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Hsu SH, Hung WC. Protein arginine methyltransferase 3: A crucial regulator in metabolic reprogramming and gene expression in cancers. Cancer Lett 2023; 554:216008. [PMID: 36400311 DOI: 10.1016/j.canlet.2022.216008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Post-translational modification (PTM) of proteins increases proteome diversity, which is critical for maintaining cellular homeostasis. The importance of protein methylation in the regulation of diverse biological processes has been highlighted in the past decades. Methylation of the arginine residue on proteins is catalyzed by members of the protein arginine methyltransferase (PRMT) family. PRMTs play indispensable roles in various pathways that regulate cancer development, progression, and drug response. In this review, we discuss the role of PRMT3, a member of the PRMT family, in controlling oncogenic processes. Additionally, the effects of PRMT3 on the methylation of regulatory proteins involved in transcription, post-transcriptional control, ribosomal maturation, translation, biological synthesis, and metabolic signaling are summarized. Moreover, recent progresses in the development of PRMT3 inhibitors are introduced. Overall, this review highlights the importance of PRMT3 in tumorigenesis and discusses the underlying mechanisms by which PRMT3 modulates cellular metabolism and gene expression. These results also provide a molecular basis for therapeutic modalities by targeting PRMT3.
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Affiliation(s)
- Shih-Han Hsu
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, 802, Taiwan.
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2
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Sun X, Bieber JM, Hammerlindl H, Chalkley RJ, Li KH, Burlingame AL, Jacobson MP, Wu LF, Altschuler SJ. Modulating environmental signals to reveal mechanisms and vulnerabilities of cancer persisters. SCIENCE ADVANCES 2022; 8:eabi7711. [PMID: 35089788 PMCID: PMC8797778 DOI: 10.1126/sciadv.abi7711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Cancer persister cells are able to survive otherwise lethal doses of drugs through nongenetic mechanisms, which can lead to cancer regrowth and drug resistance. The broad spectrum of molecular differences observed between persisters and their treatment-naïve counterparts makes it challenging to identify causal mechanisms underlying persistence. Here, we modulate environmental signals to identify cellular mechanisms that promote the emergence of persisters and to pinpoint actionable vulnerabilities that eliminate them. We found that interferon-γ (IFNγ) can induce a pro-persistence signal that can be specifically eliminated by inhibition of type I protein arginine methyltransferase (PRMT) (PRMTi). Mechanistic investigation revealed that signal transducer and activator of transcription 1 (STAT1) is a key component connecting IFNγ's pro-persistence and PRMTi's antipersistence effects, suggesting a previously unknown application of PRMTi to target persisters in settings with high STAT1 expression. Modulating environmental signals can accelerate the identification of mechanisms that promote and eliminate cancer persistence.
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Affiliation(s)
| | | | | | | | | | | | | | - Lani F. Wu
- Corresponding author. (S.J.A.); (L.F.W.)
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3
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Verma M, Khan MIK, Kadumuri RV, Chakrapani B, Awasthi S, Mahesh A, Govindaraju G, Chavali PL, Rajavelu A, Chavali S, Dhayalan A. PRMT3 interacts with ALDH1A1 and regulates gene-expression by inhibiting retinoic acid signaling. Commun Biol 2021; 4:109. [PMID: 33495566 PMCID: PMC7835222 DOI: 10.1038/s42003-020-01644-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 12/15/2020] [Indexed: 12/23/2022] Open
Abstract
Protein arginine methyltransferase 3 (PRMT3) regulates protein functions by introducing asymmetric dimethylation marks at the arginine residues in proteins. However, very little is known about the interaction partners of PRMT3 and their functional outcomes. Using yeast-two hybrid screening, we identified Retinal dehydrogenase 1 (ALDH1A1) as a potential interaction partner of PRMT3 and confirmed this interaction using different methods. ALDH1A1 regulates variety of cellular processes by catalyzing the conversion of retinaldehyde to retinoic acid. By molecular docking and site-directed mutagenesis, we identified the specific residues in the catalytic domain of PRMT3 that facilitate interaction with the C-terminal region of ALDH1A1. PRMT3 inhibits the enzymatic activity of ALDH1A1 and negatively regulates the expression of retinoic acid responsive genes in a methyltransferase activity independent manner. Our findings show that in addition to regulating protein functions by introducing methylation modifications, PRMT3 could also regulate global gene expression through protein-protein interactions. Here, the authors demonstrate that protein arginine methyltransferase 3 (PRMT3) interacts with and inhibits the retinal dehydrogenase ALDH1A1, negatively regulating the expression of retinoic acid responsive genes. This study shows that PRMT3 affects diverse biological processes not only by globally regulating protein function through methylation but also by regulating gene expression.
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Affiliation(s)
- Mamta Verma
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Mohd Imran K Khan
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Rajashekar Varma Kadumuri
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India
| | - Baskar Chakrapani
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Sharad Awasthi
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Arun Mahesh
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Gayathri Govindaraju
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, 695014, India
| | - Pavithra L Chavali
- CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Arumugam Rajavelu
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, 695014, India
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India.
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India.
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Hsu MC, Tsai YL, Lin CH, Pan MR, Shan YS, Cheng TY, Cheng SHC, Chen LT, Hung WC. Protein arginine methyltransferase 3-induced metabolic reprogramming is a vulnerable target of pancreatic cancer. J Hematol Oncol 2019; 12:79. [PMID: 31324208 PMCID: PMC6642535 DOI: 10.1186/s13045-019-0769-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The biological function of protein arginine methyltransferase 3 (PRMT3) is not well known because very few physiological substrates of this methyltransferase have been identified to date. METHODS The clinical significance of PRMT3 in pancreatic cancer was studied by database analysis. The PRMT3 protein level of human pancreatic tumors was detected by immunoblotting and immunohistochemical staining. PRMT3-associated proteins and the methylation sites on the proteins were investigated using mass spectrometry. Seahorse Bioscience analyzed the metabolic reprogramming. Combination index analysis and xenograft animal model were conducted to explore the effects of combination of inhibitors of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and oxidative phosphorylation on tumor growth. RESULTS We found that the expression of PRMT3 is upregulated in pancreatic cancer, and its expression is associated with poor survival. We identified GAPDH as a PRMT3-binding protein and demonstrated that GAPDH is methylated at R248 by PRMT3 in vivo. The methylation of GAPDH by PRMT3 enhanced its catalytic activity while the mutation of R248 abolished the effect. In cells, PRMT3 overexpression triggered metabolic reprogramming and enhanced glycolysis and mitochondrial respiration simultaneously in a GAPDH-dependent manner. PRMT3-overexpressing cancer cells were addicted to GAPDH-mediated metabolism and sensitive to the inhibition of GAPDH and mitochondrial respiration. The combination of inhibitors of GAPDH and oxidative phosphorylation induced a synergistic inhibition on cellular growth in vitro and in vivo. CONCLUSION Our results suggest that PRMT3 mediates metabolic reprogramming and cellular proliferation through methylating R248 of GAPDH, and double blockade of GAPDH and mitochondrial respiration could be a novel strategy for the treatment of PRMT3-overexpressing pancreatic cancer.
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Affiliation(s)
- Ming-Chuan Hsu
- National Institute of Cancer Research, National Health Research Institutes, No. 367, Shengli Road, Tainan, 704, Taiwan
| | - Ya-Li Tsai
- National Institute of Cancer Research, National Health Research Institutes, No. 367, Shengli Road, Tainan, 704, Taiwan
| | - Chia-Hsien Lin
- National Institute of Cancer Research, National Health Research Institutes, No. 367, Shengli Road, Tainan, 704, Taiwan
| | - Mei-Ren Pan
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Yan-Shen Shan
- Institute of Clinical Medicine, National Cheng Kung University, Tainan, 704, Taiwan.,Department of Surgery, National Cheng Kung University Hospital, Tainan, 704, Taiwan
| | - Tsung-Yen Cheng
- Department of Surgery, Koo Foundation Sun Yat-Sen Cancer Center, Taipei, 112, Taiwan
| | - Skye Hung-Chun Cheng
- Department of Radiation Oncology, Koo Foundation Sun Yat-Sen Cancer Center, Taipei, 112, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, No. 367, Shengli Road, Tainan, 704, Taiwan.,Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, 704, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, No. 367, Shengli Road, Tainan, 704, Taiwan. .,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
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5
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Kühn U, Buschmann J, Wahle E. The nuclear poly(A) binding protein of mammals, but not of fission yeast, participates in mRNA polyadenylation. RNA (NEW YORK, N.Y.) 2017; 23:473-482. [PMID: 28096519 PMCID: PMC5340911 DOI: 10.1261/rna.057026.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 01/04/2017] [Indexed: 05/22/2023]
Abstract
The nuclear poly(A) binding protein (PABPN1) has been suggested, on the basis of biochemical evidence, to play a role in mRNA polyadenylation by strongly increasing the processivity of poly(A) polymerase. While experiments in metazoans have tended to support such a role, the results were not unequivocal, and genetic data show that the S. pombe ortholog of PABPN1, Pab2, is not involved in mRNA polyadenylation. The specific model in which PABPN1 increases the rate of poly(A) tail elongation has never been examined in vivo. Here, we have used 4-thiouridine pulse-labeling to examine the lengths of newly synthesized poly(A) tails in human cells. Knockdown of PABPN1 strongly reduced the synthesis of full-length tails of ∼250 nucleotides, as predicted from biochemical data. We have also purified S. pombe Pab2 and the S. pombe poly(A) polymerase, Pla1, and examined their in vitro activities. Whereas PABPN1 strongly increases the activity of its cognate poly(A) polymerase in vitro, Pab2 was unable to stimulate Pla1 to any significant extent. Thus, in vitro and in vivo data are consistent in supporting a role of PABPN1 but not S. pombe Pab2 in the polyadenylation of mRNA precursors.
