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Fukudome A, Ishiga Y, Nagashima Y, Davidson KH, Chou HA, Mysore KS, Koiwa H. Functional diversity of Medicago truncatula RNA polymerase II CTD phosphatase isoforms produced in the Arabidopsis thaliana superexpression platform. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111309. [PMID: 35696909 DOI: 10.1016/j.plantsci.2022.111309] [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: 01/01/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Medicago truncatula is a model system for legume plants, which has substantially expanded the genome relative to the prototypical model dicot plant, Arabidopsis thaliana. An essential transcriptional regulator, FCP1 (transcription factor IIF-interacting RNA polymerase II carboxyl-terminal phosphatase 1) ortholog, is encoded by a single essential gene CPL4 (CTD-phosphatase-like 4), whereas M. truncatula genome contains four genes homologous to FCP1/AtCPL4, and splicing variants of MtCPL4 are observed. Functional diversification of MtCPL4 family proteins was analyzed using recombinant proteins (MtCPL4a1, MtCPL4a2, and MtCPL4b) produced in Arabidopsis cell culture system developed for plant protein overexpression. In vitro CTD phosphatase assay using highly purified MtCPL4 preparations revealed a potent CTD phosphatase activity in MtCPL4b, but not two splicing variants of MtCPL4a. On the other hand, in planta binding assay to RNA polymerase II (pol II) revealed a greater pol II-binding activity of both MtCPL4a variants. Our results indicate functional diversification of MtCPL4 isoforms and suggest the presence of a large number of functionally specialized CTD-phosphatase-like proteins in plants.
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Affiliation(s)
- Akihito Fukudome
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Yasuhiro Ishiga
- Noble Research Institute, LLC., Ardmore, OK 73401, USA; Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yukihiro Nagashima
- Vegetable and Fruit Development Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Katherine H Davidson
- Vegetable and Fruit Development Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Hsiu-An Chou
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Kirankumar S Mysore
- Noble Research Institute, LLC., Ardmore, OK 73401, USA; Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401, USA; Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma 74044, USA
| | - Hisashi Koiwa
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX 77843, USA; Vegetable and Fruit Development Center, Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA.
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2
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Medellin B, Yang W, Konduri S, Dong J, Irani S, Wu H, Matthews WL, Zhang ZY, Siegel D, Zhang Y. Targeted Covalent Inhibition of Small CTD Phosphatase 1 to Promote the Degradation of the REST Transcription Factor in Human Cells. J Med Chem 2022; 65:507-519. [PMID: 34931516 PMCID: PMC8826594 DOI: 10.1021/acs.jmedchem.1c01655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The repressor element-1 silencing transcription factor (REST) represses neuronal gene expression, whose dysregulation is implicated in brain tumors and neurological diseases. A high level of REST protein drives the tumor growth in some glioblastoma cells. While transcription factors like REST are challenging targets for small-molecule inhibitors, the inactivation of a regulatory protein, small CTD phosphatase 1 (SCP1), promotes REST degradation and reduces transcriptional activity. This study rationally designed a series of α,β-unsaturated sulfones to serve as potent and selective covalent inhibitors against SCP1. The compounds inactivate SCP1 via covalent modification of Cys181 located at the active site entrance. Cellular studies showed that the inhibitors inactivate SCP1 in a time- and dose-dependent manner with an EC50 ∼1.5 μM, reducing REST protein levels and activating specific REST-suppressed genes. These compounds represent a promising line of small-molecule inhibitors as a novel lead for glioblastoma whose growth is driven by REST transcription activity.
