151
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Zurita-Lopez CI, Sandberg T, Kelly R, Clarke SG. Human protein arginine methyltransferase 7 (PRMT7) is a type III enzyme forming ω-NG-monomethylated arginine residues. J Biol Chem 2012; 287:7859-70. [PMID: 22241471 DOI: 10.1074/jbc.m111.336271] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Full-length human protein arginine methyltransferase 7 (PRMT7) expressed as a fusion protein in Escherichia coli was initially found to generate only ω-N(G)-monomethylated arginine residues in small peptides, suggesting that it is a type III enzyme. A later study, however, characterized fusion proteins of PRMT7 expressed in bacterial and mammalian cells as a type II/type I enzyme, capable of producing symmetrically dimethylated arginine (type II activity) as well as small amounts of asymmetric dimethylarginine (type I activity). We have sought to clarify the enzymatic activity of human PRMT7. We analyzed the in vitro methylation products of a glutathione S-transferase (GST)-PRMT7 fusion protein with robust activity using a variety of arginine-containing synthetic peptides and protein substrates, including a GST fusion with the N-terminal domain of fibrillarin (GST-GAR), myelin basic protein, and recombinant human histones H2A, H2B, H3, and H4. Regardless of the methylation reaction conditions (incubation time, reaction volume, and substrate concentration), we found that PRMT7 only produces ω-N(G)-monomethylarginine with these substrates. In control experiments, we showed that mammalian GST-PRMT1 and Myc-PRMT5 were, unlike PRMT7, able to dimethylate both peptide P-SmD3 and SmB/D3 to give the expected asymmetric and symmetric products, respectively. These experiments show that PRMT7 is indeed a type III human methyltransferase capable of forming only ω-N(G)-monomethylarginine, not asymmetric ω-N(G),N(G)-dimethylarginine or symmetric ω-N(G),N(G')-dimethylarginine, under the conditions tested.
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Affiliation(s)
- Cecilia I Zurita-Lopez
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
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152
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Liokatis S, Edlich C, Soupsana K, Giannios I, Panagiotidou P, Tripsianes K, Sattler M, Georgatos SD, Politou AS. Solution structure and molecular interactions of lamin B receptor Tudor domain. J Biol Chem 2012; 287:1032-42. [PMID: 22052904 PMCID: PMC3256899 DOI: 10.1074/jbc.m111.281303] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Revised: 11/02/2011] [Indexed: 11/06/2022] Open
Abstract
Lamin B receptor (LBR) is a polytopic protein of the nuclear envelope thought to connect the inner nuclear membrane with the underlying nuclear lamina and peripheral heterochromatin. To better understand the function of this protein, we have examined in detail its nucleoplasmic region, which is predicted to harbor a Tudor domain (LBR-TD). Structural analysis by multidimensional NMR spectroscopy establishes that LBR-TD indeed adopts a classical β-barrel Tudor fold in solution, which, however, features an incomplete aromatic cage. Removal of LBR-TD renders LBR more mobile at the plane of the nuclear envelope, but the isolated module does not bind to nuclear lamins, heterochromatin proteins (MeCP2), and nucleosomes, nor does it associate with methylated Arg/Lys residues through its aromatic cage. Instead, LBR-TD exhibits tight and stoichiometric binding to the "histone-fold" region of unassembled, free histone H3, suggesting an interesting role in histone assembly. Consistent with such a role, robust binding to native nucleosomes is observed when LBR-TD is extended toward its carboxyl terminus, to include an area rich in Ser-Arg residues. The Ser-Arg region, alone or in combination with LBR-TD, binds both unassembled and assembled H3/H4 histones, suggesting that the TD/RS interface may operate as a "histone chaperone-like platform."