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Affiliation(s)
- Uwe Kühn
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Juliane Buschmann
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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7
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FAM98A associates with DDX1-C14orf166-FAM98B in a novel complex involved in colorectal cancer progression. Int J Biochem Cell Biol 2017; 84:1-13. [DOI: 10.1016/j.biocel.2016.12.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/14/2016] [Accepted: 12/25/2016] [Indexed: 02/08/2023]
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8
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Liu X, Li H, Liu L, Lu Y, Gao Y, Geng P, Li X, Huang B, Zhang Y, Lu J. Methylation of arginine by PRMT1 regulates Nrf2 transcriptional activity during the antioxidative response. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2093-103. [PMID: 27183873 DOI: 10.1016/j.bbamcr.2016.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/21/2016] [Accepted: 05/08/2016] [Indexed: 01/02/2023]
Abstract
The cap 'n' collar (CNC) family of transcription factors play important roles in resistance of oxidative and electrophilic stresses. Among the CNC family members, NF-E2-related factor 2 (Nrf2) is critical for regulating the antioxidant and phase II enzymes through antioxidant response element (ARE)-mediated transactivation. The activity of Nrf2 is controlled by a variety of post-translational modifications, including phosphorylation, ubiquitination, acetylation and sumoylation. Here we demonstrate that the arginine methyltransferase-1 (PRMT1) methylates Nrf2 protein at a single residue of arginine 437, both in vitro and in vivo. Using the heme oxygenase-1 (HO-1) as a model of phase II enzyme gene, we found that methylation of Nrf2 by PRMT1 led to a moderate increase of its DNA-binding activity and transactivation, which subsequently protected cells against the tBHP-induced glutathione depletion and cell death. Collectively, our results define a novel modification of Nrf2, which operates as a fine-tuning mechanism for the transcriptional activity of Nrf2 under the oxidative stress.
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Affiliation(s)
- Xin Liu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Hongyuan Li
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130021, China
| | - Lingxia Liu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Yang Lu
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130021, China
| | - Yanyan Gao
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Pengyu Geng
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130021, China
| | - Xiaoxue Li
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130021, China
| | - Baiqu Huang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Yu Zhang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Jun Lu
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130021, China.
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9
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Low JKK, Im H, Erce MA, Hart-Smith G, Snyder MP, Wilkins MR. Protein substrates of the arginine methyltransferase Hmt1 identified by proteome arrays. Proteomics 2016; 16:465-76. [DOI: 10.1002/pmic.201400564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 09/27/2015] [Accepted: 11/10/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Jason K. K. Low
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; The University of New South Wales; Sydney Australia
| | - Hogune Im
- Department of Genetics; Stanford University School of Medicine; Palo Alto CA USA
| | - Melissa A. Erce
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; The University of New South Wales; Sydney Australia
| | - Gene Hart-Smith
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; The University of New South Wales; Sydney Australia
| | - Michael P. Snyder
- Department of Genetics; Stanford University School of Medicine; Palo Alto CA USA
| | - Marc R. Wilkins
- Systems Biology Initiative; School of Biotechnology and Biomolecular Sciences; The University of New South Wales; Sydney Australia
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10
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Kaniskan HÜ, Szewczyk MM, Yu Z, Eram MS, Yang X, Schmidt K, Luo X, Dai M, He F, Zang I, Lin Y, Kennedy S, Li F, Dobrovetsky E, Dong A, Smil D, Min SJ, Landon M, Lin-Jones J, Huang XP, Roth BL, Schapira M, Atadja P, Barsyte-Lovejoy D, Arrowsmith CH, Brown PJ, Zhao K, Jin J, Vedadi M. A potent, selective and cell-active allosteric inhibitor of protein arginine methyltransferase 3 (PRMT3). Angew Chem Int Ed Engl 2015; 54:5166-70. [PMID: 25728001 PMCID: PMC4400258 DOI: 10.1002/anie.201412154] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/31/2015] [Indexed: 01/03/2023]
Abstract
PRMT3 catalyzes the asymmetric dimethylation of arginine residues of various proteins. It is essential for maturation of ribosomes, may have a role in lipogenesis, and is implicated in several diseases. A potent, selective, and cell-active PRMT3 inhibitor would be a valuable tool for further investigating PRMT3 biology. Here we report the discovery of the first PRMT3 chemical probe, SGC707, by structure-based optimization of the allosteric PRMT3 inhibitors we reported previously, and thorough characterization of this probe in biochemical, biophysical, and cellular assays. SGC707 is a potent PRMT3 inhibitor (IC50 =31±2 nM, KD =53±2 nM) with outstanding selectivity (selective against 31 other methyltransferases and more than 250 non-epigenetic targets). The mechanism of action studies and crystal structure of the PRMT3-SGC707 complex confirm the allosteric inhibition mode. Importantly, SGC707 engages PRMT3 and potently inhibits its methyltransferase activity in cells. It is also bioavailable and suitable for animal studies. This well-characterized chemical probe is an excellent tool to further study the role of PRMT3 in health and disease.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Structural and Chemical Biology, Oncological Sciences, and Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 (USA)
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11
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Geoghegan V, Guo A, Trudgian D, Thomas B, Acuto O. Comprehensive identification of arginine methylation in primary T cells reveals regulatory roles in cell signalling. Nat Commun 2015; 6:6758. [PMID: 25849564 PMCID: PMC4396391 DOI: 10.1038/ncomms7758] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 02/25/2015] [Indexed: 12/11/2022] Open
Abstract
The impact of protein arginine methylation on the regulation of immune functions is virtually unknown. Here, we apply a novel method—isomethionine methyl-SILAC—coupled with antibody-mediated arginine-methylated peptide enrichment to identify methylated peptides in human T cells by mass spectrometry. This approach allowed the identification of 2,502 arginine methylation sites from 1,257 tissue-specific and housekeeping proteins. We find that components of T cell antigen receptor signal machinery and several key transcription factors that regulate T cell fate determination are methylated on arginine. Moreover, we demonstrate changes in arginine methylation stoichiometry during cellular stimulation in a subset of proteins critical to T cell differentiation. Our data suggest that protein arginine methyltransferases exert key regulatory roles in T cell activation and differentiation, opening a new field of investigation in T cell biology. Arginine methylation is an important regulatory post-translational modification. Here, the authors present a new SILAC-based method—iMethyl-SILAC—that allows unambiguous identification of arginine-methylated peptide pairs by mass spectrometry and apply it to greatly expand the known T-cell arginine methylome.
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Affiliation(s)
- Vincent Geoghegan
- Laboratory of T cell signalling, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Ailan Guo
- Cell Signaling Technology Inc., Trask Lane, Danvers, Massachusetts 01923, USA
| | - David Trudgian
- Central Proteomics Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Benjamin Thomas
- Central Proteomics Facility, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Oreste Acuto
- Laboratory of T cell signalling, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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12
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Jiang X, Yao F, Li X, Jia B, Zhong G, Zhang J, Zou X, Hou L. Molecular cloning, characterization and expression analysis of the protein arginine N-methyltransferase 1 gene (As-PRMT1) from Artemia sinica. Gene 2015; 565:122-9. [PMID: 25843627 DOI: 10.1016/j.gene.2015.04.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/17/2015] [Accepted: 04/01/2015] [Indexed: 10/23/2022]
Abstract
Protein arginine N-methyltransferase 1 (PRMT1) is an important epigenetic regulation factor in eukaryotic genomes. PRMT1 is involved in histone arginine loci methylation modification, changes in eukaryotic genomes' chromatin structure, and gene expression regulation. In the present paper, the full-length 1201-bp cDNA sequence of the PRMT1 homolog of Artemia sinica (As-PRMT1) was cloned for the first time. The putative As-PRMT1 protein comprises 346 amino acids with a SAM domain and a PRMT5 domain. Multiple sequence alignments revealed that the putative sequence of As-PRMT1 protein was relatively conserved across species, especially in the SAM domain. As-PRMT1 is widely expressed during embryo development of A. sinica. This is followed by a dramatic upregulation after diapause termination and then downregulation from the nauplius stage. Furthermore, As-PRMT1 transcripts are highly upregulated under conditions of high salinity and low temperature stress. These findings suggested that As-PRMT1 is a stress-related factor that might promote or inhibit the expression of certain genes, play a critical role in embryonic development and in resistance to low temperature and high salinity stress.
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Affiliation(s)
- Xue Jiang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Feng Yao
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Xuejie Li
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Baolin Jia
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Guangying Zhong
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Jianfeng Zhang
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China
| | - Xiangyang Zou
- Department of Biology, Dalian Medical University, Dalian 116044, China.
| | - Lin Hou
- College of Life Sciences, Liaoning Normal University, Dalian 116081, China.