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Affiliation(s)
| | | | - Srihari Konduri
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Jiajun Dong
- Department of Medicinal Chemistry and Molecular Pharmacology and Department of Chemistry, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Seema Irani
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Haoyi Wu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Wendy L. Matthews
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology and Department of Chemistry, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Dionico Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
| | - Yan Zhang
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, United States
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3
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Rallabandi HR, Lee D, Sung J, Kim YJ. Peripheral Inhibition of Small C‐Terminal Domain Phosphatase 1 With Napthoquinone Analogs. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Harikrishna Reddy Rallabandi
- Department of Medicinal Biosciences and Nanotechnology Research CenterKonkuk University Chungju 27478 Republic of Korea
| | - Dongsun Lee
- Department of Medicinal Biosciences and Nanotechnology Research CenterKonkuk University Chungju 27478 Republic of Korea
| | - Jinmo Sung
- Department of Medicinal Biosciences and Nanotechnology Research CenterKonkuk University Chungju 27478 Republic of Korea
| | - Young Jun Kim
- Department of Medicinal Biosciences and Nanotechnology Research CenterKonkuk University Chungju 27478 Republic of Korea
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4
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Schwer B, Ghosh A, Sanchez AM, Lima CD, Shuman S. Genetic and structural analysis of the essential fission yeast RNA polymerase II CTD phosphatase Fcp1. RNA (NEW YORK, N.Y.) 2015; 21:1135-1146. [PMID: 25883047 PMCID: PMC4436666 DOI: 10.1261/rna.050286.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 02/25/2015] [Indexed: 06/04/2023]
Abstract
Protein phosphatases regulate mRNA synthesis and processing by remodeling the carboxy-terminal domain (CTD) of RNA polymerase II (Pol2) to dynamically inscribe a Pol2 CTD code. Fission yeast Fcp1 (SpFcp1) is an essential 723-amino acid CTD phosphatase that preferentially hydrolyzes Ser2-PO4 of the YS(2)PTSPS repeat. The SpFcp1 catalytic domain (aa 140-580) is composed of a DxDxT acyl-phosphatase module (FCPH) and a BRCT module. Here we conducted a genetic analysis of SpFcp1, which shows that (i) phosphatase catalytic activity is required for vegetative growth of fission yeast; (ii) the flanking amino-terminal domain (aa 1-139) and its putative metal-binding motif C(99)H(101)Cys(109)C(112) are essential; (iii) the carboxy-terminal domain (aa 581-723) is dispensable; (iv) a structurally disordered internal segment of the FCPH domain (aa 330-393) is dispensable; (v) lethal SpFcp1 mutations R271A and R299A are rescued by shortening the Pol2 CTD repeat array; and (vi) CTD Ser2-PO4 is not the only essential target of SpFcp1 in vivo. Recent studies highlight a second CTD code involving threonine phosphorylation of a repeat motif in transcription elongation factor Spt5. We find that Fcp1 can dephosphorylate Thr1-PO4 of the fission yeast Spt5 CTD nonamer repeat T(1)PAWNSGSK. We identify Arg271 as a governor of Pol2 versus Spt5 CTD substrate preference. Our findings implicate Fcp1 as a versatile sculptor of both the Pol2 and Spt5 CTD codes. Finally, we report a new 1.45 Å crystal structure of SpFcp1 with Mg(2+) and AlF3 that mimics an associative phosphorane transition state of the enzyme-aspartyl-phosphate hydrolysis reaction.
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Affiliation(s)
- Beate Schwer
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Agnidipta Ghosh
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Ana M Sanchez
- Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA Howard Hughes Medical Institute, Sloan-Kettering Institute, New York, New York 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10065, USA
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5
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Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
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6
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Zheng J, Yates SP, Jia Z. Structural and mechanistic insights into the bifunctional enzyme isocitrate dehydrogenase kinase/phosphatase AceK. Philos Trans R Soc Lond B Biol Sci 2012; 367:2656-68. [PMID: 22889914 DOI: 10.1098/rstb.2011.0426] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The switch between the Krebs cycle and the glyoxylate bypass is controlled by isocitrate dehydrogenase kinase/phosphatase (AceK). AceK, a bifunctional enzyme, phosphorylates and dephosphorylates isocitrate dehydrogenase (IDH) with its unique active site that harbours both the kinase and ATP/ADP-dependent phosphatase activities. AceK was the first example of prokaryotic phosphorylation identified, and the recent characterization of the structures of AceK and its complex with its protein substrate, IDH, now offers a new understanding of both previous and future endeavours. AceK is structurally similar to the eukaryotic protein kinase superfamily, sharing many of the familiar catalytic and regulatory motifs, demonstrating a close evolutionary relationship. Although the active site is shared by both the kinase and phosphatase functions, the catalytic residues needed for phosphatase function are readily seen when compared with the DXDX(T/V) family of phosphatases, despite the fact that the phosphatase function of AceK is strictly ATP/ADP-dependent. Structural analysis has also allowed a detailed look at regulation and its stringent requirements for interacting with IDH.
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Affiliation(s)
- Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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7
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Xiang K, Manley JL, Tong L. An unexpected binding mode for a Pol II CTD peptide phosphorylated at Ser7 in the active site of the CTD phosphatase Ssu72. Genes Dev 2012; 26:2265-70. [PMID: 23070812 DOI: 10.1101/gad.198853.112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ssu72, an RNA polymerase II C-terminal domain (CTD) phospho-Ser5 (pSer5) phosphatase, was recently reported to have pSer7 phosphatase activity as well. We report here the crystal structure of a ternary complex of the N-terminal domain of human symplekin, human Ssu72, and a 10-mer pSer7 CTD peptide. Surprisingly, the peptide is bound in the Ssu72 active site with its backbone running in the opposite direction compared with a pSer5 peptide. The pSer7 phosphatase activity of Ssu72 is ∼4000-fold lower than its pSer5 phosphatase activity toward a peptide substrate, consistent with the structural observations.
