1
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Carrocci TJ, DeMario S, He K, Zeps NJ, Harkner CT, Chanfreau GF, Hoskins AA. Functional analysis of the zinc finger modules of the Saccharomyces cerevisiae splicing factor Luc7. RNA (NEW YORK, N.Y.) 2024; 30:1058-1069. [PMID: 38719745 PMCID: PMC11251517 DOI: 10.1261/rna.079956.124] [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: 01/21/2024] [Accepted: 04/14/2024] [Indexed: 05/21/2024]
Abstract
Identification of splice sites is a critical step in pre-messenger RNA (pre-mRNA) splicing because the definition of the exon/intron boundaries controls what nucleotides are incorporated into mature mRNAs. The intron boundary with the upstream exon is initially identified through interactions with the U1 small nuclear ribonucleoprotein (snRNP). This involves both base-pairing between the U1 snRNA and the pre-mRNA as well as snRNP proteins interacting with the 5' splice site (5'ss)/snRNA duplex. In yeast, this duplex is buttressed by two conserved protein factors, Yhc1 and Luc7. Luc7 has three human paralogs (LUC7L, LUC7L2, and LUC7L3), which play roles in alternative splicing. What domains of these paralogs promote splicing at particular sites is not yet clear. Here, we humanized the zinc finger (ZnF) domains of the yeast Luc7 protein in order to understand their roles in splice site selection using reporter assays, transcriptome analysis, and genetic interactions. Although we were unable to determine a function for the first ZnF domain, humanization of the second ZnF domain to mirror that found in LUC7L or LUC7L2 resulted in altered usage of nonconsensus 5'ss. In contrast, the corresponding ZnF domain of LUC7L3 could not support yeast viability. Further, humanization of Luc7 can suppress mutation of the ATPase Prp28, which is involved in U1 release and exchange for U6 at the 5'ss. Our work reveals a role for the second ZnF of Luc7 in splice site selection and suggests that different ZnF domains may have different ATPase requirements for release by Prp28.
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Affiliation(s)
- Tucker J Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Samuel DeMario
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Kevin He
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Natalie J Zeps
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Cade T Harkner
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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2
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Wang J, Saviola AJ, Welty R, Liu S, Vaeth KF, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. RNA (NEW YORK, N.Y.) 2024; 30:1070-1088. [PMID: 38688558 PMCID: PMC11251525 DOI: 10.1261/rna.079917.123] [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: 12/08/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
The recognition of the 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand, the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 (yU1) snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yU1 snRNA and the 5' ss RNA duplex. We replaced the zinc-finger (ZnF) domain of yeast U1C (yU1C) with its human counterpart, which resulted in a cold-sensitive growth phenotype and moderate splicing defects. We next added an auxin-inducible degron to yeast Luc7 (yLuc7) protein (to mimic the lack of Luc7Ls in human U1 snRNP). We found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of Prp40 and Snu71 (two other essential yU1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yU1 snRNP, and splicing plays a major role in the regulation of mitochondrial function in yeast.
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Affiliation(s)
- Subbaiah Chalivendra
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Shasha Shi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Zhiling Kuang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Joseph Giovinazzo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - John Rossi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas 66047, USA
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Robb Welty
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Katherine F Vaeth
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, USA
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3
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Senn KA, Hoskins AA. Mechanisms and regulation of spliceosome-mediated pre-mRNA splicing in Saccharomyces cerevisiae. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1866. [PMID: 38972853 DOI: 10.1002/wrna.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 07/09/2024]
Abstract
Pre-mRNA splicing, the removal of introns and ligation of flanking exons, is a crucial step in eukaryotic gene expression. The spliceosome, a macromolecular complex made up of five small nuclear RNAs (snRNAs) and dozens of proteins, assembles on introns via a complex pathway before catalyzing the two transesterification reactions necessary for splicing. All of these steps have the potential to be highly regulated to ensure correct mRNA isoform production for proper cellular function. While Saccharomyces cerevisiae (yeast) has a limited set of intron-containing genes, many of these genes are highly expressed, resulting in a large number of transcripts in a cell being spliced. As a result, splicing regulation is of critical importance for yeast. Just as in humans, yeast splicing can be influenced by protein components of the splicing machinery, structures and properties of the pre-mRNA itself, or by the action of trans-acting factors. It is likely that further analysis of the mechanisms and pathways of splicing regulation in yeast can reveal general principles applicable to other eukaryotes. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Katherine Anne Senn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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4
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Zhang Z, Kumar V, Dybkov O, Will CL, Zhong J, Ludwig SEJ, Urlaub H, Kastner B, Stark H, Lührmann R. Structural insights into the cross-exon to cross-intron spliceosome switch. Nature 2024; 630:1012-1019. [PMID: 38778104 PMCID: PMC11208138 DOI: 10.1038/s41586-024-07458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/23/2024] [Indexed: 05/25/2024]
Abstract
Early spliceosome assembly can occur through an intron-defined pathway, whereby U1 and U2 small nuclear ribonucleoprotein particles (snRNPs) assemble across the intron1. Alternatively, it can occur through an exon-defined pathway2-5, whereby U2 binds the branch site located upstream of the defined exon and U1 snRNP interacts with the 5' splice site located directly downstream of it. The U4/U6.U5 tri-snRNP subsequently binds to produce a cross-intron (CI) or cross-exon (CE) pre-B complex, which is then converted to the spliceosomal B complex6,7. Exon definition promotes the splicing of upstream introns2,8,9 and plays a key part in alternative splicing regulation10-16. However, the three-dimensional structure of exon-defined spliceosomal complexes and the molecular mechanism of the conversion from a CE-organized to a CI-organized spliceosome, a pre-requisite for splicing catalysis, remain poorly understood. Here cryo-electron microscopy analyses of human CE pre-B complex and B-like complexes reveal extensive structural similarities with their CI counterparts. The results indicate that the CE and CI spliceosome assembly pathways converge already at the pre-B stage. Add-back experiments using purified CE pre-B complexes, coupled with cryo-electron microscopy, elucidate the order of the extensive remodelling events that accompany the formation of B complexes and B-like complexes. The molecular triggers and roles of B-specific proteins in these rearrangements are also identified. We show that CE pre-B complexes can productively bind in trans to a U1 snRNP-bound 5' splice site. Together, our studies provide new mechanistic insights into the CE to CI switch during spliceosome assembly and its effect on pre-mRNA splice site pairing at this stage.
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Affiliation(s)
- Zhenwei Zhang
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- State Key Laboratory of Biotherapy and Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Vinay Kumar
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Olexandr Dybkov
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Cindy L Will
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jiayun Zhong
- State Key Laboratory of Biotherapy and Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Sebastian E J Ludwig
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Vincerx Pharma, Monheim am Rhein, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Berthold Kastner
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Reinhard Lührmann
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.
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5
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Zhang W, Zhang X, Zhan X, Bai R, Lei J, Yan C, Shi Y. Structural insights into human exon-defined spliceosome prior to activation. Cell Res 2024; 34:428-439. [PMID: 38658629 PMCID: PMC11143319 DOI: 10.1038/s41422-024-00949-w] [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: 01/25/2024] [Accepted: 03/01/2024] [Indexed: 04/26/2024] Open
Abstract
Spliceosome is often assembled across an exon and undergoes rearrangement to span a neighboring intron. Most states of the intron-defined spliceosome have been structurally characterized. However, the structure of a fully assembled exon-defined spliceosome remains at large. During spliceosome assembly, the pre-catalytic state (B complex) is converted from its precursor (pre-B complex). Here we report atomic structures of the exon-defined human spliceosome in four sequential states: mature pre-B, late pre-B, early B, and mature B. In the previously unknown late pre-B state, U1 snRNP is already released but the remaining proteins are still in the pre-B state; unexpectedly, the RNAs are in the B state, with U6 snRNA forming a duplex with 5'-splice site and U5 snRNA recognizing the 3'-end of the exon. In the early and mature B complexes, the B-specific factors are stepwise recruited and specifically recognize the exon 3'-region. Our study reveals key insights into the assembly of the exon-defined spliceosomes and identifies mechanistic steps of the pre-B-to-B transition.
