1
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Zheng K, Chen S, Ren Z, Wang Y. Protein arginine methylation in viral infection and antiviral immunity. Int J Biol Sci 2023; 19:5292-5318. [PMID: 37928266 PMCID: PMC10620831 DOI: 10.7150/ijbs.89498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Protein arginine methyltransferase (PRMT)-mediated arginine methylation is an important post-transcriptional modification that regulates various cellular processes including epigenetic gene regulation, genome stability maintenance, RNA metabolism, and stress-responsive signal transduction. The varying substrates and biological functions of arginine methylation in cancer and neurological diseases have been extensively discussed, providing a rationale for targeting PRMTs in clinical applications. An increasing number of studies have demonstrated an interplay between arginine methylation and viral infections. PRMTs have been found to methylate and regulate several host cell proteins and different functional types of viral proteins, such as viral capsids, mRNA exporters, transcription factors, and latency regulators. This modulation affects their activity, subcellular localization, protein-nucleic acid and protein-protein interactions, ultimately impacting their roles in various virus-associated processes. In this review, we discuss the classification, structure, and regulation of PRMTs and their pleiotropic biological functions through the methylation of histones and non-histones. Additionally, we summarize the broad spectrum of PRMT substrates and explore their intricate effects on various viral infection processes and antiviral innate immunity. Thus, comprehending the regulation of arginine methylation provides a critical foundation for understanding the pathogenesis of viral diseases and uncovering opportunities for antiviral therapy.
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Affiliation(s)
- Kai Zheng
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Siyu Chen
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Zhe Ren
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research on Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research on Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
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2
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Chang K, Gao D, Yan J, Lin L, Cui T, Lu S. Critical Roles of Protein Arginine Methylation in the Central Nervous System. Mol Neurobiol 2023; 60:6060-6091. [PMID: 37415067 DOI: 10.1007/s12035-023-03465-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/24/2023] [Indexed: 07/08/2023]
Abstract
A remarkable post-transitional modification of both histones and non-histone proteins is arginine methylation. Methylation of arginine residues is crucial for a wide range of cellular process, including signal transduction, DNA repair, gene expression, mRNA splicing, and protein interaction. Arginine methylation is modulated by arginine methyltransferases and demethylases, like protein arginine methyltransferase (PRMTs) and Jumonji C (JmjC) domain containing (JMJD) proteins. Symmetric dimethylarginine and asymmetric dimethylarginine, metabolic products of the PRMTs and JMJD proteins, can be changed by abnormal expression of these proteins. Many pathologies including cancer, inflammation and immune responses have been closely linked to aberrant arginine methylation. Currently, the majority of the literature discusses the substrate specificity and function of arginine methylation in the pathogenesis and prognosis of cancers. Numerous investigations on the roles of arginine methylation in the central nervous system (CNS) have so far been conducted. In this review, we display the biochemistry of arginine methylation and provide an overview of the regulatory mechanism of arginine methyltransferases and demethylases. We also highlight physiological functions of arginine methylation in the CNS and the significance of arginine methylation in a variety of neurological diseases such as brain cancers, neurodegenerative diseases and neurodevelopmental disorders. Furthermore, we summarize PRMT inhibitors and molecular functions of arginine methylation. Finally, we pose important questions that require further research to comprehend the roles of arginine methylation in the CNS and discover more effective targets for the treatment of neurological diseases.
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Affiliation(s)
- Kewei Chang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Dan Gao
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Jidong Yan
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Liyan Lin
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Tingting Cui
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Shemin Lu
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China.
- Department of Biochemistry and Molecular Biology, and Institute of Molecular and Translational Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China.
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3
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Mishra PK, Au WC, Castineira PG, Ali N, Stanton J, Boeckmann L, Takahashi Y, Costanzo M, Boone C, Bloom KS, Thorpe PH, Basrai MA. Misregulation of cell cycle-dependent methylation of budding yeast CENP-A contributes to chromosomal instability. Mol Biol Cell 2023; 34:ar99. [PMID: 37436802 PMCID: PMC10551700 DOI: 10.1091/mbc.e23-03-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/15/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2023] Open
Abstract
Centromere (CEN) identity is specified epigenetically by specialized nucleosomes containing evolutionarily conserved CEN-specific histone H3 variant CENP-A (Cse4 in Saccharomyces cerevisiae, CENP-A in humans), which is essential for faithful chromosome segregation. However, the epigenetic mechanisms that regulate Cse4 function have not been fully defined. In this study, we show that cell cycle-dependent methylation of Cse4-R37 regulates kinetochore function and high-fidelity chromosome segregation. We generated a custom antibody that specifically recognizes methylated Cse4-R37 and showed that methylation of Cse4 is cell cycle regulated with maximum levels of methylated Cse4-R37 and its enrichment at the CEN chromatin occur in the mitotic cells. Methyl-mimic cse4-R37F mutant exhibits synthetic lethality with kinetochore mutants, reduced levels of CEN-associated kinetochore proteins and chromosome instability (CIN), suggesting that mimicking the methylation of Cse4-R37 throughout the cell cycle is detrimental to faithful chromosome segregation. Our results showed that SPOUT methyltransferase Upa1 contributes to methylation of Cse4-R37 and overexpression of UPA1 leads to CIN phenotype. In summary, our studies have defined a role for cell cycle-regulated methylation of Cse4 in high-fidelity chromosome segregation and highlight an important role of epigenetic modifications such as methylation of kinetochore proteins in preventing CIN, an important hallmark of human cancers.