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Affiliation(s)
- Kehui Xiang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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8
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Jasnovidova O, Stefl R. The CTD code of RNA polymerase II: a structural view. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 4:1-16. [DOI: 10.1002/wrna.1138] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Xiang K, Manley JL, Tong L. The yeast regulator of transcription protein Rtr1 lacks an active site and phosphatase activity. Nat Commun 2012; 3:946. [PMID: 22781759 PMCID: PMC3522426 DOI: 10.1038/ncomms1947] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 06/07/2012] [Indexed: 01/16/2023] Open
Abstract
The activity of RNA polymerase II (Pol II) is controlled in part by the phosphorylation state of the C-terminal domain (CTD) of its largest subunit. Recent reports have suggested that yeast regulator of transcription protein, Rtr1, and its human homologue RPAP2, possess Pol II CTD Ser5 phosphatase activity. Here we report the crystal structure of Kluyveromyces lactis Rtr1, which reveals a new type of zinc finger protein and does not have any close structural homologues. Importantly, the structure does not show evidence of an active site, and extensive experiments to demonstrate its CTD phosphatase activity have been unsuccessful, suggesting that Rtr1 has a non-catalytic role in CTD dephosphorylation.
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Affiliation(s)
- Kehui Xiang
- Department of Biological Sciences, Columbia University, New York 10027, USA
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10
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Zhang DW, Rodríguez-Molina JB, Tietjen JR, Nemec CM, Ansari AZ. Emerging Views on the CTD Code. GENETICS RESEARCH INTERNATIONAL 2012; 2012:347214. [PMID: 22567385 PMCID: PMC3335543 DOI: 10.1155/2012/347214] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/03/2011] [Indexed: 12/21/2022]
Abstract
The C-terminal domain (CTD) of RNA polymerase II (Pol II) consists of conserved heptapeptide repeats that function as a binding platform for different protein complexes involved in transcription, RNA processing, export, and chromatin remodeling. The CTD repeats are subject to sequential waves of posttranslational modifications during specific stages of the transcription cycle. These patterned modifications have led to the postulation of the "CTD code" hypothesis, where stage-specific patterns define a spatiotemporal code that is recognized by the appropriate interacting partners. Here, we highlight the role of CTD modifications in directing transcription initiation, elongation, and termination. We examine the major readers, writers, and erasers of the CTD code and examine the relevance of describing patterns of posttranslational modifications as a "code." Finally, we discuss major questions regarding the function of the newly discovered CTD modifications and the fundamental insights into transcription regulation that will necessarily emerge upon addressing those challenges.
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Affiliation(s)
- David W. Zhang
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Juan B. Rodríguez-Molina
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Joshua R. Tietjen
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Corey M. Nemec
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - Aseem Z. Ansari
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
- Genome Center of Wisconsin, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
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11
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Zhang M, Gill GN, Zhang Y. Bio-molecular architects: a scaffold provided by the C-terminal domain of eukaryotic RNA polymerase II. NANO REVIEWS 2010; 1:NANO-1-5502. [PMID: 22110856 PMCID: PMC3215212 DOI: 10.3402/nano.v1i0.5502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 07/30/2010] [Accepted: 08/03/2010] [Indexed: 11/14/2022]
Abstract
In eukaryotic cells, the transcription of genes is accurately orchestrated both spatially and temporally by the C-terminal domain of RNA polymerase II (CTD). The CTD provides a dynamic platform to recruit different regulators of the transcription apparatus. Different posttranslational modifications are precisely applied to specific sites of the CTD to coordinate transcription process. Regulators of the RNA polymerase II must identify specific sites in the CTD for cellular survival, metabolism, and development. Even though the CTD is disordered in the eukaryotic RNA polymerase II crystal structures due to its intrinsic flexibility, recent advances in the complex structural analysis of the CTD with its binding partners provide essential clues for understanding how selectivity is achieved for individual site recognition. The recent discoveries of the interactions between the CTD and histone modification enzymes disclose an important role of the CTD in epigenetic control of the eukaryotic gene expression. The intersection of the CTD code with the histone code discloses an intriguing yet complicated network for eukaryotic transcriptional regulation.
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Affiliation(s)
- Mengmeng Zhang
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, USA
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12
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Abstract
The reversible phosphorylation of proteins is accomplished by opposing activities of kinases and phosphatases. Relatively few protein serine/threonine phosphatases (PSPs) control the specific dephosphorylation of thousands of phosphoprotein substrates. Many PSPs, exemplified by protein phosphatase 1 (PP1) and PP2A, achieve substrate specificity and regulation through combinatorial interactions between conserved catalytic subunits and a large number of regulatory subunits. Other PSPs, represented by PP2C and FCP/SCP, contain both catalytic and regulatory domains within the same polypeptide chain. Here, we discuss biochemical and structural investigations that advance the mechanistic understanding of the three major classes of PSPs, with a focus on PP2A.