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Affiliation(s)
- Wenyu Zhang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaofeng Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xiechao Zhan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Rui Bai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Jianlin Lei
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chuangye Yan
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Yigong Shi
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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6
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White DS, Dunyak BM, Vaillancourt FH, Hoskins AA. A Sequential Binding Mechanism for 5' Splice Site Recognition and Modulation for the Human U1 snRNP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590139. [PMID: 38659798 PMCID: PMC11042371 DOI: 10.1101/2024.04.18.590139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Splice site recognition is essential for defining the transcriptome. Drugs like risdiplam and branaplam change how U1 snRNP recognizes particular 5' splice sites (5'SS) and promote U1 snRNP binding and splicing at these locations. Despite the therapeutic potential of 5'SS modulators, the complexity of their interactions and snRNP substrates have precluded defining a mechanism for 5'SS modulation. We have determined a sequential binding mechanism for modulation of -1A bulged 5'SS by branaplam using a combination of ensemble kinetic measurements and colocalization single molecule spectroscopy (CoSMoS). Our mechanism establishes that U1-C protein binds reversibly to U1 snRNP, and branaplam binds to the U1 snRNP/U1-C complex only after it has engaged a -1A bulged 5'SS. Obligate orders of binding and unbinding explain how reversible branaplam interactions cause formation of long-lived U1 snRNP/5'SS complexes. Branaplam is a ribonucleoprotein, not RNA duplex alone, targeting drug whose action depends on fundamental properties of 5'SS recognition.
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Affiliation(s)
- David S. White
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI
- Present Address: Element Biosciences, San Diego, CA
| | | | | | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI
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7
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Bai R, Yuan M, Zhang P, Luo T, Shi Y, Wan R. Structural basis of U12-type intron engagement by the fully assembled human minor spliceosome. Science 2024; 383:1245-1252. [PMID: 38484052 DOI: 10.1126/science.adn7272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/09/2024] [Indexed: 03/19/2024]
Abstract
The minor spliceosome, which is responsible for the splicing of U12-type introns, comprises five small nuclear RNAs (snRNAs), of which only one is shared with the major spliceosome. In this work, we report the 3.3-angstrom cryo-electron microscopy structure of the fully assembled human minor spliceosome pre-B complex. The atomic model includes U11 small nuclear ribonucleoprotein (snRNP), U12 snRNP, and U4atac/U6atac.U5 tri-snRNP. U11 snRNA is recognized by five U11-specific proteins (20K, 25K, 35K, 48K, and 59K) and the heptameric Sm ring. The 3' half of the 5'-splice site forms a duplex with U11 snRNA; the 5' half is recognized by U11-35K, U11-48K, and U11 snRNA. Two proteins, CENATAC and DIM2/TXNL4B, specifically associate with the minor tri-snRNP. A structural analysis uncovered how two conformationally similar tri-snRNPs are differentiated by the minor and major prespliceosomes for assembly.
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Affiliation(s)
- Rui Bai
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, 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, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Meng Yuan
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pu Zhang
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ting Luo
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, 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, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Yigong Shi
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, 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, Xihu District, Hangzhou 310024, Zhejiang Province, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Research Center for Industries of the Future, Key Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Xihu District, 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, Xihu District, Hangzhou 310024, Zhejiang Province, China
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8
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Zhang Z, Kumar V, Dybkov O, Will CL, Urlaub H, Stark H, Lührmann R. Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. EMBO J 2024; 43:1065-1088. [PMID: 38383864 PMCID: PMC10943123 DOI: 10.1038/s44318-024-00052-1] [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: 09/27/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
The B complex is a key intermediate stage of spliceosome assembly. To improve the structural resolution of monomeric, human spliceosomal B (hB) complexes and thereby generate a more comprehensive hB molecular model, we determined the cryo-EM structure of B complex dimers formed in the presence of ATP γ S. The enhanced resolution of these complexes allows a finer molecular dissection of how the 5' splice site (5'ss) is recognized in hB, and new insights into molecular interactions of FBP21, SNU23 and PRP38 with the U6/5'ss helix and with each other. It also reveals that SMU1 and RED are present as a heterotetrameric complex and are located at the interface of the B dimer protomers. We further show that MFAP1 and UBL5 form a 5' exon binding channel in hB, and elucidate the molecular contacts stabilizing the 5' exon at this stage. Our studies thus yield more accurate models of protein and RNA components of hB complexes. They further allow the localization of additional proteins and protein domains (such as SF3B6, BUD31 and TCERG1) whose position was not previously known, thereby uncovering new functions for B-specific and other hB proteins during pre-mRNA splicing.
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Affiliation(s)
- Zhenwei Zhang
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Vinay Kumar
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Olexandr Dybkov
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Cindy L Will
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Reinhard Lührmann
- Cellular Biochemistry, Max-Planck-Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
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9
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Carrocci TJ, DeMario S, He K, Zeps NJ, Harkner CT, Chanfreau G, Hoskins AA. Functional Analysis of the Zinc Finger Modules of the S. cerevisiae Splicing Factor Luc7. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578419. [PMID: 38352541 PMCID: PMC10862913 DOI: 10.1101/2024.02.04.578419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Identification of splice sites is a critical step in pre-mRNA splicing since definition of the exon/intron boundaries controls what nucleotides are incorporated into mature mRNAs. The intron boundary with the upstream exon is initially identified through interactions with the U1 snRNP. This involves both base pairing between the U1 snRNA and the pre-mRNA as well as snRNP proteins interacting with the 5' splice site/snRNA duplex. In yeast, this duplex is buttressed by two conserved protein factors, Yhc1 and Luc7. Luc7 has three human paralogs (LUC7L, LUC7L2, and LUC7L3) which play roles in alternative splicing. What domains of these paralogs promote splicing at particular sites is not yet clear. Here, we humanized the zinc finger domains of the yeast Luc7 protein in order to understand their roles in splice site selection using reporter assays, transcriptome analysis, and genetic interactions. While we were unable to determine a function for the first zinc finger domain, humanization of the second zinc finger domain to mirror that found in LUC7L or LUC7L2 resulted in altered usage of nonconsensus 5' splice sites. In contrast, the corresponding zinc finger domain of LUC7L3 could not support yeast viability. Further, humanization of Luc7 can suppress mutation of the ATPase Prp28, which is involved in U1 release and exchange for U6 at the 5' splice site. Our work reveals a role for the second zinc finger of Luc7 in splice site selection and suggests that different zinc finger domains may have different ATPase requirements for release by Prp28.
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Affiliation(s)
- Tucker J. Carrocci
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel DeMario
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin He
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Natalie J. Zeps
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cade T. Harkner
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Guillaume Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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10
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Chalivendra S, Shi S, Li X, Kuang Z, Giovinazzo J, Zhang L, Rossi J, Saviola AJ, Wang J, Welty R, Liu S, Vaeth K, Zhou ZH, Hansen KC, Taliaferro JM, Zhao R. Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571893. [PMID: 38168357 PMCID: PMC10760170 DOI: 10.1101/2023.12.15.571893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The recognition of 5' splice site (5' ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5' ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5' ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5' ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe 2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.
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11
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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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12
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Cartwright-Acar CH, Osterhoudt K, Suzuki JMNGL, Gomez D, Katzman S, Zahler AM. A forward genetic screen in C. elegans identifies conserved residues of spliceosomal proteins PRP8 and SNRNP200/BRR2 with a role in maintaining 5' splice site identity. Nucleic Acids Res 2022; 50:11834-11857. [PMID: 36321655 PMCID: PMC9723624 DOI: 10.1093/nar/gkac991] [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: 11/24/2021] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
The spliceosome undergoes extensive rearrangements as it assembles onto precursor messenger RNAs. In the earliest assembly step, U1snRNA identifies the 5' splice site. However, U1snRNA leaves the spliceosome relatively early in assembly, and 5' splice site identity is subsequently maintained through interactions with U6snRNA, protein factor PRP8, and other components during the rearrangements that build the catalytic site. Using a forward genetic screen in Caenorhabditis elegans, we have identified suppressors of a locomotion defect caused by a 5'ss mutation. Here we report three new suppressor alleles from this screen, two in PRP8 and one in SNRNP200/BRR2. mRNASeq studies of these suppressor strains indicate that they also affect specific native alternative 5'ss, especially for suppressor PRP8 D1549N. A strong suppressor at the unstructured N-terminus of SNRNP200, N18K, indicates a novel role for this region. By examining distinct changes in the splicing of native genes, examining double mutants between suppressors, comparing these new suppressors to previously identified splicing suppressors from yeast, and mapping conserved suppressor residues onto cryoEM structural models of assembling human spliceosomes, we conclude that there are multiple interactions at multiple stages in spliceosome assembly responsible for maintaining the initial 5'ss identified by U1snRNA for entry into the catalytic core.