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Affiliation(s)
- Prashant K. Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Pedro G. Castineira
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Nazrin Ali
- Queen Mary University of London, E1 4NS, UK
| | - John Stanton
- University of North Carolina, Chapel Hill, NC 27599
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yoshimitsu Takahashi
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | | | | | - Munira A. Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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4
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Singh AP, Kumar R, Gupta D. Structural insights into the mechanism of human methyltransferase hPRMT4. J Biomol Struct Dyn 2022; 40:10821-10834. [PMID: 34308797 DOI: 10.1080/07391102.2021.1950567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Human PRMT4, also known as CARM1, is a type I arginine methyltransferase protein that catalyse the formation of asymmetrical dimethyl arginine product. Structural studies done to date on PRMT4 have shown that the N-terminal region, Rossmann fold and dimerization arm play an important role in PRMT4 activity. Elucidating the functions of these regions in catalysis remains to be explored. Studies have shown the existence of communication pathways in PRMT4, which need further elucidation. The molecular dynamics (MD) simulations performed in this study show differences in different monomeric and dimeric forms of hPRMT4, revealing the role of the N-terminal region, Rossmann fold and dimerization arm. The study shows the conformational changes that occur during dimerization and SAM binding. Our cross-correlation analysis showed a correlation between these regions. Further, we performed PSN and network analysis to establish the existence of communication networks and an allosteric pathway. This study shows the use of MD simulations and network analysis to explore the aspects of PRMT4 dimerization, SAM binding and demonstrates the existence of an allosteric network. These findings shed novel insights into the conformational changes associated with hPRMT4, the mechanism of its dimerization, SAM binding and clues for better inhibitor designs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amar Pratap Singh
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Rakesh Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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5
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Cura V, Cavarelli J. Structure, Activity and Function of the PRMT2 Protein Arginine Methyltransferase. Life (Basel) 2021; 11:1263. [PMID: 34833139 PMCID: PMC8623767 DOI: 10.3390/life11111263] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
PRMT2 belongs to the protein arginine methyltransferase (PRMT) family, which catalyzes the arginine methylation of target proteins. As a type I enzyme, PRMT2 produces asymmetric dimethyl arginine and has been shown to have weak methyltransferase activity on histone substrates in vitro, suggesting that its authentic substrates have not yet been found. PRMT2 contains the canonical PRMT methylation core and a unique Src homology 3 domain. Studies have demonstrated its clear implication in many different cellular processes. PRMT2 acts as a coactivator of several nuclear hormone receptors and is known to interact with a multitude of splicing-related proteins. Furthermore, PRMT2 is aberrantly expressed in several cancer types, including breast cancer and glioblastoma. These reports highlight the crucial role played by PRMT2 and the need for a better characterization of its activity and cellular functions.
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Affiliation(s)
- Vincent Cura
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR 7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
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6
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Dong R, Li X, Lai KO. Activity and Function of the PRMT8 Protein Arginine Methyltransferase in Neurons. Life (Basel) 2021; 11:life11111132. [PMID: 34833008 PMCID: PMC8621972 DOI: 10.3390/life11111132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
Among the nine mammalian protein arginine methyltransferases (PRMTs), PRMT8 is unusual because it has restricted expression in the nervous system and is the only membrane-bound PRMT. Emerging studies have demonstrated that this enzyme plays multifaceted roles in diverse processes in neurons. Here we will summarize the unique structural features of PRMT8 and describe how it participates in various neuronal functions such as dendritic growth, synapse maturation, and synaptic plasticity. Recent evidence suggesting the potential role of PRMT8 function in neurological diseases will also be discussed.
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7
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Lei Y, Han P, Tian D. Protein arginine methyltransferases and hepatocellular carcinoma: A review. Transl Oncol 2021; 14:101194. [PMID: 34365222 PMCID: PMC8353347 DOI: 10.1016/j.tranon.2021.101194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 12/27/2022] Open
Abstract
Protein arginine methylation is essential in multiple biological processes. The family of PRMTs is a novel regulator of liver diseases. Deregulation of PRMTs is correlated with HCC prognosis and clinical features. PRMTs play a vital role in HCC malignancy, immune responses and metabolism. PRMTs may represent druggable targets as novel strategies for HCC therapy.
Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed cancers with a high mortality rate worldwide. The complexity of HCC initiation and progression poses a great challenge to the diagnosis and treatment. An increasing number of studies have focused on the emerging roles of protein arginine methylation in cancers, including tumor growth, invasion, metastasis, metabolism, immune responses, chemotherapy sensitivity, etc. The family of protein arginine methyltransferases (PRMTs) is the most important proteins that mediate arginine methylation. The deregulation of PRMTs’ expression and functions in cancers have been gradually unveiled, and many PRMTs inhibitors are in preclinical and clinical investigations now. This review focuses predominantly on the aberrant expression of PRMTs, underlying mechanisms, as well as their potential applications in HCC, and provide novel insights into HCC therapy.
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Affiliation(s)
- Yu Lei
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Ping Han
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China.
| | - Dean Tian
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China.