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Kaniskan HÜ, Szewczyk MM, Yu Z, Eram MS, Yang X, Schmidt K, Luo X, Dai M, He F, Zang I, Lin Y, Kennedy S, Li F, Dobrovetsky E, Dong A, Smil D, Min SJ, Landon M, Lin-Jones J, Huang XP, Roth BL, Schapira M, Atadja P, Barsyte-Lovejoy D, Arrowsmith CH, Brown PJ, Zhao K, Jin J, Vedadi M. A Potent, Selective and Cell-Active Allosteric Inhibitor of Protein Arginine Methyltransferase 3 (PRMT3). Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Kim DI, Park MJ, Lim SK, Park JI, Yoon KC, Han HJ, Gustafsson JÅ, Lim JH, Park SH. PRMT3 regulates hepatic lipogenesis through direct interaction with LXRα. Diabetes 2015; 64:60-71. [PMID: 25187371 DOI: 10.2337/db13-1394] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Arginine methylation is responsible for diverse biological functions and is mediated by protein arginine methyltransferases (PRMTs). Nonalcoholic fatty liver disease (NAFLD) is accompanied by excessive hepatic lipogenesis via liver X receptor α (LXRα). Thus we examined the pathophysiological role of PRMTs in NAFLD and their relationship with LXRα. In this study, palmitic acid (PA) treatment increased PRMT3, which is correlated with the elevation of hepatic lipogenic proteins. The expression of lipogenic proteins was increased by PRMT3 overexpression, but decreased by PRMT3 silencing and use of the PRMT3 knockout (KO) mouse embryonic fibroblast cell line. PRMT3 also increased the transcriptional activity of LXRα by directly binding with LXRα in a methylation-independent manner. In addition, PA treatment translocated PRMT3 to the nucleus. In animal models, a high-fat diet increased the LXRα and PRMT3 expressions and binding, which was not observed in LXRα KO mice. Furthermore, increased PRMT3 expression and its binding with LXRα were observed in NAFLD patients. Taken together, LXRα and PRMT3 expression was increased in cellular and mouse models of NAFLD and human patients, and PRMT3 translocated into the nucleus bound with LXRα as a transcriptional cofactor, which induced lipogenesis. In conclusion, PRMT3 translocation by PA is coupled to the binding of LXRα, which is responsible for the onset of fatty liver.
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Affiliation(s)
- Dong-il Kim
- College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Min-jung Park
- College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Seul-ki Lim
- Metabolism and Functionality Research Group, R&D Division, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Jae-il Park
- Korea Basic Science Institute, Gwangju Center at Chonnam National University, Gwangju, Republic of Korea
| | - Kyung-chul Yoon
- Department of Ophthalmology, Chonnam National University Medical School and Hospital, Gwangju, Republic of Korea
| | - Ho-jae Han
- Department of Verterinary Physiology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jan-åke Gustafsson
- Molecular Nutrition Unit, Department of Bioscience and Nutrition, Karolinska Institutet, Stockholm, Sweden Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX
| | - Jae-hyang Lim
- Department of Microbiology, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Soo-hyun Park
- College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
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15
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Abstract
Mounting evidence suggests that protein methyltransferases (PMTs), which catalyze methylation of histone and nonhistone proteins, play a crucial role in diverse biological processes and human diseases. In particular, PMTs have been recognized as major players in regulating gene expression and chromatin state. PMTs are divided into two categories: protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs). There has been a steadily growing interest in these enzymes as potential therapeutic targets and therefore discovery of PMT inhibitors has also been pursued increasingly over the past decade. Here, we present a perspective on selective, small-molecule inhibitors of PMTs with an emphasis on their discovery, characterization, and applicability as chemical tools for deciphering the target PMTs' physiological functions and involvement in human diseases. We highlight the current state of PMT inhibitors and discuss future directions and opportunities for PMT inhibitor discovery.
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Affiliation(s)
- H Ümit Kaniskan
- Department of Structural and Chemical Biology, ‡Department of Oncological Sciences, §Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
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16
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Wigington CP, Williams KR, Meers MP, Bassell GJ, Corbett AH. Poly(A) RNA-binding proteins and polyadenosine RNA: new members and novel functions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2014; 5:601-22. [PMID: 24789627 PMCID: PMC4332543 DOI: 10.1002/wrna.1233] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/07/2014] [Accepted: 03/06/2014] [Indexed: 02/05/2023]
Abstract
Poly(A) RNA-binding proteins (Pabs) bind with high affinity and specificity to polyadenosine RNA. Textbook models show a nuclear Pab, PABPN1, and a cytoplasmic Pab, PABPC, where the nuclear PABPN1 modulates poly(A) tail length and the cytoplasmic PABPC stabilizes poly(A) RNA in the cytoplasm and also enhances translation. While these conventional roles are critically important, the Pab family has expanded recently both in number and in function. A number of novel roles have emerged for both PAPBPN1 and PABPC that contribute to the fine-tuning of gene expression. Furthermore, as the characterization of the nucleic acid binding properties of RNA-binding proteins advances, additional proteins that show high affinity and specificity for polyadenosine RNA are being discovered. With this expansion of the Pab family comes a concomitant increase in the potential for Pabs to modulate gene expression. Further complication comes from an expansion of the potential binding sites for Pab proteins as revealed by an analysis of templated polyadenosine stretches present within the transcriptome. Thus, Pabs could influence mRNA fate and function not only by binding to the nontemplated poly(A) tail but also to internal stretches of adenosine. Understanding the diverse functions of Pab proteins is not only critical to understand how gene expression is regulated but also to understand the molecular basis for tissue-specific diseases that occur when Pab proteins are altered. Here we describe both conventional and recently emerged functions for PABPN1 and PABPC and then introduce and discuss three new Pab family members, ZC3H14, hnRNP-Q1, and LARP4.
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Affiliation(s)
- Callie P. Wigington
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Kathryn R. Williams
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael P. Meers
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Gary J. Bassell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anita H. Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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17
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McMurray M. Lean forward: Genetic analysis of temperature-sensitive mutants unfolds the secrets of oligomeric protein complex assembly. Bioessays 2014; 36:836-46. [PMID: 25048147 DOI: 10.1002/bies.201400062] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Multisubunit protein complexes are essential for cellular function. Genetic analysis of essential processes requires special tools, among which temperature-sensitive (Ts) mutants have historically been crucial. Many researchers assume that the effect of temperature on such mutants is to drive their proteolytic destruction. In fact, degradation-mediated elimination of mutant proteins likely explains only a fraction of the phenotypes associated with Ts mutants. Here I discuss insights gained from analysis of Ts mutants in oligomeric proteins, with particular focus on the study of septins, GTP-binding subunits of cytoskeletal filaments whose structures and functions are the subject of current investigation in my and many other labs. I argue that the kinds of unbiased forward genetic approaches that generate Ts mutants provide information that is largely inaccessible to modern reverse genetic methodologies, and will continue to drive our understanding of higher-order assembly by septins and other oligomeric proteins.
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Affiliation(s)
- Michael McMurray
- Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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18
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Low JK, Hart-Smith G, Erce MA, Wilkins MR. Analysis of the Proteome of Saccharomyces cerevisiae for Methylarginine. J Proteome Res 2013; 12:3884-99. [DOI: 10.1021/pr400556c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Jason K.K. Low
- Systems Biology Laboratory, School of Biotechnology
and Biomolecular Sciences, The University of New South Wales, NSW 2052 Sydney, Australia
| | - Gene Hart-Smith
- Systems Biology Laboratory, School of Biotechnology
and Biomolecular Sciences, The University of New South Wales, NSW 2052 Sydney, Australia
| | - Melissa A. Erce
- Systems Biology Laboratory, School of Biotechnology
and Biomolecular Sciences, The University of New South Wales, NSW 2052 Sydney, Australia
| | - Marc R. Wilkins
- Systems Biology Laboratory, School of Biotechnology
and Biomolecular Sciences, The University of New South Wales, NSW 2052 Sydney, Australia
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19
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Thapar R, Denmon AP. Signaling pathways that control mRNA turnover. Cell Signal 2013; 25:1699-710. [PMID: 23602935 PMCID: PMC3703460 DOI: 10.1016/j.cellsig.2013.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 03/29/2013] [Indexed: 02/06/2023]
Abstract
Cells regulate their genomes mainly at the level of transcription and at the level of mRNA decay. While regulation at the level of transcription is clearly important, the regulation of mRNA turnover by signaling networks is essential for a rapid response to external stimuli. Signaling pathways result in posttranslational modification of RNA binding proteins by phosphorylation, ubiquitination, methylation, acetylation etc. These modifications are important for rapid remodeling of dynamic ribonucleoprotein complexes and triggering mRNA decay. Understanding how these posttranslational modifications alter gene expression is therefore a fundamental question in biology. In this review we highlight recent findings on how signaling pathways and cell cycle checkpoints involving phosphorylation, ubiquitination, and arginine methylation affect mRNA turnover.
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Affiliation(s)
- Roopa Thapar
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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20
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Banerjee A, Apponi LH, Pavlath GK, Corbett AH. PABPN1: molecular function and muscle disease. FEBS J 2013; 280:4230-50. [PMID: 23601051 DOI: 10.1111/febs.12294] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/03/2013] [Accepted: 04/11/2013] [Indexed: 12/17/2022]
Abstract
The polyadenosine RNA binding protein polyadenylate-binding nuclear protein 1 (PABPN1) plays key roles in post-transcriptional processing of RNA. Although PABPN1 is ubiquitously expressed and presumably contributes to control of gene expression in all tissues, mutation of the PABPN1 gene causes the disease oculopharyngeal muscular dystrophy (OPMD), in which a limited set of skeletal muscles are affected. A major goal in the field of OPMD research is to understand why mutation of a ubiquitously expressed gene leads to a muscle-specific disease. PABPN1 plays a well-documented role in controlling the poly(A) tail length of RNA transcripts but new functions are emerging through studies that exploit a variety of unbiased screens as well as model organisms. This review addresses (a) the molecular function of PABPN1 incorporating recent findings that reveal novel cellular functions for PABPN1 and (b) the approaches that are being used to understand the molecular defects that stem from expression of mutant PABPN1. The long-term goal in this field of research is to understand the key molecular functions of PABPN1 in muscle as well as the mechanisms that underlie the pathological consequences of mutant PABPN1. Armed with this information, researchers can seek to develop therapeutic approaches to enhance the quality of life for patients afflicted with OPMD.