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Affiliation(s)
- Catiana H Cartwright-Acar
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Kenneth Osterhoudt
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Jessie M N G L Suzuki
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Destiny R Gomez
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Sol Katzman
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Alan M Zahler
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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13
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Gildea MA, Dwyer ZW, Pleiss JA. Transcript-specific determinants of pre-mRNA splicing revealed through in vivo kinetic analyses of the 1 st and 2 nd chemical steps. Mol Cell 2022; 82:2967-2981.e6. [PMID: 35830855 PMCID: PMC9391291 DOI: 10.1016/j.molcel.2022.06.020] [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: 10/13/2020] [Revised: 01/31/2022] [Accepted: 06/12/2022] [Indexed: 10/17/2022]
Abstract
We generate high-precision measurements of the in vivo rates of both chemical steps of pre-mRNA splicing across the genome-wide complement of substrates in yeast by coupling metabolic labeling, multiplexed primer-extension sequencing, and kinetic modeling. We demonstrate that the rates of intron removal vary widely, splice-site sequences are primary determinants of 1st step but have little apparent impact on 2nd step rates, and the 2nd step is generally faster than the 1st step. Ribosomal protein genes (RPGs) are spliced faster than non-RPGs at each step, and RPGs share evolutionarily conserved properties that may contribute to their faster splicing. A genetic variant defective in the 1st step of the pathway reveals a genome-wide defect in the 1st step but an unexpected, transcript-specific change in the 2nd step. Our work demonstrates that extended co-transcriptional association is an important determinant of splicing rate, a conclusion at odds with recent claims of ultra-fast splicing.
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Affiliation(s)
- Michael A Gildea
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Zachary W Dwyer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Jeffrey A Pleiss
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA.
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14
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Hansen SR, White DS, Scalf M, Corrêa IR, Smith LM, Hoskins AA. Multi-step recognition of potential 5' splice sites by the Saccharomyces cerevisiae U1 snRNP. eLife 2022; 11:70534. [PMID: 35959885 PMCID: PMC9436412 DOI: 10.7554/elife.70534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, splice sites define the introns of pre-mRNAs and must be recognized and excised with nucleotide precision by the spliceosome to make the correct mRNA product. In one of the earliest steps of spliceosome assembly, the U1 small nuclear ribonucleoprotein (snRNP) recognizes the 5' splice site (5' SS) through a combination of base pairing, protein-RNA contacts, and interactions with other splicing factors. Previous studies investigating the mechanisms of 5' SS recognition have largely been done in vivo or in cellular extracts where the U1/5' SS interaction is difficult to deconvolute from the effects of trans-acting factors or RNA structure. In this work we used colocalization single-molecule spectroscopy (CoSMoS) to elucidate the pathway of 5' SS selection by purified yeast U1 snRNP. We determined that U1 reversibly selects 5' SS in a sequence-dependent, two-step mechanism. A kinetic selection scheme enforces pairing at particular positions rather than overall duplex stability to achieve long-lived U1 binding. Our results provide a kinetic basis for how U1 may rapidly surveil nascent transcripts for 5' SS and preferentially accumulate at these sequences rather than on close cognates.
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Affiliation(s)
- Sarah R Hansen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - David S White
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, United States
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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15
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Zhao C, Li Y, Qiu C, Chen J, Wu H, Wang Q, Ma X, Song K, Kong B. Splicing Factor DDX23, Transcriptionally Activated by E2F1, Promotes Ovarian Cancer Progression by Regulating FOXM1. Front Oncol 2021; 11:749144. [PMID: 34966670 PMCID: PMC8710544 DOI: 10.3389/fonc.2021.749144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/23/2021] [Indexed: 12/19/2022] Open
Abstract
Ovarian carcinoma remains the most lethal gynecological carcinoma. Abnormal expression of splicing factors is closely related to the occurrence and development of tumors. The DEAD-box RNA helicases are important members of the splicing factor family. However, their role in the occurrence and progression of ovarian cancer is still unclear. In this study, we identified DEAD-box helicase 23 (DDX23) as a key DEAD-box RNA helicase in ovarian cancer using bioinformatics methods. We determined that DDX23 was upregulated in ovarian cancer and its high expression predicted poor prognosis. Functional assays indicated that DDX23 silencing significantly impeded cell proliferation/invasion in vitro and tumor growth in vivo. Mechanistically, transcriptomic analysis showed that DDX23 was involved in mRNA processing in ovarian cancer cells. Specifically, DDX23 regulated the mRNA processing of FOXM1. DDX23 silencing reduced the production of FOXM1C, the major oncogenic transcript of FOXM1 in ovarian cancer, thereby decreasing the FOXM1 protein expression and attenuating the malignant progression of ovarian cancer. Rescue assays indicated that FOXM1 was a key executor in DDX23-induced malignant phenotype of ovarian cancer. Furthermore, we confirmed that DDX23 was transcriptionally activated by the transcription factor (TF) E2F1 in ovarian cancer using luciferase reporter assays and chromatin immunoprecipitation (ChIP) assays. In conclusion, our study demonstrates that high DDX23 expression is involved in malignant behavior of ovarian cancer and DDX23 may become a potential target for precision therapy of ovarian cancer.
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Affiliation(s)
- Chen Zhao
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Chunping Qiu
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Jingying Chen
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Huan Wu
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Qiuman Wang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Xinyue Ma
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Gynecology Oncology Key Laboratory, Qilu Hospital, Shandong University, Jinan, China
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16
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Yeh FL, Chang SL, Ahmed GR, Liu HI, Tung L, Yeh CS, Lanier LS, Maeder C, Lin CM, Tsai SC, Hsiao WY, Chang WH, Chang TH. Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling. Nat Commun 2021; 12:3082. [PMID: 34035302 PMCID: PMC8149812 DOI: 10.1038/s41467-021-23459-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 04/29/2021] [Indexed: 11/10/2022] Open
Abstract
Splicing, a key step in the eukaryotic gene-expression pathway, converts precursor messenger RNA (pre-mRNA) into mRNA by excising introns and ligating exons. This task is accomplished by the spliceosome, a macromolecular machine that must undergo sequential conformational changes to establish its active site. Each of these major changes requires a dedicated DExD/H-box ATPase, but how these enzymes are activated remain obscure. Here we show that Prp28, a yeast DEAD-box ATPase, transiently interacts with the conserved 5' splice-site (5'SS) GU dinucleotide and makes splicing-dependent contacts with the U1 snRNP protein U1C, and U4/U6.U5 tri-snRNP proteins, Prp8, Brr2, and Snu114. We further show that Prp28's ATPase activity is potentiated by the phosphorylated Npl3, but not the unphosphorylated Npl3, thus suggesting a strategy for regulating DExD/H-box ATPases. We propose that Npl3 is a functional counterpart of the metazoan-specific Prp28 N-terminal region, which can be phosphorylated and serves as an anchor to human spliceosome.
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Affiliation(s)
- Fu-Lung Yeh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | | | - Hsin-I Liu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Luh Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Leah Stands Lanier
- Department of Biology, Washington and Lee University, Lexington, VA, USA
| | - Corina Maeder
- Department of Chemistry, Trinity University, San Antonio, TX, USA
| | - Che-Min Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Shu-Chun Tsai
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Yi Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
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17
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Shao W, Ding Z, Zheng ZZ, Shen JJ, Shen YX, Pu J, Fan YJ, Query CC, Xu YZ. Prp5-Spt8/Spt3 interaction mediates a reciprocal coupling between splicing and transcription. Nucleic Acids Res 2020; 48:5799-5813. [PMID: 32399566 PMCID: PMC7293005 DOI: 10.1093/nar/gkaa311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 04/08/2020] [Accepted: 05/03/2020] [Indexed: 01/23/2023] Open
Abstract
Transcription and pre-mRNA splicing are coupled to promote gene expression and regulation. However, mechanisms by which transcription and splicing influence each other are still under investigation. The ATPase Prp5p is required for pre-spliceosome assembly and splicing proofreading at the branch-point region. From an open UV mutagenesis screen for genetic suppressors of prp5 defects and subsequent targeted testing, we identify components of the TBP-binding module of the Spt–Ada–Gcn5 Acetyltransferase (SAGA) complex, Spt8p and Spt3p. Spt8Δ and spt3Δ rescue the cold-sensitivity of prp5-GAR allele, and prp5 mutants restore growth of spt8Δ and spt3Δ strains on 6-azauracil. By chromatin immunoprecipitation (ChIP), we find that prp5 alleles decrease recruitment of RNA polymerase II (Pol II) to an intron-containing gene, which is rescued by spt8Δ. Further ChIP-seq reveals that global effects on Pol II-binding are mutually rescued by prp5-GAR and spt8Δ. Inhibited splicing caused by prp5-GAR is also restored by spt8Δ. In vitro assays indicate that Prp5p directly interacts with Spt8p, but not Spt3p. We demonstrate that Prp5p's splicing proofreading is modulated by Spt8p and Spt3p. Therefore, this study reveals that interactions between the TBP-binding module of SAGA and the spliceosomal ATPase Prp5p mediate a balance between transcription initiation/elongation and pre-spliceosome assembly.