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Affiliation(s)
| | - Christian Edlich
- the Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany
| | - Katerina Soupsana
- Biology, School of Medicine, University of Ioannina, GR-45110 Ioannina, Greece
- the Biomedical Research Institute, Foundation for Research and Technology (BRI-FORTH), GR-45110 Ioannina, Greece
| | - Ioannis Giannios
- Biology, School of Medicine, University of Ioannina, GR-45110 Ioannina, Greece
- the Biomedical Research Institute, Foundation for Research and Technology (BRI-FORTH), GR-45110 Ioannina, Greece
| | | | - Konstantinos Tripsianes
- the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany, and
- the Department Chemie, Munich Center for Integrated Protein Science (CiPSM),Technische Universität München, 85747 Garching, Germany
| | - Michael Sattler
- the Structural and Computational Biology Unit, European Molecular Biology Laboratory, D-69012 Heidelberg, Germany
- the Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany, and
- the Department Chemie, Munich Center for Integrated Protein Science (CiPSM),Technische Universität München, 85747 Garching, Germany
| | - Spyros D. Georgatos
- Biology, School of Medicine, University of Ioannina, GR-45110 Ioannina, Greece
- the Biomedical Research Institute, Foundation for Research and Technology (BRI-FORTH), GR-45110 Ioannina, Greece
| | - Anastasia S. Politou
- From the Laboratories of Biological Chemistry and
- the Biomedical Research Institute, Foundation for Research and Technology (BRI-FORTH), GR-45110 Ioannina, Greece
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153
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Rajakumara E, Wang Z, Ma H, Hu L, Chen H, Lin Y, Guo R, Wu F, Li H, Lan F, Shi YG, Xu Y, Patel DJ, Shi Y. PHD finger recognition of unmodified histone H3R2 links UHRF1 to regulation of euchromatic gene expression. Mol Cell 2012; 43:275-284. [PMID: 21777816 DOI: 10.1016/j.molcel.2011.07.006] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 07/06/2011] [Accepted: 07/07/2011] [Indexed: 01/20/2023]
Abstract
Histone methylation occurs on both lysine and arginine residues, and its dynamic regulation plays a critical role in chromatin biology. Here we identify the UHRF1 PHD finger (PHD(UHRF1)), an important regulator of DNA CpG methylation, as a histone H3 unmodified arginine 2 (H3R2) recognition modality. This conclusion is based on binding studies and cocrystal structures of PHD(UHRF1) bound to histone H3 peptides, where the guanidinium group of unmodified R2 forms an extensive intermolecular hydrogen bond network, with methylation of H3R2, but not H3K4 or H3K9, disrupting complex formation. We have identified direct target genes of UHRF1 from microarray and ChIP studies. Importantly, we show that UHRF1's ability to repress its direct target gene expression is dependent on PHD(UHRF1) binding to unmodified H3R2, thereby demonstrating the functional importance of this recognition event and supporting the potential for crosstalk between histone arginine methylation and UHRF1 function.
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Affiliation(s)
- Eerappa Rajakumara
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Zhentian Wang
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Honghui Ma
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lulu Hu
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Hao Chen
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yan Lin
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Rui Guo
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Feizhen Wu
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Haitao Li
- Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fei Lan
- Constellation Pharmaceuticals, Cambridge, MA 02140, USA
| | - Yujiang Geno Shi
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhui Xu
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Yang Shi
- Laboratory of Epigenetics, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China.,Department of Biochemistry, Fudan University Medical School, Shanghai 200032, China.,Division of Newborn Medicine and Program in Epigenetics, Department of Medicine, Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
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154
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Cheng D, Vemulapalli V, Bedford MT. Methods applied to the study of protein arginine methylation. Methods Enzymol 2012; 512:71-92. [PMID: 22910203 DOI: 10.1016/b978-0-12-391940-3.00004-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Arginine methylation was discovered in the mid-1960s. About 15 years ago, the first protein arginine N-methyltransferase (PRMT) enzyme was described. The PRMT family now stands at nine members, and these enzymes play a key role in regulating a multitude of cellular events. The majority of the PRMTs have been deleted in mice, thus providing genetically tractable systems for in vivo and cell-based studies. These studies have implicated this posttranslational modification in chromatin remodeling, transcriptional regulation, RNA processing, protein/RNA trafficking, signal transduction, and DNA repair. In this chapter, we introduce different approaches that have been developed to assess protein arginine methylation levels and characterize PRMT substrates.
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Affiliation(s)
- Donghang Cheng
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas, USA.