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8
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Couto E Silva A, Wu CYC, Clemons GA, Acosta CH, Chen CT, Possoit HE, Citadin CT, Lee RHC, Brown JI, Frankel A, Lin HW. Protein arginine methyltransferase 8 modulates mitochondrial bioenergetics and neuroinflammation after hypoxic stress. J Neurochem 2021; 159:742-761. [PMID: 34216036 DOI: 10.1111/jnc.15462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/26/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022]
Abstract
Protein arginine methyltransferases (PRMTs) are a family of enzymes involved in gene regulation and protein/histone modifications. PRMT8 is primarily expressed in the central nervous system, specifically within the cellular membrane and synaptic vesicles. Recently, PRMT8 has been described to play key roles in neuronal signaling such as a regulator of dendritic arborization, synaptic function and maturation, and neuronal differentiation and plasticity. Here, we examined the role of PRMT8 in response to hypoxia-induced stress in brain metabolism. Our results from liquid chromatography mass spectrometry, mitochondrial oxygen consumption rate (OCR), and protein analyses indicate that PRMT8(-/-) knockout mice presented with altered membrane phospholipid composition, decreased mitochondrial stress capacity, and increased neuroinflammatory markers, such as TNF-α and ionized calcium binding adaptor molecule 1 (Iba1, a specific marker for microglia/macrophage activation) after hypoxic stress. Furthermore, adenovirus-based overexpression of PRMT8 reversed the changes in membrane phospholipid composition, mitochondrial stress capacity, and neuroinflammatory markers. Together, our findings establish PRMT8 as an important regulatory component of membrane phospholipid composition, short-term memory function, mitochondrial function, and neuroinflammation in response to hypoxic stress.
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Affiliation(s)
| | | | | | | | - Chuck T Chen
- National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA
| | - HarLee E Possoit
- Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | | | | | - Jennifer I Brown
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Hung Wen Lin
- Department of Cellular Biology & Anatomy.,Louisiana State University Health Sciences Center, Shreveport, LA, USA
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9
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Samuel SF, Barry A, Greenman J, Beltran-Alvarez P. Arginine methylation: the promise of a 'silver bullet' for brain tumours? Amino Acids 2021; 53:489-506. [PMID: 33404912 PMCID: PMC8107164 DOI: 10.1007/s00726-020-02937-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Despite intense research efforts, our pharmaceutical repertoire against high-grade brain tumours has not been able to increase patient survival for a decade and life expectancy remains at less than 16 months after diagnosis, on average. Inhibitors of protein arginine methyltransferases (PRMTs) have been developed and investigated over the past 15 years and have now entered oncology clinical trials, including for brain tumours. This review collates recent advances in the understanding of the role of PRMTs and arginine methylation in brain tumours. We provide an up-to-date literature review on the mechanisms for PRMT regulation. These include endogenous modulators such as alternative splicing, miRNA, post-translational modifications and PRMT-protein interactions, and synthetic inhibitors. We discuss the relevance of PRMTs in brain tumours with a particular focus on PRMT1, -2, -5 and -8. Finally, we include a future perspective where we discuss possible routes for further research on arginine methylation and on the use of PRMT inhibitors in the context of brain tumours.
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Affiliation(s)
| | - Antonia Barry
- Department of Biomedical Sciences, University of Hull, Hull, UK
| | - John Greenman
- Department of Biomedical Sciences, University of Hull, Hull, UK
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10
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Wu CYC, Couto E Silva A, Citadin CT, Clemons GA, Acosta CH, Knox BA, Grames MS, Rodgers KM, Lee RHC, Lin HW. Palmitic acid methyl ester inhibits cardiac arrest-induced neuroinflammation and mitochondrial dysfunction. Prostaglandins Leukot Essent Fatty Acids 2021; 165:102227. [PMID: 33445063 PMCID: PMC8174449 DOI: 10.1016/j.plefa.2020.102227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/25/2022]
Abstract
We previously discovered that palmitic acid methyl ester (PAME) is a potent vasodilator released from the sympathetic ganglion with vasoactive properties. Post-treatment with PAME can enhance cortical cerebral blood flow and functional learning and memory, while inhibiting neuronal cell death in the CA1 region of the hippocampus under pathological conditions (i.e. cerebral ischemia). Since mechanisms underlying PAME-mediated neuroprotection remain unclear, we investigated the possible neuroprotective mechanisms of PAME after 6 min of asphyxial cardiac arrest (ACA, an animal model of global cerebral ischemia). Our results from capillary-based immunoassay (for the detection of proteins) and cytokine array suggest that PAME (0.02 mg/kg) can decrease neuroinflammatory markers, such as ionized calcium binding adaptor molecule 1 (Iba1, a specific marker for microglia/macrophage activation) and inflammatory cytokines after cardiopulmonary resuscitation. Additionally, the mitochondrial oxygen consumption rate (OCR) and respiratory function in the hippocampal slices were restored following ACA (via Seahorse XF24 Extracellular Flux Analyzer) suggesting that PAME can ameliorate mitochondrial dysfunction. Finally, hippocampal protein arginine methyltransferase 1 (PRMT1) and PRMT8 are enhanced in the presence of PAME to suggest a possible pathway of methylated fatty acids to modulate arginine-based enzymatic methylation. Altogether, our findings suggest that PAME can provide neuroprotection in the presence of ACA to alleviate neuroinflammation and ameliorate mitochondrial dysfunction.
