1
|
Zhang X, Zhan X, Bian T, Yang F, Li P, Lu Y, Xing Z, Fan R, Zhang QC, Shi Y. Structural insights into branch site proofreading by human spliceosome. Nat Struct Mol Biol 2024; 31:835-845. [PMID: 38196034 DOI: 10.1038/s41594-023-01188-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/23/2023] [Indexed: 01/11/2024]
Abstract
Selection of the pre-mRNA branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is crucial to prespliceosome (A complex) assembly. The RNA helicase PRP5 proofreads BS selection but the underlying mechanism remains unclear. Here we report the atomic structures of two sequential complexes leading to prespliceosome assembly: human 17S U2 snRNP and a cross-exon pre-A complex. PRP5 is anchored on 17S U2 snRNP mainly through occupation of the RNA path of SF3B1 by an acidic loop of PRP5; the helicase domain of PRP5 associates with U2 snRNA; the BS-interacting stem-loop (BSL) of U2 snRNA is shielded by TAT-SF1, unable to engage the BS. In the pre-A complex, an initial U2-BS duplex is formed; the translocated helicase domain of PRP5 stays with U2 snRNA and the acidic loop still occupies the RNA path. The pre-A conformation is specifically stabilized by the splicing factors SF1, DNAJC8 and SF3A2. Cancer-derived mutations in SF3B1 damage its association with PRP5, compromising BS proofreading. Together, these findings reveal key insights into prespliceosome assembly and BS selection or proofreading by PRP5.
Collapse
Affiliation(s)
- Xiaofeng Zhang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC; MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Xiechao Zhan
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Tong Bian
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Fenghua Yang
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Pan Li
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yichen Lu
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Zhihan Xing
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Rongyan Fan
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
| | - Qiangfeng Cliff Zhang
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China
| | - Yigong Shi
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure; Tsinghua-Peking Joint Center for Life Sciences; School of Life Sciences, Tsinghua University, Beijing, China.
| |
Collapse
|
2
|
Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. Nat Commun 2023; 14:897. [PMID: 36797247 PMCID: PMC9935549 DOI: 10.1038/s41467-023-36489-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
Three RNA helicases - DDX42, DDX46 and DHX15 - are found to be associated with human U2 snRNP, but their roles and mechanisms in U2 snRNP and spliceosome assembly are insufficiently understood. Here we report the cryo-electron microscopy (cryo-EM) structures of the DDX42-SF3b complex and a putative assembly precursor of 17S U2 snRNP that contains DDX42 (DDX42-U2 complex). DDX42 is anchored on SF3B1 through N-terminal sequences, with its N-plug occupying the RNA path of SF3B1. The binding mode of DDX42 to SF3B1 is in striking analogy to that of DDX46. In the DDX42-U2 complex, the N-terminus of DDX42 remains anchored on SF3B1, but the helicase domain has been displaced by U2 snRNA and TAT-SF1. Through in vitro assays, we show DDX42 and DDX46 are mutually exclusive in terms of binding to SF3b. Cancer-driving mutations of SF3B1 target the residues in the RNA path that directly interact with DDX42 and DDX46. These findings reveal the distinct roles of DDX42 and DDX46 in assembly of 17S U2 snRNP and provide insights into the mechanisms of SF3B1 cancer mutations.
Collapse
|
3
|
Molecular mechanisms in governing genomic stability and tumor suppression by the SETD2 H3K36 methyltransferase. Int J Biochem Cell Biol 2022; 144:106155. [PMID: 34990836 DOI: 10.1016/j.biocel.2021.106155] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 01/15/2023]
Abstract
Epigenetic dysregulation is an important contributor to carcinogenesis. This is not surprising, as chromatin-genomic DNA organized around structural histone scaffolding-serves as the template on which occurs essential nuclear processes, such as transcription, DNA replication and DNA repair. Histone H3 lysine 36 (H3K36) methyltransferases, such as the SET-domain 2 protein (SETD2), have emerged as critical tumor suppressors. Previous work on mammalian SETD2 and its counterpart in model organisms, Set2, has highlighted the role of this protein in governing genomic stability through transcriptional elongation and splicing, as well as in DNA damage response processes and cell cycle progression. A compendium of SETD2 mutations have been documented, garnered from sequenced cancer patient genome data, and these findings underscore the cancer-driving properties of SETD2 loss-of-function. In this review, we consolidate the molecular mechanisms regulated by SETD2/Set2 and discuss evidence of its dysregulation in tumorigenesis. Insight into the genetic interactions that exist between SETD2 and various canonical intracellular signaling pathways has not only empowered pharmacological intervention by taking advantage of synthetic lethality but underscores SETD2 as a druggable target for precision cancer therapy.
Collapse
|
4
|
A deep learning approach to identify gene targets of a therapeutic for human splicing disorders. Nat Commun 2021; 12:3332. [PMID: 34099697 PMCID: PMC8185002 DOI: 10.1038/s41467-021-23663-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/07/2021] [Indexed: 01/16/2023] Open
Abstract
Pre-mRNA splicing is a key controller of human gene expression. Disturbances in splicing due to mutation lead to dysregulated protein expression and contribute to a substantial fraction of human disease. Several classes of splicing modulator compounds (SMCs) have been recently identified and establish that pre-mRNA splicing represents a target for therapy. We describe herein the identification of BPN-15477, a SMC that restores correct splicing of ELP1 exon 20. Using transcriptome sequencing from treated fibroblast cells and a machine learning approach, we identify BPN-15477 responsive sequence signatures. We then leverage this model to discover 155 human disease genes harboring ClinVar mutations predicted to alter pre-mRNA splicing as targets for BPN-15477. Splicing assays confirm successful correction of splicing defects caused by mutations in CFTR, LIPA, MLH1 and MAPT. Subsequent validations in two disease-relevant cellular models demonstrate that BPN-15477 increases functional protein, confirming the clinical potential of our predictions.
Collapse
|
5
|
Wu NY, Cheng SC. Functional analysis of Cwc24 ZF-domain in 5' splice site selection. Nucleic Acids Res 2019; 47:10327-10339. [PMID: 31504764 PMCID: PMC6821175 DOI: 10.1093/nar/gkz733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/07/2019] [Accepted: 08/15/2019] [Indexed: 11/30/2022] Open
Abstract
The essential splicing factor Cwc24 contains a zinc-finger (ZF) domain required for its function in splicing. Cwc24 binds over the 5' splice site after the spliceosome is activated, and its binding prior to Prp2-mediated spliceosome remodeling is important for proper interactions of U5 and U6 with the 5' splice site sequence and selection of the 5' splice site. Here, we show that Cwc24 transiently interacts with the 5' splice site in formation of the functional RNA catalytic core during spliceosome remodeling, and the ZF-motif is required for specific interaction of Cwc24 with the 5' splice site. Deletion of the ZF domain or mutation of the conserved ZF residues greatly weakened the association of Cwc24 with the spliceosome, and lowered the affinity and specificity of its interaction with the 5' splice site, resulting in atypical interactions of U5, U6 and Prp8 with the 5' splice site, and aberrant cleavage at the 5' splice site. Our results reveal a crucial role of the Cwc24 ZF-motif for defining 5' splice site selection in the first splicing step.
Collapse
Affiliation(s)
- Nan-Ying Wu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| |
Collapse
|
6
|
Chung CS, Tseng CK, Lai YH, Wang HF, Newman AJ, Cheng SC. Dynamic protein-RNA interactions in mediating splicing catalysis. Nucleic Acids Res 2019; 47:899-910. [PMID: 30395327 PMCID: PMC6344849 DOI: 10.1093/nar/gky1089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/19/2018] [Indexed: 11/16/2022] Open
Abstract
The spliceosome is assembled via sequential interactions of pre-mRNA with five small nuclear RNAs and many proteins. Recent determination of cryo-EM structures for several spliceosomal complexes has provided deep insights into interactions between spliceosomal components and structural changes of the spliceosome between steps, but information on how the proteins interact with pre-mRNA to mediate the reaction is scarce. By systematic analysis of proteins interacting with the splice sites (SSs), we have identified many previously unknown interactions of spliceosomal components with the pre-mRNA. Prp8 directly binds over the 5′SS and the branch site (BS) for the first catalytic step, and the 5′SS and 3′SS for the second step. Switching the Prp8 interaction from the BS to the 3′SS requires Slu7, which interacts dynamically with pre-mRNA first, and then interacts stably with the 3′-exon after Prp16-mediated spliceosome remodeling. Our results suggest that Prp8 plays a key role in positioning the 5′SS and 3′SS, facilitated by Slu7 through interactions with Prp8 and substrate RNA to advance exon ligation. We also provide evidence that Prp16 first docks on the intron 3′ tail, then translocates in the 3′ to 5′ direction on remodeling the spliceosome.
Collapse
Affiliation(s)
- Che-Sheng Chung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Chi-Kang Tseng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| | - Yung-Hua Lai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Hui-Fang Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan 112, Republic of China
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 115, Republic of China
| |
Collapse
|
7
|
Role of Cwc24 in the First Catalytic Step of Splicing and Fidelity of 5' Splice Site Selection. Mol Cell Biol 2017; 37:MCB.00580-16. [PMID: 27994011 DOI: 10.1128/mcb.00580-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/11/2016] [Indexed: 12/17/2022] Open
Abstract
Cwc24 is an essential splicing factor but only transiently associates with the spliceosome, with an unknown function. The protein contains a RING finger and a zinc finger domain in the carboxyl terminus. The human ortholog of Cwc24, RNF113A, has been associated with the disorder trichothiodystrophy. Here, we show that the zinc finger domain is essential for Cwc24 function, while the RING finger domain is dispensable. Cwc24 binds to the spliceosome after the Prp19-associated complex and is released upon Prp2 action. Cwc24 is not required for Prp2-mediated remodeling of the spliceosome, but the spliceosome becomes inactive if remodeling occurs before the addition of Cwc24. Cwc24 binds directly to pre-mRNA at the 5' splice site, spanning the splice junction. In the absence of Cwc24, U5 and U6 modes of interaction with the 5' splice site are altered, and splicing is very inefficient, with aberrant cleavage at the 5' splice site. Our data suggest roles for Cwc24 in orchestrating organization of the spliceosome into an active configuration prior to Prp2-mediated spliceosome remodeling and in promoting specific interaction of U5 and U6 with the 5' splice site for fidelity of 5' splice site selection.