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Affiliation(s)
- Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China.,State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Zhan Ding
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zeng-Zhang Zheng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ji-Jia Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Yu-Xian Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jia Pu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu-Jie Fan
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
| | - Charles C Query
- Department of Cell Biology, Albert Einstein College of Medicine, NY 10461, USA
| | - Yong-Zhen Xu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei 430072, China
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18
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Aslanzadeh V, Beggs JD. Revisiting the window of opportunity for cotranscriptional splicing in budding yeast. RNA (NEW YORK, N.Y.) 2020; 26:1081-1085. [PMID: 32439718 PMCID: PMC7430680 DOI: 10.1261/rna.075895.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We reported previously that, in budding yeast, transcription rate affects both the efficiency and fidelity of pre-mRNA splicing, especially of ribosomal protein transcripts. Here, we report that the majority of ribosomal protein transcripts with non-consensus 5' splice sites are spliced less efficiently when transcription is faster, and more efficiently with slower transcription. These results support the "window of opportunity" model, and we suggest a possible mechanism to explain these findings.
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Affiliation(s)
- Vahid Aslanzadeh
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Jean D Beggs
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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19
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Fica SM. Cryo-EM snapshots of the human spliceosome reveal structural adaptions for splicing regulation. Curr Opin Struct Biol 2020; 65:139-148. [PMID: 32717639 DOI: 10.1016/j.sbi.2020.06.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/28/2022]
Abstract
Introns are excised from pre-messenger RNAs by the spliceosome, which produces mRNAs with continuous protein-coding information. In humans, most pre-mRNAs undergo alternative splicing to expand proteomic diversity. Cryo-electron microscopy (cryo-EM) structures of the yeast spliceosome elucidated how proteins stabilize and remodel an RNA-based active site to effect splicing catalysis. More recent cryo-EM snapshots of the human spliceosome reveal a complex protein scaffold and provide insights into the role of specific human proteins in modulating spliceosome activation, splice site positioning, and the ATPase-mediated dynamics of the active site. The emerging molecular picture highlights how, compared to its yeast counterpart, the human spliceosome has coopted additional protein factors to allow increased plasticity of splice site recognition and remodeling, and potentially to regulate alternative splicing.
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Affiliation(s)
- Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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20
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Abstract
Splicing of the precursor messenger RNA, involving intron removal and exon ligation, is mediated by the spliceosome. Together with biochemical and genetic investigations of the past four decades, structural studies of the intact spliceosome at atomic resolution since 2015 have led to mechanistic delineation of RNA splicing with remarkable insights. The spliceosome is proven to be a protein-orchestrated metalloribozyme. Conserved elements of small nuclear RNA (snRNA) constitute the splicing active site with two catalytic metal ions and recognize three conserved intron elements through duplex formation, which are delivered into the splicing active site for branching and exon ligation. The protein components of the spliceosome stabilize the conformation of the snRNA, drive spliceosome remodeling, orchestrate the movement of the RNA elements, and facilitate the splicing reaction. The overall organization of the spliceosome and the configuration of the splicing active site are strictly conserved between human and yeast.
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Affiliation(s)
- Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China;,
| | - Rui Bai
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310024, China
| | - Xiechao Zhan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China;,
| | - Yigong Shi
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China;,
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310024, China
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21
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Abstract
The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5' splice site (5'SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5'SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5'SS, producing a free 5' exon. Removal of the BP adenosine from the active site allows the 3'SS to bind, so that the 5' exon attacks the 3'SS to produce mature mRNA and an excised lariat intron.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
| | - Clément Charenton
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; ,
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22
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van der Feltz C, Hoskins AA. Structural and functional modularity of the U2 snRNP in pre-mRNA splicing. Crit Rev Biochem Mol Biol 2019; 54:443-465. [PMID: 31744343 DOI: 10.1080/10409238.2019.1691497] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The U2 small nuclear ribonucleoprotein (snRNP) is an essential component of the spliceosome, the cellular machine responsible for removing introns from precursor mRNAs (pre-mRNAs) in all eukaryotes. U2 is an extraordinarily dynamic splicing factor and the most frequently mutated in cancers. Cryo-electron microscopy (cryo-EM) has transformed our structural and functional understanding of the role of U2 in splicing. In this review, we synthesize these and other data with respect to a view of U2 as an assembly of interconnected functional modules. These modules are organized by the U2 small nuclear RNA (snRNA) for roles in spliceosome assembly, intron substrate recognition, and protein scaffolding. We describe new discoveries regarding the structure of U2 components and how the snRNP undergoes numerous conformational and compositional changes during splicing. We specifically highlight large scale movements of U2 modules as the spliceosome creates and rearranges its active site. U2 serves as a compelling example for how cellular machines can exploit the modular organization and structural plasticity of an RNP.
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Affiliation(s)
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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23
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Kastner B, Will CL, Stark H, Lührmann R. Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes. Cold Spring Harb Perspect Biol 2019; 11:a032417. [PMID: 30765414 PMCID: PMC6824238 DOI: 10.1101/cshperspect.a032417] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spliceosome is a highly complex, dynamic ribonucleoprotein molecular machine that undergoes numerous structural and compositional rearrangements that lead to the formation of its active site. Recent advances in cyroelectron microscopy (cryo-EM) have provided a plethora of near-atomic structural information about the inner workings of the spliceosome. Aided by previous biochemical, structural, and functional studies, cryo-EM has confirmed or provided a structural basis for most of the prevailing models of spliceosome function, but at the same time allowed novel insights into splicing catalysis and the intriguing dynamics of the spliceosome. The mechanism of pre-mRNA splicing is highly conserved between humans and yeast, but the compositional dynamics and ribonucleoprotein (RNP) remodeling of the human spliceosome are more complex. Here, we summarize recent advances in our understanding of the molecular architecture of the human spliceosome, highlighting differences between the human and yeast splicing machineries.
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Affiliation(s)
- Berthold Kastner
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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24
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Toroney R, Nielsen KH, Staley JP. Termination of pre-mRNA splicing requires that the ATPase and RNA unwindase Prp43p acts on the catalytic snRNA U6. Genes Dev 2019; 33:1555-1574. [PMID: 31558568 PMCID: PMC6824469 DOI: 10.1101/gad.328294.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/03/2019] [Indexed: 11/25/2022]
Abstract
In this study, Toroney et al. set out to identify the mechanism of Prp43p action in splicing. The authors use biochemical approaches to demonstrate that the 3' end of U6 acts as the key substrate by which Prp43p promotes disassembly and intron release, thereby terminating splicing. The termination of pre-mRNA splicing functions to discard suboptimal substrates, thereby enhancing fidelity, and to release excised introns in a manner coupled to spliceosome disassembly, thereby allowing recycling. The mechanism of termination, including the RNA target of the DEAH-box ATPase Prp43p, remains ambiguous. We discovered a critical role for nucleotides at the 3′ end of the catalytic U6 small nuclear RNA in splicing termination. Although conserved sequence at the 3′ end is not required, 2′ hydroxyls are, paralleling requirements for Prp43p biochemical activities. Although the 3′ end of U6 is not required for recruiting Prp43p to the spliceosome, the 3′ end cross-links directly to Prp43p in an RNA-dependent manner. Our data indicate a mechanism of splicing termination in which Prp43p translocates along U6 from the 3′ end to disassemble the spliceosome and thereby release suboptimal substrates or excised introns. This mechanism reveals that the spliceosome becomes primed for termination at the same stage it becomes activated for catalysis, implying a requirement for stringent control of spliceosome activity within the cell.
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Affiliation(s)
- Rebecca Toroney
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
| | - Klaus H Nielsen
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
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25
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Li S, Xu R, Li A, Liu K, Gu L, Li M, Zhang H, Zhang Y, Zhuang S, Wang Q, Gao G, Li N, Zhang C, Li Y, Yu B. SMA1, a homolog of the splicing factor Prp28, has a multifaceted role in miRNA biogenesis in Arabidopsis. Nucleic Acids Res 2019; 46:9148-9159. [PMID: 29982637 PMCID: PMC6158494 DOI: 10.1093/nar/gky591] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 06/19/2018] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs that repress gene expression. In plants, the RNase III enzyme Dicer-like (DCL1) processes primary miRNAs (pri-miRNAs) into miRNAs. Here, we show that SMALL1 (SMA1), a homolog of the DEAD-box pre-mRNA splicing factor Prp28, plays essential roles in miRNA biogenesis in Arabidopsis. A hypomorphic sma1-1 mutation causes growth defects and reduces miRNA accumulation correlated with increased target transcript levels. SMA1 interacts with the DCL1 complex and positively influences pri-miRNA processing. Moreover, SMA1 binds the promoter region of genes encoding pri-miRNAs (MIRs) and is required for MIR transcription. Furthermore, SMA1 also enhances the abundance of the DCL1 protein levels through promoting the splicing of the DCL1 pre-mRNAs. Collectively, our data provide new insights into the function of SMA1/Prp28 in regulating miRNA abundance in plants.
