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Zuberek J, Warzecha M, Dobrowolski M, Modrak-Wojcik A. An intramolecular disulphide bond in human 4E-T affects its binding to eIF4E1a protein. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:497-510. [PMID: 37798395 PMCID: PMC10618305 DOI: 10.1007/s00249-023-01684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/07/2023]
Abstract
The cap at the 5'terminus of mRNA is a key determinant of gene expression in eukaryotic cells, which among others is required for cap dependent translation and protects mRNA from degradation. These properties of cap are mediated by several proteins. One of them is 4E-Transporter (4E-T), which plays an important role in translational repression, mRNA decay and P-bodies formation. 4E-T is also one of several proteins that interact with eukaryotic initiation factor 4E (eIF4E), a cap binding protein which is a key component of the translation initiation machinery. The molecular mechanisms underlying the interactions of these two proteins are crucial for mRNA processing. Studying the interactions between human eIF4E1a and the N-terminal fragment of 4E-T that possesses unstructured 4E-binding motifs under non-reducing conditions, we observed that 4E-T preferentially forms an intramolecular disulphide bond. This "disulphide loop" reduces affinity of 4E-T for eIF4E1a by about 300-fold. Considering that only human 4E-T possesses two cysteines located between the 4E binding motifs, we proposed that the disulphide bond may act as a switch to regulate interactions between the two proteins.
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Affiliation(s)
- Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
| | - Marek Warzecha
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Mateusz Dobrowolski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Anna Modrak-Wojcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
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Cai Z, Zhang J, Xiong J, Ma C, Yang B, Li H. New insights into the potential mechanisms of spermatogenic failure in patients with idiopathic azoospermia. Mol Hum Reprod 2020; 26:469-484. [PMID: 32402059 DOI: 10.1093/molehr/gaaa033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/14/2020] [Indexed: 12/20/2022] Open
Abstract
Abstract
Idiopathic azoospermia (IA) refers to azoospermia without a clear aetiology. Due to the unclear aetiology and pathological mechanism of IA, there is no effective treatment for IA. The development of assisted reproductive and microsperm extraction technologies has brought hope to patients with IA with fertility problems. However, there are still many patients with IA whose testes lack healthy sperm, causing infertility. Therefore, it is key to identify how testicular spermatogenic failure can be reversed to promote spermatogenesis in patients with IA to resolve fertility problems; these goals are a great challenge in reproductive medicine. The underlying genetic factors seem to be important pathological factors of IA. Understanding the role of genetic factors in the pathological mechanism of spermatogenic failure in patients with IA is of great value for future studies and treatments and is also an important reference for the reproductive health of males and their offspring. A method combining sequencing technology and bioinformatics analysis is an important means to understand the genetic pathological mechanisms. We used bioinformatics analysis to study the public human IA dataset. We found that the pathogenic mechanism of IA may be related to abnormal ciliary structure and function and disrupted RNA metabolism in spermatogenic cells. Disrupted m6A regulation of spermatogenesis may be an important pathological mechanism of IA and warrants attention. Finally, we screened for key genes and potential therapeutic drugs to determine future research directions.
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Affiliation(s)
- Zhonglin Cai
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jianzhong Zhang
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jian Xiong
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Chengquan Ma
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Bin Yang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongjun Li
- Department of Urology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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3
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Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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4
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Gonatopoulos-Pournatzis T, Cowling VH. Cap-binding complex (CBC). Biochem J 2014. [PMID: 24354960 DOI: 10.1042/bj2013121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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Affiliation(s)
| | - Victoria H Cowling
- *MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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Raczynska KD, Simpson CG, Ciesiolka A, Szewc L, Lewandowska D, McNicol J, Szweykowska-Kulinska Z, Brown JWS, Jarmolowski A. Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana. Nucleic Acids Res 2009; 38:265-78. [PMID: 19864257 PMCID: PMC2800227 DOI: 10.1093/nar/gkp869] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The nuclear cap-binding protein complex (CBC) participates in 5′ splice site selection of introns that are proximal to the mRNA cap. However, it is not known whether CBC has a role in alternative splicing. Using an RT–PCR alternative splicing panel, we analysed 435 alternative splicing events in Arabidopsis thaliana genes, encoding mainly transcription factors, splicing factors and stress-related proteins. Splicing profiles were determined in wild type plants, the cbp20 and cbp80(abh1) single mutants and the cbp20/80 double mutant. The alternative splicing events included alternative 5′ and 3′ splice site selection, exon skipping and intron retention. Significant changes in the ratios of alternative splicing isoforms were found in 101 genes. Of these, 41% were common to all three CBC mutants and 15% were observed only in the double mutant. The cbp80(abh1) and cbp20/80 mutants had many more changes in alternative splicing in common than did cbp20 and cbp20/80 suggesting that CBP80 plays a more significant role in alternative splicing than CBP20, probably being a platform for interactions with other splicing factors. Cap-binding proteins and the CBC are therefore directly involved in alternative splicing of some Arabidopsis genes and in most cases influenced alternative splicing of the first intron, particularly at the 5′ splice site.
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Kierzkowski D, Kmieciak M, Piontek P, Wojtaszek P, Szweykowska-Kulinska Z, Jarmolowski A. The Arabidopsis CBP20 targets the cap-binding complex to the nucleus, and is stabilized by CBP80. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:814-25. [PMID: 19453442 DOI: 10.1111/j.1365-313x.2009.03915.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The cap-binding protein complex (CBC) binds to the caps of all RNA polymerase II transcripts, and plays an important role in RNA metabolism. We characterized interactions, localization and nuclear-cytoplasmic transport of two subunits of the Arabidopsis thaliana cap-binding protein complex (AtCBC): AtCBP20 and AtCBP80. Using CFP/YFP-tagged proteins, we show that transport of AtCBC from the cytoplasm to the nucleus in the plant cell is different from that described in other eukaryotic cells. We show that the smaller subunit of the complex, AtCBP20, plays a crucial role in the nuclear import of AtCBC. The C-terminal part of AtCBP20 contains two functionally independent nuclear localization signals (NLSs). At least one of these two NLSs is required for the import of CBC into the plant nucleus. The interaction between the A. thaliana CBP20 and CBP80 was also analyzed in detail, using the yeast two-hybrid system and fluorescence resonance energy transfer (FRET) assays. The N-terminal part of AtCBP20 is essential for interaction with AtCBP80. Furthermore, AtCBP80 is important for the protein stability of the smaller subunit of CBC. Based on these data, we propose a model for the nuclear-cytoplasmic trafficking of the CBC complex in plants.
