)81127-g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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40
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Affiliation(s)
- G W Zieve
- Department of Basic Sciences, Hutchinson Cancer Research, Seattle, Washington
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41
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Bach M, Bringmann P, Lührmann R. Purification of small nuclear ribonucleoprotein particles with antibodies against modified nucleosides of small nuclear RNAs. Methods Enzymol 1990; 181:232-57. [PMID: 2143251 DOI: 10.1016/0076-6879(90)81125-e] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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42
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Temsamani J, Alibert C, Tazi J, Rucheton M, Capony JP, Jeanteur P, Cathala G, Brunel C. B-B' proteins from small nuclear ribonucleoproteins have an endoribonuclease catalytic domain inactive in native particles. J Mol Biol 1989; 206:439-49. [PMID: 2523974 DOI: 10.1016/0022-2836(89)90492-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Native small nuclear ribonucleoproteins (snRNPs) purified by several conventional procedures or reconstituted in vitro have no ribonuclease activity. However, when these same snRNPs are centrifuged in cesium chloride gradients at low [Mg2+] and in the presence of sarkosyl, an endoribonuclease is unmasked at the density of core particles (i.e. containing only the set of low molecular weight proteins common to all snRNPs), while an inhibitory component is released in soluble form. The nature of this inhibitor was not further investigated and the molecular events underlying this inhibition/activation process remained only a matter of speculation. On the other hand, evidence was obtained that the nuclease activity is carried by B-B' on the basis of its comigration with B-B' as well as with two of their cleavage products after SDS/polyacrylamide gel electrophoresis of snRNP proteins. One was identified by a B-B'-specific monoclonal antibody. Another one, especially prominent and migrating between D and E core proteins, was identified as the N-terminal half of B-B' by microsequence analysis. Although tightly associated with core snRNPs, the activity is not dependent upon the presence of an snRNA. For the time being, the functional significance of this nuclease remains entirely elusive.
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Affiliation(s)
- J Temsamani
- UA CNRS 1191, Laboratoire de Biochimie, Centre Val d'Aurelle-Paul Lamarque, Montpellier, France
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43
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Tan EM. Antinuclear antibodies: diagnostic markers for autoimmune diseases and probes for cell biology. Adv Immunol 1989; 44:93-151. [PMID: 2646863 DOI: 10.1016/s0065-2776(08)60641-0] [Citation(s) in RCA: 1081] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- E M Tan
- W. M. Keck Autoimmune Disease Center, Scripps Clinic and Research Foundation, La Jolla, California 92037
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44
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Rauh AJ, Hornig H, Lührmann R. At least three distinct B cell epitopes reside in the C-terminal half of La protein, as determined by a recombinant DNA approach. Eur J Immunol 1988; 18:2049-57. [PMID: 2464497 DOI: 10.1002/eji.1830181227] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The La antigen is a nuclear protein that is one of the major target antigens of autoantibodies found in the sera of patients with primary Sjögren's syndrome. The formation of such autoantibodies is therefore likely to reflect the basic immunopathogenesis of this disorder. A recombinant DNA strategy has been used to examine the La protein for sequences that encode autoimmunizing B cell epitopes. We have isolated and characterized a 1.2-kb-long cDNA from a human liver cDNA library encoding a region of the La protein; this region contains 296 amino acids, including the C terminus. A sub-library of recombinant DNA in the expression vector pEX was made from portions of the La cDNA. Individual fusion proteins were tested by immunoblotting and enzyme-linked immunosorbent assay for their ability to react with anti-La autoantibodies contained in sera from patients with Sjögren's syndrome. In this way, we have identified at least three distinct epitopes in the C-terminal half of the La protein. Every anti-La serum tested contained antibodies against all three of the antigenic regions identified. Furthermore, most of the sera display similar ratios between the titers of antibodies with the three kinds of specificity. Our data suggest that the production of anti-La autoantibodies may be antigen driven.