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Affiliation(s)
- Celeste Yin-Chieh Wu
- Department of Neurology, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA.
| | - Alexandre Couto E Silva
- Department of Cellular Biology and Anatomy, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Cristiane T Citadin
- Department of Cellular Biology and Anatomy, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Garrett A Clemons
- Department of Cellular Biology and Anatomy, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Christina H Acosta
- Department of Cellular Biology and Anatomy, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Brianne A Knox
- Department of Neurology, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Mychal S Grames
- Department of Pharmacology, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Krista M Rodgers
- Department of Neurology, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA; Department of Cellular Biology and Anatomy, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Reggie Hui-Chao Lee
- Department of Neurology, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA; Department of Pharmacology, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Hung Wen Lin
- Department of Neurology, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA; Department of Cellular Biology and Anatomy, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA; Department of Pharmacology, Toxicology & Neuroscience Louisiana State University Health Sciences Center, Shreveport, LA, USA
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11
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Khella MS, Bröhm A, Weirich S, Jeltsch A. Mechanistic Insights into the Allosteric Regulation of the Clr4 Protein Lysine Methyltransferase by Autoinhibition and Automethylation. Int J Mol Sci 2020; 21:ijms21228832. [PMID: 33266419 PMCID: PMC7700585 DOI: 10.3390/ijms21228832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/12/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Clr4 is a histone H3 lysine 9 methyltransferase in Schizosaccharomyces pombe that is essential for heterochromatin formation. Previous biochemical and structural studies have shown that Clr4 is in an autoinhibited state in which an autoregulatory loop (ARL) blocks the active site. Automethylation of lysine residues in the ARL relieves autoinhibition. To investigate the mechanism of Clr4 regulation by autoinhibition and automethylation, we exchanged residues in the ARL by site-directed mutagenesis leading to stimulation or inhibition of automethylation and corresponding changes in Clr4 catalytic activity. Furthermore, we demonstrate that Clr4 prefers monomethylated (H3K9me1) over unmodified (H3K9me0) histone peptide substrates, similar to related human enzymes and, accordingly, H3K9me1 is more efficient in overcoming autoinhibition. Due to enzyme activation by automethylation, we observed a sigmoidal dependence of Clr4 activity on the AdoMet concentration, with stimulation at high AdoMet levels. In contrast, an automethylation-deficient mutant showed a hyperbolic Michaelis–Menten type relationship. These data suggest that automethylation of the ARL could act as a sensor for AdoMet levels in cells and regulate the generation and maintenance of heterochromatin accordingly. This process could connect epigenome modifications with the metabolic state of cells. As other human protein lysine methyltransferases (for example, PRC2) also use automethylation/autoinhibition mechanisms, our results may provide a model to describe their regulation as well.
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Affiliation(s)
- Mina S. Khella
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (M.S.K.); (A.B.); (S.W.)
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, African Union Organization Street, Abbassia, Cairo 11566, Egypt
| | - Alexander Bröhm
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (M.S.K.); (A.B.); (S.W.)
| | - Sara Weirich
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (M.S.K.); (A.B.); (S.W.)
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany; (M.S.K.); (A.B.); (S.W.)
- Correspondence: or ; Tel.: +49-711-685-64390; Fax: +49-711-685-64392
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12
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Hartley AV, Lu T. Modulating the modulators: regulation of protein arginine methyltransferases by post-translational modifications. Drug Discov Today 2020; 25:1735-1743. [PMID: 32629172 DOI: 10.1016/j.drudis.2020.06.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/14/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023]
Abstract
The therapeutic potential of targeting protein arginine methyltransferases (PRMTs) is inextricably linked to their key roles in various cellular functions, including splicing, proliferation, cell cycle regulation, differentiation, and DNA damage signaling. Unsurprisingly, the development of inhibitors against these enzymes has become a rapidly expanding research area. However, effective targeting of PRMTs requires a deeper understanding of the mechanistic details behind their regulation at multiple levels, involving those mechanisms that alter their activity, interactions, and localization. Recently, post-translational modifications (PTMs) of PRMTs have emerged as another crucial aspect of this regulation. Here, we review the regulatory role of PTMs in the activity and function of PRMTs, with emphasis on the contribution of these PTMs to pathological states, such as cancer.
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Affiliation(s)
- Antja-Voy Hartley
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; Department of Medicine, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Tao Lu
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, 975 W. Walnut Street, Indianapolis, IN 46202, USA.
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13
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Wang YC, Chang CP, Tsai YJ, Lee YJ, Li C. Alternative 3' splice site selection of intron 5 within the prmt8 gene results in a novel variant widely distributed in vertebrates and specifically abundant in Aves. Gene 2020; 747:144684. [PMID: 32311412 DOI: 10.1016/j.gene.2020.144684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 11/18/2022]
Abstract
PRMT8 is a neuron-specific protein arginine methyltransferase in vertebrates. From data mining, we found a novel prmt8e6+43 splicing variant with a 43-nucleotide (nt) extension at the 5' of exon 6 in chicken. RT-PCR analyses confirmed the existence of two splicing variants but also detected a third upper signal. The triplet pattern detected in chicken suggests that one strand from the prmt8e6+43 transcript and one strand from the regular splicing products form a heteroduplex with a bulb conformation and the two transcripts are of similar abundance. One short plus one faint upper heteroduplex signal detected in mouse and human indicate that the level of the variant is much less than the normal one in mammals. The relative expression of the normal and prmt8e6+43 variants in different species can be inferred from the reads of intron 5 that contains the 43-nt extension or not in the RNA-seq data of NCBI Gene database. The results of the analyses showed that the prmt8e6+43 variant is relatively abundant in birds but much less or even not detected in mammalian species. As conserved intron 5 sequences and evidences of alternative splicing (AS) are detected in elephant shark, a cartilaginous fish with the slowest-evolving genome, we propose that the prmt8e6+43 variant is present in the common ancestor of jawed vertebrates. The prmt8e6+43 variant includes a premature termination codon and thus should encode a truncated PRMT8 with deletion from the dimerization arm. Western blot analyses showed very weak low-molecular-weight signals in chicken, which might be the C-terminal truncated PRMT8. Why avian species maintain high RNA but not protein levels of the prmt8e6+43 variant and whether the evolutionary conserved sequence and AS might regulate PRMT8 expression require further investigation.