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Affiliation(s)
- Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0666, USA.,School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Aixia Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0666, USA.,School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA
| | - Liqing Gu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mu Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0666, USA.,School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA
| | - Hairui Zhang
- School of Life Science, Shanxi Normal University, Linfen 041004, China
| | - Yueying Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shangshang Zhuang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Quanhui Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Gang Gao
- School of Life Science, Shanxi Normal University, Linfen 041004, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0666, USA.,School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588-0666, USA.,School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA
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26
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Talkish J, Igel H, Hunter O, Horner SW, Jeffery NN, Leach JR, Jenkins JL, Kielkopf CL, Ares M. Cus2 enforces the first ATP-dependent step of splicing by binding to yeast SF3b1 through a UHM-ULM interaction. RNA (NEW YORK, N.Y.) 2019; 25:1020-1037. [PMID: 31110137 PMCID: PMC6633205 DOI: 10.1261/rna.070649.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/15/2019] [Indexed: 05/16/2023]
Abstract
Stable recognition of the intron branchpoint (BP) by the U2 snRNP to form the pre-spliceosome is the first ATP-dependent step of splicing. Genetic and biochemical data from yeast indicate that Cus2 aids U2 snRNA folding into the stem IIa conformation prior to pre-spliceosome formation. Cus2 must then be removed by an ATP-dependent function of Prp5 before assembly can progress. However, the location from which Cus2 is displaced and the nature of its binding to the U2 snRNP are unknown. Here, we show that Cus2 contains a conserved UHM (U2AF homology motif) that binds Hsh155, the yeast homolog of human SF3b1, through a conserved ULM (U2AF ligand motif). Mutations in either motif block binding and allow pre-spliceosome formation without ATP. A 2.0 Å resolution structure of the Hsh155 ULM in complex with the UHM of Tat-SF1, the human homolog of Cus2, and complementary binding assays show that the interaction is highly similar between yeast and humans. Furthermore, we show that Tat-SF1 can replace Cus2 function by enforcing ATP dependence of pre-spliceosome formation in yeast extracts. Cus2 is removed before pre-spliceosome formation, and both Cus2 and its Hsh155 ULM binding site are absent from available cryo-EM structure models. However, our data are consistent with the apparent location of the disordered Hsh155 ULM between the U2 stem-loop IIa and the HEAT repeats of Hsh155 that interact with Prp5. We propose a model in which Prp5 uses ATP to remove Cus2 from Hsh155 such that extended base-pairing between U2 snRNA and the intron BP can occur.
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Affiliation(s)
- Jason Talkish
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Oarteze Hunter
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Steven W Horner
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Nazish N Jeffery
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Justin R Leach
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Jermaine L Jenkins
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Clara L Kielkopf
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
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27
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Bao P, Boon KL, Will CL, Hartmuth K, Lührmann R. Multiple RNA-RNA tertiary interactions are dispensable for formation of a functional U2/U6 RNA catalytic core in the spliceosome. Nucleic Acids Res 2019; 46:12126-12138. [PMID: 30335160 PMCID: PMC6294511 DOI: 10.1093/nar/gky966] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 01/24/2023] Open
Abstract
The active 3D conformation of the spliceosome's catalytic U2/U6 RNA core is stabilised by a network of secondary and tertiary RNA interactions, but also depends on spliceosomal proteins for its formation. To determine the contribution towards splicing of specific RNA secondary and tertiary interactions in the U2/U6 RNA core, we introduced mutations in critical U6 nucleotides and tested their effect on splicing using a yeast in vitro U6 depletion/complementation system. Elimination of selected RNA tertiary interactions involving the U6 catalytic triad, or deletions of the bases of U6-U80 or U6-A59, had moderate to no effect on splicing, showing that the affected secondary and tertiary interactions are not required for splicing catalysis. However, removal of the base of U6-G60 of the catalytic triad completely blocked splicing, without affecting assembly of the activated spliceosome or its subsequent conversion into a B*-like complex. Our data suggest that the catalytic configuration of the RNA core that allows catalytic metal M1 binding can be maintained by Protein–RNA contacts. However, RNA stacking interactions in the U2/U6 RNA core are required for productive coordination of metal M2. The functional conformation of the U2/U6 RNA core is thus highly buffered, with overlapping contributions from RNA–RNA and Protein–RNA interactions.
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Affiliation(s)
- Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Kum-Loong Boon
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Klaus Hartmuth
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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28
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Plaschka C, Newman AJ, Nagai K. Structural Basis of Nuclear pre-mRNA Splicing: Lessons from Yeast. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032391. [PMID: 30765413 DOI: 10.1101/cshperspect.a032391] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Noncoding introns are removed from nuclear precursor messenger RNA (pre-mRNA) in a two-step phosphoryl transfer reaction by the spliceosome, a dynamic multimegadalton enzyme. Cryo-electron microscopy (cryo-EM) structures of the Saccharomyces cerevisiae spliceosome were recently determined in eight key states. Combined with the wealth of available genetic and biochemical data, these structures have revealed new insights into the mechanisms of spliceosome assembly, activation, catalysis, and disassembly. The structures show how a single RNA catalytic center forms during activation and accomplishes both steps of the splicing reaction. The structures reveal how spliceosomal helicases remodel the spliceosome for active site formation, substrate docking, reaction product undocking, and spliceosome disassembly and how they facilitate splice site proofreading. Although human spliceosomes contain additional proteins, their cryo-EM structures suggest that the underlying mechanism is conserved across all eukaryotes. In this review, we summarize the current structural understanding of pre-mRNA splicing.
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Affiliation(s)
- Clemens Plaschka
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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29
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Charenton C, Wilkinson ME, Nagai K. Mechanism of 5' splice site transfer for human spliceosome activation. Science 2019; 364:362-367. [PMID: 30975767 DOI: 10.1126/science.aax3289] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
The prespliceosome, comprising U1 and U2 small nuclear ribonucleoproteins (snRNPs) bound to the precursor messenger RNA 5' splice site (5'SS) and branch point sequence, associates with the U4/U6.U5 tri-snRNP to form the fully assembled precatalytic pre-B spliceosome. Here, we report cryo-electron microscopy structures of the human pre-B complex captured before U1 snRNP dissociation at 3.3-angstrom core resolution and the human tri-snRNP at 2.9-angstrom resolution. U1 snRNP inserts the 5'SS-U1 snRNA helix between the two RecA domains of the Prp28 DEAD-box helicase. Adenosine 5'-triphosphate-dependent closure of the Prp28 RecA domains releases the 5'SS to pair with the nearby U6 ACAGAGA-box sequence presented as a mobile loop. The structures suggest that formation of the 5'SS-ACAGAGA helix triggers remodeling of an intricate protein-RNA network to induce Brr2 helicase relocation to its loading sequence in U4 snRNA, enabling Brr2 to unwind the U4/U6 snRNA duplex to allow U6 snRNA to form the catalytic center of the spliceosome.
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Affiliation(s)
| | | | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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30
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Xia X. RNA-Seq approach for accurate characterization of splicing efficiency of yeast introns. Methods 2019; 176:25-33. [PMID: 30926533 DOI: 10.1016/j.ymeth.2019.03.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/12/2019] [Accepted: 03/19/2019] [Indexed: 01/21/2023] Open
Abstract
Introns in different genes, or even different introns within the same gene, often have different splice sites and differ in splicing efficiency (SE). One expects mass-transcribed genes to have introns with higher SE than weakly transcribed genes. However, such a simple expectation cannot be tested directly because variable SE for these genes is often not measured. Mechanistically, SE should depend on signal strength at key splice sites (SS) such as 5'SS, 3'SS and branchpoint site (BPS), i.e., SE = F(5'SS, 3'SS, BPS). However, without SE, we again cannot model how these splice sites contribute to SE. Here I present an RNA-Seq approach to quantify SE for each of the 304 introns in yeast (Saccharomyces cerevisiae) genes, including 24 in the 5'UTR, by measuring 1) number of reads mapped to exon-exon junctions (NEE) as a proxy for the abundance of spliced form, and 2) number of reads mapped to exon-intron junction (NEI5 and NEI3 at 5' and 3' ends of intron) as a proxy for the abundance of unspliced form. The total mRNA is NTotal = NEE + p * NEI5 + (1-p) * NEI3, with the simplest p = 0.5 but statistical methods were presented to estimate p from data. An estimated p is needed because NEI5 is expected to be smaller than NEI3 due to 1) step 1 splicing occurs before step 2 so EI5 is broken before EI3, 2) enrichment of poly(A) mRNA by oligo-dT, and 3) 5' degradation. SE is defined as the proportion (NEE/NTotal). Application of the method shows that ribosomal protein messages are efficiently and mostly cotranscriptionally spliced. Yeast genes with long introns are also spliced efficiently. HAC1/YFL031W is poorly spliced partly because its splicing involves a nonspliceosome mechanism and partly because Ire1p, which participate in splicing HAC1, is hardly expressed. Many putative yeast genes have low SE, and some splice sites are incorrectly annotated.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa K1N 6N5, Canada; Ottawa Institute of Systems Biology, Ottawa, Ontario K1H 8M5, Canada.