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Affiliation(s)
- A J Rauh
- Max-Planck-Institut für molekulare Genetik, Otto-Warburg-Laboratorium, Berlin, FRG
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45
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Thomas JD, Conrad RC, Blumenthal T. The C. elegans trans-spliced leader RNA is bound to Sm and has a trimethylguanosine cap. Cell 1988; 54:533-9. [PMID: 3401926 DOI: 10.1016/0092-8674(88)90075-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
mRNA splicing in C. elegans is unusual: most introns are very short (approximately 50 bases), and many mRNAs receive a leader by trans-splicing. The donor in trans-splicing is a 94 nucleotide molecule, termed the leader RNA, that contributes its 5' 22 nucleotides to a variety of mRNAs. We show here that C. elegans has the usual snRNAs, which presumably catalyze the splicing reactions. As expected, they are bound to the Sm antigen and have 2,2,7-methylguanosine caps. Remarkably, the trans-spliced leader RNA is also Sm-associated and has this special cap. Hence, a molecule discovered as a substate of splicing has properties of molecules heretofore known only to facilitate splicing of other RNAs. Mature mRNAs that have received the leader evidently lack 2,2,7-methylguanosine caps, suggesting that these caps are removed or altered during processing.
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Affiliation(s)
- J D Thomas
- Department of Biology Indiana University, Bloomington 47405
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46
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Nigg EA. Nuclear function and organization: the potential of immunochemical approaches. INTERNATIONAL REVIEW OF CYTOLOGY 1988; 110:27-92. [PMID: 3053500 DOI: 10.1016/s0074-7696(08)61847-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- E A Nigg
- Swiss Institute for Experimental Cancer Research, Chemin des Boveresses, Epalinges s/Lausanne
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47
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Bochnig P, Reuter R, Bringmann P, Lührmann R. A monoclonal antibody against 2,2,7-trimethylguanosine that reacts with intact, class U, small nuclear ribonucleoproteins as well as with 7-methylguanosine-capped RNAs. EUROPEAN JOURNAL OF BIOCHEMISTRY 1987; 168:461-7. [PMID: 2959477 DOI: 10.1111/j.1432-1033.1987.tb13439.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A hybridoma secreting a monoclonal antibody (H-20) that recognizes the 2,2,7-trimethylguanosine(m3G)-containing cap structure of U snRNAs was derived from a mouse which was immunized with a m3G-containing human serum albumin conjugate. The antibody specifically reacts with intact small nuclear ribonucleoprotein particles, U snRNPs, and allows the snRNPs U1 to U6 to be isolated in one step from nuclear extracts of eucaryotic cells by affinity chromatography on a preparative scale. Antibody-bound snRNPs are desorbed from the affinity column by elution with excess of the cross-reactive nucleoside 7-methylguanosine (m7G), which guarantees maintenance of their native structure. The 20 affinity column also allows the snRNPs U1, U2 and U5 to be separated from U4/U6 RNPs by sequential elution of the particles with m7G under differential salt concentrations. As determined by competitive radioimmunoassay and protein-A--Sepharose immunoprecipitation, mAb H-20 crossreacts with intact m7G cap structures. In particular we could show that non-denatured m7G-capped SP6/beta-globin RNA was precipitated efficiently by the antibody while GpppG-capped or non-capped RNAs did not react. Thus the monoclonal antibody H-20 should have a wide application, not only for studying the molecular biology and immunology of the U snRNPs from diverse organisms, but also for the characterization and isolation of m7G-capped transcripts.
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Affiliation(s)
- P Bochnig
- Max-Planck-Insitut für Molekulare Genetik, Otto-Warburg-Laboratorium, Berlin
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48
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Konings DA, Mattaj IW. Mutant U2 snRNAs of Xenopus which can form an altered higher order RNA structure are unable to enter the nucleus. Exp Cell Res 1987; 172:329-39. [PMID: 2958304 DOI: 10.1016/0014-4827(87)90391-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We studied the nuclear targeting of U snRNAs by microinjection of wild-type and mutant U2 small nuclear RNA transcripts into the cytoplasm of Xenopus oocytes. It has previously been shown that a mutant U2 RNA (delta C) which does not bind certain common U snRNP proteins, some of which carry epitopes recognized by anti-Sm antisera, does not enter the nucleus. We show here that several mutant U2 RNAs which bind to Sm antigens do not enter the nucleus, demonstrating that this RNA-protein interaction is insufficient to produce a nuclear targeting signal. Computer predictions of the secondary structures of the RNAs, derived from minimal energy calculations, show that those which are unable to enter the nucleus have the potential to form an additional secondary structure interaction due to base complementarity between sequences near to their 5' and 3' ends. The data suggest that this structural feature inhibits nuclear targeting.