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Affiliation(s)
- Ayan Banerjee
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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21
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Liu F, Li F, Ma A, Dobrovetsky E, Dong A, Gao C, Korboukh I, Liu J, Smil D, Brown PJ, Frye SV, Arrowsmith CH, Schapira M, Vedadi M, Jin J. Exploiting an allosteric binding site of PRMT3 yields potent and selective inhibitors. J Med Chem 2013; 56:2110-24. [PMID: 23445220 PMCID: PMC4319713 DOI: 10.1021/jm3018332] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein arginine methyltransferases (PRMTs) play an important role in diverse biological processes. Among the nine known human PRMTs, PRMT3 has been implicated in ribosomal biosynthesis via asymmetric dimethylation of the 40S ribosomal protein S2 and in cancer via interaction with the DAL-1 tumor suppressor protein. However, few selective inhibitors of PRMTs have been discovered. We recently disclosed the first selective PRMT3 inhibitor, which occupies a novel allosteric binding site and is noncompetitive with both the peptide substrate and cofactor. Here we report comprehensive structure-activity relationship studies of this series, which resulted in the discovery of multiple PRMT3 inhibitors with submicromolar potencies. An X-ray crystal structure of compound 14u in complex with PRMT3 confirmed that this inhibitor occupied the same allosteric binding site as our initial lead compound. These studies provide the first experimental evidence that potent and selective inhibitors can be created by exploiting the allosteric binding site of PRMT3.
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Affiliation(s)
- Feng Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Anqi Ma
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Elena Dobrovetsky
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Cen Gao
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ilia Korboukh
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jing Liu
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David Smil
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jian Jin
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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22
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Mallet PL, Bachand F. A Proline-Tyrosine Nuclear Localization Signal (PY-NLS) Is Required for the Nuclear Import of Fission Yeast PAB2, but Not of Human PABPN1. Traffic 2013; 14:282-94. [DOI: 10.1111/tra.12036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/20/2012] [Accepted: 12/26/2012] [Indexed: 12/27/2022]
Affiliation(s)
- Pierre-Luc Mallet
- RNA Group, Department of Biochemistry; Université de Sherbrooke; Sherbrooke; QC; Canada
| | - François Bachand
- RNA Group, Department of Biochemistry; Université de Sherbrooke; Sherbrooke; QC; Canada
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23
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Low JKK, Wilkins MR. Protein arginine methylation in Saccharomyces cerevisiae. FEBS J 2012; 279:4423-43. [PMID: 23094907 DOI: 10.1111/febs.12039] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/10/2012] [Accepted: 10/19/2012] [Indexed: 11/27/2022]
Abstract
Recent research has implicated arginine methylation as a major regulator of cellular processes, including transcription, translation, nucleocytoplasmic transport, signalling, DNA repair, RNA processing and splicing. Arginine methylation is evolutionarily conserved, and it is now thought that it may rival other post-translational modifications such as phosphorylation in terms of its occurrence in the proteome. In addition, multiple recent examples demonstrate an exciting new theme: the interplay between methylation and other post-translational modifications such as phosphorylation. In this review, we summarize our current understanding of arginine methylation and the recent advances made, with a focus on the lower eukaryote Saccharomyces cerevisiae. We cover the types of methylated proteins, their responsible methyltransferases, where and how the effects of arginine methylation are seen in the cell, and, finally, discuss the conservation of the biological function of methylarginines between S. cerevisiae and mammals.
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Affiliation(s)
- Jason K K Low
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
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24
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Arginine methylation next to the PY-NLS modulates Transportin binding and nuclear import of FUS. EMBO J 2012; 31:4258-75. [PMID: 22968170 PMCID: PMC3501225 DOI: 10.1038/emboj.2012.261] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/17/2012] [Indexed: 12/13/2022] Open
Abstract
Fused in sarcoma (FUS) is a nuclear protein that carries a proline-tyrosine nuclear localization signal (PY-NLS) and is imported into the nucleus via Transportin (TRN). Defects in nuclear import of FUS have been implicated in neurodegeneration, since mutations in the PY-NLS of FUS cause amyotrophic lateral sclerosis (ALS). Moreover, FUS is deposited in the cytosol in a subset of frontotemporal lobar degeneration (FTLD) patients. Here, we show that arginine methylation modulates nuclear import of FUS via a novel TRN-binding epitope. Chemical or genetic inhibition of arginine methylation restores TRN-mediated nuclear import of ALS-associated FUS mutants. The unmethylated arginine-glycine-glycine domain preceding the PY-NLS interacts with TRN and arginine methylation in this domain reduces TRN binding. Inclusions in ALS-FUS patients contain methylated FUS, while inclusions in FTLD-FUS patients are not methylated. Together with recent findings that FUS co-aggregates with two related proteins of the FET family and TRN in FTLD-FUS but not in ALS-FUS, our study provides evidence that these two diseases may be initiated by distinct pathomechanisms and implicates alterations in arginine methylation in pathogenesis.
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25
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Siarheyeva A, Senisterra G, Allali-Hassani A, Dong A, Dobrovetsky E, Wasney GA, Chau I, Marcellus R, Hajian T, Liu F, Korboukh I, Smil D, Bolshan Y, Min J, Wu H, Zeng H, Loppnau P, Poda G, Griffin C, Aman A, Brown PJ, Jin J, Al-Awar R, Arrowsmith CH, Schapira M, Vedadi M. An allosteric inhibitor of protein arginine methyltransferase 3. Structure 2012; 20:1425-35. [PMID: 22795084 DOI: 10.1016/j.str.2012.06.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 05/24/2012] [Accepted: 06/02/2012] [Indexed: 10/28/2022]
Abstract
PRMT3, a protein arginine methyltransferase, has been shown to influence ribosomal biosynthesis by catalyzing the dimethylation of the 40S ribosomal protein S2. Although PRMT3 has been reported to be a cytosolic protein, it has been shown to methylate histone H4 peptide (H4 1-24) in vitro. Here, we report the identification of a PRMT3 inhibitor (1-(benzo[d][1,2,3]thiadiazol-6-yl)-3-(2-cyclohexenylethyl)urea; compound 1) with IC50 value of 2.5 μM by screening a library of 16,000 compounds using H4 (1-24) peptide as a substrate. The crystal structure of PRMT3 in complex with compound 1 as well as kinetic analysis reveals an allosteric mechanism of inhibition. Mutating PRMT3 residues within the allosteric site or using compound 1 analogs that disrupt interactions with allosteric site residues both abrogated binding and inhibitory activity. These data demonstrate an allosteric mechanism for inhibition of protein arginine methyltransferases, an emerging class of therapeutic targets.
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Affiliation(s)
- Alena Siarheyeva
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
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26
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Asymmetric dimethylarginine, an endogenous NOS inhibitor, is actively metabolized in rat erythrocytes. Biosci Biotechnol Biochem 2012; 76:1334-42. [PMID: 22785485 DOI: 10.1271/bbb.120086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
N(G), N(G)-Dimethyl-L-arginine (asymmetric dimethylarginine: ADMA) is an endogenous competitive inhibitor of nitric oxide synthase (NOS). Plasma ADMA concentrations have been reported to increase in connection with diseases associated with an impaired endothelial L-arginine/NO pathway. In this study, we investigated the metabolism of ADMA in circulating blood cell populations to elucidate the regulatory mechanism of elevation of plasma ADMA, a novel risk factor for cardiovascular disease. We found by RT-PCR and Western blot analyses that protein arginine methyltransferase (PRMT)1 and dimethylarginine dimethylaminohydrolase (DDAH)-1, responsible for the biosynthesis and degradation of ADMA respectively, are expressed in erythrocytes (ECs), leukocytes, and platelets. We also identified a major ADMA-containing protein in ECs as catalase, confirmed by GST-pull down assay to bind to PRMT1 in vitro. This is the first report that the ADMA-metabolizing system, including the arginine methylation of proteins and the breakdown of free ADMA, occurs in circulating blood cell-populations, and that catalase in ECs might be a potential protein targeted by PRMT1.
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27
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Kölbel K, Ihling C, Kühn U, Neundorf I, Otto S, Stichel J, Robaa D, Beck-Sickinger AG, Sinz A, Wahle E. Peptide Backbone Conformation Affects the Substrate Preference of Protein Arginine Methyltransferase I. Biochemistry 2012; 51:5463-75. [DOI: 10.1021/bi300373b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Knut Kölbel
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse
3, 06120 Halle, Germany
| | - Christian Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Germany
| | - Uwe Kühn
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse
3, 06120 Halle, Germany
| | - Ines Neundorf
- Institute of Biochemistry, University of Leipzig, Brüderstrasse 34, 04103
Leipzig, Germany
| | - Silke Otto
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse
3, 06120 Halle, Germany
| | - Jan Stichel
- Institute of Biochemistry, University of Leipzig, Brüderstrasse 34, 04103
Leipzig, Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Germany
| | | | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse
3, 06120 Halle, Germany
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28
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Shia WJ, Okumura AJ, Yan M, Sarkeshik A, Lo MC, Matsuura S, Komeno Y, Zhao X, Nimer SD, Yates JR, Zhang DE. PRMT1 interacts with AML1-ETO to promote its transcriptional activation and progenitor cell proliferative potential. Blood 2012; 119:4953-62. [PMID: 22498736 PMCID: PMC3367897 DOI: 10.1182/blood-2011-04-347476] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 03/23/2012] [Indexed: 01/04/2023] Open
Abstract
Fusion protein AML1-ETO, resulting from t(8;21) translocation, is highly related to leukemia development. It has been reported that full-length AML1-ETO blocks AML1 function and requires additional mutagenic events to promote leukemia. We have previously shown that the expression of AE9a, a splice isoform of AML1-ETO, can rapidly cause leukemia in mice. To understand how AML1-ETO is involved in leukemia development, we took advantage of our AE9a leukemia model and sought to identify its interacting proteins from primary leukemic cells. Here, we report the discovery of a novel AE9a binding partner PRMT1 (protein arginine methyltransferase 1). PRMT1 not only interacts with but also weakly methylates arginine 142 of AE9a. Knockdown of PRMT1 affects expression of a specific group of AE9a-activated genes. We also show that AE9a recruits PRMT1 to promoters of AE9a-activated genes, resulting in enrichment of H4 arginine 3 methylation, H3 Lys9/14 acetylation, and transcription activation. More importantly, knockdown of PRMT1 suppresses the self-renewal capability of AE9a, suggesting a potential role of PRMT1 in regulating leukemia development.