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Affiliation(s)
- Yigong Shi
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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13
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Mallavarapu A, Thomson M, Ullian B, Gunawardena J. Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface 2009; 6:257-70. [PMID: 18647734 PMCID: PMC2659579 DOI: 10.1098/rsif.2008.0205] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mathematical models are increasingly used to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations presents a fundamental barrier to progress. Overcoming this requires modularity, enabling sub-systems to be specified independently and combined incrementally, and abstraction, enabling generic properties of biological processes to be specified independently of specific instances. These, in turn, require models to be represented as programs rather than as datatypes. Programmable modularity and abstraction enables libraries of modules to be created, which can be instantiated and reused repeatedly in different contexts with different components. We have developed a computational infrastructure that accomplishes this. We show here why such capabilities are needed, what is required to implement them and what can be accomplished with them that could not be done previously.
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Affiliation(s)
- Aneil Mallavarapu
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Cambridge, MA 02115, USA.
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14
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Sajiki K, Hatanaka M, Nakamura T, Takeda K, Shimanuki M, Yoshida T, Hanyu Y, Hayashi T, Nakaseko Y, Yanagida M. Genetic control of cellular quiescence in S. pombe. J Cell Sci 2009; 122:1418-29. [PMID: 19366728 DOI: 10.1242/jcs.046466] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transition from proliferation to quiescence brings about extensive changes in cellular behavior and structure. However, the genes that are crucial for establishing and/or maintaining quiescence are largely unknown. The fission yeast Schizosaccharomyces pombe is an excellent model in which to study this problem, because it becomes quiescent under nitrogen starvation. Here, we characterize 610 temperature-sensitive mutants, and identify 33 genes that are required for entry into and maintenance of quiescence. These genes cover a broad range of cellular functions in the cytoplasm, membrane and nucleus. They encode proteins for stress-responsive and cell-cycle kinase signaling pathways, for actin-bound and osmo-controlling endosome formation, for RNA transcription, splicing and ribosome biogenesis, for chromatin silencing, for biosynthesis of lipids and ATP, for cell-wall and membrane morphogenesis, and for protein trafficking and vesicle fusion. We specifically highlight Fcp1, a CTD phosphatase of RNA polymerase II, which differentially affects the transcription of genes that are involved in quiescence and proliferation. We propose that the transcriptional role of Fcp1 is central in differentiating quiescence from proliferation.
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Affiliation(s)
- Kenichi Sajiki
- Okinawa Institute of Science and Technology (OIST), Initial Research Project, Uruma 904-2234, Okinawa, Japan
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15
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Ghosh A, Shuman S, Lima CD. The structure of Fcp1, an essential RNA polymerase II CTD phosphatase. Mol Cell 2009; 32:478-90. [PMID: 19026779 DOI: 10.1016/j.molcel.2008.09.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 08/22/2008] [Accepted: 09/11/2008] [Indexed: 11/24/2022]
Abstract
Kinases and phosphatases regulate mRNA synthesis and processing by phosphorylating and dephosphorylating the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. Fcp1 is an essential CTD phosphatase that preferentially hydrolyzes Ser2-PO(4) of the tandem YSPTSPS CTD heptad array. Fcp1 crystal structures were captured at two stages of the reaction pathway: a Mg-BeF(3) complex that mimics the aspartylphosphate intermediate and a Mg-AlF(4)(-) complex that mimics the transition state of the hydrolysis step. Fcp1 is a Y-shaped protein composed of an acylphosphatase domain located at the base of a deep canyon formed by flanking modules that are missing from the small CTD phosphatase (SCP) clade: an Fcp1-specific helical domain and a C-terminal BRCA1 C-terminal (BRCT) domain. The structure and mutational analysis reveals that Fcp1 and Scp1 (a Ser5-selective phosphatase) adopt different CTD-binding modes; we surmise the CTD threads through the Fcp1 canyon to access the active site.
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Affiliation(s)
- Agnidipta Ghosh
- Structural Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA
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16
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Abstract
Reversible protein phosphorylation on multiple sites is a key regulatory mechanism in most cellular processes. We consider here a kinase-phosphatase-substrate system with two sites, under mass-action kinetics, with no restrictions on the order of phosphorylation or dephosphorylation. We show that the concentrations of the four phosphoforms at steady state satisfy an algebraic formula-an invariant-that is independent of the other chemical species, such as free enzymes or enzyme-substrate complexes, and holds irrespective of the starting conditions and the total amounts of enzymes and substrate. Such invariants allow stringent quantitative predictions to be made without requiring any knowledge of site-specific parameter values. We introduce what we believe are novel methods from algebraic geometry-Gröbner bases, rational curves-to calculate invariants. These methods are particularly significant because they make it possible to treat parameters symbolically without having to specify their numerical values, and thereby allow us to sidestep the parameter problem. We anticipate that this approach will have much wider applications in biological modeling.