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Affiliation(s)
- Daniel Kierzkowski
- Department of Molecular and Cellular Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska, Poland
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Kmieciak M, Simpson CG, Lewandowska D, Brown JWS, Jarmolowski A. Cloning and characterization of two subunits of Arabidopsis thaliana nuclear cap-binding complex. Gene 2002; 283:171-83. [PMID: 11867224 DOI: 10.1016/s0378-1119(01)00859-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this report we characterize two Arabidopsis thaliana proteins, named AtCBP20 and AtCBP80, that are homologues of human subunits of a nuclear cap-binding protein complex (CBC). AtCBP20 has a calculated molecular mass of 29.9 kDa, and AtCBP80 is a 96.5 kDa protein. AtCBP20 exhibits 68% identity and 82% similarity to human CBP20. Like its human homologue, AtCBP20 contains a canonical RNA binding domain (RBD) with single RNP2 and RNP1 motifs. In addition to the N-terminal part, which is similar to the human protein, AtCBP20 has a long C-terminus rich in arginine, glycine and aspartate residues. The second subunit of the Arabidopsis cap-binding complex, AtCBP80, shows 28% identity and 50% similarity to its homologue from HeLa cells. The protein contains a MIF4G domain at its N-terminus, the feature characteristic to all analyzed CBP80s. This domain, described also in eIF4G and NMD2 proteins, is thought to be involved in protein-protein and also in protein--RNA interactions. Both proteins AtCBP20 and AtCBP80 are encoded by single-copy genes in the A. thaliana genome. The AtCBP20 gene is located on chromosome V, and the AtCBP80 gene is encoded by chromosome II. Among introns identified in the AtCBP20 gene, we discovered an U12 type intervening sequence (an AT-AC intron). This intron is spliced out very efficiently in plants, but when isolated and tested for splicing in tobacco protoplasts, the efficiency of the U12 intron excision was low. Splicing efficiency of the U12 intron is improved by the addition of exon and intron sequences upstream or downstream of the U12 intron. AtCBP20 and AtCBP80 are constitutively expressed in all examined organs of A. thaliana, including roots, stems, leaves and flowers. Interestingly, the steady-state level of both transcripts seem to be very similar in all tissues analyzed.
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Affiliation(s)
- Maciej Kmieciak
- Department of Gene Expression, Adam Mickiewicz University, Miedzychodzka 5, 60-371, Poznan, Poland
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O'Mullane L, Eperon IC. The pre-mRNA 5' cap determines whether U6 small nuclear RNA succeeds U1 small nuclear ribonucleoprotein particle at 5' splice sites. Mol Cell Biol 1998; 18:7510-20. [PMID: 9819436 PMCID: PMC109331 DOI: 10.1128/mcb.18.12.7510] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Efficient splicing of the 5'-most intron of pre-mRNA requires a 5' m7G(5')ppp(5')N cap, which has been implicated in U1 snRNP binding to 5' splice sites. We demonstrate that the cap alters the kinetic profile of U1 snRNP binding, but its major effect is on U6 snRNA binding. With two alternative wild-type splice sites in an adenovirus pre-mRNA, the cap selectively alters U1 snRNA binding at the site to which cap-independent U1 snRNP binding is stronger and that is used predominantly in splicing; with two consensus sites, the cap acts on both, even though one is substantially preferred for splicing. However, the most striking quantitative effect of the 5' cap is neither on U1 snRNP binding nor on the assembly of large complexes but on the replacement of U1 snRNP by U6 snRNA at the 5' splice site. Inhibition of splicing by a cap analogue is correlated with the loss of U6 interactions at the 5' splice site and not with any loss of U1 snRNP binding.
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Affiliation(s)
- L O'Mullane
- Department of Biochemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
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9
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Yamada-Okabe T, Mio T, Matsui M, Kashima Y, Arisawa M, Yamada-Okabe H. Isolation and characterization of the Candida albicans gene for mRNA 5'-triphosphatase: association of mRNA 5'-triphosphatase and mRNA 5'-guanylyltransferase activities is essential for the function of mRNA 5'-capping enzyme in vivo. FEBS Lett 1998; 435:49-54. [PMID: 9755857 DOI: 10.1016/s0014-5793(98)01037-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The amino acid sequence of the Saccharomyces cerevisiae mRNA 5'-triphosphatase (TPase) diverges from those of higher eukaryotes. In order to confirm the sequence divergence of TPases in lower and higher eukaryotes, the Candida albicans gene for TPase was identified and characterized. This gene designated CaCET1 (C. albicans mRNA 5'-capping enzyme triphosphatase 1) has an open reading frame of 1.5 kb, which can encode a 59-kDa protein. Although the N-terminal one-fifth of S. cerevisiae TPase (ScCet1p) is missing in CaCet1p, CaCet1p shares significant sequence similarity with ScCet1p over the entire region of the protein; the recombinant CaCet1p, which was expressed as a fusion protein with glutathione S-transferase (GST), displayed TPase activity in vitro. CaCET1 rescued CET1-deficient S. cerevisiae cells when expressed under the control of the ADH1 promoter, whereas the human capping enzyme derivatives that are active for TPase activity but defective in mRNA 5'-guanylyltransferase (GTase) activity did not. Yeast two-hybrid analysis revealed that C. albicans Cet1p can bind to the S. cerevisiae GTase in addition to its own partner, the C. albicans GTase. In contrast, neither the full-length human capping enzyme nor its TPase domain interacted with the yeast GTase. These results indicate that the failure of the human TPase activity to complement an S. cerevisiae cet1delta null mutation is attributable, at least in part, to the inability of the human capping enzyme to associate with the yeast GTase, and that the physical association of GTase and TPase is essential for the function of the capping enzyme in vivo.