Collapse
|
8
|
Eifler TT, Shao W, Bartholomeeusen K, Fujinaga K, Jäger S, Johnson JR, Luo Z, Krogan NJ, Peterlin BM. Cyclin-dependent kinase 12 increases 3' end processing of growth factor-induced c-FOS transcripts. Mol Cell Biol 2015; 35:468-78. [PMID: 25384976 PMCID: PMC4272423 DOI: 10.1128/mcb.01157-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Revised: 10/07/2014] [Accepted: 11/01/2014] [Indexed: 01/05/2023] Open
Abstract
Transcriptional cyclin-dependent kinases (CDKs) regulate RNA polymerase II initiation and elongation as well as cotranscriptional mRNA processing. In this report, we describe an important role for CDK12 in the epidermal growth factor (EGF)-induced c-FOS proto-oncogene expression in mammalian cells. This kinase was found in the exon junction complexes (EJC) together with SR proteins and was thus recruited to RNA polymerase II. In cells depleted of CDK12 or eukaryotic translation initiation factor 4A3 (eIF4A3) from the EJC, EGF induced fewer c-FOS transcripts. In these cells, phosphorylation of serines at position 2 in the C-terminal domain (CTD) of RNA polymerase II, as well as levels of cleavage-stimulating factor 64 (Cstf64) and 73-kDa subunit of cleavage and polyadenylation specificity factor (CPSF73), was reduced at the c-FOS gene. These effects impaired 3' end processing of c-FOS transcripts. Mutant CDK12 proteins lacking their Arg-Ser-rich (RS) domain or just the RS domain alone acted as dominant negative proteins. Thus, CDK12 plays an important role in cotranscriptional processing of c-FOS transcripts.
Collapse
Affiliation(s)
- Tristan T Eifler
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Wei Shao
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Koen Bartholomeeusen
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Koh Fujinaga
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Stefanie Jäger
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California, USA California Institute for Quantitative Biosciences, QB3, San Francisco, California, USA
| | - Jeff R Johnson
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California, USA California Institute for Quantitative Biosciences, QB3, San Francisco, California, USA
| | - Zeping Luo
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California, USA California Institute for Quantitative Biosciences, QB3, San Francisco, California, USA
| | - B Matija Peterlin
- Department of Medicine, Microbiology and Immunology, University of California at San Francisco, San Francisco, California, USA
| |
Collapse
|
9
|
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength. Genome Biol 2015; 16:201. [PMID: 26392272 PMCID: PMC4578845 DOI: 10.1186/s13059-015-0749-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/27/2015] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. The core spliceosome component PRPF8 is essential for spliceosome assembly through its participation in ribonucleoprotein (RNP) complexes for splice-site recognition, branch-point formation and catalysis. PRPF8 deficiency is linked to human diseases like retinitis pigmentosa or myeloid neoplasia, but its genome-wide effects on constitutive and alternative splicing remain unclear. RESULTS Here, we show that alterations in RNA splicing patterns across the human transcriptome that occur in conditions of restricted cellular PRPF8 abundance are defined by the altered splicing of introns with weak 5' splice sites. iCLIP of spliceosome components reveals that PRPF8 depletion decreases RNP complex formation at most splice sites in exon-intron junctions throughout the genome. However, impaired splicing affects only a subset of human transcripts, enriched for mitotic cell cycle factors, leading to mitotic arrest. Preferentially retained introns and differentially used exons in the affected genes contain weak 5' splice sites, but are otherwise indistinguishable from adjacent spliced introns. Experimental enhancement of splice-site strength in mini-gene constructs overcomes the effects of PRPF8 depletion on the kinetics and fidelity of splicing during transcription. CONCLUSIONS Competition for PRPF8 availability alters the transcription-coupled splicing of RNAs in which weak 5' splice sites predominate, enabling diversification of human gene expression during biological processes like mitosis. Our findings exemplify the regulatory potential of changes in the core spliceosome machinery, which may be relevant to slow-onset human genetic diseases linked to PRPF8 deficiency.
Collapse
Affiliation(s)
- Vihandha O. Wickramasinghe
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Mar Gonzàlez-Porta
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - David Perera
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Arthur R. Bartolozzi
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| | - Christopher R. Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Martina Hallegger
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG UK
| | - John C. Marioni
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ashok R. Venkitaraman
- The Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Box 197, Cambridge, CB2 0XZ UK
| |
Collapse
|
10
|
Howard JM, Sanford JR. The RNAissance family: SR proteins as multifaceted regulators of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:93-110. [PMID: 25155147 DOI: 10.1002/wrna.1260] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 07/09/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Abstract
Serine and arginine-rich (SR) proteins play multiple roles in the eukaryotic gene expression pathway. Initially described as constitutive and alternative splicing factors, now it is clear that SR proteins are key determinants of exon identity and function as molecular adaptors, linking the pre-messenger RNA (pre-mRNA) to the splicing machinery. In addition, now SR proteins are implicated in many aspects of mRNA and noncoding RNA (ncRNA) processing well beyond splicing. These unexpected roles, including RNA transcription, export, translation, and decay, may prove to be the rule rather than the exception. To simply define, this family of RNA-binding proteins as splicing factors belies the broader roles of SR proteins in post-transcriptional gene expression.
Collapse
Affiliation(s)
- Jonathan M Howard
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | | |
Collapse
|
11
|
Ilagan JO, Chalkley RJ, Burlingame A, Jurica MS. Rearrangements within human spliceosomes captured after exon ligation. RNA (NEW YORK, N.Y.) 2013; 19:400-12. [PMID: 23345524 PMCID: PMC3677250 DOI: 10.1261/rna.034223.112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 12/11/2012] [Indexed: 05/20/2023]
Abstract
In spliceosomes, dynamic RNA/RNA and RNA/protein interactions position the pre-mRNA substrate for the two chemical steps of splicing. Not all of these interactions have been characterized, in part because it has not been possible to arrest the complex at clearly defined states relative to chemistry. Previously, it was shown in yeast that the DEAD/H-box protein Prp22 requires an extended 3' exon to promote mRNA release from the spliceosome following second-step chemistry. In line with that observation, we find that shortening the 3' exon blocks cleaved lariat intron and mRNA release in human splicing extracts, which allowed us to stall human spliceosomes in a new post-catalytic complex (P complex). In comparison to C complex, which is blocked at a point following first-step chemistry, we detect specific differences in RNA substrate interactions near the splice sites. These differences include extended protection across the exon junction and changes in protein crosslinks to specific sites in the 5' and 3' exons. Using selective reaction monitoring (SRM) mass spectrometry, we quantitatively compared P and C complex proteins and observed enrichment of SF3b components and loss of the putative RNA-dependent ATPase DHX35. Electron microscopy revealed similar structural features for both complexes. Notably, additional density is present when complexes are chemically fixed, which reconciles our results with previously reported C complex structures. Our ability to compare human spliceosomes before and after second-step chemistry has opened a new window to rearrangements near the active site of spliceosomes, which may play roles in exon ligation and mRNA release.
Collapse
Affiliation(s)
- Janine O. Ilagan
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Robert J. Chalkley
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94122, USA
| | - A.L. Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94122, USA
| | - Melissa S. Jurica
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
- Corresponding authorE-mail
| |
Collapse
|
12
|
Factors affecting splicing strength of yeast genes. Comp Funct Genomics 2011; 2011:212146. [PMID: 22162666 PMCID: PMC3226532 DOI: 10.1155/2011/212146] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Accepted: 09/06/2011] [Indexed: 01/30/2023] Open
Abstract
Accurate and efficient splicing is of crucial importance for highly-transcribed intron-containing genes (ICGs) in rapidly replicating unicellular eukaryotes such as the budding yeast Saccharomyces cerevisiae. We characterize the 5' and 3' splice sites (ss) by position weight matrix scores (PWMSs), which is the highest for the consensus sequence and the lowest for splice sites differing most from the consensus sequence and used PWMS as a proxy for splicing strength. HAC1, which is known to be spliced by a nonspliceosomal mechanism, has the most negative PWMS for both its 5' ss and 3' ss. Several genes under strong splicing regulation and requiring additional splicing factors for their splicing also have small or negative PWMS values. Splicing strength is higher for highly transcribed ICGs than for lowly transcribed ICGs and higher for transcripts that bind strongly to spliceosomes than those that bind weakly. The 3' splice site features a prominent poly-U tract before the 3'AG. Our results suggest the potential of using PWMS as a screening tool for ICGs that are either spliced by a nonspliceosome mechanism or under strong splicing regulation in yeast and other fungal species.