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17
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Kerk D, Templeton G, Moorhead GBG. Evolutionary radiation pattern of novel protein phosphatases revealed by analysis of protein data from the completely sequenced genomes of humans, green algae, and higher plants. PLANT PHYSIOLOGY 2008; 146:351-67. [PMID: 18156295 PMCID: PMC2245839 DOI: 10.1104/pp.107.111393] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In addition to the major serine/threonine-specific phosphoprotein phosphatase, Mg(2+)-dependent phosphoprotein phosphatase, and protein tyrosine phosphatase families, there are novel protein phosphatases, including enzymes with aspartic acid-based catalysis and subfamilies of protein tyrosine phosphatases, whose evolutionary history and representation in plants is poorly characterized. We have searched the protein data sets encoded by the well-finished nuclear genomes of the higher plants Arabidopsis (Arabidopsis thaliana) and Oryza sativa, and the latest draft data sets from the tree Populus trichocarpa and the green algae Chlamydomonas reinhardtii and Ostreococcus tauri, for homologs to several classes of novel protein phosphatases. The Arabidopsis proteins, in combination with previously published data, provide a complete inventory of known types of protein phosphatases in this organism. Phylogenetic analysis of these proteins reveals a pattern of evolution where a diverse set of protein phosphatases was present early in the history of eukaryotes, and the division of plant and animal evolution resulted in two distinct sets of protein phosphatases. The green algae occupy an intermediate position, and show similarity to both plants and animals, depending on the protein. Of specific interest are the lack of cell division cycle (CDC) phosphatases CDC25 and CDC14, and the seeming adaptation of CDC14 as a protein interaction domain in higher plants. In addition, there is a dramatic increase in proteins containing RNA polymerase C-terminal domain phosphatase-like catalytic domains in the higher plants. Expression analysis of Arabidopsis phosphatase genes differentially amplified in plants (specifically the C-terminal domain phosphatase-like phosphatases) shows patterns of tissue-specific expression with a statistically significant number of correlated genes encoding putative signal transduction proteins.
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Affiliation(s)
- David Kerk
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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18
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Zhu H, Smith P, Wang LK, Shuman S. Structure-function analysis of the 3' phosphatase component of T4 polynucleotide kinase/phosphatase. Virology 2007; 366:126-36. [PMID: 17493655 PMCID: PMC2761019 DOI: 10.1016/j.virol.2007.03.059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Revised: 03/11/2007] [Accepted: 03/27/2007] [Indexed: 10/23/2022]
Abstract
T4 polynucleotide kinase/phosphatase (Pnkp) exemplifies a family of bifunctional enzymes with 5'-kinase and 3' phosphatase activities that function in nucleic acid repair. T4 Pnkp is a homotetramer of a 301-aa polypeptide, which consists of an N-terminal kinase domain of the P-loop phosphotransferase superfamily and a C-terminal phosphatase domain of the DxD acylphosphatase superfamily. The homotetramer is formed via pairs of phosphatase-phosphatase and kinase-kinase homodimer interfaces. Here we identify four side chains-Asp187, Ser211, Lys258, and Asp277-that are required for 3' phosphatase activity. Alanine mutations at these positions abolished phosphatase activity without affecting kinase function or tetramerization. Conservative substitutions of asparagine or glutamate for Asp187 did not revive the 3' phosphatase, nor did arginine or glutamine substitutions for Lys258. Threonine in lieu of Ser211 and glutamate in lieu of Asp277 restored full activity, whereas asparagine at position 277 had no salutary effect. We report a 3.0 A crystal structure of the Pnkp tetramer, in which a sulfate ion is coordinated between Arg246 and Arg279 in a position that we propose mimics one of the penultimate phosphodiesters (5'NpNpNp-3') of the polynucleotide 3'-PO(4) substrate. The amalgam of mutational and structural data engenders a plausible catalytic mechanism for the phosphatase that includes covalent catalysis (via Asp165), general acid-base catalysis (via Asp167), metal coordination (by Asp165, Asp277 and Asp278), and transition state stabilization (via Lys258, Ser211, backbone amides, and the divalent cation). Other critical side chains play architectural roles (Arg176, Asp187, Arg213, Asp254). To probe the role of oligomerization in phosphatase function, we introduced six double-alanine cluster mutations at the phosphatase-phosphatase domain interface, two of which (R297A-Q295A and E292A-D300A) converted Pnkp from a tetramer to a dimer and ablated phosphatase activity.
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19
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Qian H, Ji C, Zhao S, Chen J, Jiang M, Zhang Y, Yan M, Zheng D, Sun Y, Xie Y, Mao Y. Expression and characterization of HSPC129, a RNA polymerase II C-terminal domain phosphatase. Mol Cell Biochem 2007; 303:183-8. [PMID: 17487459 DOI: 10.1007/s11010-007-9472-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Accepted: 04/03/2007] [Indexed: 11/25/2022]
Abstract
Phosphorylation status of RNA polymerase (RNAP) II's largest subunit C-terminal domain (CTD) plays an important role during transcription cycles. The reversible phosphorylation mainly occurs at serine 2 and serine 5 of CTD heptapeptide repeats and regulates RNAP II's activity during transcription initiation, elongation and RNA processing. Here we expressed and characterized HSPC129, a putative human protein bearing a CTD phosphatase domain (CPD). PCR analysis showed that it was ubiquitously expressed. HSPC129DeltaTM, the truncate HSPC129 with first 156 N terminal amino acids deleted, exhibited Mg(2+) dependent phosphatase activity at pH 5.0. Its specific CTD phosphatase activity was verified in vitro. Our research suggests that HSPC129 may regulate the dynamic phosphorylation of RNAP II CTD.