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10
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Yamada-Okabe T, Doi R, Shimmi O, Arisawa M, Yamada-Okabe H. Isolation and characterization of a human cDNA for mRNA 5'-capping enzyme. Nucleic Acids Res 1998; 26:1700-6. [PMID: 9512541 PMCID: PMC147440 DOI: 10.1093/nar/26.7.1700] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The human mRNA 5'-capping enzyme cDNA was identified. Three highly related cDNAs, HCE1 (human mRNAcappingenzyme1), HCE1A and HCE1B , were isolated from a HeLa cDNA library. The HCE1 cDNA has the longest ORF, which can encode a 69 kDa protein. A short region of 69 bp in the 3'-half of the HCE1 ORF was missing in HCE1A and HCE1B , and, additionally, HCE1B has an early translation termination signal, which suggests that the latter two cDNAs represent alternatively spliced product. When expressed in Escherichia coli as a fusion protein with glutathione S -transferase, Hce1p displayed both mRNA 5'-triphosphatase (TPase) and mRNA 5'-guanylyltransferase (GTase) activities, and it formed a cap structure at the 5'-triphosphate end of RNA, demonstrating that it indeed specifies an active mRNA 5'-capping enzyme. The recombinant proteins derived from HCE1A and HCE1B possessed only TPase activity. When expressed from ADH1 promoter, HCE1 but not HCE1A and HCE1B complemented Saccharomyces cerevisiae CEG1 and CET1 , the genes for GTase and TPase, respectively. These results demonstrate that the N-terminal part of Hce1p is responsible for TPase activity and the C-terminal part is essential for GTase activity. In addition, the human TPase domain cannot functionally substitute for the yeast enzyme in vivo.
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Affiliation(s)
- T Yamada-Okabe
- Department of Hygiene, School of Medicine, Yokohama City University, 3-9, Fukuura, Kanazawa, Yokohama 236, Japan
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11
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Haller AA, Sarnow P. In vitro selection of a 7-methyl-guanosine binding RNA that inhibits translation of capped mRNA molecules. Proc Natl Acad Sci U S A 1997; 94:8521-6. [PMID: 9238009 PMCID: PMC22984 DOI: 10.1073/pnas.94.16.8521] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Using systematic evolution of ligands by exponential enrichment (SELEX), an RNA molecule was isolated that displays a 1,000-fold higher affinity for guanosine residues that carry an N-7 methyl group than for nonmethylated guanosine residues. The methylated guanosine residue closely resembles the 5' terminal cap structure present on all eukaryotic mRNA molecules. The cap-binding RNA specifically inhibited the translation of capped but not uncapped mRNA molecules in cell-free lysates prepared from either human HeLa cells or from Saccharomyces cerevisiae. These findings indicate that the cap-binding RNA will also be useful in studies of other cap-dependent processes such as pre-mRNA splicing and nucleocytoplasmic mRNA transport.
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Affiliation(s)
- A A Haller
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305-5402, USA
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12
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Lewis JD, Izaurralde E. The role of the cap structure in RNA processing and nuclear export. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 247:461-9. [PMID: 9266685 DOI: 10.1111/j.1432-1033.1997.00461.x] [Citation(s) in RCA: 184] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The cap structure that is characteristic of all polymerase-II-transcribed RNAs has been shown to play an important role in many aspects of RNA metabolism including RNA processing, RNA nuclear transport, and translation initiation. The effects of the cap structure on these different processes is mediated by proteins that recognise and bind to it, and are therefore generically called cap-binding proteins. For example, the cap-binding protein eIF4E, in a complex with other proteins, mediates the effect of the cap on the initiation of translation. EIF-4E is predominantly localised in the cytoplasm. In the last five years, it has been demonstrated that a second cap-binding protein complex, which is mainly localised in the nucleus, mediates the stimulatory effects of the cap in nuclear processes such as pre-mRNA splicing, RNA 3'-end formation, and RNA nuclear export. The purpose of this review is to summarise our current knowledge on the role of the cap structure and of the cap-binding protein complex in nuclear RNA metabolism and present evidence that at least some processes may be coupled in vivo.
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Affiliation(s)
- J D Lewis
- Institute of Cell and Molecular Biology, University of Edinburgh, Scotland.
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13
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Graessmann M, Eul J, Berg B, Zimmermann C, Graessmann A. SV40 T1-mRNA trans-splicing and translation requires that the in vitro synthesized cRNA is capped before microinjection. FEBS Lett 1996; 394:233-6. [PMID: 8843170 DOI: 10.1016/0014-5793(96)00956-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The purpose of this investigation was to study the effect on cap structure for trans-splicing in mammalian cells. The early SV40 Bst/Bam pre-mRNA (cRNA) was synthesized in vitro in both capped (cap-Bst/Bam-cRNA) and non-capped (Bst/Bam-cRNA) versions and microinjected into the nuclei of TC7 cells. Trans-splicing was monitored by immunofluorescence staining (T1-antigen) and by RT-PCR analysis. Cap-Bst/Bam-cRNA was trans-spliced with high efficiency, but not the Bst/Bam-cRNA molecules. Northern blot analysis revealed that both the capped and uncapped cRNA molecules had similar stability in the microinjected cells. The coinjected m7G(5')ppp(5')G cap analog did not inhibit the trans-splicing reaction in vivo and did not prevent nuclear export of the mRNA.