Collapse
|
13
|
Levit A, Nutman D, Osher E, Kamhi E, Navon R. Two novel exonic point mutations in HEXA identified in a juvenile Tay-Sachs patient: role of alternative splicing and nonsense-mediated mRNA decay. Mol Genet Metab 2010; 100:176-83. [PMID: 20363167 DOI: 10.1016/j.ymgme.2010.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/13/2010] [Accepted: 03/14/2010] [Indexed: 11/30/2022]
Abstract
We have identified three mutations in the beta-hexoseaminidase A (HEXA) gene in a juvenile Tay-Sachs disease (TSD) patient, which exhibited a reduced level of HEXA mRNA. Two mutations are novel, c.814G>A (p.Gly272Arg) and c.1305C>T (p.=), located in exon 8 and in exon 11, respectively. The third mutation, c.1195A>G (p.Asn399Asp) in exon 11, has been previously characterized as a common polymorphism in African-Americans. Hex A activity measured in TSD Glial cells, transfected with HEXA cDNA constructs bearing these mutations, was unaltered from the activity level measured in normal HEXA cDNA. Analysis of RT-PCR products revealed three aberrant transcripts in the patient, one where exon 8 was absent, one where exon 11 was absent and a third lacking both exons 10 and 11. All three novel transcripts contain frameshifts resulting in premature termination codons (PTCs). Transfection of mini-gene constructs carrying the c.814G>A and c.1305C>T mutations proved that the two mutations result in exon skipping. mRNAs that harbor a PTC are detected and degraded by the nonsense-mediated mRNA decay (NMD) pathway to prevent synthesis of abnormal proteins. However, although NMD is functional in the patient's fibroblasts, aberrant transcripts are still present. We suggest that the level of correctly spliced transcripts as well as the efficiency in which NMD degrade the PTC-containing transcripts, apparently plays an important role in the phenotype severity of the unique patient and thus should be considered as a potential target for drug therapy.
Collapse
Affiliation(s)
- A Levit
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | | | | | | |
Collapse
|
14
|
Ilagan J, Yuh P, Chalkley RJ, Burlingame AL, Jurica MS. The role of exon sequences in C complex spliceosome structure. J Mol Biol 2009; 394:363-75. [PMID: 19761775 DOI: 10.1016/j.jmb.2009.09.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 08/04/2009] [Accepted: 09/09/2009] [Indexed: 02/05/2023]
Abstract
Pre-mRNA splicing is catalyzed by a large ribonucleoprotein complex called the spliceosome. Previous electron microscopy reconstruction of C complex spliceosomes arrested between the two chemical steps of splicing revealed an averaged core structure consisting of three primary domains surrounding a central cavity. Here we characterize the involvement of pre-mRNA in this structured core of C complex by protection mapping. We find that the 3' end of the cleaved 5' exon and intron sequences flanking the branched lariat are buried in the complex. Upstream regions of the 5' exon and the entire 3' exon, including the mutant 3' splice site, are accessible and can be removed by nucleolytic cleavage. Furthermore, we show that the second-step active site of the complex, which is arrested by a 3' splice site mutation, can accept a normal 3' splice site in trans to catalyze exon ligation. Removal of the accessible exon regions alters the protein composition of the complex, but the core spliceosome proteins associated with the uridine-rich small nuclear ribonucleoproteins U2, U5, and U6 and the Prp19 complex as well as several other proteins remain intact. Two-dimensional averaged images of an exon-trimmed complex closely resemble C complex assembled on full-length pre-mRNA, supporting the hypothesis that the electron microscopy model of C complex reflects the core structure of a catalytically competent particle. Trimming the 3' exon does, however, alter the distribution of particles that appear to be missing some density, suggesting that the exon plays a role in stabilizing C complex.
Collapse
Affiliation(s)
- Janine Ilagan
- Department of Molecular, Cell and Developmental Biology, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
| | | | | | | | | |
Collapse
|
15
|
The CUGBP2 splicing factor regulates an ensemble of branchpoints from perimeter binding sites with implications for autoregulation. PLoS Genet 2009; 5:e1000595. [PMID: 19680430 PMCID: PMC2715136 DOI: 10.1371/journal.pgen.1000595] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 07/13/2009] [Indexed: 12/30/2022] Open
Abstract
Alternative pre-mRNA splicing adjusts the transcriptional output of the genome by generating related mRNAs from a single primary transcript, thereby expanding protein diversity. A fundamental unanswered question is how splicing factors achieve specificity in the selection of target substrates despite the recognition of information-poor sequence motifs. The CUGBP2 splicing regulator plays a key role in the brain region-specific silencing of the NI exon of the NMDA R1 receptor. However, the sequence motifs utilized by this factor for specific target exon selection and its role in splicing silencing are not understood. Here, we use chemical modification footprinting to map the contact sites of CUGBP2 to GU-rich motifs closely positioned at the boundaries of the branch sites of the NI exon, and we demonstrate a mechanistic role for this specific arrangement of motifs for the regulation of branchpoint formation. General support for a branch site-perimeter–binding model is indicated by the identification of a group of novel target exons with a similar configuration of motifs that are silenced by CUGBP2. These results reveal an autoregulatory role for CUGBP2 as indicated by its direct interaction with functionally significant RNA motifs surrounding the branch sites upstream of exon 6 of the CUGBP2 transcript itself. The perimeter-binding model explains how CUGBP2 can effectively embrace the branch site region to achieve the specificity needed for the selection of exon targets and the fine-tuning of alternative splicing patterns. Alternative splicing is a precisely controlled process that determines whether an exon will be included or skipped in the mature mRNA transcript. Factors that control alternative splicing bind to RNA sequence motifs in the exon or flanking introns and guide tissue and developmental specific splicing events. CUGBP2 is a dual functional regulator of alternative splicing that can cause inclusion or skipping of a target exon, depending on the context of its binding motifs. Previously, the mechanisms of regulation by this protein and the positional significance of its target motifs have not been characterized. In this study, the authors dissected the mechanism of exon skipping by CUGBP2 and demonstrate that a specific configuration of motifs at the perimeters of a functional reference point are intimately involved in this event. Furthermore, this mechanism of regulation is shown to have general significance because novel CUGBP2 target exons contain a similar arrangement of motifs. The most interesting of this group is an exon within the CUGBP2 transcript itself. This study underscores the importance of a functional reference point in the specificity of regulation by an alternative splicing factor and reveals a novel autoregulatory role for CUGBP2.
Collapse
|
16
|
Kershaw CJ, Barrass JD, Beggs JD, O'Keefe RT. Mutations in the U5 snRNA result in altered splicing of subsets of pre-mRNAs and reduced stability of Prp8. RNA (NEW YORK, N.Y.) 2009; 15:1292-304. [PMID: 19447917 PMCID: PMC2704078 DOI: 10.1261/rna.1347409] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The U5 snRNA loop 1 aligns the 5' and 3' exons for ligation during the second step of pre-mRNA splicing. U5 is intimately associated with Prp8, which mediates pre-mRNA repositioning within the catalytic core of the spliceosome and interacts directly with U5 loop 1. The genome-wide effect of three U5 loop 1 mutants has been assessed by microarray analysis. These mutants exhibited impaired and improved splicing of subsets of pre-mRNAs compared to wild-type U5. Analysis of pre-mRNAs that accumulate revealed a change in base prevalence at specific positions near the splice sites. Analysis of processed pre-mRNAs exhibiting mRNA accumulation revealed a bias in base prevalence at one position within the 5' exon. While U5 loop 1 can interact with some of these positions the base bias is not directly related to sequence changes in loop 1. All positions that display a bias in base prevalence are at or next to positions known to interact with Prp8. Analysis of Prp8 in the presence of the three U5 loop 1 mutants revealed that the most severe mutant displayed reduced Prp8 stability. Depletion of U5 snRNA in vivo also resulted in reduced Prp8 stability. Our data suggest that certain mutations in U5 loop 1 perturb the stability of Prp8 and may affect interactions of Prp8 with a subset of pre-mRNAs influencing their splicing. Therefore, the integrity of U5 is important for the stability of Prp8 during splicing and provides one possible explanation for why U5 loop 1 and Prp8 are so highly conserved.
Collapse
Affiliation(s)
- Christopher J Kershaw
- Faculty of Life Sciences, The University of Manchester, Manchester M139PT, United Kingdom
| | | | | | | |
Collapse
|
17
|
Mesa A, Somarelli JA, Herrera RJ. Spliceosomal immunophilins. FEBS Lett 2008; 582:2345-51. [PMID: 18544344 DOI: 10.1016/j.febslet.2008.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 05/16/2008] [Accepted: 06/02/2008] [Indexed: 11/17/2022]
Abstract
The spliceosome is a dynamic, macromolecular complex, which removes non-protein-coding introns from pre-mRNA to form mature mRNA in a process known as splicing. This ribonucleoprotein assembly is comprised of five uridine-rich small nuclear RNAs (snRNAs) as well as over 300 proteins. In humans, several of the known proteinaceous splicing factors are members of the immunophilin superfamily. Immunophilins are peptidyl-prolyl cis-trans isomerases that catalyze the conversion of proteins from cis to trans at Xaa-Pro bonds. Our review of the data indicates that some members of this protein family are activators of spliceosomal proteins by way of folding and transport.
Collapse
Affiliation(s)
- Annia Mesa
- Florida International University, Department of Biological Sciences, University Park, 11200 SW 8th Street, OE 304, Miami, FL 33199, United States
| | | | | |
Collapse
|
18
|
Alcid EA, Jurica MS. A protein-based EM label for RNA identifies the location of exons in spliceosomes. Nat Struct Mol Biol 2008; 15:213-5. [PMID: 18223660 DOI: 10.1038/nsmb.1378] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 01/02/2008] [Indexed: 11/09/2022]
Abstract
To locate key RNA features in the structure of the spliceosome by EM, we fused a sequence-specific RNA binding protein to a protein with a distinct donut-shaped structure. We used this fusion to label spliceosomes assembled on a pre-mRNA that contained the target sequence in the exons. The label is clearly visible in EM images of the spliceosome, and subsequent image processing with averaging shows that the exons sit close to each other in the complex. This labeling strategy will serve as a general tool for analyzing the structures of RNA-containing macromolecular complexes.