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31
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An Allosteric Network for Spliceosome Activation Revealed by High-Throughput Suppressor Analysis in Saccharomyces cerevisiae. Genetics 2019; 212:111-124. [PMID: 30898770 DOI: 10.1534/genetics.119.301922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 03/15/2019] [Indexed: 12/30/2022] Open
Abstract
Selection of suppressor mutations that correct growth defects caused by substitutions in an RNA or protein can reveal functionally important molecular structures and interactions in living cells. This approach is particularly useful for the study of complex biological pathways involving many macromolecules, such as premessenger RNA (pre-mRNA) splicing. When a sufficiently large number of suppressor mutations is obtained and structural information is available, it is possible to generate detailed models of molecular function. However, the laborious and expensive task of identifying suppressor mutations in whole-genome selections limits the utility of this approach. Here I show that a custom targeted sequencing panel can greatly accelerate the identification of suppressor mutations in the Saccharomyces cerevisiae genome. Using a panel that targets 112 genes encoding pre-mRNA splicing factors, I identified 27 unique mutations in six protein-coding genes that each overcome the cold-sensitive block to spliceosome activation caused by a substitution in U4 small nuclear RNA. When mapped to existing structures of spliceosomal complexes, the identified suppressors implicate specific molecular contacts between the proteins Brr2, Prp6, Prp8, Prp31, Sad1, and Snu114 as functionally important in an early step of catalytic activation of the spliceosome. This approach shows great promise for elucidating the allosteric cascade of molecular interactions that direct accurate and efficient pre-mRNA splicing and should be broadly useful for understanding the dynamics of other complex biological assemblies or pathways.
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32
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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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33
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Domain Requirements and Genetic Interactions of the Mud1 Subunit of the Saccharomyces cerevisiae U1 snRNP. G3-GENES GENOMES GENETICS 2019; 9:145-151. [PMID: 30413416 PMCID: PMC6325900 DOI: 10.1534/g3.118.200781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mud1 is an inessential 298-amino acid protein subunit of the Saccharomyces cerevisiae U1 snRNP. Mud1 consists of N-terminal and C-terminal RRM domains (RRM1 and RRM2) separated by a linker domain. Synthetic lethal interactions of mud1∆ with deletions of inessential spliceosome components Nam8, Mud2, and Msl1, or missense mutations in the branchpoint-binding protein Msl5 enabled us to dissect genetically the domain requirements for Mud1 function. We find that the biological activities of Mud1 can be complemented by co-expressing separately the RRM1 (aa 1-127) and linker-RRM2 (aa 128-298) modules. Whereas RRM1 and RRM2 (aa 197-298) per se are inactive in all tests of functional complementation, the linker-RRM2 by itself partially complements a subset of synthetic lethal mud1∆ interactions. Linker segment aa 155 to 196 contains a nuclear localization signal rich in basic amino acids that is necessary for RRM2 activity in mud1∆ complementation. Alanine scanning mutagenesis indicates that none of the individual RRM1 amino acid contacts to U1 snRNA in the cryo-EM model of the yeast U1 snRNP is necessary for mud1∆ complementation activity.
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34
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Mechanisms of Yeast Adaptation to Wine Fermentations. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:37-59. [PMID: 30911888 DOI: 10.1007/978-3-030-13035-0_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cells face genetic and/or environmental changes in order to outlast and proliferate. Characterization of changes after stress at different "omics" levels is crucial to understand the adaptation of yeast to changing conditions. Wine fermentation is a stressful situation which yeast cells have to cope with. Genome-wide analyses extend our cellular physiology knowledge by pointing out the mechanisms that contribute to sense the stress caused by these perturbations (temperature, ethanol, sulfites, nitrogen, etc.) and related signaling pathways. The model organism, Saccharomyces cerevisiae, was studied in response to industrial stresses and changes at different cellular levels (transcriptomic, proteomic, and metabolomics), which were followed statically and/or dynamically in the short and long terms. This chapter focuses on the response of yeast cells to the diverse stress situations that occur during wine fermentations, which induce perturbations, including nutritional changes, ethanol stress, temperature stress, oxidative stress, etc.
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35
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Zhan X, Yan C, Zhang X, Lei J, Shi Y. Structures of the human pre-catalytic spliceosome and its precursor spliceosome. Cell Res 2018; 28:1129-1140. [PMID: 30315277 PMCID: PMC6274647 DOI: 10.1038/s41422-018-0094-7] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/13/2022] Open
Abstract
The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (Bact complex). The pre-B-to-B and B-to-Bact transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5'-exon is anchored to loop I of U5 snRNA, and the 5'-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome.
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Affiliation(s)
- Xiechao Zhan
- 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.
| | - Xiaofeng Zhang
- 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, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang, 310024, China.
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36
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Structural studies of the spliceosome: past, present and future perspectives. Biochem Soc Trans 2018; 46:1407-1422. [PMID: 30420411 DOI: 10.1042/bst20170240] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/18/2022]
Abstract
The spliceosome is a multi-subunit RNA-protein complex involved in the removal of non-coding segments (introns) from between the coding regions (exons) in precursors of messenger RNAs (pre-mRNAs). Intron removal proceeds via two transesterification reactions, occurring between conserved sequences at intron-exon junctions. A tightly regulated, hierarchical assembly with a multitude of structural and compositional rearrangements posed a great challenge for structural studies of the spliceosome. Over the years, X-ray crystallography dominated the field, providing valuable high-resolution structural information that was mostly limited to individual proteins and smaller sub-complexes. Recent developments in the field of cryo-electron microscopy allowed the visualisation of fully assembled yeast and human spliceosomes, providing unprecedented insights into substrate recognition, catalysis, and active site formation. This has advanced our mechanistic understanding of pre-mRNA splicing enormously.
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37
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Chang SL, Wang HK, Tung L, Chang TH. Adaptive transcription-splicing resynchronization upon losing an essential splicing factor. Nat Ecol Evol 2018; 2:1818-1823. [PMID: 30297747 DOI: 10.1038/s41559-018-0684-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/31/2018] [Indexed: 01/21/2023]
Abstract
Essential genes form the core of a genome and are therefore thought to be indispensable for cellular viability. However, recent findings have challenged this notion in that cells may survive in the absence of some essential genes provided that relevant genetic modifiers are in existence. We therefore hypothesized that the loss of an essential gene may not always be fatefully detrimental; instead, it may pave the way towards genome evolution. We experimentally tested this hypothesis in the context of pre-messenger RNA splicing by evolving yeast cells harbouring a permanent loss of the essential splicing factor Prp28 in the presence of a genetic modifier. Here, we show that cellular fitness can be restored by compensatory mutations that alter either the splicing machinery per se or the Spt-Ada-Gcn5 acetyltransferase transcription co-activator complex in the cells with no Prp28. Biochemical and genetic analysis revealed that slowing down transcription compensates for splicing deficiency, which in turn boosts cellular fitness. In addition, we found that inefficient splicing also conversely decreases nascent RNA production. Taken together, our data suggest that transcription-splicing synchronization contributes to robustness in the gene-expression pathway and argue that the intrinsic interconnectivity within a biological system can be exploited for compensatory evolution and system re-optimization.
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Affiliation(s)
| | - Hsuan-Kai Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Luh Tung
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Tien-Hsien Chang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan. .,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan.
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38
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Wong MS, Kinney JB, Krainer AR. Quantitative Activity Profile and Context Dependence of All Human 5' Splice Sites. Mol Cell 2018; 71:1012-1026.e3. [PMID: 30174293 DOI: 10.1016/j.molcel.2018.07.033] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/18/2018] [Accepted: 07/23/2018] [Indexed: 02/02/2023]
Abstract
Pre-mRNA splicing is an essential step in the expression of most human genes. Mutations at the 5' splice site (5'ss) frequently cause defective splicing and disease due to interference with the initial recognition of the exon-intron boundary by U1 small nuclear ribonucleoprotein (snRNP), a component of the spliceosome. Here, we use a massively parallel splicing assay (MPSA) in human cells to quantify the activity of all 32,768 unique 5'ss sequences (NNN/GYNNNN) in three different gene contexts. Our results reveal that although splicing efficiency is mostly governed by the 5'ss sequence, there are substantial differences in this efficiency across gene contexts. Among other uses, these MPSA measurements facilitate the prediction of 5'ss sequence variants that are likely to cause aberrant splicing. This approach provides a framework to assess potential pathogenic variants in the human genome and streamline the development of splicing-corrective therapies.