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MESH Headings
- Animals
- Antigens, Polyomavirus Transforming/analysis
- Antigens, Polyomavirus Transforming/genetics
- Blotting, Northern
- Cell Nucleus/metabolism
- Cells, Cultured
- DNA Primers
- Electrophoresis, Agar Gel
- Fluorescent Antibody Technique
- Microinjections
- Microscopy, Fluorescence
- Polymerase Chain Reaction
- Protein Biosynthesis
- RNA Caps
- RNA Precursors/chemical synthesis
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splicing
- RNA, Complementary/genetics
- RNA, Complementary/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Rats
- Simian virus 40/genetics
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Affiliation(s)
- M Graessmann
- Institut für Molekularbiologie und Biochemie der Freien Universität Berlin, Germany
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14
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Lewis JD, Görlich D, Mattaj IW. A yeast cap binding protein complex (yCBC) acts at an early step in pre-mRNA splicing. Nucleic Acids Res 1996; 24:3332-6. [PMID: 8811086 PMCID: PMC146107 DOI: 10.1093/nar/24.17.3332] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The function in splicing of a heterodimeric nuclear cap binding complex (yCBC) from the yeast Saccharomyces cerevisiae has been examined. Immunodepletion of splicing extracts with antibodies directed against one component of the complex, yCBP80, results in the efficient co-depletion of the second component, yCBP20, producing CBC-deficient splicing extract. This extract exhibits strongly reduced splicing efficiency and similar reductions in the assembly of both spliceosomes and of the earliest defined precursors to spliceosomes, commitment complexes. The addition of highly purified yCBC substantially restores these defects. These results, together with other data, suggest that CBCs play a highly conserved role in the recognition of pre-mRNA substrates at an early step in the splicing process.
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Affiliation(s)
- J D Lewis
- European Molecular Biology Laboratory, Heidelberg, Germany
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15
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Lewis JD, Izaurralde E, Jarmolowski A, McGuigan C, Mattaj IW. A nuclear cap-binding complex facilitates association of U1 snRNP with the cap-proximal 5' splice site. Genes Dev 1996; 10:1683-98. [PMID: 8682298 DOI: 10.1101/gad.10.13.1683] [Citation(s) in RCA: 179] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The mechanism by which intron-containing RNAs are recognized by the splicing machinery is only partly understood. A nuclear cap-binding complex (CBC), which specifically recognizes the monomethyl guanosine cap structure carried by RNA polymerase II transcripts, has previously been shown to play a role in pre-mRNA splicing. Using a combination of splicing complex and psoralen cross-linking analysis we demonstrate that CBC is required for efficient recognition of the 5' splice site by U1 snRNP during formation of E (early) complex on a pre-mRNA containing a single intron. However, in a pre-mRNA containing two introns, CBC is not required for splicing of the cap distal intron. In this case, the presence of an intact polypyrimidine tract in the cap-proximal intron renders splicing of the cap-distal intron independent of CBC. These results support models in which the splice sites in a pre-mRNA are originally recognized by interactions spanning exons. The defects in splicing and U1 snRNP binding caused by CBC depletion can be specifically reversed by recombinant CBC. In summary, efficient recognition of the cap-proximal 5' splice site by U1 snRNP is facilitated by CBC in what may be one of the earliest steps in pre-mRNA recognition. Data in Colot et al. (this issue) indicate that this function of CBC is conserved in humans and yeast.
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Affiliation(s)
- J D Lewis
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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16
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Kataoka N, Ohno M, Moda I, Shimura Y. Identification of the factors that interact with NCBP, an 80 kDa nuclear cap binding protein. Nucleic Acids Res 1995; 23:3638-41. [PMID: 7478990 PMCID: PMC307259 DOI: 10.1093/nar/23.18.3638] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
It has been shown that the monomethylated cap structure plays important roles in pre-mRNA splicing and nuclear export of RNA. As a candidate for the factor involved in these nuclear events we have previously purified an 80 kDa nuclear cap binding protein (NCBP) from a HeLa cell nuclear extract and isolated its full-length cDNA. In this report, in order to obtain a clue to the cellular functions of NCBP, we attempted to identify a factor(s) that interacts with NCBP. Using the yeast two-hybrid system we isolated three clones from a HeLa cell cDNA library. We designated the proteins encoded by these clones NIPs (NCBP interacting proteins). NIP1 and NIP2 have an RNP consensus-type RNA binding domain, whereas NIP3 contains a unique domain of Arg-Glu or Lys-Glu dipeptide repeats. We also show that NCBP requires NIP1 for binding to the cap structure. Possible roles of NIPs in cap-dependent nuclear processes are discussed.
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Affiliation(s)
- N Kataoka
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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17
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Izaurralde E, Lewis J, Gamberi C, Jarmolowski A, McGuigan C, Mattaj IW. A cap-binding protein complex mediating U snRNA export. Nature 1995; 376:709-12. [PMID: 7651522 DOI: 10.1038/376709a0] [Citation(s) in RCA: 259] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cap structures are added cotranscriptionally to all RNA polymerase II transcripts. They affect several processes including RNA stability, pre-messenger RNA splicing, RNA export from the nucleus and translation initiation. The effect of the cap on translation is mediated by the initiation factor eIF-4F, whereas the effect on pre-mRNA splicing involves a nuclear complex (CBC) composed of two cap binding proteins, CBP80 and CBP20. A role for CBC in the nuclear export of capped RNAs has also been proposed. We report here the characterization of human and Xenopus CBP20s. Antibodies against recombinant CBP20 prevent interaction of CBC with capped RNAs in vitro. Following microinjection into Xenopus oocytes, the antibodies inhibit both pre-mRNA splicing and export of U small nuclear RNAs to the cytoplasm. These results demonstrate that CBC mediates the effect of the cap structure in U snRNA export, and provide direct evidence for the involvement of a cellular RNA-binding factor in the transport of RNA to the cytoplasm.
