1
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Gonzales LR, Blom S, Henriques R, Bachem CWB, Immink RGH. LncRNAs: the art of being influential without protein. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00021-9. [PMID: 38368122 DOI: 10.1016/j.tplants.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/19/2024]
Abstract
The plant long noncoding (lnc)RNA field is on the brink of transitioning from large-scale identification of lncRNAs to their functional characterization. Due to the cross-kingdom conservation of interaction types and molecular functions, there is much to be learned from mammalian lncRNA research. Here, we discuss the different molecular processes involving lncRNAs from the regulation of chromatin to splicing. Furthermore, we discuss the lncRNA interactome, which includes proteins, other RNAs, and DNA. We explore and discuss how mammalian lncRNA functionalities could be reflected in similar pathways in plants and hypothesize that several breakthroughs in mammalian research could lead to the discovery of novel plant lncRNA molecular functions. Expanding our knowledge of the biological role of lncRNAs and their multiple applications paves the way for future agricultural applications.
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Affiliation(s)
| | - Suze Blom
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands; Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Rossana Henriques
- School of Biological, Earth, and Environmental Sciences, University College Cork, Cork, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
| | - Christian W B Bachem
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands; Bioscience, Wageningen University and Research, Wageningen, The Netherlands.
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2
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Gonçalves M, Santos JI, Coutinho MF, Matos L, Alves S. Development of Engineered-U1 snRNA Therapies: Current Status. Int J Mol Sci 2023; 24:14617. [PMID: 37834063 PMCID: PMC10572768 DOI: 10.3390/ijms241914617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Splicing of pre-mRNA is a crucial regulatory stage in the pathway of gene expression. The majority of human genes that encode proteins undergo alternative pre-mRNA splicing and mutations that affect splicing are more prevalent than previously thought. Targeting aberrant RNA(s) may thus provide an opportunity to correct faulty splicing and potentially treat numerous genetic disorders. To that purpose, the use of engineered U1 snRNA (either modified U1 snRNAs or exon-specific U1s-ExSpeU1s) has been applied as a potentially therapeutic strategy to correct splicing mutations, particularly those affecting the 5' splice-site (5'ss). Here we review and summarize a vast panoply of studies that used either modified U1 snRNAs or ExSpeU1s to mediate gene therapeutic correction of splicing defects underlying a considerable number of genetic diseases. We also focus on the pre-clinical validation of these therapeutic approaches both in vitro and in vivo, and summarize the main obstacles that need to be overcome to allow for their successful translation to clinic practice in the future.
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Affiliation(s)
- Mariana Gonçalves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, Inov4Agro, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Juliana Inês Santos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Liliana Matos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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3
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Du J, Li Y, Su Y, Zhi W, Zhang J, Zhang C, Wang J, Deng W, Zhao S. LncRNA Pnky Positively Regulates Neural Stem Cell Migration by Modulating mRNA Splicing and Export of Target Genes. Cell Mol Neurobiol 2023; 43:1199-1218. [PMID: 35748966 DOI: 10.1007/s10571-022-01241-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 06/06/2022] [Indexed: 11/28/2022]
Abstract
Directed migration of neural stem cells (NSCs) is critical for embryonic neurogenesis and the healing of neurological injuries. The long noncoding RNA (lncRNA) Pnky has been reported to regulate neuronal differentiation of NSCs by interacting with PTBP1. However, its regulatory effect on NSC migration remains to be determined. Herein, we identified that Pnky is also a key regulator of NSC migration in mice, as underscored by the finding that Pnky silencing suppressed but Pnky overexpression promoted the in vitro migration of both C17.2 and NE4C murine NSCs. Additionally, in vivo cell tracking demonstrated that Pnky depletion attenuated but Pnky overexpression facilitated the migration of NE4C cells in the spinal canal after transplantation via injection into the spinal canal. Mechanistically, Pnky regulated the expression of a core set of critical regulators that direct NSC migration, including MMP2, MMP9, Connexin43, Paxillin, AKT, ERK, and P38MAPK. Using catRAPID, a web server for large-scale prediction of protein-RNA interactions, the splicing factors U2AF1 and U2AF1L4, as well as the mRNA export adaptors SARNP, Aly/Ref, and THOC7, were predicted to interact strongly with Pnky. Further investigations using colocalization and RNA immunoprecipitation (RIP) assays confirmed the direct binding of Pnky to U2AF1, SARNP, Aly/Ref, and THOC7. Transcriptomic profiling revealed that as many as 5319 differential splicing events of 3848 genes, which were highly enriched in focal adhesion, PI3K-Akt and MAPK signaling pathways, were affected by Pnky depletion. The predominant subtype of differential splicing by Pnky depletion is intron retention, followed by alternative 5' and 3' splice sites and mutually exclusive exons. Moreover, Pnky knockdown substantially blocked but Pnky overexpression facilitated the export of MMP2, Paxillin, AKT, p38MAPK, and other mRNAs to the cytosol. Collectively, our data showed that through interacting with U2AF1, SARNP, Aly/Ref, and THOC7, Pnky couples and modulates the splicing and export of target mRNAs, which consequently controlling NSC migration. These findings provide a possible theoretical basis of NSC migration regulation.
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Affiliation(s)
- Jiannan Du
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Yuan Li
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Yuting Su
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Wenqian Zhi
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Jiale Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Cheng Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Juan Wang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China
| | - Wensheng Deng
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China.
| | - Shasha Zhao
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei, 430065, People's Republic of China.
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4
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Movilla S, Roca M, Moliner V, Magistrato A. Molecular Basis of RNA-Driven ATP Hydrolysis in DExH-Box Helicases. J Am Chem Soc 2023; 145:6691-6701. [PMID: 36926902 DOI: 10.1021/jacs.2c11980] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
The spliceosome machinery catalyzes precursor messenger (pre-m)RNA splicing. In each cycle, the spliceosome experiences massive compositional and conformational remodeling fueled by the concerted action of specific RNA-dependent ATPases/helicases. Intriguingly, these enzymes are allosterically activated to perform ATP hydrolysis and trigger helicase activity only upon pre-mRNA binding. Yet, the molecular mechanism underlying the RNA-driven regulation of their ATPase function remains elusive. Here, we focus on the Prp2 ATPase/helicase which contributes to reshaping the spliceosome into its catalytic competent state. By performing classical and quantum-classical molecular dynamics simulations, we unprecedentedly unlock the molecular terms governing the Prp2 ATPase/helicase function. Namely, we dissect the molecular mechanism of ATP hydrolysis, and we disclose that RNA binding allosterically triggers the formation of a set of interactions linking the RNA binding tunnel to the catalytic site. This activates the Prp2's ATPase function by optimally placing the nucleophilic water and the general base of the enzymatic process to perform ATP hydrolysis. The key structural motifs, mechanically coupling RNA gripping and the ATPase/helicase functions, are conserved across all DExH-box helicases. This mechanism could thus be broadly applicable to all DExH-box helicase family.
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Affiliation(s)
- Santiago Movilla
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Maite Roca
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Alessandra Magistrato
- Department National Research Council of Italy (CNR), Institute of Material (IOM) c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy
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5
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Abolhasani S, Hejazian SS, Karpisheh V, Khodakarami A, Mohammadi H, Gholizadeh Navashenaq J, Hojjat-Farsangi M, Jadidi-Niaragh F. The role of SF3B1 and NOTCH1 in the pathogenesis of leukemia. IUBMB Life 2023; 75:257-278. [PMID: 35848163 DOI: 10.1002/iub.2660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/18/2022] [Indexed: 11/09/2022]
Abstract
The discovery of new genes/pathways improves our knowledge of cancer pathogenesis and presents novel potential therapeutic options. For instance, splicing factor 3b subunit 1 (SF3B1) and NOTCH1 genetic alterations have been identified at a high frequency in hematological malignancies, such as leukemia, and may be related to the prognosis of involved patients because they change the nature of malignancies in different ways like mediating therapeutic resistance; therefore, studying these gene/pathways is essential. This review aims to discuss SF3B1 and NOTCH1 roles in the pathogenesis of various types of leukemia and the therapeutic potential of targeting these genes or their mutations to provide a foundation for leukemia treatment.
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Affiliation(s)
- Shiva Abolhasani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Vahid Karpisheh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Atefeh Khodakarami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Mohammadi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Mohammad Hojjat-Farsangi
- Bioclinicum, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.,The Persian Gulf Marine Biotechnology Medicine Research Center, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Farhad Jadidi-Niaragh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Research Center for Integrative Medicine in Aging, Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran
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6
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Jian Y, Chen X, Sun K, Liu Z, Cheng D, Cao J, Liu J, Cheng X, Wu L, Zhang F, Luo Y, Hahn M, Ma Z, Yin Y. SUMOylation regulates pre-mRNA splicing to overcome DNA damage in fungi. THE NEW PHYTOLOGIST 2023; 237:2298-2315. [PMID: 36539920 DOI: 10.1111/nph.18692] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Pathogenic fungi are subject to DNA damage stress derived from host immune responses during infection. Small ubiquitin-like modifier (SUMO) modification and precursor (pre)-mRNA splicing are both involved in DNA damage response (DDR). However, the mechanisms of how SUMOylation and splicing coordinated in DDR remain largely unknown. Combining with biochemical analysis, RNA-Seq method, and biological analysis, we report that SUMO pathway participates in DDR and virulence in Fusarium graminearum, a causal agent of Fusarium head blight of cereal crops world-wide. Interestingly, a key transcription factor FgSR is SUMOylated upon DNA damage stress. SUMOylation regulates FgSR nuclear-cytoplasmic partitioning and its phosphorylation by FgMec1, and promotes its interaction with chromatin remodeling complex SWI/SNF for activating the expression of DDR-related genes. Moreover, the SWI/SNF complex was found to further recruit splicing-related NineTeen Complex, subsequently modulates pre-mRNA splicing during DDR. Our findings reveal a novel function of SUMOylation in DDR by regulating a transcription factor to orchestrate gene expression and pre-mRNA splicing to overcome DNA damage during the infection of F. graminearum, which advances the understanding of the delicate regulation of DDR by SUMOylation in pathogenic fungi, and extends the knowledge of cooperation of SUMOylation and pre-mRNA splicing in DDR in eukaryotes.