Collapse
Affiliation(s)
- Eric A Alcid
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, 1156 High Street, Santa Cruz, California 95064, USA
| | | |
Collapse
|
19
|
Dönmez G, Hartmuth K, Kastner B, Will CL, Lührmann R. The 5′ End of U2 snRNA Is in Close Proximity to U1 and Functional Sites of the Pre-mRNA in Early Spliceosomal Complexes. Mol Cell 2007; 25:399-411. [PMID: 17289587 DOI: 10.1016/j.molcel.2006.12.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Revised: 12/06/2006] [Accepted: 12/20/2006] [Indexed: 10/23/2022]
Abstract
Recognition and pairing of the correct 5' and 3' splice sites (ss) of a pre-mRNA are critical events that occur early during spliceosome assembly. Little is known about the spatial organization in early spliceosomal complexes of the U1 and U2 snRNPs, which together with several non-snRNP proteins, are involved in juxtapositioning the functional sites of the pre-mRNA. To better understand the molecular mechanisms of splice-site recognition/pairing, we have examined the organization of U2 relative to U1 and pre-mRNA in spliceosomal complexes via hydroxyl-radical probing with Fe-BABE-tethered U2 snRNA. These studies reveal that functional sites of the pre-mRNA are located close to the 5' end of U2 both in E and A complexes. U2 is also positioned close to U1 in a defined orientation already in the E complex, and their relative spatial organization remains largely unchanged during the E to A transition.
Collapse
Affiliation(s)
- Gizem Dönmez
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | | | | |
Collapse
|
20
|
Matlin AJ, Moore MJ. Spliceosome assembly and composition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:14-35. [PMID: 18380338 DOI: 10.1007/978-0-387-77374-2_2] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cells control alternative splicing by modulating assembly of the pre-mRNA splicing machinery at competing splice sites. Therefore, a working knowledge of spliceosome assembly is essential for understanding how alternative splice site choices are achieved. In this chapter, we review spliceosome assembly with particular emphasis on the known steps and factors subject to regulation during alternative splice site selection in mammalian cells. We also review recent advances regarding similarities and differences between the in vivo and in vitro assembly pathways, as well as proofreading mechanisms contributing to the fidelity of splice site selection.
Collapse
Affiliation(s)
- Arianne J Matlin
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
| | | |
Collapse
|
21
|
Turner IA, Norman CM, Churcher MJ, Newman AJ. Dissection of Prp8 protein defines multiple interactions with crucial RNA sequences in the catalytic core of the spliceosome. RNA (NEW YORK, N.Y.) 2006; 12:375-86. [PMID: 16431982 PMCID: PMC1383577 DOI: 10.1261/rna.2229706] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Current models of the core of the spliceosome include a network of RNA-RNA interactions involving the pre-mRNA and the U2, U5, and U6 snRNAs. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor. However, the sequence of Prp8 is almost entirely novel, and it offers few clues to the molecular basis of Prp8-RNA interactions. We have used an innovative transposon-based strategy to establish that catalytic core RNAs make multiple contacts in the central region of Prp8, underscoring the intimate relationship between this protein and the catalytic center of the spliceosome. Our analysis of RNA interactions identifies a discrete, highly conserved region of Prp8 as a prime candidate for the role of cofactor for the spliceosome's RNA core.
Collapse
MESH Headings
- Base Sequence
- Binding Sites
- Conserved Sequence
- Endopeptidases/genetics
- Models, Molecular
- Mutagenesis, Insertional
- Nucleic Acid Conformation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splicing
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear
- Ribonucleoprotein, U5 Small Nuclear
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Spliceosomes/metabolism
Collapse
Affiliation(s)
- Ian A Turner
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | | | | | | |
Collapse
|
22
|
Görnemann J, Kotovic KM, Hujer K, Neugebauer KM. Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. Mol Cell 2005; 19:53-63. [PMID: 15989964 DOI: 10.1016/j.molcel.2005.05.007] [Citation(s) in RCA: 213] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2005] [Revised: 04/05/2005] [Accepted: 05/09/2005] [Indexed: 10/25/2022]
Abstract
Coupling between transcription and pre-mRNA splicing is a key regulatory mechanism in gene expression. Here, we investigate cotranscriptional spliceosome assembly in yeast, using in vivo crosslinking to determine the distribution of spliceosome components along intron-containing genes. Accumulation of the U1, U2, and U5 small nuclear ribonucleoprotein particles (snRNPs) and the 3' splice site binding factors Mud2p and BBP was detected in patterns indicative of progressive and complete spliceosome assembly; recruitment of the nineteen complex (NTC) component Prp19p suggests that splicing catalysis is also cotranscriptional. The separate dynamics of the U1, U2, and U5 snRNPs are consistent with stepwise recruitment of individual snRNPs rather than a preformed "penta-snRNP", as recently proposed. Finally, we show that the cap binding complex (CBC) is necessary, but not sufficient, for cotranscriptional spliceosome assembly. Thus, the demonstration of an essential link between CBC and spliceosome assembly in vivo indicates that 5' end capping couples pre-mRNA splicing to transcription.
Collapse
Affiliation(s)
- Janina Görnemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | | | | | | |
Collapse
|
23
|
Hass M, Hannoun C, Kalinina T, Sommer G, Manegold C, Günther S. Functional analysis of hepatitis B virus reactivating in hepatitis B surface antigen-negative individuals. Hepatology 2005; 42:93-103. [PMID: 15962285 DOI: 10.1002/hep.20748] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological properties of latent or occult hepatitis B virus (HBV) have been poorly characterized as a result of the extremely low virus concentration. This report describes the phenotype of HBV reactivating in two patients after an HBsAg-negative latency period. One patient had latent HBV infection for at least 12 years without detectable viremia and symptoms of liver disease. Several full-length HBV genomes were cloned at reactivation, sequenced, and functionally tested by transfection into HuH7 cells. Genomes from both patients showed a low replication phenotype. It was caused at the level of RNA encapsidation or HBV DNA synthesis, but was not attributable to uncommon mutations in the terminal protein domain of P protein. A substantial subpopulation ( approximately 50%) of genomes from one patient did not express pre-S2/S mRNA and HBsAg. Site-directed mutagenesis identified a single G-A mutation within the S gene (position 458) to be responsible for this effect. The G458A mutation was also effective if the S gene was placed under control of a heterologous promoter. Furthermore, nuclear run-on transcription showed that the G458A mutation acts at the posttranscriptional level. The mutation affected a 5' splice site and prevented splicing of the pre-S2/S mRNA from position 458 to 1305. In conclusion, HBV latency may be characterized by viruses with reduced replication competence and antigen expression. In one patient, HBsAg expression was terminated by an as yet undescribed posttranscriptional mechanism. A single mutation inactivated a 5' splice site that is obviously essential for pre-S2/S mRNA accumulation. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html).
Collapse
Affiliation(s)
- Meike Hass
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | | | | | | |
Collapse
|
24
|
Abstract
Pre-messenger RNA (pre-mRNA) splicing is a central step in gene expression. Lying between transcription and protein synthesis, pre-mRNA splicing removes sequences (introns) that would otherwise disrupt the coding potential of intron-containing transcripts. This process takes place in the nucleus, catalyzed by a large RNA-protein complex called the spliceosome. Prp8p, one of the largest and most highly conserved of nuclear proteins, occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there. Recently, Prp8p has also come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa.Prp8 is unique, having no obvious homology to other proteins; however, using bioinformatical analysis we reveal the presence of a conserved RNA recognition motif (RRM), an MPN/JAB domain and a putative nuclear localization signal (NLS). Here, we review biochemical and genetical data, mostly related to the human and yeast proteins, that describe Prp8's central role within the spliceosome and its molecular interactions during spliceosome formation, as splicing proceeds, and in post-splicing complexes.
Collapse
Affiliation(s)
- Richard J Grainger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3JR, United Kingdom
| | | |
Collapse
|
25
|
Masuyama K, Taniguchi I, Kataoka N, Ohno M. SR proteins preferentially associate with mRNAs in the nucleus and facilitate their export to the cytoplasm. Genes Cells 2004; 9:959-65. [PMID: 15461666 DOI: 10.1111/j.1365-2443.2004.00774.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Different classes of RNA are exported to the cytoplasm by distinct mechanisms. Each class of RNA forms distinct complexes with nuclear proteins prior to its export to the cytoplasm. In our attempt to obtain comprehensive information of protein factors that specifically associate with mRNAs in the nucleus, we performed in vivo UV-crosslinking analysis after microinjection of various RNAs into Xenopus oocyte nucleus. We found a group of proteins preferentially crosslinked to mRNAs. Immunoprecipitation experiments revealed that some of the crosslinked signals corresponded to SR (serine/arginine-rich) proteins, a family of essential RNA-binding proteins involved in pre-mRNA splicing. It was previously suggested that some members of SR protein family are involved in export of a specific intronless mRNA, histone H2A mRNA and some spliced mRNAs. However, it is still to be clarified if SR proteins are involved in export of general mRNAs, especially general intronless mRNAs that do not contain specific RNA export elements. When we microinjected an antibody against SR proteins into the nucleus, export of mRNAs was severely inhibited, regardless of whether the mRNAs were produced via pre-mRNA splicing or not, whereas export of other RNAs was not affected. These results unequivocally showed that SR proteins are involved in export of both general intronless and spliced mRNAs.