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Affiliation(s)
- Hui Qian
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Room 602, Science Building, Shanghai, PR China
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20
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Reyes-Reyes M, Hampsey M. Role for the Ssu72 C-terminal domain phosphatase in RNA polymerase II transcription elongation. Mol Cell Biol 2007; 27:926-36. [PMID: 17101794 PMCID: PMC1800697 DOI: 10.1128/mcb.01361-06] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 08/18/2006] [Accepted: 11/01/2006] [Indexed: 12/31/2022] Open
Abstract
The RNA polymerase II (RNAP II) transcription cycle is accompanied by changes in the phosphorylation status of the C-terminal domain (CTD), a reiterated heptapeptide sequence (Y(1)S(2)P(3)T(4)S(5)P(6)S(7)) present at the C terminus of the largest RNAP II subunit. One of the enzymes involved in this process is Ssu72, a CTD phosphatase with specificity for serine-5-P. Here we report that the ssu72-2-encoded Ssu72-R129A protein is catalytically impaired in vitro and that the ssu72-2 mutant accumulates the serine-5-P form of RNAP II in vivo. An in vitro transcription system derived from the ssu72-2 mutant exhibits impaired elongation efficiency. Mutations in RPB1 and RPB2, the genes encoding the two largest subunits of RNAP II, were identified as suppressors of ssu72-2. The rpb1-1001 suppressor encodes an R1281A replacement, whereas rpb2-1001 encodes an R983G replacement. This information led us to identify the previously defined rpb2-4 and rpb2-10 alleles, which encode catalytically slow forms of RNAP II, as additional suppressors of ssu72-2. Furthermore, deletion of SPT4, which encodes a subunit of the Spt4-Spt5 early elongation complex, also suppresses ssu72-2, whereas the spt5-242 allele is suppressed by rpb2-1001. These results define Ssu72 as a transcription elongation factor. We propose a model in which Ssu72 catalyzes serine-5-P dephosphorylation subsequent to addition of the 7-methylguanosine cap on pre-mRNA in a manner that facilitates the RNAP II transition into the elongation stage of the transcription cycle.
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Affiliation(s)
- Mariela Reyes-Reyes
- Department of Biochemistry, Robert Wood Johnson Medical School, 683 Hoes Lane West, Piscataway, NJ 08854, USA
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21
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Zhang Y, Kim Y, Genoud N, Gao J, Kelly JW, Pfaff SL, Gill GN, Dixon JE, Noel JP. Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1. Mol Cell 2007; 24:759-770. [PMID: 17157258 PMCID: PMC2859291 DOI: 10.1016/j.molcel.2006.10.027] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 09/08/2006] [Accepted: 10/19/2006] [Indexed: 10/23/2022]
Abstract
Phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) represent a critical regulatory checkpoint for transcription. Transcription initiation requires Fcp1/Scp1-mediated dephosphorylation of phospho-CTD. Fcp1 and Scp1 belong to a family of Mg2+ -dependent phosphoserine (P.Ser)/phosphothreonine (P.Thr)-specific phosphatases. We recently showed that Scp1 is an evolutionarily conserved regulator of neuronal gene silencing. Here, we present the X-ray crystal structures of a dominant-negative form of human Scp1 (D96N mutant) bound to mono- and diphosphorylated peptides encompassing the CTD heptad repeat (Y1S2P3T4S5P6S7). Moreover, kinetic and thermodynamic analyses of Scp1-phospho-CTD peptide complexes support the structures determined. This combined structure-function analysis discloses the residues in Scp1 involved in CTD binding and its preferential dephosphorylation of P.Ser5 of the CTD heptad repeat. Moreover, these results provide a template for the design of specific inhibitors of Scp1 for the study of neuronal stem cell development.
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Affiliation(s)
- Yan Zhang
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Youngjun Kim
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093
| | - Nicolas Genoud
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Jianmin Gao
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Jeffery W Kelly
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Samuel L Pfaff
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037
| | - Gordon N Gill
- Department of Medicine, University of California, San Diego, La Jolla, California 92093; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093
| | - Joseph P Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037.