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Affiliation(s)
- Yi-Chun Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chien-Ping Chang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Yun-Jung Tsai
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Jen Lee
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chuan Li
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan.
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14
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Morettin A, Bourassa J, Mahadevan K, Trinkle-Mulcahy L, Cote J. Using affinity purification coupled with stable isotope labeling by amino acids in cell culture quantitative mass spectrometry to identify novel interactors/substrates of protein arginine methyltransferases. Methods 2020; 175:44-52. [PMID: 31794835 DOI: 10.1016/j.ymeth.2019.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
The protein arginine methyltransferase family (PRMT) is known as being the catalytic driving force for arginine methylation. This specific type of post translational modification is extensively used in biological processes, and therefore is highly relevant in the pathology of a profusion of diseases. Since altered PRMT expression or deregulation has been shown to contribute to a vast range of those diseases including cancer, their study is of great interest. Although an increasing number of substrates are being discovered for each PRMT, large scale proteomic methods can be used to identify novel interactors/substrates, further elucidating the role that PRMTs perform in physiological or disease states. Here, we describe the use of affinity purification (AP) coupled with stable isotope labeling with amino acids in cell culture (SILAC) quantitative mass spectrometry (MS) to identify protein interactors and substrates of PRMTs. We also explore the possibility of exploiting the fact most PRMTs display lower dissociation rates with their hypomethylated substrates as a strategy to increase the proportion of substrates identified in AP/MS studies.
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Affiliation(s)
- Alan Morettin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Julie Bourassa
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kohila Mahadevan
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jocelyn Cote
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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15
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Bollenbach A, Gambaryan S, Mindukshev I, Pich A, Tsikas D. GC-MS and LC-MS/MS pilot studies on the guanidine (N G)-dimethylation in native, asymmetrically and symmetrically N G-dimethylated arginine-vasopressin peptides and proteins in human red blood cells. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1141:122024. [PMID: 32062367 DOI: 10.1016/j.jchromb.2020.122024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/16/2022]
Abstract
Protein-arginine methyltransferases catalyze the methylation of the guanidine (NG) group of proteinic L-arginine (Arg) to produce monomethyl and dimethylarginine proteins. Their proteolysis releases the free amino acids monomethylarginine (MMA), symmetric dimethylarginine (SDMA) and asymmetric dimethylarginine (ADMA), respectively. MMA, SDMA and ADMA are inhibitors of the nitric oxide synthase (NOS) activity. High circulating and low urinary concentrations of ADMA and SDMA are considered risk factors in the cardiovascular and renal systems, mainly due to their inhibitory action on NOS activity. Identity, biological activity and concentration of NG-methylated proteins are largely unknown. The present study addressed these issues by using GC-MS and LC-MS/MS approaches. GC-MS was used to quantify free ADMA released by classical HCl-catalyzed hydrolysis of three synthetic Arg-vasopressin (V) peptides and of unknown endogenous NG-dimethylated proteins. The cyclic (c) disulfide forms of Arg-vasopressin analogs, i.e., Arg-vasopressin (cV-Arg-Gly-NH2), asymmetrically NG-dimethylated vasopressin (cV-ADMA-Gly-NH2) and symmetrically NG-dimethylated vasopressin (cV-SDMA-Gly-NH2) were used as model peptides in quantitative GC-MS analyses of ADMA, SDMA and other expected amino acids from the hydrolyzed Arg-vasopressin analogs. cV-ADMA-Gly-NH2 and cV-SDMA-Gly-NH2 were discriminated from cV-Arg-Gly-NH2 by LC-MS and LC-MS/MS, yet they were indistinguishable from each other. The same applies to the respective open (o) reduced and di-S-acetamide forms of oV-ADMA-Gly-NH2, oV-SDMA-Gly-NH2 and oV-Arg-Gly-NH2. Our LC-MS and LC-MS/MS studies suggest that the Arg-vasopressin analogs form [(M-H)]+ and [(M-H)+H]+ in the positive ESI mode and undergo in part conversion of their terminal Gly-NH2 (NH2, 16 Da) group to Gly-OH (OH, 17 Da). The product ion mass spectra of the di-S-acetamide forms are complex and contain several intense mass fragments differing by 1 Da. cV-ADMA-Gly-NH2 and cV-SDMA-Gly-NH2 induced platelet aggregation in platelet-rich human plasma with moderately different initial velocity and maximal aggregation rates compared to cV-Arg-Gly-NH2. Previous studies showed that human red blood cells are rich in large (>50 kDa) ADMA-containing proteins of unknown identity. Our LC-MS/MS proteomic study identified several membrane and cytosolic erythrocytic NG-dimethylated proteins, including spectrin-α (280 kDa), spectrin-β (247 kDa) and protein 4.1 (80 kDa). Being responsible for the stability of the erythrocyte membrane, the newly identified main targets for NG-dimethylation in human erythrocytes should be given a closer look in erythrocytic diseases like hereditary spherocytosis.