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Affiliation(s)
- Yunqing Jian
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xia Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kewei Sun
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zunyong Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Danni Cheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiaofei Cheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Liang Wu
- Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Feng Zhang
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Matthias Hahn
- Department of Biology, University of Kaiserslautern, PO Box 3049, 67653, Kaiserslautern, Germany
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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7
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Borišek J, Aupič J, Magistrato A. Establishing the catalytic and regulatory mechanism of
RNA
‐based machineries. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jure Borišek
- Theory Department National Institute of Chemistry Ljubljana Slovenia
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8
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Barthel T, Wollenhaupt J, Lima GMA, Wahl MC, Weiss MS. Large-Scale Crystallographic Fragment Screening Expedites Compound Optimization and Identifies Putative Protein-Protein Interaction Sites. J Med Chem 2022; 65:14630-14641. [PMID: 36260741 DOI: 10.1021/acs.jmedchem.2c01165] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The identification of starting points for compound development is one of the key steps in early-stage drug discovery. Information-rich techniques such as crystallographic fragment screening can potentially increase the efficiency of this step by providing the structural information of the binding mode of the ligands in addition to the mere binding information. Here, we present the crystallographic screening of our 1000-plus-compound F2X-Universal Library against the complex of the yeast spliceosomal Prp8 RNaseH-like domain and the snRNP assembly factor Aar2. The observed 269 hits are distributed over 10 distinct binding sites on the surface of the protein-protein complex. Our work shows that hit clusters from large-scale crystallographic fragment screening campaigns identify known interaction sites with other proteins and suggest putative additional interaction sites. Furthermore, the inherent binding pose validation within the hit clusters may accelerate downstream compound optimization.
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Affiliation(s)
- Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | | | - Markus C Wahl
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany.,Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 6, 14195 Berlin, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, 12489 Berlin, Germany
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9
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Fasimoye RY, Spencer R, Soto-Martin E, Eijlers P, Elmassoudi H, Brivio S, Mangana C, Sabele V, Rechtorikova R, Wenzel M, Connolly B, Pettitt J, Müller B. A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex. Nucleic Acids Res 2022; 50:7591-7607. [PMID: 35736244 PMCID: PMC9303266 DOI: 10.1093/nar/gkac534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022] Open
Abstract
Spliced leader trans-splicing is essential for gene expression in many eukaryotes. To elucidate the molecular mechanism of this process, we characterise the molecules associated with the Caenorhabditis elegans major spliced leader snRNP (SL1 snRNP), which donates the spliced leader that replaces the 5' untranslated region of most pre-mRNAs. Using a GFP-tagged version of the SL1 snRNP protein SNA-1 created by CRISPR-mediated genome engineering, we immunoprecipitate and identify RNAs and protein components by RIP-Seq and mass spectrometry. This reveals the composition of the SL1 snRNP and identifies associations with spliceosome components PRP-8 and PRP-19. Significantly, we identify a novel, nematode-specific protein required for SL1 trans-splicing, which we designate SNA-3. SNA-3 is an essential, nuclear protein with three NADAR domains whose function is unknown. Mutation of key residues in NADAR domains inactivates the protein, indicating that domain function is required for activity. SNA-3 interacts with the CBC-ARS2 complex and other factors involved in RNA metabolism, including SUT-1 protein, through RNA or protein-mediated contacts revealed by yeast two-hybrid assays, localisation studies and immunoprecipitations. Our data are compatible with a role for SNA-3 in coordinating trans-splicing with target pre-mRNA transcription or in the processing of the Y-branch product of the trans-splicing reaction.
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Affiliation(s)
- Rotimi Yemi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Rosie Elizabeth Barker Spencer
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Eva Soto-Martin
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Peter Eijlers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Haitem Elmassoudi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Sarah Brivio
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Carolina Mangana
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Viktorija Sabele
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Radoslava Rechtorikova
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Marius Wenzel
- Centre of Genome-Enabled Biology and Medicine, University of Aberdeen, 23 St Machar Drive, Aberdeen AB24 3RY, Scotland, UK
| | - Bernadette Connolly
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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10
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Shao C, Cai F, Zhang Y, Bao Z, Shi G, Bao M, Zhang J. Regulation of alternative splicing of PaFT and PaFDL1, the FT and FD homologs in Platanus acerifolia. Gene 2022; 830:146506. [PMID: 35447236 DOI: 10.1016/j.gene.2022.146506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/16/2022] [Accepted: 04/14/2022] [Indexed: 11/04/2022]
Abstract
Alternative splicing (AS) selects different alternative splice sites and produces a variety of transcripts with different exon/intron combinations, which may result in multiple protein isoforms. The splicing signals include cis-elements and RNA structures; however, the mechanisms of AS regulation in plants have yet to be elucidated. Previous studies have shown that in Platanus acerifolia, the FLOWERING LOCUS T (FT) homolog PaFT has a unique and complex AS pattern, in which most of the splice forms of PaFT involve the first and/or second intron, and the FD homolog PaFDL1 produces two transcripts via AS, whereas the other FT homolog PaFTL is not regulated by AS. In this study, the regulatory mechanism of the AS of PaFT was demonstrated to be conserved in different plant species. To define the distribution of the AS regulatory signals, the intron-swap, site-directed mutagenesis of alternative splice sites, and deletion experiment were performed. For the PaFT gene, all the signals that regulate the AS of the first intron were located within this intron, while the usage of the first alternative splice site in the second intron was determined by the first intron. Meanwhile, the AS of PaFDL1 might be co-regulated by exons and the first intron. Additionally, the first alternative splice site and adjacent region in PaFT intron 1 might contain cis-elements and/or RNA structures that affect the use of the other sites. This study had provided a deeper insight into the distribution of AS signals in plants, namely the AS signals of different splice sites might exist in the intron where the sites were present, and might also be distributed in exons or other introns.
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Affiliation(s)
- Changsheng Shao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Fangfang Cai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Present address: Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China.
| | - Yanping Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Zhiru Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Gehui Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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11
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Zhan X, Lu Y, Zhang X, Yan C, Shi Y. Mechanism of exon ligation by human spliceosome. Mol Cell 2022; 82:2769-2778.e4. [PMID: 35705093 DOI: 10.1016/j.molcel.2022.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/07/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022]
Abstract
Pre-mRNA splicing involves two sequential reactions: branching and exon ligation. The C complex after branching undergoes remodeling to become the C∗ complex, which executes exon ligation. Here, we report cryo-EM structures of two intermediate human spliceosomal complexes, pre-C∗-I and pre-C∗-II, both at 3.6 Å. In both structures, the 3' splice site is already docked into the active site, the ensuing 3' exon sequences are anchored on PRP8, and the step II factor FAM192A contacts the duplex between U2 snRNA and the branch site. In the transition of pre-C∗-I to pre-C∗-II, the step II factors Cactin, FAM32A, PRKRIP1, and SLU7 are recruited. Notably, the RNA helicase PRP22 is positioned quite differently in the pre-C∗-I, pre-C∗-II, and C∗ complexes, suggesting a role in 3' exon binding and proofreading. Together with information on human C and C∗ complexes, our studies recapitulate a molecular choreography of the C-to-C∗ transition, revealing mechanistic insights into exon ligation.
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Affiliation(s)
- Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China.
| | - Yichen Lu
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; College of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaofeng Zhang
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China; Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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12
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A Quality Control Mechanism of Splice Site Selection Abrogated under Stress and in Cancer. Cancers (Basel) 2022; 14:cancers14071750. [PMID: 35406522 PMCID: PMC8996931 DOI: 10.3390/cancers14071750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
Simple Summary Splicing and alternative splicing play a major role in regulating gene expression, and mis-regulation of splicing can lead to several diseases, including cancer. The aim of this review is to summarize the current knowledge of a quality control mechanism of splice site selection termed Suppression of Splicing (SOS), proposed to protect cells from splicing at the numerous intronic unused 5′ splice sites, and emphasize its relevance to cancer. This relevance stems from the finding that SOS is abrogated under stress and in cancer resulting in the expression of thousands of aberrant nonsense mRNAs that may be toxic to cells. These findings highlight the unexplored potential of such aberrant isoforms as novel targets for cancer diagnosis and therapies. Abstract Latent 5’ splice sites, highly abundant in human introns, are not normally used. This led to the proposal of a quality control mechanism, Suppression of Splicing (SOS), which protects cells from splicing at the numerous intronic latent sites, and whose activation can generate nonsense mRNAs. SOS was shown to be independent of Nonsense-Mediated mRNA Decay (NMD). Efforts to decipher the SOS mechanism revealed a pivotal role for initiator-tRNA, independent of protein translation. Recently, nucleolin (a multifunctional protein) was found to directly and specifically bind the initiator-tRNA in the nucleus and was shown to be a protein component of SOS, enabling an updated model of the SOS mechanism. Importantly, SOS is abrogated under stress and in cancer (e.g., in breast cancer cells and gliomas), generating thousands of nonsense mRNAs due to activation of latent splicing. The resulting affected human genes cover a variety of functional groups, including genes involved in cell proliferation and differentiation. Furthermore, in oligodendroglioma, the extent of activation of latent splicing increases with the severity of the cancer. Interesting examples are genes expressing aberrant nonsense mRNAs in both breast cancer and glioma, due to latent splicing activation. These findings highlight the unexplored potential of such aberrant isoforms as novel targets for cancer diagnosis and therapies.