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22
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Suh MH, Ye P, Zhang M, Hausmann S, Shuman S, Gnatt AL, Fu J. Fcp1 directly recognizes the C-terminal domain (CTD) and interacts with a site on RNA polymerase II distinct from the CTD. Proc Natl Acad Sci U S A 2005; 102:17314-9. [PMID: 16301539 PMCID: PMC1297677 DOI: 10.1073/pnas.0507987102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Indexed: 01/22/2023] Open
Abstract
Fcp1 is an essential protein phosphatase that hydrolyzes phosphoserines within the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II). Fcp1 plays a major role in the regulation of CTD phosphorylation and, hence, critically influences the function of Pol II throughout the transcription cycle. The basic understanding of Fcp1-CTD interaction has remained ambiguous because two different modes have been proposed: the "dockingsite" model versus the "distributive" mechanism. Here we demonstrate biochemically that Fcp1 recognizes and dephosphorylates the CTD directly, independent of the globular non-CTD part of the Pol II structure. We point out that the recognition of CTD by the phosphatase is based on random access and is not driven by Pol II conformation. Results from three different types of experiments reveal that the overall interaction between Fcp1 and Pol II is not stable but dynamic. In addition, we show that Fcp1 also interacts with a region on the polymerase distinct from the CTD. We emphasize that this non-CTD site is functionally distinct from the docking site invoked previously as essential for the CTD phosphatase activity of Fcp1. We speculate that Fcp1 interaction with the non-CTD site may mediate its stimulatory effect on transcription elongation reported previously.
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Affiliation(s)
- Man-Hee Suh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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23
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Hausmann S, Koiwa H, Krishnamurthy S, Hampsey M, Shuman S. Different strategies for carboxyl-terminal domain (CTD) recognition by serine 5-specific CTD phosphatases. J Biol Chem 2005; 280:37681-8. [PMID: 16148005 DOI: 10.1074/jbc.m505292200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The phosphorylated carboxyl-terminal domain (CTD) of RNA polymerase II, consisting of ((1)YSPTSPS(7))(n) heptad repeats, encodes information about the state of the transcriptional apparatus that can be conveyed to factors that regulate mRNA synthesis and processing. Here we describe how the CTD code is read by two classes of protein phosphatases, plant CPLs and yeast Ssu72, that specifically dephosphorylate Ser(5) in vitro. The CPLs and Ssu72 recognize entirely different positional cues in the CTD primary structure. Whereas the CPLs rely on Tyr(1) and Pro(3) located on the upstream side of the Ser(5)-PO(4) target site, Ssu72 recognizes Thr(4) and Pro(6) flanking the target Ser(5)-PO(4) plus the downstream Tyr(1) residue of the adjacent heptad. We surmise that the reading of the CTD code does not obey uniform rules with respect to the location and phasing of specificity determinants. Thus, CTD code, like the CTD structure, is plastic.
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Affiliation(s)
- Stéphane Hausmann
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA
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24
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Zheng H, Ji C, Gu S, Shi B, Wang J, Xie Y, Mao Y. Cloning and characterization of a novel RNA polymerase II C-terminal domain phosphatase. Biochem Biophys Res Commun 2005; 331:1401-7. [PMID: 15883030 DOI: 10.1016/j.bbrc.2005.04.065] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Indexed: 12/12/2022]
Abstract
Reversible phosphorylation of RNA polymerase (RNAP) II's largest subunit C-terminal domain (CTD) is a key event during mRNA metabolism. The CTD phosphatase, FCP1, catalyzes the dephosphorylation of RNAP II and is thought to play a major role in polymerase recycling. In this study, we isolated a novel phosphatase gene by large-scale sequencing analysis of a human fetal brain cDNA library. Its cDNA is 2215 bp in length, encoding a 318-amino acid polypeptide that contains a ubiquitin-like domain and a CTD phosphatase domain. Therefore, it was termed ubiquitin-like domain containing CTD phosphatase 1 (UBLCP1). Reverse transcription PCR (RT-PCR) revealed that UBLCP1 was expressed with relatively lower levels in most adult normal tissues and higher levels in fast growing or tumor tissues. Transient transfection experiment suggested that UBLCP1 was localized in the nucleus of COS-7 cells. Significantly, UBLCP1 could dephosphorylate GST-CTD in vitro. Accordingly, UBLCP1 may play a role in the regulation of phosphorylation state of RNA polymerase II C-terminal domain.
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Affiliation(s)
- Huarui Zheng
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China
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25
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Meinhart A, Kamenski T, Hoeppner S, Baumli S, Cramer P. A structural perspective of CTD function. Genes Dev 2005; 19:1401-15. [PMID: 15964991 DOI: 10.1101/gad.1318105] [Citation(s) in RCA: 255] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events by binding proteins involved in mRNA biogenesis. CTD-binding proteins recognize a specific CTD phosphorylation pattern, which changes during the transcription cycle, due to the action of CTD-modifying enzymes. Structural and functional studies of CTD-binding and -modifying proteins now reveal some of the mechanisms underlying CTD function. Proteins recognize CTD phosphorylation patterns either directly, by contacting phosphorylated residues, or indirectly, without contact to the phosphate. The catalytic mechanisms of CTD kinases and phosphatases are known, but the basis for CTD specificity of these enzymes remains to be understood.