Collapse
Affiliation(s)
- Kaoru Masuyama
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, and CREST, JST (Japan Science and Technology Agency), Kawaguchi, Saitama 332-0012, Japan
| | | | | | | |
Collapse
|
26
|
Carriero S, Damha MJ. Inhibition of pre-mRNA splicing by synthetic branched nucleic acids. Nucleic Acids Res 2003; 31:6157-67. [PMID: 14576302 PMCID: PMC275466 DOI: 10.1093/nar/gkg824] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2003] [Revised: 08/27/2003] [Accepted: 09/10/2003] [Indexed: 11/15/2022] Open
Abstract
The cellular transformation of a precursor mRNA (pre-mRNA) into its mature or functional form proceeds by way of a splicing reaction, in which the exons are ligated to form the mature linear RNA and the introns are excised as branched or lariat RNAs. We have prepared a series of branched compounds (bRNA and bDNA), and studied the effects of such molecules on the efficiency of mammalian pre-mRNA splicing in vitro. Y-shaped RNAs containing an unnatural L-2'-deoxycytidine unit (L-dC) at the 3' termini are highly stabilized against exonuclease hydrolysis in HeLa nuclear extracts, and are potent inhibitors of the splicing pathway. A bRNA containing internal 2'-O-methyl ribopyrimidine units and L-dC at the 3' ends was at least twice as potent as the most potent of the bRNAs containing no 2' modifications, with an IC50 of approximately 5 micro M. Inhibitory activity was maintained in a branched molecule containing an arabino-adenosine branchpoint which, unlike the native bRNAs, resisted cleavage by the lariat- debranching enzyme. The data obtained suggest that binding and sequestering of a branch recognition factor by the branched nucleic acids is an early event, which occurs prior to the first chemical step of splicing. Probably, an early recognition element preferentially binds to the synthetic branched molecules over the native pre-mRNA. As such, synthetic bRNAs may prove to be invaluable tools for the purification and identification of the putative branchpoint recognition factor.
Collapse
Affiliation(s)
- Sandra Carriero
- Department of Chemistry, Otto Maass Chemistry Building, McGill University, 801 Sherbrooke St West, Montreal, QC, H3A 2K6, Canada
| | | |
Collapse
|
27
|
Soret J, Tazi J. Phosphorylation-dependent control of the pre-mRNA splicing machinery. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2003; 31:89-126. [PMID: 12494764 DOI: 10.1007/978-3-662-09728-1_4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Affiliation(s)
- J Soret
- Institut de Génétique Moléculaire, UMR5535 du CNRS, IFR 24, 1919 Route de Mende, 34293 Montpellier, France
| | | |
Collapse
|
28
|
Reichert VL, Le Hir H, Jurica MS, Moore MJ. 5' exon interactions within the human spliceosome establish a framework for exon junction complex structure and assembly. Genes Dev 2002; 16:2778-91. [PMID: 12414731 PMCID: PMC187475 DOI: 10.1101/gad.1030602] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A general consequence of pre-mRNA splicing is the stable deposition of several proteins 20-24 nucleotides (nt) upstream of exon-exon junctions on spliced mRNAs. This exon junction complex (EJC) contains factors involved in mRNA export, cytoplasmic localization, and nonsense-mediated mRNA decay. Here we probed the mechanism and timing of EJC assembly. Over the course of splicing, the 5' exon is subject to numerous dynamic protein-RNA interactions involving at least nine distinct polypeptides. Within the fully assembled spliceosome, these interactions afford protection to the last 25-27 nt of the 5' exon intermediate. Coincident with exon ligation, interactions at the 3' end of the 5' exon disappear, and new species associate with position -24. Mass spectrometry and Western blotting of purified H, C, and mRNP complexes revealed that at least one EJC component, REF/Aly, can interact with pre-mRNA prior to spliceosome assembly, whereas Y14, Magoh, RNPS1, UAP56, and SRm160 are found in intermediate-containing spliceosomes. Upon exon ligation, association of RNPS1, UAP56, and SRm160 is destabilized. In contrast, REF/Aly, Y14, and Magoh remain stably bound to spliced mRNA, indicating that these three proteins are components of the EJC core.
Collapse
Affiliation(s)
- Vienna L Reichert
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, Massachusetts 02454, USA
| | | | | | | |
Collapse
|
29
|
Kuhn AN, Reichl EM, Brow DA. Distinct domains of splicing factor Prp8 mediate different aspects of spliceosome activation. Proc Natl Acad Sci U S A 2002; 99:9145-9. [PMID: 12087126 PMCID: PMC123108 DOI: 10.1073/pnas.102304299] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2002] [Accepted: 05/21/2002] [Indexed: 11/18/2022] Open
Abstract
Prp8 is the largest and most highly conserved protein in the spliceosome yet its mechanism of function is poorly understood. Our previous studies implicate Prp8 in control of spliceosome activation for the first catalytic step of splicing, because substitutions in five distinct regions (a-e) of Prp8 suppress a cold-sensitive block to activation caused by a mutation in U4 RNA. Catalytic activation of the spliceosome is thought to require unwinding of the U1 RNA/5' splice site and U4/U6 RNA helices by the Prp28 and Prp44/Brr2 DExD/H-box helicases, respectively. Here we show that mutations in regions a, d, and e of Prp8 exhibit allele-specific genetic interactions with mutations in Prp28, Prp44/Brr2, and U6 RNA, respectively. These results indicate that Prp8 coordinates multiple processes in spliceosome activation and enable an initial correlation of Prp8 structure and function. Furthermore, additional genetic interactions with U4-cs1 support a two-state model for this RNA conformational switch and implicate another splicing factor, Prp31, in Prp8-mediated spliceosome activation.
Collapse
Affiliation(s)
- Andreas N Kuhn
- Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532, USA
| | | | | |
Collapse
|
30
|
Kafasla P, Patrinou-Georgoula M, Lewis JD, Guialis A. Association of the 72/74-kDa proteins, members of the heterogeneous nuclear ribonucleoprotein M group, with the pre-mRNA at early stages of spliceosome assembly. Biochem J 2002; 363:793-9. [PMID: 11964181 PMCID: PMC1222533 DOI: 10.1042/0264-6021:3630793] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We have investigated the role played in precursor mRNA (pre-mRNA) splicing by the protein pair of molecular size 72/74 kDa, which are integral components of a discrete subset of heterogeneous nuclear (hn) ribonucleoproteins (RNPs) named large heterogeneous nuclear RNP (LH-nRNP). This 72/74 kDa pair of proteins has been shown to belong to the hnRNP M group, and are referred to as 72/74(M). By applying specific immunoprecipitation assays in a consecutive series of splicing reactions in vitro, the antigenic 72/74(M) protein species were found to associate with the pre-mRNA and not the intermediate or final products of splicing. Kinetic studies, combined with isolation of pre-spliceosomal and spliceosomal complexes from the splicing reaction, indicated a loose association of 72/74(M) with both the initially formed H assembly and the first splicing-committed E complex. Stable binding was seen at a later stage of the reaction, well in advance of the appearance of the first intermediate products of RNA splicing. Evidence is provided that supports the almost exclusive association of 72/74(M) with pre-mRNA within the pre-spliceosomal A complex. This dynamic binding appeared to involve pre-mRNA sites similar to those of spliceosomal U1 and U2 small nuclear RNP complexes. Moreover, a preferential binding to a truncated RNA containing the 5' exon-intron part, rather than the intron-3' exon part, of pre-mRNA was observed.
Collapse
Affiliation(s)
- Panayiota Kafasla
- Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, 48 Vas. Constantinou Ave., 11635 Athens, Greece
| | | | | | | |
Collapse
|
31
|
Collins CA, Guthrie C. Genetic interactions between the 5' and 3' splice site consensus sequences and U6 snRNA during the second catalytic step of pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2001; 7:1845-1854. [PMID: 11780639 PMCID: PMC1370222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The YAG/ consensus sequence at the 3' end of introns (the slash indicates the location of the 3' splice site) is essential for catalysis of the second step of pre-mRNA splicing. Little is known about the interactions formed by these three nucleotides in the spliceosome. Although previous observations have suggested that the G of the YAG/ interacts with the first nucleotide of the /GUA consensus sequence at the 5' end of the intron, additional interactions have not been identified. Here we report several striking genetic interactions between A+3 of the 5' /GUA with Y-3 of the 3' YAG/ and G50 of the highly conserved ACAGAG motif in U6 snRNA. Two mutations in U6 G50 of the ACAGAG can weakly suppress two mutations in A+3 of the 5' /GUA. This suppression is significantly enhanced upon the inclusion of a specific mutation Y-3 in the 3' YAG/. RNA analysis confirmed that the severe splicing defect observed in A+3 and Y-3 double mutants can be rescued to near wild-type levels by the mutations in U6 G50. The contributions of each mutation to the genetic interaction and the strong position specificity of suppression, combined with previous findings, support a model in which the 5' /GUA and the GAG of U6 function in binding the 3' YAG/ during the second catalytic step.
Collapse
Affiliation(s)
- C A Collins
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143, USA
| | | |
Collapse
|
32
|
Dagher SF, Fu XD. Evidence for a role of Sky1p-mediated phosphorylation in 3' splice site recognition involving both Prp8 and Prp17/Slu4. RNA (NEW YORK, N.Y.) 2001; 7:1284-97. [PMID: 11565750 PMCID: PMC1370172 DOI: 10.1017/s1355838201016077] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The SRPK family of kinases is specific for RS domain-containing splicing factors and known to play a critical role in protein-protein interaction and intracellular distribution of their substrates in both yeast and mammalian cells. However, the function of these kinases in pre-mRNA splicing remains unclear. Here we report that SKY1, a SRPK family member in Saccharomyces cerevisiae, genetically interacts with PRP8 and PRP17/SLU4, both of which are involved in splice site selection during pre-mRNA splicing. Prp8 is essential for splicing and is known to interact with both 5' and 3' splice sites in the spliceosomal catalytic center, whereas Prp17/Slu4 is nonessential and is required only for efficient recognition of the 3' splice site. Interestingly, deletion of SKY1 was synthetically lethal with all prp17 mutants tested, but only with specific prp8 alleles in a domain implicated in governing fidelity of 3'AG recognition. Indeed, deletion of SKY1 specifically suppressed 3'AG mutations in ACT1-CUP1 splicing reporters. These results suggest for the first time that 3' AG recognition may be subject to phosphorylation regulation by Sky1p during pre-mRNA splicing.