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Affiliation(s)
- Wei-Jong Shia
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
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29
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Cheng Y, Frazier M, Lu F, Cao X, Redinbo MR. Crystal structure of the plant epigenetic protein arginine methyltransferase 10. J Mol Biol 2011; 414:106-22. [PMID: 21986201 PMCID: PMC3217299 DOI: 10.1016/j.jmb.2011.09.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/20/2011] [Accepted: 09/24/2011] [Indexed: 01/07/2023]
Abstract
Protein arginine methyltransferase 10 (PRMT10) is a type I arginine methyltransferase that is essential for regulating flowering time in Arabidopsis thaliana. We present a 2.6 Å resolution crystal structure of A. thaliana PRMT 10 (AtPRMT10) in complex with a reaction product, S-adenosylhomocysteine. The structure reveals a dimerization arm that is 12-20 residues longer than PRMT structures elucidated previously; as a result, the essential AtPRMT10 dimer exhibits a large central cavity and a distinctly accessible active site. We employ molecular dynamics to examine how dimerization facilitates AtPRMT10 motions necessary for activity, and we show that these motions are conserved in other PRMT enzymes. Finally, functional data reveal that the 10 N-terminal residues of AtPRMT10 influence substrate specificity, and that enzyme activity is dependent on substrate protein sequences distal from the methylation site. Taken together, these data provide insights into the molecular mechanism of AtPRMT10, as well as other members of the PRMT family of enzymes. They highlight differences between AtPRMT10 and other PRMTs but also indicate that motions are a conserved element of PRMT function.
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Affiliation(s)
- Yuan Cheng
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Monica Frazier
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Falong Lu
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China,Graduate School, Chinese Academy of Sciences, Beijing, 100039, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Matthew R. Redinbo
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Program in Molecular & Cellular Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,Correspondence: Matthew R. Redinbo, Ph.D., Department of Chemistry, Campus Box 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599. Tel.:919-843-8910, Fax: 919-962-2388,
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30
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Fronz K, Güttinger S, Burkert K, Kühn U, Stöhr N, Schierhorn A, Wahle E. Arginine methylation of the nuclear poly(a) binding protein weakens the interaction with its nuclear import receptor, transportin. J Biol Chem 2011; 286:32986-94. [PMID: 21808065 PMCID: PMC3190935 DOI: 10.1074/jbc.m111.273912] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/28/2011] [Indexed: 11/06/2022] Open
Abstract
The nuclear poly(A) binding protein, PABPN1, promotes mRNA polyadenylation in the cell nucleus by increasing the processivity of poly(A) polymerase and contributing to poly(A) tail length control. In its C-terminal domain, the protein carries 13 arginine residues that are all asymmetrically dimethylated. The function of this modification in PABPN1 has been unknown. Part of the methylated domain serves as nuclear localization signal, binding the import receptor transportin. Here we report that arginine methylation weakens the affinity of PABPN1 for transportin. Recombinant, unmethylated PABPN1 binds more strongly to transportin than its methylated counterpart from mammalian tissue, and in vitro methylation reduces the affinity. Transportin and RNA compete for binding to PABPN1. Methylation favors RNA binding. Transportin also inhibits in vitro methylation of the protein. Finally, a peptide corresponding to the nuclear localization signal of PABPN1 competes with transportin-dependent nuclear import of the protein in a permeabilized cell assay and does so less efficiently when it is methylated. We hypothesize that transportin binding might delay methylation of PABPN1 until after nuclear import. In the nucleus, arginine methylation may favor the transition of PABPN1 to the competing ligand RNA and serve to reduce the risk of the protein being reexported to the cytoplasm by transportin.
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Affiliation(s)
- Katharina Fronz
- From the Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Stefan Güttinger
- the Institute of Biochemistry, Swiss Federal Institute of Technology (ETH Zürich), Schafmattstrasse 18, 8093 Zürich, Switzerland, and
| | - Kerstin Burkert
- From the Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Uwe Kühn
- From the Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Nadine Stöhr
- the Section for Molecular Cell Biology, Department of Medicine, Martin Luther University Halle-Wittenberg, 06097 Halle, Germany
| | - Angelika Schierhorn
- From the Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Elmar Wahle
- From the Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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Waldmann T, Izzo A, Kamieniarz K, Richter F, Vogler C, Sarg B, Lindner H, Young NL, Mittler G, Garcia BA, Schneider R. Methylation of H2AR29 is a novel repressive PRMT6 target. Epigenetics Chromatin 2011; 4:11. [PMID: 21774791 PMCID: PMC3164600 DOI: 10.1186/1756-8935-4-11] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 07/20/2011] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Covalent histone modifications are central to all DNA-dependent processes. Modifications of histones H3 and H4 are becoming well characterised, but knowledge of how H2A modifications regulate chromatin dynamics and gene expression is still very limited. RESULTS To understand the function of H2A modifications, we performed a systematic analysis of the histone H2A methylation status. We identified and functionally characterised two new methylation sites in H2A: R11 (H2AR11) and R29 (H2AR29). Using an unbiased biochemical approach in combination with candidate assays we showed that protein arginine methyltransferase (PRMT) 1 and PRMT6 are unique in their ability to catalyse these modifications. Importantly we found that H2AR29me2 is specifically enriched at genes repressed by PRMT6, implicating H2AR29me2 in transcriptional repression. CONCLUSIONS Our data establishes R11 and R29 as new arginine methylation sites in H2A. We identified the specific modifying enzymes involved, and uncovered a novel functional role of H2AR29me2 in gene silencing in vivo. Thus this work reveals novel insights into the function of H2A methylation and in the mechanisms of PRMT6-mediated transcriptional repression.
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Affiliation(s)
- Tanja Waldmann
- MPI for Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
- University of Konstanz, Doerenkamp-Zbinden chair, Universitätsstr. 10, 78457 Konstanz, Germany
| | - Annalisa Izzo
- MPI for Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Kinga Kamieniarz
- MPI for Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Florian Richter
- MPI for Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Christine Vogler
- MPI for Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Bettina Sarg
- Innsbruck Medical University, Division of Clinical Biochemistry, Biocenter, Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria
| | - Herbert Lindner
- Innsbruck Medical University, Division of Clinical Biochemistry, Biocenter, Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria
| | - Nicolas L Young
- Princeton University, Department of Molecular Biology, 415 Shultz Laboratory, Princeton, NJ 08540, USA
| | - Gerhard Mittler
- MPI for Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Benjamin A Garcia
- Princeton University, Department of Molecular Biology, 415 Shultz Laboratory, Princeton, NJ 08540, USA
| | - Robert Schneider
- MPI for Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
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32
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Abstract
Protozoa constitute the earliest branch of the eukaryotic lineage, and several groups of protozoans are serious parasites of humans and other animals. Better understanding of biochemical pathways that are either in common with or divergent from those of higher eukaryotes is integral in the defense against these parasites. In yeast and humans, the posttranslational methylation of arginine residues in proteins affects myriad cellular processes, including transcription, RNA processing, DNA replication and repair, and signal transduction. The protein arginine methyltransferases (PRMTs) that catalyze these reactions, which are unique to the eukaryotic kingdom of organisms, first become evident in protozoa. In this review, we focus on the current understanding of arginine methylation in multiple species of parasitic protozoa, including Trichomonas, Entamoeba, Toxoplasma, Plasmodium, and Trypanosoma spp., and discuss how arginine methylation may play important and unique roles in each type of parasite. We mine available genomic and transcriptomic data to inventory the families of PRMTs in different parasites and the changes in their abundance during the life cycle. We further review the limited functional studies on the roles of arginine methylation in parasites, including epigenetic regulation in Apicomplexa and RNA processing in trypanosomes. Interestingly, each of the parasites considered herein has significantly differing sets of PRMTs, and we speculate on the importance of this diversity in aspects of parasite biology, such as differentiation and antigenic variation.
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Takahashi Y, Daitoku H, Hirota K, Tamiya H, Yokoyama A, Kako K, Nagashima Y, Nakamura A, Shimada T, Watanabe S, Yamagata K, Yasuda K, Ishii N, Fukamizu A. Asymmetric arginine dimethylation determines life span in C. elegans by regulating forkhead transcription factor DAF-16. Cell Metab 2011; 13:505-16. [PMID: 21531333 DOI: 10.1016/j.cmet.2011.03.017] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 01/20/2011] [Accepted: 03/17/2011] [Indexed: 12/20/2022]
Abstract
Arginine methylation is a widespread posttranslational modification of proteins catalyzed by a family of protein arginine methyltransferases (PRMTs). It is well established that PRMTs are implicated in various cellular processes, but their physiological roles remain unclear. Using nematodes with a loss-of-function mutation, we show that prmt-1, the major asymmetric arginine methyltransferase, is a positive regulator of longevity in C. elegans. This regulation is dependent on both its enzymatic activity and DAF-16/FoxO transcription factor, which is negatively regulated by AKT-mediated phosphorylation downstream of the DAF-2/insulin signaling. prmt-1 is also required for stress tolerance and fat storage but not dauer formation in daf-2 mutants. Biochemical analyses indicate that PRMT-1 methylates DAF-16, thereby blocking its phosphorylation by AKT. Disruption of PRMT-1 induces phosphorylation of DAF-16 with a concomitant reduction in the expression of longevity-related genes. Thus, we provide a mechanism by which asymmetric arginine dimethylation acts as an antiaging modification in C. elegans.