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Affiliation(s)
- E Izaurralde
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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18
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Mao X, Schwer B, Shuman S. Yeast mRNA cap methyltransferase is a 50-kilodalton protein encoded by an essential gene. Mol Cell Biol 1995; 15:4167-74. [PMID: 7623811 PMCID: PMC230655 DOI: 10.1128/mcb.15.8.4167] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
RNA (guanine-7-)methyltransferase, the enzyme responsible for methylating the 5' cap structure of eukaryotic mRNA, was isolated from extracts of Saccharomyces cerevisiae. The yeast enzyme catalyzed methyl group transfer from S-adenosyl-L-methionine to the guanosine base of capped, unmethylated poly(A). Cap methylation was stimulated by low concentrations of salt and was inhibited by S-adenosyl-L-homocysteine, a presumptive product of the reaction, but not by S-adenosyl-D-homocysteine. The methyltransferase sedimented in a glycerol gradient as a single discrete component of 3.2S. A likely candidate for the gene encoding yeast cap methyltransferase was singled out on phylogenetic grounds. The ABD1 gene, located on yeast chromosome II, encodes a 436-amino-acid (50-kDa) polypeptide that displays regional similarity to the catalytic domain of the vaccinia virus cap methyltransferase. That the ABD1 gene product is indeed RNA (guanine-7-)methyltransferase was established by expressing the ABD1 protein in bacteria, purifying the protein to homogeneity, and characterizing the cap methyltransferase activity intrinsic to recombinant ABD1. The physical and biochemical properties of recombinant ABD1 methyltransferase were indistinguishable from those of the cap methyltransferase isolated and partially purified from whole-cell yeast extracts. Our finding that the ABD1 gene is required for yeast growth provides the first genetic evidence that a cap methyltransferase (and, by inference, the cap methyl group) plays an essential role in cellular function in vivo.
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Affiliation(s)
- X Mao
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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19
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Abstract
The cap-binding complex eIF-4F plays a major role in the control of translation initiation, and overexpression of its limiting subunit, eIF-4E, leads to the deregulation of cellular growth. The recent cloning of eIF-4E binding proteins (4E-BPs) has uncovered a previously unsuspected pathway for the regulation of eIF-4E activity, through sequestration of eIF-4E as a complex with 4E-BPs.
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Affiliation(s)
- S Mader
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
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20
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Shuman S. Capping enzyme in eukaryotic mRNA synthesis. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1995; 50:101-29. [PMID: 7754031 DOI: 10.1016/s0079-6603(08)60812-0] [Citation(s) in RCA: 126] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- S Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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21
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Kataoka N, Ohno M, Kangawa K, Tokoro Y, Shimura Y. Cloning of a complementary DNA encoding an 80 kilodalton nuclear cap binding protein. Nucleic Acids Res 1994; 22:3861-5. [PMID: 7937105 PMCID: PMC308381 DOI: 10.1093/nar/22.19.3861] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
It has been shown that the monomethylated cap structure plays important roles in nuclear events. The cap structure has been implicated in the enhancement of pre-mRNA splicing. More recently, this structure has also been suggested to facilitate RNA transport from the nucleus to the cytoplasm. We have previously identified and purified an 80kD Nuclear Cap Binding Protein (NCBP) from a HeLa cell nuclear extract, which could possibly mediate these nuclear activities. In this report, we describe cloning of complementary DNA (cDNA) encoding NCBP. The partial protein sequences of NCBP were determined, and the full-length cDNA of NCBP was isolated from HeLa cDNA libraries. This cDNA encoded an open reading frame of 790 amino acids with a calculated molecular mass of 91,734 daltons, which contained most of the determined protein sequences. However, the protein sequence had no significant homology to any known proteins. Transfection experiments demonstrated that the epitope-tagged NCBP, transiently expressed in HeLa cells, was localized exclusively in the nucleoplasm. Similar experiments using a truncated NCBP cDNA indicated that this nuclear localization activity is conferred by the N-terminal 70 amino-acid region.
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Affiliation(s)
- N Kataoka
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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22
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Izaurralde E, Lewis J, McGuigan C, Jankowska M, Darzynkiewicz E, Mattaj IW. A nuclear cap binding protein complex involved in pre-mRNA splicing. Cell 1994; 78:657-68. [PMID: 8069914 DOI: 10.1016/0092-8674(94)90530-4] [Citation(s) in RCA: 393] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A cap-binding protein complex (CBC) present in the nuclei of HeLa cells has been characterized. Purified CBC consists of two previously identified proteins, CBP80 and CBP20. These proteins are shown to cofractionate to apparent homogeneity and to be coimmunoprecipitable with anti-CBP80 antibodies. Analysis of the inhibition of pre-mRNA splicing in vitro and in vivo by chemically modified analogs of the cap structure, and of the binding of these analogs to CBC in vitro, suggests a role for the complex in splicing. Extracts immunodepleted of CBC do not efficiently splice an adenoviral pre-mRNA owing to blockage of an early step in splicing complex formation. CBC may therefore play a role in pre-mRNA recognition.
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Affiliation(s)
- E Izaurralde
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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23
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Trypanosoma brucei spliced-leader RNA methylations are required for trans splicing in vivo. Mol Cell Biol 1992. [PMID: 1406666 DOI: 10.1128/mcb.12.11.4844] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Trypanosoma brucei spliced leader (SL) RNA donates its 5' leader sequence to all nuclear pre-mRNAs via trans RNA splicing. The SL RNA is a small-nuclear U RNA-like molecule which is present in the cell as part of a small ribonucleoprotein particle. However, unlike the trimethylguanosine-capped small nuclear U RNAs, the SL RNA has a highly modified 5' terminus containing an m7G cap and methylations on the first four transcribed nucleotides. Here, we show that incubation of procyclic-form T. brucei in the presence of the S-adenosylmethionine analog, sinefungin, leads to a rapid inhibition of SL RNA methylation. A concomitant inhibition of trans splicing and an accumulation of high-molecular-weight tubulin transcripts were also observed. The effects of sinefungin on SL RNA methylation and on trans splicing were correlated by labeling of cells incubated in the presence of the antibiotic. The results indicate that 5' modifications of the SL RNA are necessary for it to participate in trans splicing. SL RNA modification is not required for assembly of the core SL ribonucleoprotein, as these Cs2SO4-resistant particles can be formed with either methylated or undermethylated SL RNA.