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Affiliation(s)
- Mandy S Wong
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Justin B Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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39
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Prespliceosome structure provides insights into spliceosome assembly and regulation. Nature 2018; 559:419-422. [PMID: 29995849 PMCID: PMC6141012 DOI: 10.1038/s41586-018-0323-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/16/2018] [Indexed: 11/17/2022]
Abstract
The spliceosome catalyzes the excision of introns from pre-mRNA in two steps, branching
and exon ligation, and is assembled from five small nuclear ribonucleoprotein
particles (snRNPs; U1, U2, U4, U5, U6) and numerous non-snRNP factors1. For branching, the intron
5'-splice site (5'SS) and the branch point (BP) sequence are
selected and brought into the prespliceosome by the U1 and U2 snRNPs1, which is a focal point for the regulation
by alternative splicing factors2. The
U4/U6.U5 tri-snRNP subsequently joins the prespliceosome to form the complete
pre-catalytic spliceosome. Recent studies have revealed the structural basis of
the branching and exon-ligation reactions3. However, the structural basis of early spliceosome assembly events
remains poorly understood4. Here we report
the cryo-electron microscopy structure of the yeast Saccharomyces
cerevisiae prespliceosome at near-atomic resolution. The structure
reveals an induced stabilization of the 5'SS in the U1 snRNP, and
provides structural insights into the functions of the human alternative
splicing factors LUC7-like (yeast Luc7) and TIA-1 (yeast Nam8) that are linked
to human disease5,6. In the prespliceosome, the U1 snRNP associates with the
U2 snRNP through a stable contact with the U2 3' domain and a transient
yeast-specific contact with the U2 SF3b-containing 5' region, leaving its
tri-snRNP-binding interface fully exposed. The results suggest mechanisms for
5'SS transfer to the U6 ACAGAGA region within the assembled spliceosome
and for its subsequent conversion to the activation-competent B complex
spliceosome7,8. Taken together, the data provide a working model to
investigate the early steps of spliceosome assembly.
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40
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Bai R, Wan R, Yan C, Lei J, Shi Y. Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation. Science 2018; 360:1423-1429. [PMID: 29794219 DOI: 10.1126/science.aau0325] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 05/16/2018] [Indexed: 11/02/2022]
Abstract
The precatalytic spliceosome (B complex) is preceded by the pre-B complex. Here we report the cryo-electron microscopy structures of the Saccharomyces cerevisiae pre-B and B complexes at average resolutions of 3.3 to 4.6 and 3.9 angstroms, respectively. In the pre-B complex, the duplex between the 5' splice site (5'SS) and U1 small nuclear RNA (snRNA) is recognized by Yhc1, Luc7, and the Sm ring. In the B complex, U1 small nuclear ribonucleoprotein is dissociated, the 5'-exon-5'SS sequences are translocated near U6 snRNA, and three B-specific proteins may orient the precursor messenger RNA. In both complexes, U6 snRNA is anchored to loop I of U5 snRNA, and the duplex between the branch point sequence and U2 snRNA is recognized by the SF3b complex. Structural analysis reveals the mechanism of assembly and activation for the yeast spliceosome.
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Affiliation(s)
- Rui Bai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China
| | - Ruixue Wan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Schools of Life Sciences and 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, Schools of Life Sciences and Medicine, Tsinghua University, Beijing 100084, China. .,Institute of Biology, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou 310064, Zhejiang Province, China
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41
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Didychuk AL, Butcher SE, Brow DA. The life of U6 small nuclear RNA, from cradle to grave. RNA (NEW YORK, N.Y.) 2018; 24:437-460. [PMID: 29367453 PMCID: PMC5855946 DOI: 10.1261/rna.065136.117] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Removal of introns from precursor messenger RNA (pre-mRNA) and some noncoding transcripts is an essential step in eukaryotic gene expression. In the nucleus, this process of RNA splicing is carried out by the spliceosome, a multi-megaDalton macromolecular machine whose core components are conserved from yeast to humans. In addition to many proteins, the spliceosome contains five uridine-rich small nuclear RNAs (snRNAs) that undergo an elaborate series of conformational changes to correctly recognize the splice sites and catalyze intron removal. Decades of biochemical and genetic data, along with recent cryo-EM structures, unequivocally demonstrate that U6 snRNA forms much of the catalytic core of the spliceosome and is highly dynamic, interacting with three snRNAs, the pre-mRNA substrate, and >25 protein partners throughout the splicing cycle. This review summarizes the current state of knowledge on how U6 snRNA is synthesized, modified, incorporated into snRNPs and spliceosomes, recycled, and degraded.
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Affiliation(s)
- Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
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42
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Wilkinson ME, Lin PC, Plaschka C, Nagai K. Cryo-EM Studies of Pre-mRNA Splicing: From Sample Preparation to Model Visualization. Annu Rev Biophys 2018; 47:175-199. [PMID: 29494253 DOI: 10.1146/annurev-biophys-070317-033410] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The removal of noncoding introns from pre-messenger RNA (pre-mRNA) is an essential step in eukaryotic gene expression and is catalyzed by a dynamic multi-megadalton ribonucleoprotein complex called the spliceosome. The spliceosome assembles on pre-mRNA substrates by the stepwise addition of small nuclear ribonucleoprotein particles and numerous protein factors. Extensive remodeling is required to form the RNA-based active site and to mediate the pre-mRNA branching and ligation reactions. In the past two years, cryo-electron microscopy (cryo-EM) structures of spliceosomes captured in different assembly and catalytic states have greatly advanced our understanding of its mechanism. This was made possible by long-standing efforts in the purification of spliceosome intermediates as well as recent developments in cryo-EM imaging and computational methodology. The resulting high-resolution densities allow for de novo model building in core regions of the complexes. In peripheral and less ordered regions, the combination of cross-linking, bioinformatics, biochemical, and genetic data is essential for accurate modeling. Here, we summarize these achievements and highlight the critical steps in obtaining near-atomic resolution structures of the spliceosome.
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Affiliation(s)
- Max E Wilkinson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Pei-Chun Lin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Clemens Plaschka
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; , , ,
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43
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Galej WP, Toor N, Newman AJ, Nagai K. Molecular Mechanism and Evolution of Nuclear Pre-mRNA and Group II Intron Splicing: Insights from Cryo-Electron Microscopy Structures. Chem Rev 2018; 118:4156-4176. [PMID: 29377672 DOI: 10.1021/acs.chemrev.7b00499] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear pre-mRNA splicing and group II intron self-splicing both proceed by two-step transesterification reactions via a lariat intron intermediate. Recently determined cryo-electron microscopy (cryo-EM) structures of catalytically active spliceosomes revealed the RNA-based catalytic core and showed how pre-mRNA substrates and reaction products are positioned in the active site. These findings highlight a strong structural similarity to the group II intron active site, strengthening the notion that group II introns and spliceosomes evolved from a common ancestor. Prp8, the largest and most conserved protein in the spliceosome, cradles the active site RNA. Prp8 and group II intron maturase have a similar domain architecture, suggesting that they also share a common evolutionary origin. The interactions between maturase and key group II intron RNA elements, such as the exon-binding loop and domains V and VI, are recapitulated in the interactions between Prp8 and key elements in the spliceosome's catalytic RNA core. Structural comparisons suggest that the extensive RNA scaffold of the group II intron was gradually replaced by proteins as the spliceosome evolved. A plausible model of spliceosome evolution is discussed.