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13
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Liu J, Gu L, Zhang D, Li W. Determining the Prognostic Value of Spliceosome-Related Genes in Hepatocellular Carcinoma Patients. Front Mol Biosci 2022; 9:759792. [PMID: 35281269 PMCID: PMC8907852 DOI: 10.3389/fmolb.2022.759792] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/08/2022] [Indexed: 02/05/2023] Open
Abstract
Background: The spliceosome plays an important role in mRNA alternative splicing and is aberrantly expressed in several tumors. However, the potential roles of spliceosome-related genes in the progression of hepatocellular carcinoma (HCC) remain poorly understood. Materials and Methods: Patient data were acquired from public databases. Expression differences and survival analyses were used to assess the importance of spliceosome-related genes in HCC prognosis. To explore the potential regulatory mechanisms of these genes, a protein-protein interaction network was constructed and screened using univariate and multivariate Cox regression and random forest analyses. This was used to create a five-gene prognostic model. The prognostic value and predictive power of the five-gene signature were assessed using the Kaplan-Meier and time-dependent receiver operating characteristic analyses in the training set. These results were further validated in an independent external set. To facilitate clinical application, a nomogram was prepared to predict the overall survival of HCC patients. The relative expression of five genes was detected using real-time quantitative polymerase chain reaction. Results: The analysis revealed that LSM1-7, SNRPB, SNRPD1-3, SNRPE, SNRPF, SNRPG, and SNRPN could be used as prognostic biomarkers in HCC patients. Moreover, the five-gene risk model could clearly distinguish between the high-and low-risk groups. Furthermore, the risk model was associated with the tumor mutation burden, immune cell infiltration of CD8+ T cells, natural killer T cells, M2 macrophages, and immune checkpoint inhibitors, which also demonstrated the predictive efficacy of this risk model in HCC immunotherapy. Conclusion: Spliceosome-related genes and the five-gene signature could serve as novel prognostic biomarkers for HCC patients, aiding clinical patient monitoring and follow-up.
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Affiliation(s)
- Jun Liu
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
- Medical Research Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
| | - Liming Gu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
- Department of Microbiology and Immunology, Center of Pathogen Biology and Immunology, Shantou University Medical College, Shantou, China
| | - Dangui Zhang
- Research Center of Translational Medicine, Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Wenli Li
- Reproductive Medicine Center, Yue Bei People’s Hospital, Shantou University Medical College, Shaoguan, China
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14
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Liu L, Li X, Yuan L, Zhang G, Gao H, Xu X, Zhao H. XAP5 CIRCADIAN TIMEKEEPER specifically modulates 3' splice site recognition and is important for circadian clock regulation partly by alternative splicing of LHY and TIC. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 172:151-157. [PMID: 35065375 DOI: 10.1016/j.plaphy.2022.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Pre-mRNA splicing is an essential step during gene expression, which takes place in the spliceosome, a large dynamic ribonucleoprotein complex assembled in a stepwise manner. During the last decade, several spliceosomal mutants were functionally identified to cause a lengthened circadian period by introducing intron retention defects into circadian clock genes in Arabidopsis. However, the spliceosomal components that play opposite roles in the circadian period via alternative 3' splice site (Alt 3'ss) are largely unknown. Here, we demonstrated that XCT (XAP5 CIRCADIAN TIMEKEEPER) is a key spliceosomal component associated with multiple splicing factors. Moreover, genome-wide analysis revealed that inactivation of XCT particularly results in defects in Alt 3'ss recognition by RNA sequencing. Further analysis indicated that a strong alteration in the 3' splice sites of LHY and TIC partly accounts for the shortened circadian period of the xct mutant. Therefore, our results demonstrated that mutations in XCT shortened the circadian period partly by alternative splicing of LHY and TIC particularly in 3' splice site recognition, which provides new insight into the link between alternative splicing and the circadian clock.
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Affiliation(s)
- Lei Liu
- Jiangsu Key Laboratory for Eco-agriculture Biotechnology Around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai'an, 223300, China.
| | - Xiaoyun Li
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Li Yuan
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Guofang Zhang
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hui Gao
- College of Marine Resources and Environment, Hebei Normal University of Science and Technology, Qinhuangdao, 066600, China
| | - Xiaodong Xu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Hongtao Zhao
- College of Life Science, Hebei Normal University, Hebei, 050024, China.
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15
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Yang H, Beutler B, Zhang D. Emerging roles of spliceosome in cancer and immunity. Protein Cell 2021; 13:559-579. [PMID: 34196950 PMCID: PMC9232692 DOI: 10.1007/s13238-021-00856-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is catalyzed by an intricate ribonucleoprotein complex called the spliceosome. Although the spliceosome is considered to be general cell “housekeeping” machinery, mutations in core components of the spliceosome frequently correlate with cell- or tissue-specific phenotypes and diseases. In this review, we expound the links between spliceosome mutations, aberrant splicing, and human cancers. Remarkably, spliceosome-targeted therapies (STTs) have become efficient anti-cancer strategies for cancer patients with splicing defects. We also highlight the links between spliceosome and immune signaling. Recent studies have shown that some spliceosome gene mutations can result in immune dysregulation and notable phenotypes due to mis-splicing of immune-related genes. Furthermore, several core spliceosome components harbor splicing-independent immune functions within the cell, expanding the functional repertoire of these diverse proteins.
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Affiliation(s)
- Hui Yang
- Department of Neurosurgery, Huashan Hospital, Shanghai Key laboratory of Brain Function Restoration and Neural Regeneration, MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Duanwu Zhang
- Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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16
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Bao J, Zhang Y, Zhang L, Wang X. Effects of maternal exposure to PFOA on testes of male offspring mice. CHEMOSPHERE 2021; 272:129585. [PMID: 33465609 DOI: 10.1016/j.chemosphere.2021.129585] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
This study was conducted to explore the effects of maternal exposure to perfluorooctanoic acid (PFOA) on testicular development of male offspring mice. 20 pregnant Kunming mice were randomly divided into control group and PFOA exposure group with 10 mice of each. In PFOA exposure group, pregnant mice were given 5 mg/kg BW PFOA daily by gavage during gestation. Male offspring mice were killed to separate serum and collect testis at postpartum day 21, then tested the experimental indicators. The results showed that compared with control group, the content of PFOA in the serum of PFOA-exposed mice increased significantly and testosterone content is significantly reduced. Histological observations revealed architectural damages in testis in PFOA exposed groups and the apoptosis was increased. Transcriptome sequencing results showed that the U4/U6 snRNA coding genes snu13 and prp19 complex coding genes HSP73 were up-regulated and the U5 snRNA coding genes Brr2, Prp8 and EJC/TREX coding THOC genes were down-regulated after PFOA exposure Real-time PCR confirmed this result. These results indicate that the exposure of pregnant mice to perfluorooctanoic acid will have a damaging effect on the development of testes in male offspring mice, which may be due to blocked activation of the shear body, changes in structural functions, and inability to perform shear functions.
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Affiliation(s)
- Jialu Bao
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Yan Zhang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Linchao Zhang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China
| | - Xiaodan Wang
- College of Traditional Chinese Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China.
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17
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Huang R, Zheng Z, Liu S, Yan P, Song D, Yin H, Hu P, Zhu X, Chang Z, Liu Y, Zhuang J, Meng T, Huang Z, Zhang J. Identification of prognostic and bone metastasis-related alternative splicing signatures in mesothelioma. Cancer Med 2021; 10:4478-4492. [PMID: 34041868 PMCID: PMC8267146 DOI: 10.1002/cam4.3977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/18/2023] Open
Abstract
Mesothelioma (MESO) is an infrequent tumor derived from mesothelial cells of pleura, peritoneum, pericardium, and tunica vaginalis testis. Despite advancement in technologies and better understanding of tumor progression mechanism, the prognosis of MESO remains poor. The role of alternative splicing events (ASEs) in the oncogenesis, tumor metastasis and drug resistance has been widely discussed in multiple cancers. But the prognosis and potential therapeutic value of ASEs in MESO were not clearly studied by now. We constructed a prognostic model using RNA sequencing data and matched ASE data of MESO patients obtained from the TCGA and TCGASpliceSeq database. A total of 3,993 ASEs were identified associated with overall survival using Cox regression analysis. Eight of them were finally figured out to institute the model by lasso regression analysis. The risk score of the model can predict the prognosis independently. Among the identified 390 splicing factors (SF), HSPA1A and DDX3Y was significantly associated with 43 OS-SEs. Among these OS-SEs, SNX5-58744-AT (p = 0.048) and SNX5-58745-AT (p = 0.048) were significantly associated with bone metastasis. Co-expression analysis of signal pathways and SNX5-58744-AT, SNX5-58745-AT was also depicted using GSVA. Finally, we proposed that splicing factor (SF) HSPA1A could regulate SNX5-58744-AT (R = -0.414) and SNX5-58745-AT (R = 0.414) through the pathway "Class I MHC mediated antigen processing and presentation" (R = 0.400). In this way, tumorigenesis and bone metastasis of MESO were controlled.
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Affiliation(s)
- Runzhi Huang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Zixuan Zheng
- Tongji University School of Medicine, Shanghai, China
| | - Sijia Liu
- Tongji University School of Medicine, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dianwen Song
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Huabin Yin
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Peng Hu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaolong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhengyan Chang
- Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yihan Liu
- Tongji University School of Medicine, Shanghai, China
| | - Juanwei Zhuang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tong Meng
- Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China.,Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Zhang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.,Division of Spine, Department of Orthopedics, Tongji Hospital affiliated to Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
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18
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Wu P, Zhang M, Webster NJG. Alternative RNA Splicing in Fatty Liver Disease. Front Endocrinol (Lausanne) 2021; 12:613213. [PMID: 33716968 PMCID: PMC7953061 DOI: 10.3389/fendo.2021.613213] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Alternative RNA splicing is a process by which introns are removed and exons are assembled to construct different RNA transcript isoforms from a single pre-mRNA. Previous studies have demonstrated an association between dysregulation of RNA splicing and a number of clinical syndromes, but the generality to common disease has not been established. Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease affecting one-third of adults worldwide, increasing the risk of cirrhosis and hepatocellular carcinoma (HCC). In this review we focus on the change in alternative RNA splicing in fatty liver disease and the role for splicing regulation in disease progression.