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Affiliation(s)
- Anton Meinhart
- Department of Chemistry and Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
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26
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Koiwa H, Hausmann S, Bang WY, Ueda A, Kondo N, Hiraguri A, Fukuhara T, Bahk JD, Yun DJ, Bressan RA, Hasegawa PM, Shuman S. Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases. Proc Natl Acad Sci U S A 2004; 101:14539-44. [PMID: 15388846 PMCID: PMC521950 DOI: 10.1073/pnas.0403174101] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription and mRNA processing are regulated by phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II, which consists of tandem repeats of a Y(1)S(2)P(3)T(4)S(5)P(6)S(7) heptapeptide. Previous studies showed that members of the plant CTD phosphatase-like (CPL) protein family differentially regulate osmotic stress-responsive and abscisic acid-responsive transcription in Arabidopsis thaliana. Here we report that AtCPL1 and AtCPL2 specifically dephosphorylate Ser-5 of the CTD heptad in Arabidopsis RNA polymerase II, but not Ser-2. An N-terminal catalytic domain of CPL1, which suffices for CTD Ser-5 phosphatase activity in vitro, includes a signature DXDXT acylphosphatase motif, but lacks a breast cancer 1 CTD, which is an essential component of the fungal and metazoan Fcp1 CTD phosphatase enzymes. The CTD of CPL1, which contains two putative double-stranded RNA binding motifs, is essential for the in vivo function of CPL1 and includes a C-terminal 23-aa signal responsible for its nuclear targeting. CPL2 has a similar domain structure but contains only one double-stranded RNA binding motif. Combining mutant alleles of CPL1 and CPL2 causes synthetic lethality of the male but not the female gametes. These results indicate that CPL1 and CPL2 exemplify a unique family of CTD Ser-5-specific phosphatases with an essential role in plant growth and development.
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Affiliation(s)
- Hisashi Koiwa
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-2133, USA.
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27
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Kamenski T, Heilmeier S, Meinhart A, Cramer P. Structure and mechanism of RNA polymerase II CTD phosphatases. Mol Cell 2004; 15:399-407. [PMID: 15304220 DOI: 10.1016/j.molcel.2004.06.035] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Revised: 05/21/2004] [Accepted: 05/26/2004] [Indexed: 11/15/2022]
Abstract
Recycling of RNA polymerase II (Pol II) after transcription requires dephosphorylation of the polymerase C-terminal domain (CTD) by the phosphatase Fcp1. We report the X-ray structure of the small CTD phosphatase Scp1, which is homologous to the Fcp1 catalytic domain. The structure shows a core fold and an active center similar to those of phosphotransferases and phosphohydrolases that solely share a DXDX(V/T) signature motif with Fcp1/Scp1. We demonstrate that the first aspartate in the signature motif undergoes metal-assisted phosphorylation during catalysis, resulting in a phosphoaspartate intermediate that was structurally mimicked with the inhibitor beryllofluoride. Specificity may result from CTD binding to a conserved hydrophobic pocket between the active site and an insertion domain that is unique to Fcp1/Scp1. Fcp1 specificity may additionally arise from phosphatase recruitment near the CTD via the Pol II subcomplex Rpb4/7, which is shown to be required for binding of Fcp1 to the polymerase in vitro.
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Affiliation(s)
- Tomislav Kamenski
- Department of Chemistry and Biochemistry, Gene Center, University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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28
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Hausmann S, Schwer B, Shuman S. AnEncephalitozoon cuniculiOrtholog of the RNA Polymerase II Carboxyl-Terminal Domain (CTD) Serine Phosphatase Fcp1†. Biochemistry 2004; 43:7111-20. [PMID: 15170348 DOI: 10.1021/bi0499617] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fcp1 is an essential protein serine phosphatase that dephosphorylates Ser2 or Ser5 of the RNA polymerase II carboxyl-terminal domain (CTD) heptad repeat Y(1)S(2)P(3)T(4)S(5)P(6)S(7). The CTD of the microsporidian parasite Encephalitozoon cuniculi consists of 15 heptad repeats, which approximates the minimal CTD length requirement for cell viability in yeast. Here we show that E. cuniculi encodes a minimized 411-aa Fcp1-like protein (EcFcp1), which consists of a DxDx(T/V) phosphatase domain and a BRCA1 carboxyl terminus (BRCT) domain but lacks the large N- and C-terminal domains found in fungal and metazoan Fcp1 enzymes. Nonetheless, EcFcp1 can function in lieu of Saccharomyces cerevisiae Fcp1 to sustain yeast cell growth. Recombinant EcFcp1 is a monomeric enzyme with intrinsic phosphatase activity against nonspecific (p-nitrophenyl phosphate) and specific (CTD-PO(4)) substrates. EcFcp1 dephosphorylates CTD positions Ser2 and Ser5 with similar efficacy in vitro. We exploit synthetic CTD Ser2-PO(4) and Ser5-PO(4) peptides to define minimized substrates for EcFcp1 and to illuminate the importance of CTD primary structure in Ser2 and Ser5 phosphatase activity.
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Affiliation(s)
- Stéphane Hausmann
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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