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Affiliation(s)
- Alexander Bollenbach
- Institute of Toxicology and Core Unit Proteomics, Hannover Medical School, 30623 Hannover, Germany
| | - Stepan Gambaryan
- Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, St. Petersburg 194223, Russia
| | - Igor Mindukshev
- Sechenov Institute of Evolutionary Physiology and Biochemistry Russian Academy of Sciences, St. Petersburg 194223, Russia
| | - Andreas Pich
- Institute of Toxicology and Core Unit Proteomics, Hannover Medical School, 30623 Hannover, Germany
| | - Dimitrios Tsikas
- Institute of Toxicology and Core Unit Proteomics, Hannover Medical School, 30623 Hannover, Germany.
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16
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Protein Arginine Methyltransferases in Cardiovascular and Neuronal Function. Mol Neurobiol 2019; 57:1716-1732. [PMID: 31823198 DOI: 10.1007/s12035-019-01850-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/01/2019] [Indexed: 12/16/2022]
Abstract
The methylation of arginine residues by protein arginine methyltransferases (PRMTs) is a type of post-translational modification which is important for numerous cellular processes, including mRNA splicing, DNA repair, signal transduction, protein interaction, and transport. PRMTs have been extensively associated with various pathologies, including cancer, inflammation, and immunity response. However, the role of PRMTs has not been well described in vascular and neurological function. Aberrant expression of PRMTs can alter its metabolic products, asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA). Increased ADMA levels are recognized as an independent risk factor for cardiovascular disease and mortality. Recent studies have provided considerable advances in the development of small-molecule inhibitors of PRMTs to study their function under normal and pathological states. In this review, we aim to elucidate the particular roles of PRMTs in vascular and neuronal function as a potential target for cardiovascular and neurological diseases.
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17
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Li ASM, Li F, Eram MS, Bolotokova A, Dela Seña CC, Vedadi M. Chemical probes for protein arginine methyltransferases. Methods 2019; 175:30-43. [PMID: 31809836 DOI: 10.1016/j.ymeth.2019.11.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/29/2019] [Accepted: 11/29/2019] [Indexed: 12/28/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the transfer of methyl groups to specific arginine residues of their substrates using S-adenosylmethionine as a methyl donor, contributing to regulation of many biological processes including transcription, and DNA damage repair. Dysregulation of PRMT expression is often associated with various diseases including cancers. Different methods have been used to characterize the activities of PRMTs and determine their kinetic parameters including mass spectrometry, radiometric, and antibody-based assays. Here, we present kinetic characterization of PRMTs using a radioactivity-based assay for better comparison along with previously reported values. We also report on full characterization of PRMT9 activity with SAP145 peptide as substrate. We further review the potent, selective and cell-active PRMT inhibitors discovered in recent years to provide a better understanding of available tools to investigate the roles these proteins play in health and disease.
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Affiliation(s)
- Alice Shi Ming Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Albina Bolotokova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Carlo C Dela Seña
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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18
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Shibata Y, Okada M, Miller TC, Shi YB. Knocking out histone methyltransferase PRMT1 leads to stalled tadpole development and lethality in Xenopus tropicalis. Biochim Biophys Acta Gen Subj 2019; 1864:129482. [PMID: 31734465 DOI: 10.1016/j.bbagen.2019.129482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/15/2019] [Accepted: 10/30/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Asymmetric arginine dimethylation of histone H4R3 to H4R3me2a by protein arginine methyltransferase 1 (PRMT1) has been implicated to play a key role in gene activation throughout vertebrates. PRMT1 knockout in mouse leads to embryonic lethality. This and the uterus-enclosed nature of the mouse embryo make it difficult to determine the development role of PRMT1 in mammals. METHODS We took advantage of the external development of the diploid anuran Xenopus tropicalis and adapted the TALEN genome editing technology to knock out PRMT1 in order to investigate how PRMT1 participates in vertebrate development. RESULTS We observed that PRMT1 knockout had no apparent effect on embryogenesis because normally feeding tadpoles were formed, despite the reduced asymmetric H4R3 di-methylation (H4R3me2a) due to the knockout. However, PRMT1 knockout tadpoles had severely reduced growth even with normal growth hormone gene expression. These tadpoles were also stalled in development shortly after feeding began at stages 44/45 and died within 2 weeks, well before the onset of metamorphosis. In situ analyses revealed broad cessation or drastic reduction in cell proliferation in diverse organs including the eye, brain, spinal cord, liver, and intestine. CONCLUSIONS Our findings suggest that PRMT1 is not required for embryogenesis but is a key regulator for normal progression of vertebrate development and growth. GENERAL SIGNIFICANCE The similarities and differences between PRMT1 knockout Xenopus tropicalis and mouse suggest that two distinct phases of vertebrate development: early embryogenesis and subsequent growth/organ maturation, have different but evolutionally conserved requirement for epigenetic modifications.
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Affiliation(s)
- Yuki Shibata
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Morihiro Okada
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Thomas C Miller
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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19
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Jarrold J, Davies CC. PRMTs and Arginine Methylation: Cancer's Best-Kept Secret? Trends Mol Med 2019; 25:993-1009. [PMID: 31230909 DOI: 10.1016/j.molmed.2019.05.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/10/2019] [Accepted: 05/16/2019] [Indexed: 12/19/2022]
Abstract
Post-translational modification (PTM) of proteins is vital for increasing proteome diversity and maintaining cellular homeostasis. If the writing, reading, and removal of modifications are not controlled, cancer can develop. Arginine methylation is an understudied modification that is increasingly associated with cancer progression. Consequently protein arginine methyltransferases (PRMTs), the writers of arginine methylation, have rapidly gained interest as novel drug targets. However, for clinical success a deep mechanistic understanding of the biology of PRMTs is required. In this review we focus on advances made regarding the role of PRMTs in stem cell biology, epigenetics, splicing, immune surveillance and the DNA damage response, and highlight the rapid rise of specific inhibitors that are now in clinical trials for cancer therapy.