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Affiliation(s)
- Panyisha Wu
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, United States
| | - Moya Zhang
- University of California Los Angeles, Los Angeles, CA, United States
| | - Nicholas J. G. Webster
- VA San Diego Healthcare System, San Diego, CA, United States
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
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19
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Jia Y, Zheng J, Liu S, Li F, Chi M, Cheng S, Gu Z. A Chromosome-Level Genome Assembly of the Dark Sleeper Odontobutis potamophila. Genome Biol Evol 2021; 13:6134080. [PMID: 33576781 PMCID: PMC7883661 DOI: 10.1093/gbe/evaa271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2020] [Indexed: 01/20/2023] Open
Abstract
The dark sleeper, Odontobutis potamophila, is a commercially valuable fish that widely distributed in China and Southeast Asia countries. The phenomenon of sexual dimorphism in growth is conspicuous, which the males grow substantially larger and faster than the females. However, the high-quality genome resources for gaining insight into sex-determining mechanisms to develop sex-control breeding are still lacking. Here, a chromosomal-level genome assembly of O. potamophila was generated from a combination of Illumina reads, 10× Genomics sequencing, and Hi-C chromatin interaction sequencing. The assembled genome was 1,134.62 Mb with a contig N50 of 22.25 Mb and a scaffold N50 of 24.85 Mb, representing 94.4% completeness (Benchmarking Universal Single-Copy Orthologs). Using Hi-C data, 96.49% of the total contig bases were anchored to the 22 chromosomes, with a contig N50 of 22.25 Mb and a scaffold N50 of 47.68 Mb. Approximately 54.18% of the genome were identified as repetitive elements, and 23,923 protein-coding genes were annotated in the genome. The assembled genome can be used as a valuable resource for molecular breeding and functional studies of O. potamophila in the future.
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Affiliation(s)
- Yongyi Jia
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Jianbo Zheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shili Liu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Fei Li
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Meili Chi
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shun Cheng
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Zhimi Gu
- Key Laboratory of Genetics and Breeding, Zhejiang Institute of Freshwater Fisheries, Huzhou, China
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20
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021. [PMID: 33565261 DOI: 10.1002/wrna.1643.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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21
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Angarola BL, Anczuków O. Splicing alterations in healthy aging and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1643. [PMID: 33565261 DOI: 10.1002/wrna.1643] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Alternative RNA splicing is a key step in gene expression that allows generation of numerous messenger RNA transcripts encoding proteins of varied functions from the same gene. It is thus a rich source of proteomic and functional diversity. Alterations in alternative RNA splicing are observed both during healthy aging and in a number of human diseases, several of which display premature aging phenotypes or increased incidence with age. Age-associated splicing alterations include differential splicing of genes associated with hallmarks of aging, as well as changes in the levels of core spliceosomal genes and regulatory splicing factors. Here, we review the current known links between alternative RNA splicing, its regulators, healthy biological aging, and diseases associated with aging or aging-like phenotypes. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.,Department of Genetics and Genome Sciences, UConn Health, Farmington, Connecticut, USA.,Institute for Systems Genomics, UConn Health, Farmington, Connecticut, USA
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22
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Larsen NA. The SF3b Complex is an Integral Component of the Spliceosome and Targeted by Natural Product-Based Inhibitors. Subcell Biochem 2021; 96:409-432. [PMID: 33252738 DOI: 10.1007/978-3-030-58971-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
In this chapter, the essential role of the SF3b multi-protein complex will be discussed in the context of the overall spliceosome. SF3b is critical during spliceosome assembly for recognition of the branch point (BP) adenosine and, by de facto, selection of the 3' splice site. This complex is highly dynamic, undergoing significant conformational changes upon loading of the branch duplex RNA and in its relative positioning during spliceosomal remodeling from the A, pre-B, B, Bact and B* complexes. Ultimately, during the spliceosome activation phase, SF3b must be displaced to unmask the branch point adenosine for the first splicing reaction to occur. In certain cancers, such as the hematological malignancies CML, CLL and MDS, the SF3b subunit SF3B1 is frequently mutated. Recent studies suggest these mutations lead to inappropriate branch point selection and mis-splicing events that appear to be drivers of disease. Finally, the SF3b complex is the target for at least three different classes of natural product-based inhibitors. These inhibitors bind in the BP adenosine-binding pocket and demonstrate a pre-mRNA competitive mechanism of action resulting in either intron retention or exon skipping. These compounds are extremely useful as chemical probes to isolate and characterize early stages of spliceosome assembly. They are also being explored preclinically and clinically as possible agents for hematological cancers.
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23
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Bai R, Wan R, Yan C, Jia Q, Lei J, Shi Y. Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Science 2020; 371:science.abe8863. [PMID: 33243853 DOI: 10.1126/science.abe8863] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/04/2020] [Indexed: 01/01/2023]
Abstract
Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the function of the ATPase/helicases remains poorly understood. Here, we report atomic structures of Prp2 in isolation, Prp2 complexed with its coactivator Spp2, and Prp2-loaded activated spliceosome and the results of structure-guided biochemical analysis. Prp2 weakly associates with the spliceosome and cannot function without Spp2, which stably associates with Prp2 and anchors on the spliceosome, thus tethering Prp2 to the activated spliceosome and allowing Prp2 to function. Pre-mRNA is loaded into a featured channel between the N and C halves of Prp2, where Leu536 from the N half and Arg844 from the C half prevent backward sliding of pre-mRNA toward its 5'-end. Adenosine 5'-triphosphate binding and hydrolysis trigger interdomain movement in Prp2, which drives unidirectional stepwise translocation of pre-mRNA toward its 3'-end. These conserved mechanisms explain the coupling of spliceosome remodeling to pre-mRNA splicing.
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Affiliation(s)
- Rui Bai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Ruixue Wan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology and Advanced Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Jia
- Beijing Advanced Innovation Center for Structural Biology and Advanced Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology and Advanced Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Beijing Advanced Innovation Center for Structural Biology and Advanced Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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24
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Liu J, Ma T, Gao M, Liu Y, Liu J, Wang S, Xie Y, Wen Q, Wang L, Cheng J, Liu S, Zou J, Wu J, Li W, Xie H. Proteomic Characterization of Proliferation Inhibition of Well-Differentiated Laryngeal Squamous Cell Carcinoma Cells Under Below-Background Radiation in a Deep Underground Environment. Front Public Health 2020; 8:584964. [PMID: 33194991 PMCID: PMC7661695 DOI: 10.3389/fpubh.2020.584964] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/06/2020] [Indexed: 02/05/2023] Open
Abstract
Background: There has been a considerable concern about cancer induction in response to radiation exposure. However, only a limited number of studies have focused on the biological effects of below-background radiation (BBR) in deep underground environments. To improve our understanding of the effects of BBR on cancer, we studied its biological impact on well-differentiated laryngeal squamous cell carcinoma cells (FD-LSC-1) in a deep underground laboratory (DUGL). Methods: The growth curve, morphological, and quantitative proteomic experiments were performed on FD-LSC-1 cells cultured in the DUGL and above-ground laboratory (AGL). Results: The proliferation of FD-LSC-1 cells from the DUGL group was delayed compared to that of cells from the AGL group. Transmission electron microscopy scans of the cells from the DUGL group indicated the presence of hypertrophic endoplasmic reticulum (ER) and a higher number of ER. At a cutoff of absolute fold change ≥ 1.2 and p < 0.05, 807 differentially abundant proteins (DAPs; 536 upregulated proteins and 271 downregulated proteins in the cells cultured in the DUGL) were detected. KEGG pathway analysis of these DAPs revealed that seven pathways were enriched. These included ribosome (p < 0.0001), spliceosome (p = 0.0001), oxidative phosphorylation (p = 0.0001), protein export (p = 0.0001), thermogenesis (p = 0.0003), protein processing in the endoplasmic reticulum (p = 0.0108), and non-alcoholic fatty liver disease (p = 0.0421). Conclusion: The BBR environment inhibited the proliferation of FD-LSC-1 cells. Additionally, it induced changes in protein expression associated with the ribosome, gene spliceosome, RNA transport, and energy metabolism among others. The changes in protein expression might form the molecular basis for proliferation inhibition and enhanced survivability of cells adapting to BBR exposure in a deep underground environment. RPL26, RPS27, ZMAT2, PRPF40A, SNRPD2, SLU7, SRSF5, SRSF3, SNRPF, WFS1, STT3B, CANX, ERP29, HSPA5, COX6B1, UQCRH, and ATP6V1G1 were the core proteins associated with the BBR stress response in cells.
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Affiliation(s)
- Jifeng Liu
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China.,Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Tengfei Ma
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China.,Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mingzhong Gao
- College of Water Resources and Hydropower, Sichuan University, Chengdu, China
| | - Yilin Liu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Liu
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Shichao Wang
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yike Xie
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qiao Wen
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Wang
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Juan Cheng
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shixi Liu
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Jian Zou
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, China.,Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiang Wu
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Heping Xie
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China.,College of Water Resources and Hydropower, Sichuan University, Chengdu, China.,Institute of Deep Earth Science and Green Energy, Shenzhen University, Shenzhen, China
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25
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Ma Y, Zhang S, Bi C, Mei C, Jiang SC, Wang XF, Lu ZJ, Zhang DP. Arabidopsis exoribonuclease USB1 interacts with the PPR-domain protein SOAR1 to negatively regulate abscisic acid signaling. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5837-5851. [PMID: 32969475 PMCID: PMC7541913 DOI: 10.1093/jxb/eraa315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/23/2020] [Indexed: 05/27/2023]
Abstract
Signaling by the phytohormone abscisic acid (ABA) involves pre-mRNA splicing, a key process of post-transcriptional regulation of gene expression. However, the regulatory mechanism of alternative pre-mRNA splicing in ABA signaling remains largely unknown. We previously identified a pentatricopeptide repeat protein SOAR1 (suppressor of the ABAR-overexpressor 1) as a crucial player downstream of ABAR (putative ABA receptor) in ABA signaling. In this study, we identified a SOAR1 interaction partner USB1, which is an exoribonuclease catalyzing U6 production for spliceosome assembly. We reveal that together USB1 and SOAR1 negatively regulate ABA signaling in early seedling development. USB1 and SOAR1 are both required for the splicing of transcripts of numerous genes, including those involved in ABA signaling pathways, suggesting that USB1 and SOAR1 collaborate to regulate ABA signaling by affecting spliceosome assembly. These findings provide important new insights into the mechanistic control of alternative pre-mRNA splicing in the regulation of ABA-mediated plant responses to environmental cues.