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Affiliation(s)
- D A Konings
- European Molecular Biology Laboratorium, Heidelberg, Switzerland
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49
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Ishaq M, Ali R. Immunological characterization of small nuclear ribonucleoproteins reactive with sera of patients with systemic lupus erythematosus. J Clin Immunol 1987; 7:381-8. [PMID: 2958494 DOI: 10.1007/bf00917016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have previously reported the purification of Sm and RNP antigens from goat liver and identified two polypeptides of molecular weights 70 and 80-90 kd as RNP specific and of 14 and 30 kd as Sm specific. In this communication the effect of ribonuclease and trypsin on Sm and RNP antigens was studied at the polypeptide level. We found that the RNP antigenic determinant polypeptides of 70 and 80-90 kd are lost as a result of such treatment, whereas there is no effect on the Sm-specific 14- and 30-kd polypeptides. The role of RNA in the antigenicity of Sm and RNP was studied by dissociation and reconstitution studies. The antigens were fractionated into protein and RNA and the individual fractions were tested for Sm and RNP activity by counterimmunoelectrophoresis (CIE) and enzyme-linked immunosorbent assay (ELISA). The RNA fraction did not react alone with anti-Sm and anti-RNP sera with either of the assays. Conversely when the protein fraction was tested by CIE, only Sm antigenicity was detectable. In the ELISA both Sm and RNP activities were demonstrated in the protein fraction. These results show that the presence of RNA is important in the immunoprecipitation reactions involving only RNP antigen, whereas Sm activity is independent of RNA. In addition, when the reaction is carried out by an assay involving primary antigen-antibody reaction (e.g., ELISA), RNP antibodies react with protein fractions alone, without the presence of RNA. We also report the glycoprotein nature of Sm-specific polypeptides.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- M Ishaq
- Department of Biochemistry, Faculty of Medicine, Aligarh Muslim University, India
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50
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Guialis A, Dangli A, Sekeris CE. Distribution of snRNP complexes in rat liver nuclear extracts: biochemical and immunochemical analysis. Mol Cell Biochem 1987; 76:147-61. [PMID: 2959852 DOI: 10.1007/bf00223480] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Rat liver nuclei were extracted with 0.14 M NaCl and the extracts submitted to sucrose gradient fractionation. Aliquots of the nuclear residue remaining after the 0.14 M NaCl extraction were also extracted either with 0.3 M NaCl or 1 M urea, and the extracts similarly submitted to sucrose gradient fractionation. Thereafter, both the presence and relative distribution of individual U-snRNA (U1-U6) species was followed. Results showed an extensive association of all U-snRNAs to RNP structures of greater than or equal to 40 S. However, characteristic differences in the association of mostly U1 and U5--which were the major identifiable species in the extracts--to these structures were observed. Only a small fraction of U1 appeared complexed to less than or equal to 40 S RNP structures, while most of it sedimenting in the greater than 20 S region of the gradient. In contrast, U5-snRNA had a tight and almost exclusive association to 40 S RNP structures. No pool of 10-12 S U5-snRNP complexes was detected. Combined immunoprecipitation and immunoblotting experiments on nuclear 0.14 M NaCl extracts using anti-Sm and/or anti-RNP antisera showed that all snRNA species, whether recovered as 10-12 S complexes or segregated with greater than or equal to 40 S RNP components, existed as snRNP structures bearing at least their Sm-antigenic polypeptides. These and our previous results [Guialis, A., Arvanitopoulou, A, Patrinou-Georgoula, M. and Sekeris, C.E. (1983) FEBS Lett. 151, 127-133], support the existence of snRNP-enriched RNP structures of greater than or equal to 40 S. In such structures the core polypeptides (Mr = 32,000-45,000) of 40 S monoparticles are not obligatory components.
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Affiliation(s)
- A Guialis
- National Hellenic Research Foundation, Biological Research Center, Athens, Greece
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