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Affiliation(s)
- Yuta Takahashi
- Life Science Center, Tsukuba Advanced Research Alliance, Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Ibaraki, Japan
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34
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Yu MC. The Role of Protein Arginine Methylation in mRNP Dynamics. Mol Biol Int 2011; 2011:163827. [PMID: 22091396 PMCID: PMC3195771 DOI: 10.4061/2011/163827] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 02/12/2011] [Indexed: 12/13/2022] Open
Abstract
In eukaryotes, messenger RNA biogenesis depends on the ordered and precise assembly of a nuclear messenger ribonucleoprotein particle (mRNP) during transcription. This process requires a well-orchestrated and dynamic sequence of molecular recognition events by specific RNA-binding proteins. Arginine methylation is a posttranslational modification found in a plethora of RNA-binding proteins responsible for mRNP biogenesis. These RNA-binding proteins include both heterogeneous nuclear ribonucleoproteins (hnRNPs) and serine/arginine-rich (SR) proteins. In this paper, I discuss the mechanisms of action by which arginine methylation modulates various facets of mRNP biogenesis, and how the collective consequences of this modification impart the specificity required to generate a mature, translational- and export-competent mRNP.
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Affiliation(s)
- Michael C Yu
- Department of Biological Sciences, State University of New York at Buffalo, 109 Cooke Hall, Buffalo, NY 14260, USA
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35
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Arginine methylation of BCL-2 antagonist of cell death (BAD) counteracts its phosphorylation and inactivation by Akt. Proc Natl Acad Sci U S A 2011; 108:6085-90. [PMID: 21444773 DOI: 10.1073/pnas.1015328108] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Protein arginine methylation is a common posttranslational modification catalyzed by a family of the protein arginine methyltransferases (PRMTs). We have previously reported that PRMT1 methylates Forkhead box O transcription factors at two arginine residues within an Akt consensus phosphorylation motif (RxRxxS/T), and that this methylation blocks Akt-mediated phosphorylation of the transcription factors. These findings led us to hypothesize that the functional crosstalk between arginine methylation and phosphorylation could be extended to other Akt target proteins as well as Forkhead box O proteins. Here we identify BCL-2 antagonist of cell death (BAD) as an additional substrate for PRMT1 among several Akt target proteins. We show that PRMT1 specifically binds and methylates BAD at Arg-94 and Arg-96, both of which comprise the Akt consensus phosphorylation motif. Consistent with the hypothesis, PRMT1-mediated methylation of these two arginine residues inhibits Akt-mediated phosphorylation of BAD at Ser-99 in vitro and in vivo. We also demonstrate that the complex formation of BAD with 14-3-3 proteins, which occurs subsequent to Akt-mediated phosphorylation, is negatively regulated by PRMT1. Furthermore, PRMT1 knockdown prevents mitochondrial localization of BAD and its binding to the antiapoptotic BCL-X(L) protein. BAD overexpression causes an increase in apoptosis with concomitant activation of caspase-3, whereas PRMT1 knockdown significantly suppresses these apoptotic processes. Taken together, our results add a new dimension to the complexity of posttranslational BAD regulation and provide evidence that arginine methylation within an Akt consensus phosphorylation motif functions as an inhibitory modification against Akt-dependent survival signaling.
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36
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Tsai YJ, Pan H, Hung CM, Hou PT, Li YC, Lee YJ, Shen YT, Wu TT, Li C. The predominant protein arginine methyltransferase PRMT1 is critical for zebrafish convergence and extension during gastrulation. FEBS J 2011; 278:905-17. [PMID: 21214862 DOI: 10.1111/j.1742-4658.2011.08006.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein arginine methyltransferase (PRMT)1 is the predominant type I methyltransferase in mammals. In the present study, we used zebrafish (Danio rerio) as the model system to elucidate PRMT1 expression and function during embryogenesis. Zebrafish prmt1 transcripts were detected from the zygote period to the early larva stage. Knockdown of prmt1 by antisense morpholino oligo (AMO) resulted in delayed growth, shortened body-length, curled tails and cardiac edema. PRMT1 protein level, type I protein arginine methyltransferase activity, specific asymmetric protein arginine methylation and histone H4 R3 methylation all decreased in the AMO-injected morphants. The morphants showed defective convergence and extension and the abnormalities were more severe at the posterior than the anterior parts. Cell migration defects suggested by the phenotypes were not only observed in the morphant embryos, but also in a cellular prmt1 small-interfering RNA knockdown model. Rescue of the phenotypes by co-injection of wild-type but not catalytic defective prmt1 mRNA confirmed the specificity of the AMO and the requirement of methyltransferase activity in early development. The results obtained in the present study demonstrate a direct link of early development with protein arginine methylation catalyzed by PRMT1.
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Affiliation(s)
- Yun-Jung Tsai
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
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37
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Mort M, Evani US, Krishnan VG, Kamati KK, Baenziger PH, Bagchi A, Peters BJ, Sathyesh R, Li B, Sun Y, Xue B, Shah NH, Kann MG, Cooper DN, Radivojac P, Mooney SD. In silico functional profiling of human disease-associated and polymorphic amino acid substitutions. Hum Mutat 2010; 31:335-46. [PMID: 20052762 DOI: 10.1002/humu.21192] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An important challenge in translational bioinformatics is to understand how genetic variation gives rise to molecular changes at the protein level that can precipitate both monogenic and complex disease. To this end, we compiled datasets of human disease-associated amino acid substitutions (AAS) in the contexts of inherited monogenic disease, complex disease, functional polymorphisms with no known disease association, and somatic mutations in cancer, and compared them with respect to predicted functional sites in proteins. Using the sequence homology-based tool SIFT to estimate the proportion of deleterious AAS in each dataset, only complex disease AAS were found to be indistinguishable from neutral polymorphic AAS. Investigation of monogenic disease AAS predicted to be nondeleterious by SIFT were characterized by a significant enrichment for inherited AAS within solvent accessible residues, regions of intrinsic protein disorder, and an association with the loss or gain of various posttranslational modifications. Sites of structural and/or functional interest were therefore surmised to constitute useful additional features with which to identify the molecular disruptions caused by deleterious AAS. A range of bioinformatic tools, designed to predict structural and functional sites in protein sequences, were then employed to demonstrate that intrinsic biases exist in terms of the distribution of different types of human AAS with respect to specific structural, functional and pathological features. Our Web tool, designed to potentiate the functional profiling of novel AAS, has been made available at http://profile.mutdb.org/.
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Affiliation(s)
- Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
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38
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Martin G, Ostareck-Lederer A, Chari A, Neuenkirchen N, Dettwiler S, Blank D, Rüegsegger U, Fischer U, Keller W. Arginine methylation in subunits of mammalian pre-mRNA cleavage factor I. RNA (NEW YORK, N.Y.) 2010; 16:1646-59. [PMID: 20562214 PMCID: PMC2905762 DOI: 10.1261/rna.2164210] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Mammalian cleavage factor I (CF I(m)) is composed of two polypeptides of 25 kDa and either a 59 or 68 kDa subunit (CF I(m)25, CF I(m)59, CF I(m)68). It is part of the cleavage and polyadenylation complex responsible for processing the 3' ends of messenger RNA precursors. To investigate post-translational modifications in factors of the 3' processing complex, we systematically searched for enzymes that modify arginines by the addition of methyl groups. Protein arginine methyltransferases (PRMTs) are such enzymes that transfer methyl groups from S-adenosyl methionine to arginine residues within polypeptide chains resulting in mono- or dimethylated arginines. We found that CF I(m)68 and the nuclear poly(A) binding protein 1 (PABPN1) were methylated by HeLa cell extracts in vitro. By fractionation of these extracts followed by mass spectral analysis, we could demonstrate that the catalytic subunit PRMT5, together with its cofactor WD45, could symmetrically dimethylate CF I(m)68, whereas pICln, the third polypeptide of the complex, was stimulatory. As sites of methylation in CF I(m)68 we could exclusively identify arginines in a GGRGRGRF or "GAR" motif that is conserved in vertebrates. Further in vitro assays revealed a second methyltransferase, PRMT1, which modifies CF I(m)68 by asymmetric dimethylation of the GAR motif and also weakly methylates the C-termini of both CF I(m)59 and CF I(m)68. The results suggest that native-as compared with recombinant-protein substrates may contain additional determinants for methylation by specific PRMTs. A possible involvement of CF I(m) methylation in the context of RNA export is discussed.