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Affiliation(s)
- Yu Ma
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Shang Zhang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Chao Bi
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Chao Mei
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Shang-Chuan Jiang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Xiao-Fang Wang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Zhi John Lu
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Da-Peng Zhang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
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26
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Aceituno-Valenzuela U, Micol-Ponce R, Ponce MR. Genome-wide analysis of CCHC-type zinc finger (ZCCHC) proteins in yeast, Arabidopsis, and humans. Cell Mol Life Sci 2020; 77:3991-4014. [PMID: 32303790 PMCID: PMC11105112 DOI: 10.1007/s00018-020-03518-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 03/06/2020] [Accepted: 03/30/2020] [Indexed: 12/22/2022]
Abstract
The diverse eukaryotic proteins that contain zinc fingers participate in many aspects of nucleic acid metabolism, from DNA transcription to RNA degradation, post-transcriptional gene silencing, and small RNA biogenesis. These proteins can be classified into at least 30 types based on structure. In this review, we focus on the CCHC-type zinc fingers (ZCCHC), which contain an 18-residue domain with the CX2CX4HX4C sequence, where C is cysteine, H is histidine, and X is any amino acid. This motif, also named the "zinc knuckle", is characteristic of the retroviral Group Antigen protein and occurs alone or with other motifs. Many proteins containing zinc knuckles have been identified in eukaryotes, but only a few have been studied. Here, we review the available information on ZCCHC-containing factors from three evolutionarily distant eukaryotes-Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens-representing fungi, plants, and metazoans, respectively. We performed systematic searches for proteins containing the CX2CX4HX4C sequence in organism-specific and generalist databases. Next, we analyzed the structural and functional information for all such proteins stored in UniProtKB. Excluding retrotransposon-encoded proteins and proteins harboring uncertain ZCCHC motifs, we found seven ZCCHC-containing proteins in yeast, 69 in Arabidopsis, and 34 in humans. ZCCHC-containing proteins mainly localize to the nucleus, but some are nuclear and cytoplasmic, or exclusively cytoplasmic, and one localizes to the chloroplast. Most of these factors participate in RNA metabolism, including transcriptional elongation, polyadenylation, translation, pre-messenger RNA splicing, RNA export, RNA degradation, microRNA and ribosomal RNA biogenesis, and post-transcriptional gene silencing. Several human ZCCHC-containing factors are derived from neofunctionalized retrotransposons and act as proto-oncogenes in diverse neoplastic processes. The conservation of ZCCHCs in orthologs of these three phylogenetically distant eukaryotes suggests that these domains have biologically relevant functions that are not well known at present.
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Affiliation(s)
- Uri Aceituno-Valenzuela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202, Elche, Spain.
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27
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Sebbag-Sznajder N, Brody Y, Hochberg-Laufer H, Shav-Tal Y, Sperling J, Sperling R. Dynamic Supraspliceosomes Are Assembled on Different Transcripts Regardless of Their Intron Number and Splicing State. Front Genet 2020; 11:409. [PMID: 32499811 PMCID: PMC7243799 DOI: 10.3389/fgene.2020.00409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Splicing and alternative splicing of pre-mRNA are key sources in the formation of diversity in the human proteome. These processes have a central role in the regulation of the gene expression pathway. Yet, how spliceosomes are assembled on a multi-intronic pre-mRNA is at present not well understood. To study the spliceosomes assembled in vivo on transcripts with variable number of introns, we examined a series of three related transcripts derived from the β-globin gene, where two transcript types contained increasing number of introns, while one had only an exon. Each transcript had multiple MS2 sequence repeats that can be bound by the MS2 coat protein. Using our protocol for isolation of endogenous spliceosomes under native conditions from cell nuclei, we show that all three transcripts are found in supraspliceosomes – 21 MDa dynamic complexes, sedimenting at 200S in glycerol gradients, and composed of four native spliceosomes connected by the transcript. Affinity purification of complexes assembled on the transcript with most introns (termed E6), using the MS2 tag, confirmed the assembly of E6 in supraspliceosomes with components such as Sm proteins and PSF. Furthermore, splicing inhibition by spliceostatin A did not inhibit the assembly of supraspliceosomes on the E6 transcript, yet increased the percentage of E6 pre-mRNA supraspliceosomes. These findings were corroborated in intact cells, using RNA FISH to detect the MS2-tagged E6 mRNA, together with GFP-tagged splicing factors, showing the assembly of splicing factors SRSF2, U1-70K, and PRP8 onto the E6 transcripts under normal conditions and also when splicing was inhibited. This study shows that different transcripts with different number of introns, or lacking an intron, are assembled in supraspliceosomes even when splicing is inhibited. This assembly starts at the site of transcription and can continue during the life of the transcript in the nucleoplasm. This study further confirms the dynamic and universal nature of supraspliceosomes that package RNA polymerase II transcribed pre-mRNAs into complexes composed of four native spliceosomes connected by the transcript, independent of their length, number of introns, or splicing state.
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Affiliation(s)
| | - Yehuda Brody
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Hodaya Hochberg-Laufer
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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28
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Oshiquiri LH, Gomes SL, Georg RC. Blastocladiella emersonii spliceosome is regulated in response to the splicing inhibition caused by the metals cadmium, cobalt and manganese. Fungal Biol 2020; 124:468-474. [PMID: 32389309 DOI: 10.1016/j.funbio.2020.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 01/08/2023]
Abstract
Blastocladiella emersonii is an aquatic fungus of the phylum Blastocladiomycota, localized near the base of the fungal tree. Previous studies have shown that B. emersonii responds to heat shock and cadmium exposure inducing the transcription of a high number of genes. EST sequencing from heat shocked and cadmium exposed B. emersonii cells has shown that exposure to cadmium causes strong splicing inhibition. Despite the knowledge about splicing inhibition by cadmium, it is still unclear if other metal contaminants can cause the same response. In the present study, we have demonstrated that the effect of cadmium exposure on splicing inhibition is much stronger than that of other divalent metals such as cobalt and manganese. Data presented here also indicate that intron retention occurs randomly among the fungal transcripts, as verified by analyzing differently affected transcripts. In addition, we identified in the genome of B. emersonii the genes encoding the snRNA splicing components U1, U2, U4, U5 and U6 and observed that spliceosome snRNAs are upregulated in the presence of metals, in particular snRNA U1 in cells under cadmium exposure. This observation suggests that snRNA upregulation might be a defense of the fungal cell against the metal stress condition.
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Affiliation(s)
- Letícia Harumi Oshiquiri
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Suely Lopes Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Raphaela Castro Georg
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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29
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Liang Q, Geng Q, Jiang L, Liang M, Li L, Zhang C, Wang W. Protein methylome analysis in Arabidopsis reveals regulation in RNA-related processes. J Proteomics 2020; 213:103601. [PMID: 31809900 DOI: 10.1016/j.jprot.2019.103601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/23/2019] [Accepted: 11/25/2019] [Indexed: 01/09/2023]
Abstract
Protein methylation has been proposed as an important post-translational modification, which occurs predominantly on lysine and arginine residues. Recent discoveries have revealed that protein methylation is also present on non-histones besides histones, and plays critical roles in regulating protein stability and function. However, proteome-wide identification of methylated proteins in plants remains unexplored. Here, we present the first global survey of monomethyl arginine, symmetric and asymmetric dimethyl arginine, and monomethyl, dimethyl, trimethyl lysine modifications in the proteomes of 10-day-old Arabidopsis seedlings through a combination of immunoaffinity purification and mass spectrometry analysis. In total, we identified 617 methylation sites which mapped to 412 proteins, with 263 proteins harboring 381 lysine methylation sites and 149 proteins harboring 236 arginine methylation sites. Among them, 607 methylation sites on 408 proteins were novel findings. Motif analysis revealed that glycine preferentially flanked methylated arginine residues, whereas aspartate and glutamate enriched around mono- and dimethylated lysine sites. Methylated proteins were involved in a variety of metabolic processes, showing significant enrichment in RNA-related metabolic pathways including spliceosome, RNA transport, and ribosome. Our data provide a global view of methylated non-histone proteins in Arabidopsis, laying foundations for elucidating the biological function of protein methylation in plants. SIGNIFICANCE: Protein methylation has emerged as a common and important modification both in eukaryotes and prokaryotes. The identification of methylated sites/peptides is fundamental for further functional analysis of protein methylation. This study was the first proteome-scale identification of lysine and arginine methylation in plants. We found that methylation occurred widely on non-histone proteins in Arabidopsis and was involved in diverse biological functions. The results provide foundations for the investigation of the protein methylome in Arabidopsis and provide powerful resources for the functional analysis of protein methylation in plants.
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Affiliation(s)
- Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qinghe Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meng Liang
- Jingjie PTM BioLab (Hangzhou) Co.Ltd, Hangzhou 310018, China
| | - Linhan Li
- Jingjie PTM BioLab (Hangzhou) Co.Ltd, Hangzhou 310018, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Weixuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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30
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Frey K, Pucker B. Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites. Cells 2020; 9:E458. [PMID: 32085510 PMCID: PMC7072748 DOI: 10.3390/cells9020458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 11/17/2022] Open
Abstract
Most protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5' end and AG at the 3' end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations, which have been known for years. Recently, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here, we expand systematic investigations of non-canonical splice site combinations in plants across eukaryotes by analyzing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences, such as an apparently increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts are a likely explanation for this observation, thus indicating annotation errors. In addition, high numbers of GA-AG splice site combinations were observed in Eurytemoraaffinis and Oikopleuradioica. A variant in one U1 small nuclear RNA (snRNA) isoform might allow the recognition of GA as a 5' splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3' splice site compared to the 5' splice site across animals, fungi, and plants.
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Affiliation(s)
- Katharina Frey
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany;
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615 Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany;
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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31
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Abstract
The ribosome and RNase P are cellular ribonucleoprotein complexes that perform peptide bond synthesis and phosphodiester bond cleavage, respectively. Both are ancient biological assemblies that were already present in the last universal common ancestor of all life. The large subunit rRNA in the ribosome and the RNA subunit of RNase P are the ribozyme components required for catalysis. Here, we explore the idea that these two large ribozymes may have begun their evolutionary odyssey as an assemblage of RNA "fragments" smaller than the contemporary full-length versions and that they transitioned through distinct stages along a pathway that may also be relevant for the evolution of other non-coding RNAs.