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24
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McNally KP, Agabian N. Trypanosoma brucei spliced-leader RNA methylations are required for trans splicing in vivo. Mol Cell Biol 1992; 12:4844-51. [PMID: 1406666 PMCID: PMC360417 DOI: 10.1128/mcb.12.11.4844-4851.1992] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The Trypanosoma brucei spliced leader (SL) RNA donates its 5' leader sequence to all nuclear pre-mRNAs via trans RNA splicing. The SL RNA is a small-nuclear U RNA-like molecule which is present in the cell as part of a small ribonucleoprotein particle. However, unlike the trimethylguanosine-capped small nuclear U RNAs, the SL RNA has a highly modified 5' terminus containing an m7G cap and methylations on the first four transcribed nucleotides. Here, we show that incubation of procyclic-form T. brucei in the presence of the S-adenosylmethionine analog, sinefungin, leads to a rapid inhibition of SL RNA methylation. A concomitant inhibition of trans splicing and an accumulation of high-molecular-weight tubulin transcripts were also observed. The effects of sinefungin on SL RNA methylation and on trans splicing were correlated by labeling of cells incubated in the presence of the antibiotic. The results indicate that 5' modifications of the SL RNA are necessary for it to participate in trans splicing. SL RNA modification is not required for assembly of the core SL ribonucleoprotein, as these Cs2SO4-resistant particles can be formed with either methylated or undermethylated SL RNA.
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Affiliation(s)
- K P McNally
- Intercampus Program in Molecular Parasitology, University of California, San Francisco
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25
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Izaurralde E, Stepinski J, Darzynkiewicz E, Mattaj IW. A cap binding protein that may mediate nuclear export of RNA polymerase II-transcribed RNAs. J Cell Biol 1992; 118:1287-95. [PMID: 1522107 PMCID: PMC2289605 DOI: 10.1083/jcb.118.6.1287] [Citation(s) in RCA: 124] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
It has previously been shown that efficient export of U1 snRNA or of microinjected, in vitro synthesized, RNA transcripts from the nucleus of Xenopus oocytes is facilitated by their monomethyl guanosine cap structures. Nuclear exit of these transcripts could be competitively inhibited by microinjection of an excess of a cap analog, the dinucleotide m7GpppG (Hamm, J., and I. W. Mattaj. 1990. Cell. 63:109-118). We have now analyzed the ability of several other related cap analogs to inhibit the export of U1 snRNA from the nucleus. The results define the recognition specificity of a factor(s) involved in RNA transport, and indicate that the cap binding activity (CBA) involved in RNA export is different from cap binding proteins (CBPs) involved in the initiation of translation. A CBP, whose specificity for different analogs correlates with the ability of the analogs to inhibit U1 snRNA export, is identified in nuclear extracts prepared from HeLa cells. We propose that this protein may have a role in the export of capped RNAs from the nucleus.
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Affiliation(s)
- E Izaurralde
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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26
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Waigmann E, Barta A. Processing of chimeric introns in dicot plants: evidence for a close cooperation between 5' and 3' splice sites. Nucleic Acids Res 1992; 20:75-81. [PMID: 1738607 PMCID: PMC310328 DOI: 10.1093/nar/20.1.75] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Splice sites of vertebrate introns are generally not recognized in plant cells. Several lines of evidences have led to the proposal that the mechanism of 3' splice site selection differs in plants and animals (K. Wiebauer, J.J. Herrero, and W. Filipowicz, Mol. Cell. Biol. 8:2042-2051, 1988). To gain a better insight into the mechanistic differences between plant and animal splicing, we constructed chimeric introns consisting partly of dicotyledonous plant and partly of animal intron sequences. Splicing of these chimeric introns was analyzed in transiently transfected tobacco protoplasts. The results show that there are no principal sequence or structural differences between the 3' splice regions of plants and animals. Furthermore, evidence is provided that cooperation between 5' and 3' splice sites takes place and influences their mutual selection.
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Affiliation(s)
- E Waigmann
- Institut für Biochemie, Universität Wien, Vienna, Austria
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27
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Synthesis of gamma-[4-(benzoylphenyl)methylamido]-7-methylguanosine 5'-triphosphate, a photoaffinity-label for cap-binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1088:301-4. [PMID: 2001403 DOI: 10.1016/0167-4781(91)90067-v] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
An easy and rapid method for the synthesis of the photoreactive cap analogue gamma-[4-(benzoylphenyl)methylamido]-7-methylguanosine-5'-triphosp hate (BP-m7GTP) has been developed. Synthesis of [gamma-32P]BP-m7GTP was carried out as a two-step procedure. The first step included the phosphorylation of GDP with [32P]orthophosphate to [gamma-32P]GTP and its methylation to [gamma-32P]m7GTP. After purification, [gamma-32P]m7GTP was condensed with 4-aminomethyl-benzophenone-HCl to [gamma-32P]BP-m7GTP. Using this probe, specific labeling of nuclear cap binding proteins is demonstrated.
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28
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Bindereif A, Green MR. Identification and functional analysis of mammalian splicing factors. GENETIC ENGINEERING 1991; 12:201-24. [PMID: 1368558 DOI: 10.1007/978-1-4613-0641-2_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- A Bindereif
- Max-Planck-Institut für Molekulare Genetik Otto-Warburg-Laboratorium, Berlin, Germany
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29
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Abstract
We have identified a cap binding protein in a HeLa nuclear extract using a gel mobility shift assay probed with capped RNA. Subcellular fractionation of HeLa cells revealed that the majority (about 70%) of the cap binding activity is present in the nuclear extract, about 20% is in the cytoplasmic S100 fraction, and almost none in the ribosome-high salt wash fraction, indicating that the protein in active form localizes mainly in the nuclei. Competition experiments with various cap analogues showed that the G(5')ppp(5')N-blocking structure as well as the methyl residue at the N7 position of the blocking guanosine is important for the binding of this protein, and that the trimethylguanosine cap structure which exists at the 5' termini of many snRNAs is not recognized by this protein. Immunoprecipitation experiments using various anti-snRNP antibodies suggested that this protein is partially associated with U2 snRNP. We purified this protein to near homogeneity from a HeLa nuclear extract by several chromatographic procedures including capped RNA-Sepharose chromatography. The purified protein shows molecular weight of 80 kilodaltons, as judged by SDS gel electrophoresis, and binds specifically to the cap structure.