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Affiliation(s)
- James Jarrold
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Clare C Davies
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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20
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Rapid and direct measurement of methyltransferase activity in about 30 min. Methods 2019; 175:3-9. [PMID: 31605745 DOI: 10.1016/j.ymeth.2019.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/05/2019] [Accepted: 10/07/2019] [Indexed: 11/24/2022] Open
Abstract
Protein arginine methylation is a widespread eukaryotic posttranslational modification that occurs to both histone and non-histone proteins. The S-adenosyl-L-methionine (AdoMet or SAM)-dependent modification is catalyzed by the protein arginine methyltransferase (PRMT) family of enzymes. In the last several years a series of both direct and indirect assay formats have been described that allow the rate of methylation to be measured. Here we provide a detailed protocol to directly measure PRMT activity using radiolabeled AdoMet, reversed-phase resin-filled pipette tips (ZipTips®) and a liquid scintillation counter. Because the ZipTips® based quantitation relies only on the straightforward separation of unreacted AdoMet from a methylated substrate, this protocol should be readily adaptable to other methyltransferases. The method is fast, simple to employ with both peptide and protein substrates, and produces very little radioactive waste.
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21
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Rakow S, Pullamsetti SS, Bauer UM, Bouchard C. Assaying epigenome functions of PRMTs and their substrates. Methods 2019; 175:53-65. [PMID: 31542509 DOI: 10.1016/j.ymeth.2019.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Among the widespread and increasing number of identified post-translational modifications (PTMs), arginine methylation is catalyzed by the protein arginine methyltransferases (PRMTs) and regulates fundamental processes in cells, such as gene regulation, RNA processing, translation, and signal transduction. As epigenetic regulators, PRMTs play key roles in pluripotency, differentiation, proliferation, survival, and apoptosis, which are essential biological programs leading to development, adult homeostasis but also pathological conditions including cancer. A full understanding of the molecular mechanisms that underlie PRMT-mediated gene regulation requires the genome wide mapping of each player, i.e., PRMTs, their substrates and epigenetic marks, methyl-marks readers as well as interaction partners, in a thorough and unambiguous manner. However, despite the tremendous advances in high throughput sequencing technologies and the numerous efforts from the scientific community, the epigenomic profiling of PRMTs as well as their histone and non-histone substrates still remains a big challenge owing to obvious limitations in tools and methodologies. This review will summarize the present knowledge about the genome wide mapping of PRMTs and their substrates as well as the technical approaches currently in use. The limitations and pitfalls of the technical tools along with conventional approaches will be then discussed in detail. Finally, potential new strategies for chromatin profiling of PRMTs and histone substrates will be proposed and described.
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Affiliation(s)
- Sinja Rakow
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Soni Savai Pullamsetti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Uta-Maria Bauer
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Caroline Bouchard
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany.
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22
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Lee CH, Yu JR, Granat J, Saldaña-Meyer R, Andrade J, LeRoy G, Jin Y, Lund P, Stafford JM, Garcia BA, Ueberheide B, Reinberg D. Automethylation of PRC2 promotes H3K27 methylation and is impaired in H3K27M pediatric glioma. Genes Dev 2019; 33:1428-1440. [PMID: 31488577 PMCID: PMC6771381 DOI: 10.1101/gad.328773.119] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
In this study, Lee et al. use both in vitro and in vivo approaches to elucidate the regulation of PRC2. They demonstrate a novel PRC2 self-regulatory mechanism through its EZH1/2-mediated automethylation activity. The histone methyltransferase activity of PRC2 is central to the formation of H3K27me3-decorated facultative heterochromatin and gene silencing. In addition, PRC2 has been shown to automethylate its core subunits, EZH1/EZH2 and SUZ12. Here, we identify the lysine residues at which EZH1/EZH2 are automethylated with EZH2-K510 and EZH2-K514 being the major such sites in vivo. Automethylated EZH2/PRC2 exhibits a higher level of histone methyltransferase activity and is required for attaining proper cellular levels of H3K27me3. While occurring independently of PRC2 recruitment to chromatin, automethylation promotes PRC2 accessibility to the histone H3 tail. Intriguingly, EZH2 automethylation is significantly reduced in diffuse intrinsic pontine glioma (DIPG) cells that carry a lysine-to-methionine substitution in histone H3 (H3K27M), but not in cells that carry either EZH2 or EED mutants that abrogate PRC2 allosteric activation, indicating that H3K27M impairs the intrinsic activity of PRC2. Our study demonstrates a PRC2 self-regulatory mechanism through its EZH1/2-mediated automethylation activity.