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Affiliation(s)
- Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210.
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32
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Hou S, Qu D, Li Y, Zhu B, Liang D, Wei X, Tang W, Zhang Q, Hao J, Guo W, Wang W, Zhao S, Wang Q, Azam S, Khan M, Zhao H, Zhang L, Lei H. XAB2 depletion induces intron retention in POLR2A to impair global transcription and promote cellular senescence. Nucleic Acids Res 2019; 47:8239-8254. [PMID: 31216022 PMCID: PMC6735682 DOI: 10.1093/nar/gkz532] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/31/2019] [Accepted: 06/05/2019] [Indexed: 01/10/2023] Open
Abstract
XAB2 is a multi-functional protein participating processes including transcription, splicing, DNA repair and mRNA export. Here, we report POLR2A, the largest catalytic subunit of RNA polymerase II, as a major target gene down-regulated after XAB2 depletion. XAB2 depletion led to severe splicing defects of POLR2A with significant intron retention. Such defects resulted in substantial loss of POLR2A at RNA and protein levels, which further impaired global transcription. Treatment of splicing inhibitor madrasin induced similar reduction of POLR2A. Screen using TMT-based quantitative proteomics identified several proteins involved in mRNA surveillance including Dom34 with elevated expression. Inhibition of translation or depletion of Dom34 rescued the expression of POLR2A by stabilizing its mRNA. Immuno-precipitation further confirmed that XAB2 associated with spliceosome components important to POLR2A expression. Domain mapping revealed that TPR motifs 2–4 and 11 of XAB2 were critical for POLR2A expression by interacting with SNW1. Finally, we showed POLR2A mediated cell senescence caused by XAB2 deficiency. Depletion of XAB2 or POLR2A induced cell senescence by up-regulation of p53 and p21, re-expression of POLR2A after XAB2 depletion alleviated cellular senescence. These data together support that XAB2 serves as a guardian of POLR2A expression to ensure global gene expression and antagonize cell senescence.
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Affiliation(s)
- Shuai Hou
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Dajun Qu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Yue Li
- Breast Disease and Reconstruction Center, Breast Cancer Key Lab of Dalian, Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Baohui Zhu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Dapeng Liang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Xinyue Wei
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Wei Tang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qian Zhang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Jiaojiao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Wei Guo
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Weijie Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Siqi Zhao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Qi Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Sikandar Azam
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Misbah Khan
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Haidong Zhao
- Breast Disease and Reconstruction Center, Breast Cancer Key Lab of Dalian, Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Haixin Lei
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
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Green CM, Li Z, Smith AD, Novikova O, Bacot-Davis VR, Gao F, Hu S, Banavali NK, Thiele DJ, Li H, Belfort M. Spliceosomal Prp8 intein at the crossroads of protein and RNA splicing. PLoS Biol 2019; 17:e3000104. [PMID: 31600193 PMCID: PMC6805012 DOI: 10.1371/journal.pbio.3000104] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 10/22/2019] [Accepted: 09/13/2019] [Indexed: 01/07/2023] Open
Abstract
The spliceosome is a large ribonucleoprotein complex that removes introns from pre-mRNAs. At its functional core lies the essential pre-mRNA processing factor 8 (Prp8) protein. Across diverse eukaryotes, this protein cofactor of RNA catalysis harbors a self-splicing element called an intein. Inteins in Prp8 are extremely pervasive and are found at 7 different sites in various species. Here, we focus on the Prp8 intein from Cryptococcus neoformans (Cne), a human fungal pathogen. We solved the crystal structure of this intein, revealing structural homology among protein splicing sequences in eukaryotes, including the Hedgehog C terminus. Working with the Cne Prp8 intein in a reporter assay, we find that the biologically relevant divalent metals copper and zinc inhibit intein splicing, albeit by 2 different mechanisms. Copper likely stimulates reversible modifications on a catalytically important cysteine, whereas zinc binds at the terminal asparagine and the same critical cysteine. Importantly, we also show that copper treatment inhibits Prp8 protein splicing in Cne. Lastly, an intein-containing Prp8 precursor model is presented, suggesting that metal-induced protein splicing inhibition would disturb function of both Prp8 and the spliceosome. These results indicate that Prp8 protein splicing can be modulated, with potential functional implications for the spliceosome.
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Affiliation(s)
- Cathleen M. Green
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Zhong Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Aaron D. Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Olga Novikova
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Valjean R. Bacot-Davis
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America
| | - Fengshan Gao
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Saiyang Hu
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Nilesh K. Banavali
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
| | - Dennis J. Thiele
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, United States of America,Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hongmin Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America,* E-mail: (MB); (HL)
| | - Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, Albany, New York, United States of America,Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America,* E-mail: (MB); (HL)
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34
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Sperling R. Small non-coding RNA within the endogenous spliceosome and alternative splicing regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194406. [PMID: 31323432 DOI: 10.1016/j.bbagrm.2019.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 10/26/2022]
Abstract
Splicing and alternative splicing (AS), which occur in the endogenous spliceosome, play major roles in regulating gene expression, and defects in them are involved in numerous human diseases including cancer. Although the mechanism of the splicing reaction is well understood, the regulation of AS remains to be elucidated. A group of essential regulatory factors in gene expression are small non-coding RNAs (sncRNA): e.g. microRNA, mainly known for their inhibitory role in translation in the cytoplasm; and small nucleolar RNA, known for their role in methylating non-coding RNA in the nucleolus. Here I highlight a new aspect of sncRNAs found within the endogenous spliceosome. Assembled in non-canonical complexes and through different base pairing than their canonical ones, spliceosomal sncRNAs can potentially target different RNAs. Examples of spliceosomal sncRNAs regulating AS, regulating gene expression, and acting in a quality control of AS are reviewed, suggesting novel functions for spliceosomal sncRNAs. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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35
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Crane MM, Sands B, Battaglia C, Johnson B, Yun S, Kaeberlein M, Brent R, Mendenhall A. In vivo measurements reveal a single 5'-intron is sufficient to increase protein expression level in Caenorhabditis elegans. Sci Rep 2019; 9:9192. [PMID: 31235724 PMCID: PMC6591249 DOI: 10.1038/s41598-019-45517-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/06/2019] [Indexed: 11/29/2022] Open
Abstract
Introns can increase gene expression levels using a variety of mechanisms collectively referred to as Intron Mediated Enhancement (IME). IME has been measured in cell culture and plant models by quantifying expression of intronless and intron-bearing reporter genes in vitro. We developed hardware and software to implement microfluidic chip-based gene expression quantification in vivo. We altered position, number and sequence of introns in reporter genes controlled by the hsp-90 promoter. Consistent with plant and mammalian studies, we determined a single, natural or synthetic, 5'-intron is sufficient for the full IME effect conferred by three synthetic introns, while a 3'-intron is not. We found coding sequence can affect IME; the same three synthetic introns that increase mcherry protein concentration by approximately 50%, increase mEGFP by 80%. We determined IME effect size is not greatly affected by the stronger vit-2 promoter. Our microfluidic imaging approach should facilitate screens for factors affecting IME and other intron-dependent processes.
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Affiliation(s)
- Matthew M Crane
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Bryan Sands
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Christian Battaglia
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Brock Johnson
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Soo Yun
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Matt Kaeberlein
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Division of Basic Science, Seattle, WA, USA
| | - Alex Mendenhall
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA.
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36
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Huang W, Huang Y, Xu J, Liao JL. How Does the Spliceosome Catalyze Intron Lariat Formation? Insights from Quantum Mechanics/Molecular Mechanics Free-Energy Simulations. J Phys Chem B 2019; 123:6049-6055. [DOI: 10.1021/acs.jpcb.9b04377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Wenting Huang
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
| | - Yan Huang
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City, Guangzhou 510006, China
| | - Jie-Lou Liao
- Department of Chemical Physics, University of Science and Technology of China, JinZhai Rd. 96, Hefei, Anhui 230026, China
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37
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Singh RN, Singh NN. A novel role of U1 snRNP: Splice site selection from a distance. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:634-642. [PMID: 31042550 DOI: 10.1016/j.bbagrm.2019.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 04/15/2019] [Accepted: 04/18/2019] [Indexed: 12/23/2022]
Abstract
Removal of introns by pre-mRNA splicing is fundamental to gene function in eukaryotes. However, understanding the mechanism by which exon-intron boundaries are defined remains a challenging endeavor. Published reports support that the recruitment of U1 snRNP at the 5'ss marked by GU dinucleotides defines the 5'ss as well as facilitates 3'ss recognition through cross-exon interactions. However, exceptions to this rule exist as U1 snRNP recruited away from the 5'ss retains the capability to define the splice site, where the cleavage takes place. Independent reports employing exon 7 of Survival Motor Neuron (SMN) genes suggest a long-distance effect of U1 snRNP on splice site selection upon U1 snRNP recruitment at target sequences with or without GU dinucleotides. These findings underscore that sequences distinct from the 5'ss may also impact exon definition if U1 snRNP is recruited to them through partial complementarity with the U1 snRNA. In this review we discuss the expanded role of U1 snRNP in splice-site selection due to U1 ability to be recruited at more sites than predicted solely based on GU dinucleotides.
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Affiliation(s)
- Ravindra N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States of America.
| | - Natalia N Singh
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States of America
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38
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Belfort M, Lambowitz AM. Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools. Cold Spring Harb Perspect Biol 2019; 11:11/4/a032375. [PMID: 30936187 DOI: 10.1101/cshperspect.a032375] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Group II introns, self-splicing retrotransposons, serve as both targets of investigation into their structure, splicing, and retromobility and a source of tools for genome editing and RNA analysis. Here, we describe the first cryo-electron microscopy (cryo-EM) structure determination, at 3.8-4.5 Å, of a group II intron ribozyme complexed with its encoded protein, containing a reverse transcriptase (RT), required for RNA splicing and retromobility. We also describe a method called RIG-seq using a retrotransposon indicator gene for high-throughput integration profiling of group II introns and other retrotransposons. Targetrons, RNA-guided gene targeting agents widely used for bacterial genome engineering, are described next. Finally, we detail thermostable group II intron RTs, which synthesize cDNAs with high accuracy and processivity, for use in various RNA-seq applications and relate their properties to a 3.0-Å crystal structure of the protein poised for reverse transcription. Biological insights from these group II intron revelations are discussed.