Collapse
Affiliation(s)
- S F Dagher
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla 92093-0651, USA
| | | |
Collapse
|
33
|
Will CL, Schneider C, MacMillan AM, Katopodis NF, Neubauer G, Wilm M, Lührmann R, Query CC. A novel U2 and U11/U12 snRNP protein that associates with the pre-mRNA branch site. EMBO J 2001; 20:4536-46. [PMID: 11500380 PMCID: PMC125580 DOI: 10.1093/emboj/20.16.4536] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previous UV cross-linking studies demonstrated that, upon integration of the U2 snRNP into the spliceosome, a 14 kDa protein (p14) interacts directly with the branch adenosine, the nucleophile for the first transesterification step of splicing. We have identified the cDNA encoding this protein by microsequencing a 14 kDa protein isolated from U2-type spliceosomes. This protein contains an RNA recognition motif and is highly conserved across species. Antibodies raised against this cDNA-encoded protein precipitated the 14 kDa protein cross-linked to the branch adenosine, confirming the identity of the p14 cDNA. A combination of immunoblotting, protein microsequencing and immunoprecipitation revealed that p14 is a component of both 17S U2 and 18S U11/U12 snRNPs, suggesting that it contributes to the interaction of these snRNPs with the branch sites of U2- and U12-type pre-mRNAs, respectively. p14 was also shown to be a subunit of the heteromeric splicing factor SF3b and to interact directly with SF3b155. Immuno precipitations indicated that p14 is present in U12-type spliceosomes, consistent with the idea that branch point selection is similar in the major and minor spliceosomes.
Collapse
Affiliation(s)
- Cindy L. Will
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D-37077 Göttingen, EMBL, Protein and Peptide Group, D-69117 Heidelberg, Germany, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 and Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461-1975, USA Corresponding authors e-mail: or
| | - Claudia Schneider
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D-37077 Göttingen, EMBL, Protein and Peptide Group, D-69117 Heidelberg, Germany, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 and Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461-1975, USA Corresponding authors e-mail: or
| | - Andrew M. MacMillan
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D-37077 Göttingen, EMBL, Protein and Peptide Group, D-69117 Heidelberg, Germany, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 and Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461-1975, USA Corresponding authors e-mail: or
| | - Nikos F. Katopodis
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D-37077 Göttingen, EMBL, Protein and Peptide Group, D-69117 Heidelberg, Germany, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 and Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461-1975, USA Corresponding authors e-mail: or
| | - Gitte Neubauer
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D-37077 Göttingen, EMBL, Protein and Peptide Group, D-69117 Heidelberg, Germany, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 and Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461-1975, USA Corresponding authors e-mail: or
| | - Matthias Wilm
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D-37077 Göttingen, EMBL, Protein and Peptide Group, D-69117 Heidelberg, Germany, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 and Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461-1975, USA Corresponding authors e-mail: or
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D-37077 Göttingen, EMBL, Protein and Peptide Group, D-69117 Heidelberg, Germany, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 and Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461-1975, USA Corresponding authors e-mail: or
| | - Charles C. Query
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D-37077 Göttingen, EMBL, Protein and Peptide Group, D-69117 Heidelberg, Germany, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7 and Department of Cell Biology, Albert Einstein College of Medicine, New York, NY 10461-1975, USA Corresponding authors e-mail: or
| |
Collapse
|
34
|
Peled-Zehavi H, Berglund JA, Rosbash M, Frankel AD. Recognition of RNA branch point sequences by the KH domain of splicing factor 1 (mammalian branch point binding protein) in a splicing factor complex. Mol Cell Biol 2001; 21:5232-41. [PMID: 11438677 PMCID: PMC87247 DOI: 10.1128/mcb.21.15.5232-5241.2001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mammalian splicing factor 1 (SF1; also mammalian branch point binding protein [mBBP]; hereafter SF1/mBBP) specifically recognizes the seven-nucleotide branch point sequence (BPS) located at 3' splice sites and participates in the assembly of early spliceosomal complexes. SF1/mBBP utilizes a "maxi-K homology" (maxi-KH) domain for recognition of the single-stranded BPS and requires a cooperative interaction with splicing factor U2AF65 bound to an adjacent polypyrimidine tract (PPT) for high-affinity binding. To investigate how the KH domain of SF1/mBBP recognizes the BPS in conjunction with U2AF and possibly other proteins, we constructed a transcriptional reporter system utilizing human immunodeficiency virus type 1 Tat fusion proteins and examined the RNA-binding specificity of the complex using KH domain and RNA-binding site mutants. We first established that SF1/mBBP and U2AF cooperatively assemble in our reporter system at RNA sites composed of the BPS, PPT, and AG dinucleotide found at 3' splice sites, with endogenous proteins assembled along with the Tat fusions. We next found that the activities of the Tat fusion proteins on different BPS variants correlated well with the known splicing efficiencies of the variants, supporting a model in which the SF1/mBBP-BPS interaction helps determine splicing efficiency prior to the U2 snRNP-BPS interaction. Finally, the likely RNA-binding surface of the maxi-KH domain was identified by mutagenesis and appears similar to that used by "simple" KH domains, involving residues from two putative alpha helices, a highly conserved loop, and parts of a beta sheet. Using a homology model constructed from the cocrystal structure of a Nova KH domain-RNA complex (Lewis et al., Cell 100:323-332, 2000), we propose a plausible arrangement for SF1/mBBP-U2AF complexes assembled at 3' splice sites.
Collapse
Affiliation(s)
- H Peled-Zehavi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94143, USA
| | | | | | | |
Collapse
|
35
|
Alvi RK, Lund M, Okeefe RT. ATP-dependent interaction of yeast U5 snRNA loop 1 with the 5' splice site. RNA (NEW YORK, N.Y.) 2001; 7:1013-23. [PMID: 11453062 PMCID: PMC1370142 DOI: 10.1017/s135583820101041x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Pre-messenger RNA splicing is a two-step process by which introns are removed and exons joined together. In yeast, the U5 snRNA loop 1 interacts with the 5' exon before the first step of splicing and with the 5' and 3' exons before the second step. In vitro studies revealed that yeast U5 loop 1 is not required for the first step of splicing but is essential for holding the 5' and 3' exons for ligation during the second step. It is critical, therefore, that loop 1 contacts the 5' exon before the first step of splicing to hold this exon following cleavage from the pre-mRNA. At present it is not known how U5 loop 1 is positioned on the 5' exon prior to the first step of splicing. To address this question, we have used site-specific photoactivated crosslinking in yeast spliceosomes to investigate the interaction of U5 loop 1 with the pre-mRNA prior to the first step of splicing. We have found that the highly conserved uridines in loop 1 make ATP-dependent contacts with an approximately 8-nt region at the 5' splice site that includes the invariant GU. These interactions are dependent on functional U2 and U6 snRNAs. Our results support a model where U5 snRNA loop 1 interacts with the 5' exon in two steps during its targeting to the 5' splice site.
Collapse
Affiliation(s)
- R K Alvi
- School of Biological Sciences, University of Manchester, United Kingdom
| | | | | |
Collapse
|
36
|
Berglund JA, Rosbash M, Schultz SC. Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines. RNA (NEW YORK, N.Y.) 2001; 7:682-91. [PMID: 11350032 PMCID: PMC1370120 DOI: 10.1017/s1355838201002187] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Bulged nucleotides play a variety of important roles in RNA structure and function, frequently forming tertiary interactions and sometimes even participating in RNA catalysis. In pre-mRNA splicing, the U2 snRNA base pairs with the intron branchpoint sequence (BPS) to form a short RNA duplex that contains a bulged adenosine that ultimately serves as the nucleophile that attacks the 5' splice site. We have determined a 2.18-A resolution crystal structure of a self-complementary RNA designed to mimic the highly conserved yeast (Saccharomyces cerevisiae) branchpoint sequence (5'-UACUAACGUAGUA with the BPS italicized and the branchsite adenosine underlined) base paired with its complementary sequence from U2 snRNA. The structure shows a nearly ideal A-form helix from which two unpaired adenosines flip out. Although the adenosine adjacent to the branchsite adenosine is the one bulged out in the structure described here, either of these adenosines can serve as the nucleophile in mammalian but not in yeast pre-mRNA splicing. In addition, the packing of the bulged RNA helices within the crystal reveals a novel RNA tertiary interaction in which three RNA helices interact through bulged adenosines in the absence of any divalent metal ions.
Collapse
Affiliation(s)
- J A Berglund
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309, USA.
| | | | | |
Collapse
|
37
|
Chua K, Reed R. An upstream AG determines whether a downstream AG is selected during catalytic step II of splicing. Mol Cell Biol 2001; 21:1509-14. [PMID: 11238888 PMCID: PMC86697 DOI: 10.1128/mcb.21.5.1509-1514.2001] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Specific mechanisms must exist to ensure fidelity in selecting the AG dinucleotide that functions as the 3' splice site during the second transesterification step of splicing. Here we show that the optimal location for this AG is within a narrow distance (19 to 23 nucleotides [nt]) downstream from the branch point sequence (BPS). Contrary to previous expectations, AGs located less than 23 nt from the BPS are always recognized, even when a second AG located more optimally downstream is used in the transesterification reaction. Indeed, the AG closest to the BPS actually dictates the precise location of the AG that engages in the reaction. This mechanism, in which the AG is identified by a general localization step followed by a precise localization step, may be used to achieve fidelity while allowing flexibility in the location of 3' splice sites.
Collapse
Affiliation(s)
- K Chua
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | |
Collapse
|
38
|
Rossi D, Cozzio A, Flechsig E, Klein MA, Rülicke T, Aguzzi A, Weissmann C. Onset of ataxia and Purkinje cell loss in PrP null mice inversely correlated with Dpl level in brain. EMBO J 2001; 20:694-702. [PMID: 11179214 PMCID: PMC145426 DOI: 10.1093/emboj/20.4.694] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PrP knockout mice in which only the open reading frame was disrupted ('Zürich I') remained healthy. However, more extensive deletions resulted in ataxia, Purkinje cell loss and ectopic expression in brain of Doppel (Dpl), encoded by the downstream gene, PRND: A new PrP knockout line, 'Zürich II', with a 2.9 kb PRNP: deletion, developed this phenotype at approximately 10 months (50% morbidity). A single PRNP: allele abolished the syndrome. Compound Zürich I/Zürich II heterozygotes had half the Dpl of Zürich II mice and developed symptoms 6 months later. Zürich II mice transgenic for a PRND:-containing cosmid expressed Dpl at twice the level and became ataxic approximately 5 months earlier. Thus, Dpl levels in brain and onset of the ataxic syndrome are inversely correlated.