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Affiliation(s)
- M Ohno
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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30
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Nordqvist K, Akusjärvi G. Adenovirus early region 4 stimulates mRNA accumulation via 5' introns. Proc Natl Acad Sci U S A 1990; 87:9543-7. [PMID: 2263609 PMCID: PMC55208 DOI: 10.1073/pnas.87.24.9543] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The adenovirus major late transcription unit accounts for most virus-specific transcription late after infection. All mRNAs expressed from this unit carry a short spliced leader, the so-called tripartite leader, attached to their 5' ends. Here we describe a function for an adenovirus gene product in the control of major late mRNA abundance. We show that early region 4 (E4) stimulates mRNA accumulation from tripartite leader intron-containing transcription units approximately 10-fold in short-term transfection assays. The effect was already detectable in nuclear RNA and was not due to a transcriptional activation through any of the major late promoter elements or through an effect at nuclear to cytoplasmic mRNA transport. A surprising positional effect of the intron was noted. To be E4 responsive, the intron had to be placed close to the pre-mRNA 5' end. The same intron located far downstream in the 3' untranslated region of the mRNA was not E4 responsive. The E4 enhancement was not dependent on specific virus exon or intron sequences. These results suggest that E4 modulates a general pathway in mammalian mRNA formation.
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Affiliation(s)
- K Nordqvist
- Department of Microbial Genetics, Karolinska Institutet, Stockholm, Sweden
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31
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mRNAs that mature through trans-splicing in Caenorhabditis elegans have a trimethylguanosine cap at their 5' termini. Mol Cell Biol 1990. [PMID: 1690851 DOI: 10.1128/mcb.10.4.1769] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Approximately 10% of the mRNAs in the nematode Caenorhabditis elegans mature through a trans-splicing mechanism that involves the transfer of a 22-nucleotide spliced leader to the 5' end of the pre-mRNA. The spliced leader RNA exists as a small nuclear ribonucleoprotein particle and has the trimethylguanosine cap that is characteristic of eucaryotic small nuclear RNAs. We found that the trimethylguanosine cap present on the spliced leader RNA was transferred to the pre-mRNA during the trans-splicing reaction. Thereafter, the trimethylguanosine cap was maintained on the mature mRNA. This is the first example of eucaryotic cellular mRNAs possessing a trimethylguanosine cap structure.
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32
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Van Doren K, Hirsh D. mRNAs that mature through trans-splicing in Caenorhabditis elegans have a trimethylguanosine cap at their 5' termini. Mol Cell Biol 1990; 10:1769-72. [PMID: 1690851 PMCID: PMC362283 DOI: 10.1128/mcb.10.4.1769-1772.1990] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Approximately 10% of the mRNAs in the nematode Caenorhabditis elegans mature through a trans-splicing mechanism that involves the transfer of a 22-nucleotide spliced leader to the 5' end of the pre-mRNA. The spliced leader RNA exists as a small nuclear ribonucleoprotein particle and has the trimethylguanosine cap that is characteristic of eucaryotic small nuclear RNAs. We found that the trimethylguanosine cap present on the spliced leader RNA was transferred to the pre-mRNA during the trans-splicing reaction. Thereafter, the trimethylguanosine cap was maintained on the mature mRNA. This is the first example of eucaryotic cellular mRNAs possessing a trimethylguanosine cap structure.
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Affiliation(s)
- K Van Doren
- Department of Developmental Biology, Synergen, Inc., Boulder, Colorado 80301
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33
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Thalmann E, Blaas D, Kuechler E. Affinity chromatography of HeLa splicing extracts on m7 GTP-sepharose and photoaffinity-labeling of cap-binding proteins with gamma-[(4-benzoylphenyl) methylamido]-7-methyl-guanosine-5'-triphosphate. Mol Biol Rep 1990; 14:207. [PMID: 2362575 DOI: 10.1007/bf00360476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- E Thalmann
- Institute of Biochemistry, University of Vienna, Austria
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34
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McCubbin WD, Edery I, Altmann M, Sonenberg N, Kay CM. Circular dichroism and fluorescence studies on protein synthesis initiation factor eIF-4E and two mutant forms from the yeast Saccharomyces cerevisiae. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)77888-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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35
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Abstract
Intron A of the human growth hormone gene does not contain an A residue within 56 nucleotides preceding the 3' splice site. The analysis of the excised intron lariat revealed a C residue 28 nucleotides upstream from the 3' splice site as the major branch acceptor nucleotide. Two additional minor branched nucleotides were identified as U residues at positions -22 and -36. An adenosine substitution at position -22 results in lariat formation solely to this nucleotide. Therefore, C and U residues can function efficiently as natural branch acceptors, but an A residue is preferred if available in the proper region. In addition, the data strongly reinforce the importance of the distance constraint for lariat formation. To explain selection of the branch acceptor nucleotide, potential base-pairing interactions of branch point sequences with the U2 RNA are discussed.
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36
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Abstract
Intron A of the human growth hormone gene does not contain an A residue within 56 nucleotides preceding the 3' splice site. The analysis of the excised intron lariat revealed a C residue 28 nucleotides upstream from the 3' splice site as the major branch acceptor nucleotide. Two additional minor branched nucleotides were identified as U residues at positions -22 and -36. An adenosine substitution at position -22 results in lariat formation solely to this nucleotide. Therefore, C and U residues can function efficiently as natural branch acceptors, but an A residue is preferred if available in the proper region. In addition, the data strongly reinforce the importance of the distance constraint for lariat formation. To explain selection of the branch acceptor nucleotide, potential base-pairing interactions of branch point sequences with the U2 RNA are discussed.
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37
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Gilmartin GM, McDevitt MA, Nevins JR. Multiple factors are required for specific RNA cleavage at a poly(A) addition site. Genes Dev 1988; 2:578-87. [PMID: 2838381 DOI: 10.1101/gad.2.5.578] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An SP6 RNA containing the adenovirus 5 L3 poly(A) site is processed efficiently in a HeLa cell nuclear extract to generate correct 3' termini. Accurate 3' processing has also been demonstrated for the adenovirus E2A and SV40 early poly(A) sites, although these are processed less efficiently than the L3 site. Efficient cleavage at the poly(A) site requires the presence of a 5'-cap structure, as well as the RNA sequence motifs previously shown to be necessary for 3' processing in vivo, suggesting the presence and action of the appropriate factors in the nuclear extract. Fractionation of the nuclear extract has revealed a requirement for at least two distinct factors for cleavage at the L3 poly(A) site. One of these factors appears to possess an RNA component due to its sensitivity to micrococcal nuclease. The activity of this fraction is also sensitive to alpha-Sm monoclonal antibody, indicating the presence of an snRNP essential for the cleavage reaction. Additional factors are required for the subsequent polyadenylation reaction, indicating the involvement of a multicomponent complex in the processing of an RNA at the poly(A) site.