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Affiliation(s)
- Marlene Belfort
- Department of Biological Sciences and RNA Institute, University at Albany, State University of New York, Albany, New York 12222
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712
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39
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Yu J, Luan X, Yan Y, Qiao C, Liu Y, Zhao D, Xie B, Zheng Q, Wang M, Chen W, Shen C, He Z, Hu X, Huang X, Li H, Chen B, Zheng B, Chen X, Fang J. Small ribonucleoprotein particle protein SmD3 governs the homeostasis of germline stem cells and the crosstalk between the spliceosome and ribosome signals in Drosophila. FASEB J 2019; 33:8125-8137. [PMID: 30921522 DOI: 10.1096/fj.201802536rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ribonucleoprotein (RNP) spliceosome machinery triggers the precursor RNA splicing process in eukaryotes. Major spliceosome defects are implicated in male infertility; however, the underlying mechanistic links between the spliceosome and the ribosome in Drosophila testes remains largely unresolved. Small ribonucleoprotein particle protein SmD3 (SmD3) is a novel germline stem cell (GSC) regulatory gene identified in our previous screen of Drosophila testes. In the present study, using genetic manipulation in a Drosophila model, we demonstrated that SmD3 is required for the GSC niche and controls the self-renewal and differentiation of GSCs in the testis. Using in vitro assays in Schneider 2 cells, we showed that SmD3 also regulates the homeostasis of proliferation and apoptosis in Drosophila. Furthermore, using liquid chromatography-tandem mass spectrometry methods, SmD3 was identified as binding with ribosomal protein (Rp)L18, which is a key regulator of the large subunit in the ribosome. Moreover, SmD3 was observed to regulate spliceosome and ribosome subunit expression levels and controlled spliceosome and ribosome function via RpL18. Significantly, our findings revealed the genetic causes and molecular mechanisms underlying the stem cell niche and the crosstalk between the spliceosome and the ribosome.-Yu, J., Luan, X., Yan, Y., Qiao, C., Liu, Y., Zhao, D., Xie, B., Zheng, Q., Wang, M., Chen, W., Shen, C., He, Z., Hu, X., Huang, X., Li, H., Chen, B., Zheng, B., Chen, X., Fang, J. Small ribonucleoprotein particle protein SmD3 governs the homeostasis of germline stem cells and the crosstalk between the spliceosome and ribosome signals in Drosophila.
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Affiliation(s)
- Jun Yu
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Xiaojin Luan
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Yidan Yan
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Chen Qiao
- Department of Clinical Pharmacy, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
| | - Yuanyuan Liu
- Center for Reproduction and Genetics, Suzhou Municipal Hospital-The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Dan Zhao
- Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China.,Center for Reproduction, The Fourth Affiliated Hospital of Jiangsu University-The Fourth People's Hospital of Zhenjiang, Zhenjiang, China
| | - Bing Xie
- Department of Obstetrics and Gynecology, The Fourth Affiliated Hospital of Jiangsu University-The Fourth People's Hospital of Zhenjiang, Zhenjiang, China
| | - Qianwen Zheng
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Min Wang
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
| | - Wanyin Chen
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
| | - Cong Shen
- Center for Reproduction and Genetics, Suzhou Municipal Hospital-The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zeyu He
- Department of Clinical Medicine, China Medical University, Shenyang, China
| | - Xing Hu
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
| | - Xiaoyan Huang
- Department of Histology and Embryology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Hong Li
- Center for Reproduction and Genetics, Suzhou Municipal Hospital-The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Binghai Chen
- Department of Urology, The Affiliated Hospital of Jiangsu University
| | - Bo Zheng
- Center for Reproduction and Genetics, Suzhou Municipal Hospital-The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xia Chen
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China.,Reproductive Sciences Institute, Jiangsu University, Zhenjiang, China
| | - Jie Fang
- Department of Gynecology, The Affiliated Hospital of Jiangsu University-Jiangsu University, Zhenjiang, China
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40
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Wan R, Bai R, Yan C, Lei J, Shi Y. Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching. Cell 2019; 177:339-351.e13. [PMID: 30879786 DOI: 10.1016/j.cell.2019.02.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/10/2018] [Accepted: 02/06/2019] [Indexed: 11/17/2022]
Abstract
Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B∗) is pivotal for understanding the branching reaction. In this study, we assembled the B∗ complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B∗ complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B∗ complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state.
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Affiliation(s)
- Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Rui Bai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China.
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41
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DeNicola AB, Tang Y. Therapeutic approaches to treat human spliceosomal diseases. Curr Opin Biotechnol 2019; 60:72-81. [PMID: 30772756 DOI: 10.1016/j.copbio.2019.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023]
Abstract
Mutated RNA splicing machinery drives many human diseases and is a promising therapeutic target for engineering and small molecule therapy. In the case of mutations in individual genes that cause them to be incorrectly spliced, engineered splicing factors can be introduced to correct splicing of these aberrant transcripts and reduce the effects of the disease phenotype. Mutations that occur in certain splicing factor genes themselves have been implicated in many cancers, particularly myelodysplastic syndromes. Small molecules that target splicing factors have been developed as therapies to preferentially induce apoptosis in these cancer cells. Specifically, drugs targeting the splicing factor SF3B1 have led to recent clinical trials. Here, we review the role of alternative splicing in disease, approaches to rescue incorrect splicing using engineered splicing factors, and small molecule splicing inhibitors developed to treat hematological cancers.
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Affiliation(s)
- Anthony B DeNicola
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States.
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, United States
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42
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Zhang L, Vielle A, Espinosa S, Zhao R. RNAs in the spliceosome: Insight from cryoEM structures. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1523. [PMID: 30729694 DOI: 10.1002/wrna.1523] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/12/2018] [Accepted: 12/28/2018] [Indexed: 12/28/2022]
Abstract
Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton RNA-protein complex. The spliceosome undergoes dramatic compositional and conformational changes through the splicing cycle, forming at least 10 distinct complexes. Recent high-resolution cryoEM structures of various spliceosomal complexes revealed unprecedented details of this large molecular machine. This review highlights insight into the structure and function of the spliceosomal RNA components obtained from these new structures, with a focus on the yeast spliceosome. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Anne Vielle
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Sara Espinosa
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
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43
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Structures of the human spliceosomes before and after release of the ligated exon. Cell Res 2019; 29:274-285. [PMID: 30728453 PMCID: PMC6461851 DOI: 10.1038/s41422-019-0143-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 01/14/2019] [Indexed: 11/08/2022] Open
Abstract
Pre-mRNA splicing is executed by the spliceosome, which has eight major functional states each with distinct composition. Five of these eight human spliceosomal complexes, all preceding exon ligation, have been structurally characterized. In this study, we report the cryo-electron microscopy structures of the human post-catalytic spliceosome (P complex) and intron lariat spliceosome (ILS) at average resolutions of 3.0 and 2.9 Å, respectively. In the P complex, the ligated exon remains anchored to loop I of U5 small nuclear RNA, and the 3′-splice site is recognized by the junction between the 5′-splice site and the branch point sequence. The ATPase/helicase Prp22, along with the ligated exon and eight other proteins, are dissociated in the P-to-ILS transition. Intriguingly, the ILS complex exists in two distinct conformations, one with the ATPase/helicase Prp43 and one without. Comparison of these three late-stage human spliceosomes reveals mechanistic insights into exon release and spliceosome disassembly.
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44
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Tian Y, Chen MX, Yang JF, Achala HHK, Gao B, Hao GF, Yang GF, Dian ZY, Hu QJ, Zhang D, Zhang J, Liu YG. Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species. PLANTA 2019; 249:583-600. [PMID: 30317439 DOI: 10.1007/s00425-018-3026-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
This study systematically identifies plant SYF2/NTC31/p29 genes from 62 plant species by a combinatory bioinformatics approach, revealing the importance of this gene family in phylogenetics, duplication, transcriptional, and post-transcriptional regulation. Alternative splicing is a post-transcriptional regulatory mechanism, which is critical for plant development and stress responses. The entire process is strictly attenuated by a complex of splicing-related proteins, designated splicing factors. Human p29, also referred to as synthetic lethal with cdc forty 2 (SYF2) or the NineTeen complex 31 (NTC31), is a core protein found in the NTC complex of humans and yeast. This splicing factor participates in a variety of biological processes, including DNA damage repair, control of the cell cycle, splicing, and tumorigenesis. However, its function in plants has been seldom reported. Thus, we have systematically identified 89 putative plant SYF2s from 62 plant species among the deposited entries in the Phytozome database. The phylogenetic relationships and evolutionary history among these plant SYF2s were carefully examined. The results revealed that plant SYF2s exhibited distinct patterns regarding their gene structure, promoter sequences, and expression levels, suggesting their functional diversity in response to developmental cues or stress treatments. Although local duplication events, such as tandem duplication and retrotransposition, were found among several plant species, most of the plant species contained only one copy of SYF2, suggesting the existence of additional mechanisms to confer duplication resistance. Further investigation using the model dicot and monocot representatives Arabidopsis and rice SYF2s indicated that the splicing pattern and resulting protein isoforms might play an alternative role in the functional diversity.
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Affiliation(s)
- Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Mo-Xian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jing-Fang Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - H H K Achala
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Bei Gao
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ge-Fei Hao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | | | - Qi-Juan Hu
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Di Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianhua Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
- Department of Biology, Hong Kong Baptist University and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China.
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Yan C, Wan R, Shi Y. Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome. Cold Spring Harb Perspect Biol 2019; 11:11/1/a032409. [PMID: 30602541 DOI: 10.1101/cshperspect.a032409] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Precursor messenger RNA (pre-mRNA) splicing is executed by the spliceosome. In the past 3 years, cryoelectron microscopy (cryo-EM) structures have been elucidated for a majority of the yeast spliceosomal complexes and for a few human spliceosomes. During the splicing reaction, the dynamic spliceosome has an immobile core of about 20 protein and RNA components, which are organized around a conserved splicing active site. The divalent metal ions, coordinated by U6 small nuclear RNA (snRNA), catalyze the branching reaction and exon ligation. The spliceosome also contains a mobile but compositionally stable group of about 13 proteins and a portion of U2 snRNA, which facilitate substrate delivery into the splicing active site. The spliceosomal transitions are driven by the RNA-dependent ATPase/helicases, resulting in the recruitment and dissociation of specific splicing factors that enable the reaction. In summary, the spliceosome is a protein-directed metalloribozyme.