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Affiliation(s)
- Georges Martin
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
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39
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Guendel I, Carpio L, Pedati C, Schwartz A, Teal C, Kashanchi F, Kehn-Hall K. Methylation of the tumor suppressor protein, BRCA1, influences its transcriptional cofactor function. PLoS One 2010; 5:e11379. [PMID: 20614009 PMCID: PMC2894074 DOI: 10.1371/journal.pone.0011379] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 06/08/2010] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Approximately half of hereditary breast cancers have mutations in either BRCA1 or BRCA2. BRCA1 is a multifaceted tumor suppressor protein that has implications in processes such as cell cycle, transcription, DNA damage response and chromatin remodeling. This multifunctional nature of BRCA1 is achieved by exerting its many effects through modulation of transcription. Many cellular events are dictated by covalent modification of proteins, an important mechanism in regulating protein and genome function; of which protein methylation is an important posttranslational modification with activating or repressive effects. METHODS/PRINCIPAL FINDINGS Here we demonstrate for the first time that BRCA1 is methylated both in breast cancer cell lines and breast cancer tumor samples at arginine and lysine residues through immunoprecipitation and western blot analysis. Arginine methylation by PRMT1 was observed in vitro and the region of BRCA1 504-802 shown to be highly methylated. PRMT1 was detected in complex with BRCA1 504-802 through in vitro binding assays and co-immunoprecipitated with BRCA1. Inhibition of methylation resulted in decreased BRCA1 methylation and alteration of BRCA1 binding to promoters in vivo as shown through chromatin immunoprecipitation assays. Knockdown of PRMT1 also resulted in increased BRCA1 binding to particular promoters in vivo. Finally, following methylation inhibition, Sp1 was found to preferentially associate with hypo-methylated BRCA1 and STAT1 was found to preferentially associate with hyper-methylated BRCA1. CONCLUSIONS/SIGNIFICANCE These results suggest that methylation may influence either the ability of BRCA1 to bind to specific promoters or protein-protein interactions which alters the recruitment of BRCA1 to these promoters. Thus, given the importance of BRCA1 to genomic stability, methylation of BRCA1 may ultimately affect the tumor suppressor ability of BRCA1.
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Affiliation(s)
- Irene Guendel
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University Medical Center, Washington, D. C., United States of America
- Department of Molecular and Microbiology, National Center for Biodefense & Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Lawrence Carpio
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University Medical Center, Washington, D. C., United States of America
- Department of Molecular and Microbiology, National Center for Biodefense & Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Caitlin Pedati
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University Medical Center, Washington, D. C., United States of America
| | - Arnold Schwartz
- Department of Pathology, The George Washington University Medical Center, Washington, D. C., United States of America
| | - Christine Teal
- Breast Care Center, The George Washington University Medical Center, Washington, D. C., United States of America
| | - Fatah Kashanchi
- Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University Medical Center, Washington, D. C., United States of America
- Department of Molecular and Microbiology, National Center for Biodefense & Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
| | - Kylene Kehn-Hall
- Department of Molecular and Microbiology, National Center for Biodefense & Infectious Diseases, George Mason University, Manassas, Virginia, United States of America
- * E-mail:
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40
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Lipson RS, Webb KJ, Clarke SG. Rmt1 catalyzes zinc-finger independent arginine methylation of ribosomal protein Rps2 in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2009; 391:1658-62. [PMID: 20035717 DOI: 10.1016/j.bbrc.2009.12.112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 12/18/2009] [Indexed: 10/20/2022]
Abstract
Rps2/rpS2 is a well conserved protein of the eukaryotic ribosomal small subunit. Rps2 has previously been shown to contain asymmetric dimethylarginine residues, the addition of which is catalyzed by zinc-finger-containing arginine methyltransferase 3 (Rmt3) in the fission yeast Schizosaccharomyces pombe and protein arginine methyltransferase 3 (PRMT3) in mammalian cells. Here, we demonstrate that despite the lack of a zinc-finger-containing homolog of Rmt3/PRMT3 in the budding yeast Saccharomyces cerevisiae, Rps2 is partially modified to generate asymmetric dimethylarginine and monomethylarginine residues. We find that this modification of Rps2 is dependent upon the major arginine methyltransferase 1 (Rmt1) in S. cerevisiae. These results are suggestive of a role for Rmt1 in modifying the function of Rps2 in a manner distinct from that occurring in S. pombe and mammalian cells.
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Affiliation(s)
- Rebecca S Lipson
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, 607 Charles E Young Drive East, Los Angeles, CA 90095-1569, USA
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41
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Jarmalavicius S, Trefzer U, Walden P. Differential arginine methylation of the G‐protein pathway suppressor GPS‐2 recognized by tumor‐specific T cells in melanoma. FASEB J 2009; 24:937-46. [DOI: 10.1096/fj.09-136283] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Saulius Jarmalavicius
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
| | - Uwe Trefzer
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
| | - Peter Walden
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
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42
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Kuhn P, Xu W. Protein arginine methyltransferases: nuclear receptor coregulators and beyond. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:299-342. [PMID: 20374708 DOI: 10.1016/s1877-1173(09)87009-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein arginine methyltransferases (PRMTs) are a family of enzymes that play a crucial role in diverse cellular functions. Several PRMTs have been associated with gene expression regulation, in which PRMTs act as histone methyltransferases, secondary coregulators of transcription, or facilitate mRNA splicing and stability. Additional functions include modulation of protein localization, ribosomal assembly, and signal transduction. At the organismal level, several PRMTs appear to be important for development and may play an important role in cancer. The relationships between their cellular and organismal functions are poorly understood; at least in part due to the large body of enzymatic substrates for PRMTs and their transcriptional targets that remain to be determined. Specific PRMT inhibitors have been developed in recent years, which should help to shed light on their diverse biological roles. Connecting PRMT cellular functions with their global effects on an organism will facilitate development of novel treatments for human diseases.
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Affiliation(s)
- Peter Kuhn
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin 53706, USA
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43
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Tavanez JP, Bengoechea R, Berciano MT, Lafarga M, Carmo-Fonseca M, Enguita FJ. Hsp70 chaperones and type I PRMTs are sequestered at intranuclear inclusions caused by polyalanine expansions in PABPN1. PLoS One 2009; 4:e6418. [PMID: 19641605 PMCID: PMC2712759 DOI: 10.1371/journal.pone.0006418] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 06/26/2009] [Indexed: 02/03/2023] Open
Abstract
Genomic instability at loci with tandem arrays of simple repeats is the cause for many neurological, neurodegenerative and neuromuscular diseases. When located in coding regions, disease-associated expansions of trinucleotide repeats are translated into homopolymeric amino acid stretches of glutamine or alanine. Polyalanine expansions in the poly(A)-binding protein nuclear 1 (PABPN1) gene causes oculopharyngeal muscular dystrophy (OPMD). To gain novel insight into the molecular pathophysiology of OPMD, we studied the interaction of cellular proteins with normal and expanded PABPN1. Pull-down assays show that heat shock proteins including Hsp70, and type I arginine methyl transferases (PRMT1 and PRMT3) associate preferentially with expanded PABPN1. Immunofluorescence microscopy further reveals accumulation of these proteins at intranuclear inclusions in muscle from OPMD patients. Recombinant PABPN1 with expanded polyalanine stretches binds Hsp70 with higher affinity, and data from molecular simulations suggest that expansions of the PABPN1 polyalanine tract result in transition from a disordered, flexible conformation to a stable helical secondary structure. Taken together, our results suggest that the pathological mutation in the PABPN1 gene alters the protein conformation and induces a preferential interaction with type I PRMTs and Hsp70 chaperones. This in turn causes sequestration in intranuclear inclusions, possibly leading to a progressive cellular defect in arginine methylation and chaperone activity.
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Affiliation(s)
- João Paulo Tavanez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Rocio Bengoechea
- Department of Anatomy and Cell Biology, and “Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)”, University of Cantabria, Santander, Spain
| | - Maria T. Berciano
- Department of Anatomy and Cell Biology, and “Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)”, University of Cantabria, Santander, Spain
| | - Miguel Lafarga
- Department of Anatomy and Cell Biology, and “Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED)”, University of Cantabria, Santander, Spain
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- * E-mail:
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44
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Wolf SS. The protein arginine methyltransferase family: an update about function, new perspectives and the physiological role in humans. Cell Mol Life Sci 2009; 66:2109-21. [PMID: 19300908 PMCID: PMC11115746 DOI: 10.1007/s00018-009-0010-x] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 02/19/2009] [Accepted: 02/20/2009] [Indexed: 12/12/2022]
Abstract
Information about the family of protein arginine methyltransferases (PRMTs) has been growing rapidly over the last few years and the emerging role of arginine methylation involved in cellular processes like signaling, RNA processing, gene transcription, and cellular transport function has been investigated. To date, 11 PRMTs gene transcripts have been identified in humans. Almost all PRMTs have been shown to have enzymatic activity and to catalyze arginine methylation. This review will summarize the overall function of human PRMTs and include novel highlights on each family member.
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Affiliation(s)
- S S Wolf
- Bayer Schering Pharma AG, Global Drug Discovery, TRG Women's Healthcare, Muellerstr 178, 13353, Berlin, Germany.
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Abstract
Arginine methylation is a post-translational modification that affects many cellular processes in eukaryotes. The malaria parasite Plasmodium falciparum encodes three conserved PRMTs (protein arginine N-methyltransferases). We have determined that PfPRMT1 (P. falciparum PRMT1) has authentic type I PRMT activity to form monomethylarginines and asymmetric dimethylarginines. Compared with mammalian PRMT1s, PfPRMT1 possesses a distinctive N-terminal sequence that is approximately 50 amino acids longer and is essential for enzyme activity. Recombinant PfPRMT1 methylated histones H4 and H2A and several conserved substrates involved in RNA metabolism, including fibrillarin, poly(A)-binding protein II, ribosomal protein S2 and a putative splicing factor. Using synthetic peptides and MS, we determined target arginines in several substrates and studied the enzyme kinetics. Whereas the kinetic parameters of recombinant PfPRMT1 on an H4 peptide and S-adenosylmethionine were similar to those of mammalian PRMT1s, PfPRMT1 had much higher substrate-turnover rates. In the histone H4 N-terminus, PfPRMT1 could methylate only Arg3, a mark for transcription activation. Western blotting detected dynamic dimethylation of H4-Arg3 during parasite development, suggesting that histone-arginine methylation may play a conserved role in chromatin-mediated gene regulation. Consistent with the presence of potential substrates in both the cytoplasm and nucleus, green fluorescent protein-tagged PfPRMT1 and untagged PfPRMT1 were localized in both cellular compartments, with the majority in the cytoplasm. in vitro assays showed that PfPRMT1 could be inhibited by several small-molecule inhibitors, with IC50-values in the sub-micromolar range. Most of these compounds also effectively inhibited parasite growth, suggesting that parasite PRMTs are promising targets for developing antiparasitic drugs.