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155
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Bao J, Wang L, Lei J, Hu Y, Liu Y, Shen H, Yan W, Xu C. STK31(TDRD8) is dynamically regulated throughout mouse spermatogenesis and interacts with MIWI protein. Histochem Cell Biol 2011; 137:377-89. [PMID: 22205278 DOI: 10.1007/s00418-011-0897-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2011] [Indexed: 01/01/2023]
Abstract
Tudor-domain-containing proteins (TDRDs) are suggested to be critical regulators of germinal granules assembly involved in Piwi-interacting RNAs (piRNAs)-mediated pathways, of which associated components and the underlying functional mechanisms, however, remain to be elucidated. We herein characterized the expression pattern of STK31, a member of TDRDs subfamily (also termed as TDRD8), throughout spermatogenesis during mouse postnatal development. RT-PCR and Western blot verified its preferential expression in testis, but not in any other somatic tissues, in addition to embryonic stem cells. Immunofluorescent staining demonstrated that STK31 was confined to granules-like structures in mid-to-late spermatocyte cytoplasm and to acrosomal cap starting at steps 7-8 of spermatids. Furthermore, STK31 retained its localization to equatorial segment of acrosome during epididymal maturation, capacitation, and acrosome reaction. Co-immunoprecipitation assay in vivo and in vitro confirmed MIWI is a bona fide partner of STK31 in mice testes, in combination with LC/MS identification. We also discovered a group of heat shock proteins specifically associated with STK31 in vivo. Our findings suggest mouse STK31 could be a potential nuage-associated protein in the cytoplasm of mid-to-late spermatocytes and play pivotal roles related to fertilization.
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Affiliation(s)
- Jianqiang Bao
- Shanghai Key Laboratory for Reproductive Medicine, Department of Histology and Embryology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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156
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Khorasanizadeh S. Recognition of methylated histones: new twists and variations. Curr Opin Struct Biol 2011; 21:744-9. [PMID: 22056613 DOI: 10.1016/j.sbi.2011.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/30/2011] [Accepted: 10/11/2011] [Indexed: 10/15/2022]
Abstract
Histone tails undergo methylation at their lysines and arginines. These chemical marks act as traffic signals that direct activity of chromatin remodeling complexes to appropriate regions of the genome. A surprisingly diverse group of effector protein modules in chromatin remodeling complexes and their associated factors are involved in the recognition of histone methyllysines. Previous studies generally painted a picture of individual lysines recognized by these protein modules in a 1:1 fashion. However, recent structural studies show more complex interactions where the critical lysines are recognized in pairs, or in the context of nucleosomal DNA, or within the central pore of repeat motifs. These interactions extend our understanding of how histone tail recognition can be enhanced through coupled interactions within a single module or through the cooperation of two different molecules.
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Affiliation(s)
- Sepideh Khorasanizadeh
- Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, 6400 Sanger Road, Orlando, FL 32827, USA.
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157
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Abstract
The chromatin organization modifier domain (chromodomain) was first identified as a motif associated with chromatin silencing in Drosophila. There is growing evidence that chromodomains are evolutionary conserved across different eukaryotic species to control diverse aspects of epigenetic regulation. Although originally reported as histone H3 methyllysine readers, the chromodomain functions have now expanded to recognition of other histone and non-histone partners as well as interaction with nucleic acids. Chromodomain binding to a diverse group of targets is mediated by a conserved substructure called the chromobox homology region. This motif can be used to predict methyllysine binding and distinguish chromodomains from related Tudor "Royal" family members. In this review, we discuss and classify various chromodomains according to their context, structure and the mechanism of target recognition.
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Affiliation(s)
- Bartlomiej J Blus
- Diabetes and Obesity Research Center, Sanford-Burnham Medical Research Institute, Orlando, FL, USA
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158
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Chen C, Nott TJ, Jin J, Pawson T. Deciphering arginine methylation: Tudor tells the tale. Nat Rev Mol Cell Biol 2011; 12:629-42. [PMID: 21915143 DOI: 10.1038/nrm3185] [Citation(s) in RCA: 224] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins can be modified by post-translational modifications such as phosphorylation, methylation, acetylation and ubiquitylation, creating binding sites for specific protein domains. Methylation has pivotal roles in the formation of complexes that are involved in cellular regulation, including in the generation of small RNAs. Arginine methylation was discovered half a century ago, but the ability of methylarginine sites to serve as binding motifs for members of the Tudor protein family, and the functional significance of the protein-protein interactions that are mediated by Tudor domains, has only recently been appreciated. Tudor proteins are now known to be present in PIWI complexes, where they are thought to interact with methylated PIWI proteins and regulate the PIWI-interacting RNA (piRNA) pathway in the germ line.