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Affiliation(s)
- G M Gilmartin
- Howard Hughes Medical Institute, Rockefeller University, New York, New York 10021
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38
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39
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Masuda N, Watahiki M, Tanaka M, Yamakawa M, Shimizu K, Nagai J, Nakashima K. Molecular cloning of cDNA encoding 20 kDa variant human growth hormone and the alternative splicing mechanism. BIOCHIMICA ET BIOPHYSICA ACTA 1988; 949:125-31. [PMID: 2825811 DOI: 10.1016/0167-4781(88)90062-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
cDNA encoding the 20 kDa variant form of human growth hormone has been cloned, and its sequence analysis verified the alternative splicing mechanism for the mRNA synthesis. The cDNA sequence lacked 45 nucleotides corresponding to the sequence of 15 amino acids in the 22 kDa form of growth hormone. The cDNA clones for the 20 kDa variant hormone had the homogeneous 5'-ends, while the clones for the 22 kDa form showed a minor heterogenity, having two transcription initiation sites. The percentage of 20 kDa variant cDNA clones was approx. 7.7% of the total human growth hormone cDNA clones, consistent with the contents of 20 kDa hormone protein in human anterior pituitary and plasma.
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Affiliation(s)
- N Masuda
- Department of Biochemistry, Mie University School of Medicine, Japan
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40
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Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol Cell Biol 1988. [PMID: 3683396 DOI: 10.1128/mcb.7.10.3602] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To analyze the specificity of RNA processing reactions, we constructed hybrid genes containing RNA polymerase III promoters fused to sequences that are normally transcribed by polymerase II and assessed their transcripts following transfection into human 293 cells. Transcripts derived from these chimeric constructs were analyzed by using a combined RNase H and S1 nuclease assay to test whether RNAs containing consensus 5' and 3' splicing signals could be efficiently spliced in intact cells, even though they were transcribed by RNA polymerase III. We found that polymerase III-derived RNAs are not substrates for splicing. Similarly, we were not able to detect poly(A)+ RNAs derived from genes that contained a polymerase III promoter linked to sequences that were necessary and sufficient to direct 3'-end cleavage and polyadenylation when transcribed by RNA polymerase II. Our findings are consistent with the view that in vivo splicing and polyadenylation pathways are obligatorily coupled to transcription by RNA polymerase II.
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41
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Sonenberg N. Cap-binding proteins of eukaryotic messenger RNA: functions in initiation and control of translation. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1988; 35:173-207. [PMID: 3065823 DOI: 10.1016/s0079-6603(08)60614-5] [Citation(s) in RCA: 230] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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42
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Krämer A, Frick M, Keller W. Separation of multiple components of HeLa cell nuclear extracts required for pre-messenger RNA splicing. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)45427-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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43
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Sisodia SS, Sollner-Webb B, Cleveland DW. Specificity of RNA maturation pathways: RNAs transcribed by RNA polymerase III are not substrates for splicing or polyadenylation. Mol Cell Biol 1987; 7:3602-12. [PMID: 3683396 PMCID: PMC368014 DOI: 10.1128/mcb.7.10.3602-3612.1987] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
To analyze the specificity of RNA processing reactions, we constructed hybrid genes containing RNA polymerase III promoters fused to sequences that are normally transcribed by polymerase II and assessed their transcripts following transfection into human 293 cells. Transcripts derived from these chimeric constructs were analyzed by using a combined RNase H and S1 nuclease assay to test whether RNAs containing consensus 5' and 3' splicing signals could be efficiently spliced in intact cells, even though they were transcribed by RNA polymerase III. We found that polymerase III-derived RNAs are not substrates for splicing. Similarly, we were not able to detect poly(A)+ RNAs derived from genes that contained a polymerase III promoter linked to sequences that were necessary and sufficient to direct 3'-end cleavage and polyadenylation when transcribed by RNA polymerase II. Our findings are consistent with the view that in vivo splicing and polyadenylation pathways are obligatorily coupled to transcription by RNA polymerase II.
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Affiliation(s)
- S S Sisodia
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205
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44
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Hartmuth K, Barta A. In vitro processing of the human growth hormone primary transcript. Nucleic Acids Res 1987; 15:7005-25. [PMID: 3658671 PMCID: PMC306189 DOI: 10.1093/nar/15.17.7005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
To study the sequence of events during processing of primary RNA transcripts and to gain more insight into the mechanism of splice site selection, the in vitro processing of a 2.5 kb human growth hormone (hGH) pre-mRNA containing four introns and an alternative 3' splice site for intron B was analysed. In order to process the hGH pre-mRNA the preparation of the HeLa cell nuclear extract had to be modified, indicating differences in factor requirement for processing this pre-mRNA. After an unusual long lag phase of one hour splicing intermediates begin to accumulate. Intron A and D are removed with correct ligation of exons 1/2 and 4/5. Most splice sites are used--albeit with variable efficiencies--except the splice sites surrounding exon 3 and the 3' alternative splice site within exon 3; as a consequence "exon skipping" events take place. Using a pre-mRNA containing only intron B neither the 5' nor the 3' splice site is cleaved, indicating that the 3' splice site of intron B is not recognized. The results show that splice sites can differ considerably in their requirement for splicing factors.
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Affiliation(s)
- K Hartmuth
- Institut für Biochemie, Universität Wien, Austria
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Assembly of pre-mRNA splicing complex is cap dependent. Mol Biol Rep 1987. [DOI: 10.1007/bf00356903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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