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Affiliation(s)
- Wojciech P Galej
- EMBL Grenoble , 71 Avenue des Martyrs , 38042 Grenoble Cedex 09 , France
| | - Navtej Toor
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge CB2 0QH , U.K
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44
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Bao P, Will CL, Urlaub H, Boon KL, Lührmann R. The RES complex is required for efficient transformation of the precatalytic B spliceosome into an activated B act complex. Genes Dev 2018; 31:2416-2429. [PMID: 29330354 PMCID: PMC5795787 DOI: 10.1101/gad.308163.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/11/2017] [Indexed: 12/31/2022]
Abstract
The precise function of the trimeric retention and splicing (RES) complex in pre-mRNA splicing remains unclear. Here we dissected the role of RES during the assembly and activation of yeast spliceosomes. The efficiency of pre-mRNA splicing was significantly lower in the absence of the RES protein Snu17, and the recruitment of its binding partners, Pml1 (pre-mRNA leakage protein 1) and Bud13 (bud site selection protein 13), to the spliceosome was either abolished or substantially reduced. RES was not required for the assembly of spliceosomal B complexes, but its absence hindered efficient Bact complex formation. ΔRES spliceosomes were no longer strictly dependent on Prp2 activity for their catalytic activation, suggesting that they are structurally compromised. Addition of Prp2, Spp2, and UTP to affinity-purified ΔRES B or a mixture of B/Bact complexes formed on wild-type pre-mRNA led to their disassembly. However, no substantial disassembly was observed with ΔRES spliceosomes formed on a truncated pre-mRNA that allows Prp2 binding but blocks its activity. Thus, in the absence of RES, Prp2 appears to bind prematurely, leading to the disassembly of the ΔRES B complexes to which it binds. Our data suggest that Prp2 can dismantle B complexes with an aberrant protein composition, suggesting that it may proofread the spliceosome's RNP structure prior to activation.
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Affiliation(s)
- Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Kum-Loong Boon
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany
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45
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Bao P, Höbartner C, Hartmuth K, Lührmann R. Yeast Prp2 liberates the 5' splice site and the branch site adenosine for catalysis of pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2017; 23:1770-1779. [PMID: 28864812 PMCID: PMC5688998 DOI: 10.1261/rna.063115.117] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/31/2017] [Indexed: 05/20/2023]
Abstract
The RNA helicase Prp2 facilitates the remodeling of the spliceosomal Bact complex to the catalytically activated B* complex just before step one of splicing. As a high-resolution cryo-EM structure of the B* complex is currently lacking, the precise spliceosome remodeling events mediated by Prp2 remain poorly understood. To investigate the latter, we used chemical structure probing to compare the RNA structure of purified yeast Bact and B* complexes. Our studies reveal deviations from conventional RNA helices in the functionally important U6 snRNA internal stem-loop and U2/U6 helix Ib in the activated Bact complex, and to a lesser extent in B*. Interestingly, the N7 of U6-G60 of the catalytic triad becomes accessible to DMS modification in the B* complex, suggesting that the Hoogsteen interaction with U6-A52 is destabilized in B*. Our data show that Prp2 action does not unwind double-stranded RNA, but enhances the flexibility of the first step reactants, the pre-mRNA's 5' splice site and branch site adenosine. Prp2 therefore appears to act primarily as an RNPase to achieve catalytic activation by liberating the first step reactants in preparation for catalysis of the first step of splicing.
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Affiliation(s)
- Penghui Bao
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Claudia Höbartner
- Research Group Nucleic Acid Chemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
| | - Klaus Hartmuth
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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46
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Yeh CS, Chang SL, Chen JH, Wang HK, Chou YC, Wang CH, Huang SH, Larson A, Pleiss JA, Chang WH, Chang TH. The conserved AU dinucleotide at the 5' end of nascent U1 snRNA is optimized for the interaction with nuclear cap-binding-complex. Nucleic Acids Res 2017; 45:9679-9693. [PMID: 28934473 PMCID: PMC5766165 DOI: 10.1093/nar/gkx608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/05/2017] [Indexed: 11/13/2022] Open
Abstract
Splicing is initiated by a productive interaction between the pre-mRNA and the U1 snRNP, in which a short RNA duplex is established between the 5' splice site of a pre-mRNA and the 5' end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5'-end of the U1 snRNA is highly conserved, despite the absence of an apparent role in the formation of the duplex. To explore this conundrum, we varied this AU dinucleotide into all possible permutations and analyzed the resulting molecular consequences. This led to the unexpected findings that the AU dinucleotide dictates the optimal binding of cap-binding complex (CBC) to the 5' end of the nascent U1 snRNA, which ultimately influences the utilization of U1 snRNP in splicing. Our data also provide a structural interpretation as to why the AU dinucleotide is conserved during evolution.
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Affiliation(s)
- Chung-Shu Yeh
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Jui-Hui Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Hsuan-Kai Wang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Yue-Chang Chou
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Shih-Hsin Huang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan.,Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Amy Larson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jeffrey A Pleiss
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tien-Hsien Chang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
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47
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snRNP proteins in health and disease. Semin Cell Dev Biol 2017; 79:92-102. [PMID: 29037818 DOI: 10.1016/j.semcdb.2017.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 01/16/2023]
Abstract
Split gene architecture of most human genes requires removal of intervening sequences by mRNA splicing that occurs on large multiprotein complexes called spliceosomes. Mutations compromising several spliceosomal components have been recorded in degenerative syndromes and haematological neoplasia, thereby highlighting the importance of accurate splicing execution in homeostasis of assorted adult tissues. Moreover, insufficient splicing underlies defective development of craniofacial skeleton and upper extremities. This review summarizes recent advances in the understanding of splicing factor function deduced from cryo-EM structures. We combine these data with the characterization of splicing factors implicated in hereditary or somatic disorders, with a focus on potential functional consequences the mutations may elicit in spliceosome assembly and/or performance. Given aberrant splicing or perturbations in splicing efficiency substantially underpin disease pathogenesis, profound understanding of the mis-splicing principles may open new therapeutic vistas. In three major sections dedicated to retinal dystrophies, hereditary acrofacial syndromes, and haematological malignancies, we delineate the noticeable variety of conditions associated with dysfunctional splicing and accentuate recurrent patterns in splicing defects.
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48
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Fica SM, Nagai K. Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine. Nat Struct Mol Biol 2017; 24:791-799. [PMID: 28981077 DOI: 10.1038/nsmb.3463] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/10/2017] [Indexed: 12/18/2022]
Abstract
The spliceosome excises introns from pre-messenger RNAs using an RNA-based active site that is cradled by a dynamic protein scaffold. A recent revolution in cryo-electron microscopy (cryo-EM) has led to near-atomic-resolution structures of key spliceosome complexes that provide insight into the mechanism of activation, splice site positioning, catalysis, protein rearrangements and ATPase-mediated dynamics of the active site. The cryo-EM structures rationalize decades of observations from genetic and biochemical studies and provide a molecular framework for future functional studies.
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49
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Scheres SH, Nagai K. CryoEM structures of spliceosomal complexes reveal the molecular mechanism of pre-mRNA splicing. Curr Opin Struct Biol 2017; 46:130-139. [PMID: 28888105 DOI: 10.1016/j.sbi.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/26/2017] [Accepted: 08/07/2017] [Indexed: 01/09/2023]
Abstract
The spliceosome is an intricate molecular machine which catalyses the removal of introns from eukaryotic mRNA precursors by two trans-esterification reactions (branching and exon ligation) to produce mature mRNA with uninterrupted protein coding sequences. The structures of the spliceosome in several key states determined by electron cryo-microscopy have greatly advanced our understanding of its molecular mechanism. The catalytic RNA core is formed during the activation of the fully assembled B to Bact complex and remains largely unchanged throughout the splicing cycle. RNA helicases and step specific factors regulate docking and undocking of the substrates (branch site and 3' splice site) to the single RNA-based active site to catalyse the two trans-esterification reactions.
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Affiliation(s)
- Sjors Hw Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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50
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Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics. Proc Natl Acad Sci U S A 2017; 114:E7688-E7696. [PMID: 28839094 DOI: 10.1073/pnas.1703507114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Decades of study of the architecture and function of structured RNAs have led to the perspective that RNA tertiary structure is modular, made of locally stable domains that retain their structure across RNAs. We formalize a hypothesis inspired by this modularity-that RNA folding thermodynamics and kinetics can be quantitatively predicted from separable energetic contributions of the individual components of a complex RNA. This reconstitution hypothesis considers RNA tertiary folding in terms of ΔGalign, the probability of aligning tertiary contact partners, and ΔGtert, the favorable energetic contribution from the formation of tertiary contacts in an aligned state. This hypothesis predicts that changes in the alignment of tertiary contacts from different connecting helices and junctions (ΔGHJH) or from changes in the electrostatic environment (ΔG+/-) will not affect the energetic perturbation from a mutation in a tertiary contact (ΔΔGtert). Consistent with these predictions, single-molecule FRET measurements of folding of model RNAs revealed constant ΔΔGtert values for mutations in a tertiary contact embedded in different structural contexts and under different electrostatic conditions. The kinetic effects of these mutations provide further support for modular behavior of RNA elements and suggest that tertiary mutations may be used to identify rate-limiting steps and dissect folding and assembly pathways for complex RNAs. Overall, our model and results are foundational for a predictive understanding of RNA folding that will allow manipulation of RNA folding thermodynamics and kinetics. Conversely, the approaches herein can identify cases where an independent, additive model cannot be applied and so require additional investigation.
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