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Affiliation(s)
- Chen Chen
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
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159
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Sims RJ, Rojas LA, Beck DB, Bonasio R, Schüller R, Drury WJ, Eick D, Reinberg D. The C-terminal domain of RNA polymerase II is modified by site-specific methylation. Science 2011; 332:99-103. [PMID: 21454787 DOI: 10.1126/science.1202663] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII) in mammals undergoes extensive posttranslational modification, which is essential for transcriptional initiation and elongation. Here, we show that the CTD of RNAPII is methylated at a single arginine (R1810) by the coactivator-associated arginine methyltransferase 1 (CARM1). Although methylation at R1810 is present on the hyperphosphorylated form of RNAPII in vivo, Ser2 or Ser5 phosphorylation inhibits CARM1 activity toward this site in vitro, suggesting that methylation occurs before transcription initiation. Mutation of R1810 results in the misexpression of a variety of small nuclear RNAs and small nucleolar RNAs, an effect that is also observed in Carm1(-/-) mouse embryo fibroblasts. These results demonstrate that CTD methylation facilitates the expression of select RNAs, perhaps serving to discriminate the RNAPII-associated machinery recruited to distinct gene types.
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Affiliation(s)
- Robert J Sims
- Howard Hughes Medical Institute (HHMI), Department of Biochemistry, New York University School of Medicine, 522 First Avenue, Smilow 211, New York, NY 10016, USA
| | - Luis Alejandro Rojas
- Howard Hughes Medical Institute (HHMI), Department of Biochemistry, New York University School of Medicine, 522 First Avenue, Smilow 211, New York, NY 10016, USA
| | - David B Beck
- Howard Hughes Medical Institute (HHMI), Department of Biochemistry, New York University School of Medicine, 522 First Avenue, Smilow 211, New York, NY 10016, USA
| | - Roberto Bonasio
- Howard Hughes Medical Institute (HHMI), Department of Biochemistry, New York University School of Medicine, 522 First Avenue, Smilow 211, New York, NY 10016, USA
| | - Roland Schüller
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - William J Drury
- Howard Hughes Medical Institute (HHMI), Department of Biochemistry, New York University School of Medicine, 522 First Avenue, Smilow 211, New York, NY 10016, USA
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science Munich (CIPSM), Marchioninistrasse 25, 81377 Munich, Germany
| | - Danny Reinberg
- Howard Hughes Medical Institute (HHMI), Department of Biochemistry, New York University School of Medicine, 522 First Avenue, Smilow 211, New York, NY 10016, USA
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160
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Abstract
Histone modifications not only play important roles in regulating chromatin structure and nuclear processes but also can be passed to daughter cells as epigenetic marks. Accumulating evidence suggests that the key function of histone modifications is to signal for recruitment or activity of downstream effectors. Here, we discuss the latest discovery of histone-modification readers and how the modification language is interpreted.
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Affiliation(s)
- Miyong Yun
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390-9148, USA
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161
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162
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Di Lorenzo A, Bedford MT. Histone arginine methylation. FEBS Lett 2010; 585:2024-31. [PMID: 21074527 DOI: 10.1016/j.febslet.2010.11.010] [Citation(s) in RCA: 332] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/06/2010] [Accepted: 11/08/2010] [Indexed: 01/23/2023]
Abstract
Arginine methylation is a common posttranslational modification (PTM). This type of PTM occurs on both nuclear and cytoplasmic proteins, and is particularly abundant on shuttling proteins. In this review, we will focus on one aspect of this PTM: the diverse roles that arginine methylation of the core histone tails play in regulating chromatin function. A family of nine protein arginine methyltransferases (PRMTs) catalyze methylation reactions, and a subset target histones. Importantly, arginine methylation of histone tails can promote or prevent the docking of key transcriptional effector molecules, thus playing a central role in the orchestration of the histone code.
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Affiliation(s)
- Alessandra Di Lorenzo
- The University of Texas MD Anderson Cancer Center, Science Park-Research Division, Smithville, TX 78957, United States
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