Collapse
Affiliation(s)
| | - Antonio Cozzio
- MRC Prion Unit/Neurogenetics, Imperial College School of Medicine at St Mary’s, London W2 1PG, UK,
Institut für Neuropathologie and Biologisches Zentrallabor, Universitätsspital Zürich, 8091 Zürich, Switzerland Present address: Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA Corresponding author e-mail:
D.Rossi and A.Cozzio contributed equally to this work
| | | | - Michael A. Klein
- MRC Prion Unit/Neurogenetics, Imperial College School of Medicine at St Mary’s, London W2 1PG, UK,
Institut für Neuropathologie and Biologisches Zentrallabor, Universitätsspital Zürich, 8091 Zürich, Switzerland Present address: Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA Corresponding author e-mail:
D.Rossi and A.Cozzio contributed equally to this work
| | - Thomas Rülicke
- MRC Prion Unit/Neurogenetics, Imperial College School of Medicine at St Mary’s, London W2 1PG, UK,
Institut für Neuropathologie and Biologisches Zentrallabor, Universitätsspital Zürich, 8091 Zürich, Switzerland Present address: Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA Corresponding author e-mail:
D.Rossi and A.Cozzio contributed equally to this work
| | - Adriano Aguzzi
- MRC Prion Unit/Neurogenetics, Imperial College School of Medicine at St Mary’s, London W2 1PG, UK,
Institut für Neuropathologie and Biologisches Zentrallabor, Universitätsspital Zürich, 8091 Zürich, Switzerland Present address: Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA Corresponding author e-mail:
D.Rossi and A.Cozzio contributed equally to this work
| | - Charles Weissmann
- MRC Prion Unit/Neurogenetics, Imperial College School of Medicine at St Mary’s, London W2 1PG, UK,
Institut für Neuropathologie and Biologisches Zentrallabor, Universitätsspital Zürich, 8091 Zürich, Switzerland Present address: Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA Corresponding author e-mail:
D.Rossi and A.Cozzio contributed equally to this work
| |
Collapse
|
39
|
Le Hir H, Izaurralde E, Maquat LE, Moore MJ. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J 2000; 19:6860-9. [PMID: 11118221 PMCID: PMC305905 DOI: 10.1093/emboj/19.24.6860] [Citation(s) in RCA: 699] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic mRNAs exist in vivo as ribonucleoprotein particles (mRNPs). The protein components of mRNPs have important functions in mRNA metabolism, including effects on subcellular localization, translational efficiency and mRNA half-life. There is accumulating evidence that pre-mRNA splicing can alter mRNP structure and thereby affect downstream mRNA metabolism. Here, we report that the spliceosome stably deposits several proteins on mRNAs, probably as a single complex of approximately 335 kDa. This complex protects 8 nucleotides of mRNA from complete RNase digestion at a conserved position 20-24 nucleotides upstream of exon-exon junctions. Splicing-dependent RNase protection of this region was observed in both HeLa cell nuclear extracts and Xenopus laevis oocyte nuclei. Immunoprecipitations revealed that five components of the complex are the splicing-associated factors SRm160, DEK and RNPS1, the mRNA-associated shuttling protein Y14 and the mRNA export factor REF. Possible functions for this complex in nucleocytoplasmic transport of spliced mRNA, as well as the nonsense-mediated mRNA decay pathway, are discussed.
Collapse
Affiliation(s)
- H Le Hir
- Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | | | | | | |
Collapse
|
40
|
Guth S, Valcárcel J. Kinetic role for mammalian SF1/BBP in spliceosome assembly and function after polypyrimidine tract recognition by U2AF. J Biol Chem 2000; 275:38059-66. [PMID: 10954700 DOI: 10.1074/jbc.m001483200] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two sequences important for pre-mRNA splicing precede the 3' end of introns in higher eukaryotes, the branch point (BP) and the polypyrimidine (Py) tract. Initial recognition of these signals involves cooperative binding of the splicing factor SF1/mammalian branch point binding protein (mBBP) to the BP and of U2AF(65) to the Py tract. Both factors are required for recruitment of the U2 small nuclear ribonucleoprotein particle (U2 snRNP) to the BP in reactions reconstituted from purified components. In contrast, extensive depletion of ST1/BBP in Saccharomyces cerevisiae does not compromise spliceosome assembly or splicing significantly. As BP sequences are less conserved in mammals, these discrepancies could reflect more stringent requirements for SF1/BBP in this system. We report here that extensive depletion of SF1/mBBP from nuclear extracts of HeLa cells results in only modest reduction of their activity in spliceosome assembly and splicing. Some of these effects reflect differences in the kinetics of U2 snRNP binding. Although U2AF(65) binding was reduced in the depleted extracts, the defects caused by SF1/mBBP depletion could not be fully restored by an increase in occupancy of the Py tract by exogenously added U2AF(65), arguing for a role of SF1/mBBP in U2 snRNP recruitment distinct from promoting U2AF(65) binding.
Collapse
Affiliation(s)
- S Guth
- Gene Expression Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | | |
Collapse
|
41
|
Eperon IC, Makarova OV, Mayeda A, Munroe SH, Cáceres JF, Hayward DG, Krainer AR. Selection of alternative 5' splice sites: role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1. Mol Cell Biol 2000; 20:8303-18. [PMID: 11046128 PMCID: PMC102138 DOI: 10.1128/mcb.20.22.8303-8318.2000] [Citation(s) in RCA: 154] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first component known to recognize and discriminate among potential 5' splice sites (5'SSs) in pre-mRNA is the U1 snRNP. However, the relative levels of U1 snRNP binding to alternative 5'SSs do not necessarily determine the splicing outcome. Strikingly, SF2/ASF, one of the essential SR protein-splicing factors, causes a dose-dependent shift in splicing to a downstream (intron-proximal) site, and yet it increases U1 snRNP binding at upstream and downstream sites simultaneously. We show here that hnRNP A1, which shifts splicing towards an upstream 5'SS, causes reduced U1 snRNP binding at both sites. Nonetheless, the importance of U1 snRNP binding is shown by proportionality between the level of U1 snRNP binding to the downstream site and its use in splicing. With purified components, hnRNP A1 reduces U1 snRNP binding to 5'SSs by binding cooperatively and indiscriminately to the pre-mRNA. Mutations in hnRNP A1 and SF2/ASF show that the opposite effects of the proteins on 5'SS choice are correlated with their effects on U1 snRNP binding. Cross-linking experiments show that SF2/ASF and hnRNP A1 compete to bind pre-mRNA, and we conclude that this competition is the basis of their functional antagonism; SF2/ASF enhances U1 snRNP binding at all 5'SSs, the rise in simultaneous occupancy causing a shift in splicing towards the downstream site, whereas hnRNP A1 interferes with U1 snRNP binding such that 5'SS occupancy is lower and the affinities of U1 snRNP for the individual sites determine the site of splicing.
Collapse
Affiliation(s)
- I C Eperon
- Department of Biochemistry, University of Leicester, Leicester LE1 7RH, United Kingdom.
| | | | | | | | | | | | | |
Collapse
|
42
|
Dirksen WP, Li X, Mayeda A, Krainer AR, Rottman FM. Mapping the SF2/ASF binding sites in the bovine growth hormone exonic splicing enhancer. J Biol Chem 2000; 275:29170-7. [PMID: 10880506 DOI: 10.1074/jbc.m001126200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Splicing of the last intron (intron D) of the bovine growth hormone pre-mRNA requires the presence of a downstream exonic splicing enhancer (ESE). This enhancer is contained within a 115-nucleotide FspI-PvuII (FP) fragment located in the middle of the last exon (exon 5). Previous work showed that the splicing factor SF2/ASF binds to this FP region and stimulates splicing of intron D in vitro. However, the precise sequences recognized by SF2/ASF within the FP region had not been determined. Here we used multiple strategies to map the SF2/ASF binding sites and determine their importance for ESE function. Taking advantage of the fact that SF2/ASF ultraviolet (UV) cross-links specifically to RNA containing the FP sequence, we first mapped a major SF2/ASF binding site by UV cross-linking and reverse transcription. This strategy identified a 29-nucleotide SF2/ASF binding region in the middle of the FP sequence containing the 7-nucleotide purine-rich motif described previously. Interestingly, this binding region is neither sufficient, nor absolutely required for SF2/ASF-mediated splicing, suggesting that additional SF2/ASF binding sites are present. The location of these additional sites was determined by electrophoretic mobility shift analysis of various subfragments of the FP sequence. Antisense 2'-O-methyl oligoribonucleotides complementary to selected SF2/ASF binding sites block bovine growth hormone intron D splicing. Thus, multiple SF2/ASF binding sites within the exonic splicing enhancer contribute to maximal enhancer activity.