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Affiliation(s)
- Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310064, Zhejiang Province, China
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Fernández-Espartero CH, Rizzo A, Fulford AD, Falo-Sanjuan J, Goutte-Gattat D, Ribeiro PS. Prp8 regulates oncogene-induced hyperplastic growth in Drosophila. Development 2018; 145:dev.162156. [PMID: 30333215 PMCID: PMC6262796 DOI: 10.1242/dev.162156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 10/10/2018] [Indexed: 01/08/2023]
Abstract
Although developmental signalling pathways control tumourigenic growth, the cellular mechanisms that abnormally proliferating cells rely on are still largely unknown. Drosophila melanogaster is a genetically tractable model that is used to study how specific genetic changes confer advantageous tumourigenic traits. Despite recent efforts, the role of deubiquitylating enzymes in cancer is particularly understudied. We performed a Drosophila in vivo RNAi screen to identify deubiquitylating enzymes that modulate RasV12-induced hyperplastic growth. We identified the spliceosome core component Prp8 as a crucial regulator of Ras-, EGFR-, Notch- or RET-driven hyperplasia. Loss of prp8 function alone decreased cell proliferation, increased cell death, and affected cell differentiation and polarity. In hyperplasia, Prp8 supported tissue overgrowth independently of caspase-dependent cell death. The depletion of prp8 efficiently blocked Ras-, EGFR- and Notch-driven tumours but, in contrast, enhanced tumours that were driven by oncogenic RET, suggesting a context-specific role in hyperplasia. These data show, for the first time, that Prp8 regulates hyperplasia, and extend recent observations on the potential role of the spliceosome in cancer. Our findings suggest that targeting Prp8 could be beneficial in specific tumour types. Summary: Prp8 has been identified as a modulator of oncogenic growth in multiple Drosophila cancer models, which suggests the spliceosome as a potential context-dependent target in cancers.
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Affiliation(s)
- Cecilia H Fernández-Espartero
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Alberto Rizzo
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Alexander D Fulford
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Julia Falo-Sanjuan
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Damien Goutte-Gattat
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Paulo S Ribeiro
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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Lourencetti NMS, Wolf IR, Lacerda MPF, Valente GT, Zanelli CF, Santoni MM, Mendes-Giannini MJS, Enguita FJ, Fusco-Almeida AM. Transcriptional profile of a bioethanol production contaminant Candida tropicalis. AMB Express 2018; 8:166. [PMID: 30311091 PMCID: PMC6182018 DOI: 10.1186/s13568-018-0693-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/26/2018] [Indexed: 11/26/2022] Open
Abstract
The fermentation process is widely used in the industry for bioethanol production. Even though it is widely used, microbial contamination is unpredictable and difficult to control. The problem of reduced productivity is directly linked to competition for nutrients during contamination. Yeasts representing the Candida species are frequently isolated contaminants. Elucidating the behavior of a contaminant during the fermentation cycle is essential for combatting the contamination. Consequently, the aim of the current study was to better understand the functional and transcriptional behavior of a contaminating yeast Candida tropicalis. We used a global RNA sequencing approach (RNA-seq/MiSeq) to analyze gene expression. Genes with significantly repressed or induced expression, and related to the fermentations process, such as sugar transport, pyruvate decarboxylase, amino acid metabolism, membrane, tolerance to high concentrations of ethanol and temperatures, nutrient suppression), and transcription-linked processes, were identified. The expression pattern suggested that the functional and transcriptional behavior of the contaminating yeast during fermentation for bioethanol production is similar to that of the standard yeast Saccharomyces cerevisiae. In addition, the analysis confirmed that C. tropicalis is an important contaminant of the alcoholic fermentation process, generating bioethanol and viability through its tolerance to all the adversities of a fermentation process essential for the production of bioethanol. According on the gene expression profile, many of these mechanisms are similar to those of S. cerevisiae strains currently used for bioethanol production. These mechanisms can inform studies on antimicrobials, to combat yeast contamination during industrial bioethanol production.
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Nicolaou KC, Rhoades D, Kumar SM. Total Syntheses of Thailanstatins A-C, Spliceostatin D, and Analogues Thereof. Stereodivergent Synthesis of Tetrasubstituted Dihydro- and Tetrahydropyrans and Design, Synthesis, Biological Evaluation, and Discovery of Potent Antitumor Agents. J Am Chem Soc 2018; 140:8303-8320. [PMID: 29943984 DOI: 10.1021/jacs.8b04634] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Efficient and selective total syntheses of spliceosome modulating natural products thailanstatins A-C and spliceostatin D are reported. A number of stereoselective methods for the construction of various tetrasubstituted dihydro- and tetrahydropyrans were developed as a prerequisite for the syntheses of these naturally occurring molecules and variations thereof. The pyran-forming reactions utilize a Heck/Saegusa-Ito cascade sequence to generate hydroxy α,β,γ,δ-unsaturated aldehyde precursors followed by a catalyst-controlled oxa-Michael cyclization to furnish tetrasubstituted dihydropyrans with high stereocontrol. Subsequent optimized homogeneous or heterogeneous hydrogenations of these dihydropyran systems afford their tetrahydropyran counterparts, also in a highly stereoselective manner. The synthesized thailanstatins and related analogues were biologically evaluated for their cytotoxic properties, leading to the identification of a number of compounds with exceptionally potent antitumor activities suitable for further development as potential antibody-drug conjugate payloads, single drugs, or drug combinations for cancer therapies. Important structure-activity relationships within the thailanstatin family and structurally related compounds are discussed and are expected to be path-pointing for future studies.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, BioScience Research Collaborative , Rice University , 6100 Main Street , Houston , Texas 77005 , United States
| | - Derek Rhoades
- Department of Chemistry, BioScience Research Collaborative , Rice University , 6100 Main Street , Houston , Texas 77005 , United States
| | - S Mothish Kumar
- Department of Chemistry, BioScience Research Collaborative , Rice University , 6100 Main Street , Houston , Texas 77005 , United States
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Finci LI, Zhang X, Huang X, Zhou Q, Tsai J, Teng T, Agrawal A, Chan B, Irwin S, Karr C, Cook A, Zhu P, Reynolds D, Smith PG, Fekkes P, Buonamici S, Larsen NA. The cryo-EM structure of the SF3b spliceosome complex bound to a splicing modulator reveals a pre-mRNA substrate competitive mechanism of action. Genes Dev 2018; 32:309-320. [PMID: 29491137 PMCID: PMC5859971 DOI: 10.1101/gad.311043.117] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/07/2018] [Indexed: 12/16/2022]
Abstract
In this study, Finci et. al. present the cryo-EM structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5), part of the U2 snRNP, bound to E7107 at 3.95 A. The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action. Somatic mutations in spliceosome proteins lead to dysregulated RNA splicing and are observed in a variety of cancers. These genetic aberrations may offer a potential intervention point for targeted therapeutics. SF3B1, part of the U2 small nuclear RNP (snRNP), is targeted by splicing modulators, including E7107, the first to enter clinical trials, and, more recently, H3B-8800. Modulating splicing represents a first-in-class opportunity in drug discovery, and elucidating the structural basis for the mode of action opens up new possibilities for structure-based drug design. Here, we present the cryogenic electron microscopy (cryo-EM) structure of the SF3b subcomplex (SF3B1, SF3B3, PHF5A, and SF3B5) bound to E7107 at 3.95 Å. This structure shows that E7107 binds in the branch point adenosine-binding pocket, forming close contacts with key residues that confer resistance upon mutation: SF3B1R1074H and PHF5AY36C. The structure suggests a model in which splicing modulators interfere with branch point adenosine recognition and supports a substrate competitive mechanism of action (MOA). Using several related chemical probes, we validate the pose of the compound and support their substrate competitive MOA by comparing their activity against both strong and weak pre-mRNA substrates. Finally, we present functional data and structure–activity relationship (SAR) on the PHF5AR38C mutation that sensitizes cells to some chemical probes but not others. Developing small molecule splicing modulators represents a promising therapeutic approach for a variety of diseases, and this work provides a significant step in enabling structure-based drug design for these elaborate natural products. Importantly, this work also demonstrates that the utilization of cryo-EM in drug discovery is coming of age.
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Affiliation(s)
- Lorenzo I Finci
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaofeng Zhang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiuliang Huang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiang Zhou
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jennifer Tsai
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Teng Teng
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Anant Agrawal
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Betty Chan
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Sean Irwin
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Craig Karr
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Andrew Cook
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Ping Zhu
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | | | - Peter G Smith
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
| | - Peter Fekkes
- H3 Biomedicine, Inc., Cambridge, Massachusetts 02139, USA
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50
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All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome. Proc Natl Acad Sci U S A 2018; 115:6584-6589. [PMID: 29891649 DOI: 10.1073/pnas.1802963115] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The spliceosome (SPL) is a majestic macromolecular machinery composed of five small nuclear RNAs and hundreds of proteins. SPL removes noncoding introns from precursor messenger RNAs (pre-mRNAs) and ligates coding exons, giving rise to functional mRNAs. Building on the first SPL structure solved at near-atomic-level resolution, here we elucidate the functional dynamics of the intron lariat spliceosome (ILS) complex through multi-microsecond-long molecular-dynamics simulations of ∼1,000,000 atoms models. The ILS essential dynamics unveils (i) the leading role of the Spp42 protein, which heads the gene maturation by tuning the motions of distinct SPL components, and (ii) the critical participation of the Cwf19 protein in displacing the intron lariat/U2 branch helix. These findings provide unprecedented details on the SPL functional dynamics, thus contributing to move a step forward toward a thorough understanding of eukaryotic pre-mRNA splicing.
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