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Perreault A, Gascon S, D'Amours A, Aletta JM, Bachand F. A methyltransferase-independent function for Rmt3 in ribosomal subunit homeostasis. J Biol Chem 2009; 284:15026-37. [PMID: 19359250 DOI: 10.1074/jbc.m109.004812] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Schizosaccharomyces pombe Rmt3 is a member of the protein-arginine methyltransferase (PRMT) family and is the homolog of human PRMT3. We previously characterized Rmt3 as a ribosomal protein methyltransferase based on the identification of the 40 S Rps2 (ribosomal protein S2) as a substrate of Rmt3. RMT3-null cells produce nonmethylated Rps2 and show mis-regulation of the 40 S/60 S ribosomal subunit ratio due to a small subunit deficit. For this study, we have generated a series of RMT3 alleles that express various amino acid substitutions to characterize the functional domains of Rmt3 in Rps2 binding, Rps2 arginine methylation, and small ribosomal subunit production. Notably, catalytically inactive versions of Rmt3 restored the ribosomal subunit imbalance detected in RMT3-null cells. Consistent with a methyltransferase-independent function for Rmt3 in small ribosomal subunit production, the expression of an Rps2 variant in which the identified methylarginine residues were substituted with lysines showed normal levels of 40 S subunit. Importantly, substitutions within the zinc finger domain of Rmt3 that abolished Rps2 binding did not rescue the 40 S ribosomal subunit deficit of RMT3-null cells. Our findings suggest that the Rmt3-Rps2 interaction, rather than Rps2 methylation, is important for the function of Rmt3 in the regulation of small ribosomal subunit production.
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Affiliation(s)
- Audrey Perreault
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Québec J1H 5N4, Canada
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Arginine methylation of human adenovirus type 5 L4 100-kilodalton protein is required for efficient virus production. J Virol 2009; 83:4778-90. [PMID: 19264777 DOI: 10.1128/jvi.02493-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The adenovirus type 5 (Ad5) late region 4 (L4) 100-kDa nonstructural protein (L4-100K) mediates inhibition of cellular protein synthesis and selective translation of tripartite leader (TL)-containing viral late mRNAs via ribosome shunting. In addition, L4-100K has been implicated in the trimerization and nuclear localization of hexon protein. We previously proved that L4-100K is a substrate of the protein arginine methylation machinery, an emergent posttranslational modification system involved in a growing list of cellular processes, including transcriptional regulation, cell signaling, RNA processing, and DNA repair. As understood at present, L4-100K arginine methylation involves protein arginine methyltransferase 1 (PRMT1), which asymmetrically dimethylates arginines embedded in arginine-glycine-glycine (RGG) or glycine-arginine-rich (GAR) domains. To identify the methylated arginine residues and assess the role of L4-100K arginine methylation, we generated amino acid substitution mutations in the RGG and GAR motifs to examine their effects in Ad-infected and plasmid-transfected cells. Arginine-to-glycine exchanges in the RGG boxes significantly diminished L4-100K methylation in the course of an infection and substantially reduced virus growth, demonstrating that L4-100K methylation in RGG motifs is an important host cell function required for efficient Ad replication. Our data further indicate that PRMT1-catalyzed arginine methylation in the RGG boxes regulates the binding of L4-100K to hexon and promotes the capsid assembly of the structural protein as well as modulating TL-mRNA interaction. Furthermore, substitutions in GAR, but not RGG, regions affected L4-100K nuclear import, implying that the nuclear localization signal of L4-100K is located within the GAR sequence.
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Wang H, Straubinger RM, Aletta JM, Cao J, Duan X, Yu H, Qu J. Accurate localization and relative quantification of arginine methylation using nanoflow liquid chromatography coupled to electron transfer dissociation and orbitrap mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:507-19. [PMID: 19110445 PMCID: PMC3351756 DOI: 10.1016/j.jasms.2008.11.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2008] [Revised: 11/12/2008] [Accepted: 11/13/2008] [Indexed: 05/21/2023]
Abstract
Protein arginine (Arg) methylation serves an important functional role in eucaryotic cells, and typically occurs in domains consisting of multiple Arg in close proximity. Localization of methylarginine (MA) within Arg-rich domains poses a challenge for mass spectrometry (MS)-based methods; the peptides are highly charged under electrospray ionization (ESI), which limits the number of sequence-informative products produced by collision induced dissociation (CID), and loss of the labile methylation moieties during CID precludes effective fragmentation of the peptide backbone. Here the fragmentation behavior of Arg-rich peptides was investigated comprehensively using electron-transfer dissociation (ETD) and CID for both methylated and unmodified glycine-/Arg-rich peptides (GAR), derived from residues 679-695 of human nucleolin, which contains methylation motifs that are widely-represented in biological systems. ETD produced abundant information for sequencing and MA localization, whereas CID failed to provide credible identification for any available charge state (z = 2-4). Nevertheless, CID produced characteristic neutral losses that can be employed to distinguish among different types of MA, as suggested by previous works and confirmed here with product ion scans of high accuracy/resolution by an LTQ/Orbitrap. To analyze MA-peptides in relatively complex mixtures, a method was developed that employs nano-LC coupled to alternating CID/ETD for peptide sequencing and MA localization/characterization, and an Orbitrap for accurate precursor measurement and relative quantification of MA-peptide stoichiometries. As proof of concept, GAR-peptides methylated in vitro by protein arginine N-methyltransferases PRMT1 and PRMT7 were analyzed. It was observed that PRMT1 generated a number of monomethylated (MMA) and asymmetric-dimethylated peptides, while PRMT7 produced predominantly MMA peptides and some symmetric-dimethylated peptides. This approach and the results may advance understanding of the actions of PRMTs and the functional significance of Arg methylation patterns.
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Affiliation(s)
- Hao Wang
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
| | - Robert M. Straubinger
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
| | - John M. Aletta
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
- CH3 BioSystems LLC 1416 Sweet Home Road, Amherst, New York 14228-2784
| | - Jin Cao
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
| | - Xiaotao Duan
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
| | - Haoying Yu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
| | - Jun Qu
- The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260-1200
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St, Buffalo, NY 14203
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Herrmann F, Pably P, Eckerich C, Bedford MT, Fackelmayer FO. Human protein arginine methyltransferases in vivo--distinct properties of eight canonical members of the PRMT family. J Cell Sci 2009; 122:667-77. [PMID: 19208762 DOI: 10.1242/jcs.039933] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Methylation of arginine residues is a widespread post-translational modification of proteins catalyzed by a small family of protein arginine methyltransferases (PRMTs). Functionally, the modification appears to regulate protein functions and interactions that affect gene regulation, signalling and subcellular localization of proteins and nucleic acids. All members have been, to different degrees, characterized individually and their implication in cellular processes has been inferred from characterizing substrates and interactions. Here, we report the first comprehensive comparison of all eight canonical members of the human PRMT family with respect to subcellular localization and dynamics in living cells. We show that the individual family members differ significantly in their properties, as well as in their substrate specificities, suggesting that they fulfil distinctive, non-redundant functions in vivo. In addition, certain PRMTs display different subcellular localization in different cell types, implicating cell- and tissue-specific mechanisms for regulating PRMT functions.
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Affiliation(s)
- Frank Herrmann
- EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), c/Dr. Aiguader 88, 08003 Barcelona, Spain
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50
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Weber S, Maass F, Schuemann M, Krause E, Suske G, Bauer UM. PRMT1-mediated arginine methylation of PIAS1 regulates STAT1 signaling. Genes Dev 2009; 23:118-32. [PMID: 19136629 DOI: 10.1101/gad.489409] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To elucidate the function of the transcriptional coregulator PRMT1 (protein arginine methyltranferase 1) in interferon (IFN) signaling, we investigated the expression of STAT1 (signal transducer and activator of transcription) target genes in PRMT1-depleted cells. We show here that PRMT1 represses a subset of IFNgamma-inducible STAT1 target genes in a methyltransferase-dependent manner. These genes are also regulated by the STAT1 inhibitor PIAS1 (protein inhibitor of activated STAT1). PIAS1 is arginine methylated by PRMT1 in vitro as well as in vivo upon IFN treatment. Mutational and mass spectrometric analysis of PIAS1 identifies Arg 303 as the single methylation site. Using both methylation-deficient and methylation-mimicking mutants, we find that arginine methylation of PIAS1 is essential for the repressive function of PRMT1 in IFN-dependent transcription and for the recruitment of PIAS1 to STAT1 target gene promoters in the late phase of the IFN response. Methylation-dependent promoter recruitment of PIAS1 results in the release of STAT1 and coincides with the decline of STAT1-activated transcription. Accordingly, knockdown of PRMT1 or PIAS1 enhances the anti-proliferative effect of IFNgamma. Our findings identify PRMT1 as a novel and crucial negative regulator of STAT1 activation that controls PIAS1-mediated repression by arginine methylation.
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Affiliation(s)
- Susanne Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps-University of Marburg, 35032 Marburg, Germany
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