Collapse
Affiliation(s)
- W P Dirksen
- Department of Molecular Biology and Microbiology and the Department of Medicine, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106-4960, USA
| | | | | | | | | |
Collapse
|
43
|
Carlo T, Sierra R, Berget SM. A 5' splice site-proximal enhancer binds SF1 and activates exon bridging of a microexon. Mol Cell Biol 2000; 20:3988-95. [PMID: 10805741 PMCID: PMC85762 DOI: 10.1128/mcb.20.11.3988-3995.2000] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Internal exon size in vertebrates occurs over a narrow size range. Experimentally, exons shorter than 50 nucleotides are poorly included in mRNA unless accompanied by strengthened splice sites or accessory sequences that act as splicing enhancers, suggesting steric interference between snRNPs and other splicing factors binding simultaneously to the 3' and 5' splice sites of microexons. Despite these problems, very small naturally occurring exons exist. Here we studied the factors and mechanism involved in recognizing a constitutively included six-nucleotide exon from the cardiac troponin T gene. Inclusion of this exon is dependent on an enhancer located downstream of the 5' splice site. This enhancer contains six copies of the simple sequence GGGGCUG. The enhancer activates heterologous microexons and will work when located either upstream or downstream of the target exon, suggesting an ability to bind factors that bridge splicing units. A single copy of this sequence is sufficient for in vivo exon inclusion and is the binding site for the known bridging mammalian splicing factor 1 (SF1). The enhancer and its bound SF1 act to increase recognition of the upstream exon during exon definition, such that competition of in vitro reactions with RNAs containing the GGGGCUG repeated sequence depress splicing of the upstream intron, assembly of the spliceosome on the 3' splice site of the exon, and cross-linking of SF1. These results suggest a model in which SF1 bridges the small exon during initial assembly, thereby effectively extending the domain of the exon.
Collapse
Affiliation(s)
- T Carlo
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | |
Collapse
|
44
|
ten Dam GB, Zilch CF, Wallace D, Wieringa B, Beverley PC, Poels LG, Screaton GR. Regulation of alternative splicing of CD45 by antagonistic effects of SR protein splicing factors. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2000; 164:5287-95. [PMID: 10799890 DOI: 10.4049/jimmunol.164.10.5287] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CD45 is a transmembrane glycoprotein possessing tyrosine phosphatase activity, which is involved in cell signaling. CD45 is expressed on the surface of most leukocytes and can be alternatively spliced by the inclusion or skipping of three variable exons (4, 5, and 6 or A, B, and C) to produce up to eight isoforms. In T cells, the splicing pattern of CD45 isoforms changes after activation; naive cells express high m.w. isoforms of CD45 which predominantly express exon A (CD45RA), whereas activated cells lose expression of exon A to form low m.w. isoforms of CD45 including CD45RO. Little is known about the specific factors controlling the switch in CD45 splicing which occurs on activation. In this study, we examined the influence of the SR family of splicing factors, which, like CD45, are expressed in tissue-specific patterns and have been shown to modulate the alternative splicing of a variety of transcripts. We show that specific SR proteins have antagonistic effects on CD45 splicing, leading either to exon inclusion or skipping. Furthermore, we were able to demonstrate specific changes in the SR protein expression pattern during T cell activation.
Collapse
Affiliation(s)
- G B ten Dam
- Departments of Cell Biology and Anatomy, Faculty of Medical Sciences, University of Nijmegen, Nijmegen, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
45
|
Le Hir H, Moore MJ, Maquat LE. Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon–exon junctions. Genes Dev 2000. [DOI: 10.1101/gad.14.9.1098] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We provide direct evidence that pre-mRNA splicing alters mRNP protein composition. Using a novel in vitro cross-linking approach, we detected several proteins that associate with mRNA exon–exon junctions only as a consequence of splicing. Immunoprecipitation experiments suggested that these proteins are part of a tight complex around the junction. Two were identified as SRm160, a nuclear matrix-associated splicing coactivator, and hPrp8p, a core component of U5 snRNP and spliceosomes. Glycerol gradient fractionation showed that a subset of these proteins remain associated with mRNA after its release from the spliceosome. These results demonstrate that the spliceosome can leave behind signature proteins at exon–exon junctions. Such proteins could influence downstream metabolic events in vivo such as mRNA transport, translation, and nonsense-mediated decay.
Collapse
|
46
|
Le Hir H, Moore MJ, Maquat LE. Pre-mRNA splicing alters mRNP composition: evidence for stable association of proteins at exon-exon junctions. Genes Dev 2000; 14:1098-108. [PMID: 10809668 PMCID: PMC316578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
We provide direct evidence that pre-mRNA splicing alters mRNP protein composition. Using a novel in vitro cross-linking approach, we detected several proteins that associate with mRNA exon-exon junctions only as a consequence of splicing. Immunoprecipitation experiments suggested that these proteins are part of a tight complex around the junction. Two were identified as SRm160, a nuclear matrix-associated splicing coactivator, and hPrp8p, a core component of U5 snRNP and spliceosomes. Glycerol gradient fractionation showed that a subset of these proteins remain associated with mRNA after its release from the spliceosome. These results demonstrate that the spliceosome can leave behind signature proteins at exon-exon junctions. Such proteins could influence downstream metabolic events in vivo such as mRNA transport, translation, and nonsense-mediated decay.
Collapse
Affiliation(s)
- H Le Hir
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York 14263 USA
| | | | | |
Collapse
|
47
|
Abstract
In the current model for spliceosome assembly, U1 snRNP binds to the 5' splice site in the E complex followed by ATP-dependent binding of U2 snRNP to the branchpoint sequence (BPS) in the A complex. Here we report the characterization of highly purified, functional E complex. We provide evidence that this complex contains functional U2 snRNP and that this snRNP is required for E complex assembly. The BPS is not required for U2 snRNP binding in the E complex. These data suggest a model for spliceosome assembly in which U1 and U2 snRNPs first associate with the spliceosome in the E complex and then an ATP-dependent step results in highly stable U2 snRNP binding to the BPS in the A complex.
Collapse
Affiliation(s)
- R Das
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | |
Collapse
|
48
|
Abstract
The MSL5 gene, which codes for the splicing factor BBP/ScSF1, is essential in Saccharomyces cerevisiae, yet previous analyses failed to reveal a defect in assembly of (pre)-spliceosomes or in vitro splicing associated with its depletion. We generated 11 temperature-sensitive (ts) mutants and one cold-sensitive (cs) mutant in the corresponding gene and analyzed their phenotypes. While all mutants were blocked in the formation of commitment complex 2 (CC2) at non-permissive and permissive temperature, the ts mutants showed no defect in spliceosome formation and splicing in vitro. The cs mutant was defective in (pre)-spliceosome formation, but residual splicing activity could be detected. In vivo splicing of reporters carrying introns weakened by mutations in the 5' splice site and/or in the branchpoint region was affected in all mutants. Pre-mRNA leakage to the cytoplasm was strongly increased (up to 40-fold) in the mutants. A combination of ts mutants with a disruption of upf1, a gene involved in nonsense-mediated decay, resulted in a specific synthetic growth phenotype, suggesting that the essential function of SF1 in yeast could be related to the retention of pre-mRNA in the nucleus.
Collapse
Affiliation(s)
- B Rutz
- EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | |
Collapse
|
49
|
Lund M, Tange TO, Dyhr-Mikkelsen H, Hansen J, Kjems J. Characterization of human RNA splice signals by iterative functional selection of splice sites. RNA (NEW YORK, N.Y.) 2000; 6:528-44. [PMID: 10786844 PMCID: PMC1369934 DOI: 10.1017/s1355838200992033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
An iterative in vitro splicing strategy was employed to select for optimal 3' splicing signals from a pool of pre-mRNAs containing randomized regions. Selection of functional branchpoint sequences in HeLa cell nuclear extract yielded a sequence motif that evolved from UAA after one round of splicing toward a UACUAAC consensus after seven rounds. A significant part of the selected sequences contained a conserved AAUAAAG motif that proved to be functional both as a polyadenylation signal and a branch site in a competitive manner. Characterization of the branchpoint in these clones to either the upstream or downstream adenosines of the AAUAAAG sequence revealed that the branching process proceeded efficiently but quite promiscuously. Surprisingly, the conserved guanosine, adjacent to the common AAUAAA polyadenylation motif, was found to be required only for polyadenylation. In an independent experiment, sequences surrounding an optimal branchpoint sequence were selected from two randomized 20-nt regions. The clones selected after six rounds of splicing revealed an extended polypyrimidine tract with a high frequency of UCCU motifs and a highly conserved YAG sequence in the extreme 3' end of the randomized insert. Mutating the 3' terminal guanosine of the intron strongly affects complex A formation, implying that the invariant AG is recognized early in spliceosome assembly.
Collapse
Affiliation(s)
- M Lund
- Department of Molecular and Structural Biology, University of Aarhus, Denmark
| | | | | | | | | |
Collapse
|
50
|
McPheeters DS, Schwer B, Muhlenkamp P. Interaction of the yeast DExH-box RNA helicase prp22p with the 3' splice site during the second step of nuclear pre-mRNA splicing. Nucleic Acids Res 2000; 28:1313-21. [PMID: 10684925 PMCID: PMC111051 DOI: 10.1093/nar/28.6.1313] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using site-specific incorporation of the photo-chemical cross-linking reagent 4-thiouridine, we demonstrate the previously unknown association of two proteins with yeast 3' splice sites. One of these is an unidentified approximately 122 kDa protein that cross-links to 3' splice sites during formation of the pre--spliceosome. The other factor is the DExH-box RNA helicase, Prp22p. With substrates functional in the second step of splicing, only very weak cross-linking of Prp22p to intron sequences at the 3' splice site is observed. In contrast, substrates blocked at the second step exhibit strong cross-linking of Prp22 to intron sequences at the 3' splice site, but not to adjacent exon sequences. In vitro reconstitution experiments also show that the association of Prp22p with intron sequences at the 3' splice site is dependent on Prp16p and does not persist when release of mature mRNA from the spliceosome is blocked. Taken together, these results suggest that the 3' splice site of yeast introns is contacted much earlier than previously envisioned by a protein of approximately 120 kDa, and that a transient association of Prp22p with the 3' splice site occurs between the first and second catalytic steps.
Collapse
Affiliation(s)
- D S McPheeters
- Department of Biochemistry and the Center for RNA Moelcular Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| | | | | |
Collapse
|