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Affiliation(s)
- Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Jeffrey Granat
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ricardo Saldaña-Meyer
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Joshua Andrade
- Proteomics Laboratory, New York University School of Medicine, New York, New York 10016, USA
| | - Gary LeRoy
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ying Jin
- Shared Bioinformatics Core, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Peder Lund
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, New York University School of Medicine, New York, New York 10016, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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23
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Jain K, Clarke SG. PRMT7 as a unique member of the protein arginine methyltransferase family: A review. Arch Biochem Biophys 2019; 665:36-45. [PMID: 30802433 DOI: 10.1016/j.abb.2019.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 12/14/2022]
Abstract
Protein arginine methyltransferases (PRMTs) are found in a wide variety of eukaryotic organisms and can regulate gene expression, DNA repair, RNA splicing, and stem cell biology. In mammalian cells, nine genes encode a family of sequence-related enzymes; six of these PRMTs catalyze the formation of ω-asymmetric dimethyl derivatives, two catalyze ω-symmetric dimethyl derivatives, and only one (PRMT7) solely catalyzes ω-monomethylarginine formation. Purified recombinant PRMT7 displays a number of unique enzymatic properties including a substrate preference for arginine residues in R-X-R motifs with additional flanking basic amino acid residues and a temperature optimum well below 37 °C. Evidence has been presented for crosstalk between PRMT7 and PRMT5, where methylation of a histone H4 peptide at R17, a PRMT7 substrate, may activate PRMT5 for methylation of R3. Defects in muscle stem cells (satellite cells) and immune cells are found in mouse Prmt7 homozygous knockouts, while humans lacking PRMT7 are characterized by significant intellectual developmental delays, hypotonia, and facial dysmorphisms. The overexpression of the PRMT7 gene has been correlated with cancer metastasis in humans. Current research challenges include identifying cellular factors that control PRMT7 expression and activity, identifying the physiological substrates of PRMT7, and determining the effect of methylation on these substrates.
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Affiliation(s)
- Kanishk Jain
- Lineberger Comprehensive Cancer Center and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC, 27599, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
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24
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Haghandish N, Baldwin RM, Morettin A, Dawit HT, Adhikary H, Masson JY, Mazroui R, Trinkle-Mulcahy L, Côté J. PRMT7 methylates eukaryotic translation initiation factor 2α and regulates its role in stress granule formation. Mol Biol Cell 2019; 30:778-793. [PMID: 30699057 PMCID: PMC6589776 DOI: 10.1091/mbc.e18-05-0330] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) are a family of enzymes that modify proteins by methylating the guanidino nitrogen atoms of arginine residues to regulate cellular processes such as chromatin remodeling, pre-mRNA splicing, and signal transduction. PRMT7 is the single type III PRMT solely capable of arginine monomethylation. To date, other than histone proteins, there are very few identified substrates of PRMT7. We therefore performed quantitative mass spectrometry experiments to identify PRMT7’s interactome and potential substrates to better characterize the enzyme’s biological function(s) in cells. These experiments revealed that PRMT7 interacts with and can methylate eukaryotic translation initiation factor 2 alpha (eIF2α), in vitro and in breast cancer cells. Furthermore, we uncovered a potential regulatory interplay between eIF2α arginine methylation by PRMT7 and stress-induced phosphorylation status of eIF2α at serine 51. Finally, we demonstrated that PRMT7 is required for eIF2α-dependent stress granule formation in the face of various cellular stresses. Altogether, our findings implicate PRMT7 as a novel mediator of eIF2α-dependent cellular stress response pathways.
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Affiliation(s)
- Nasim Haghandish
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - R Mitchell Baldwin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Alan Morettin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Haben Tesfu Dawit
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Hemanta Adhikary
- Oncology Division, CHU de Québec-Université Laval, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Jean-Yves Masson
- Oncology Division, CHU de Québec-Université Laval, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Rachid Mazroui
- Oncology Division, CHU de Québec-Université Laval, Québec City, QC G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jocelyn Côté
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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25
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Kim JW, Choe YM, Shin JG, Park BL, Shin HD, Choi IG, Lee BC. Associations of BRAP polymorphisms with the risk of alcohol dependence and scores on the Alcohol Use Disorders Identification Test. Neuropsychiatr Dis Treat 2019; 15:83-94. [PMID: 30636874 PMCID: PMC6309135 DOI: 10.2147/ndt.s184067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Alcohol dependence (AD) is a common disorder that is influenced by genetic as well as environmental factors. A previous genome-wide association study (GWAS) of the Korean population performed by our research group identified a number of genes, including BRCA1-associated protein (BRAP) and protein arginine methyltransferase 8 (PRMT8), as novel genetic markers of AD. METHODS The present investigation was a fine-mapping follow-up study of 459 AD and 455 non-AD subjects of Korean descent to determine the associations between BRAP and PRMT8 polymorphisms and AD. The Alcohol Use Disorders Identification Test (AUDIT) was administered to screen for the degree of AD risk in the subjects and 58 genetic variants, 5 for BRAP and 53 for PRMT8, were genotyped for subsequent association analyses. RESULTS In the present case-control analysis, BRAP rs3782886 showed the most significant association signal with a risk of AD (P=1.29×10-16, Pcorr =7.74×10-16, OR =0.19). There were also significant differences in the overall and subcategory scores for the BRAP genetic variants, including rs3782886 (P=9.94×10-31, Pcorr =5.96×10-30 at rs3782886 for the overall AUDIT score). However, the genetic effects of PRMT8 polymorphisms observed in our previous GWAS were not replicated in the present study (minimum P=0.0005, Pcorr >0.05, OR =0.30 at rs4766139 in the recessive model). Furthermore, the single-nucleotide polymorphisms of PRMT8 were not associated with the overall and subcategory AUDIT scores. CONCLUSION The present findings suggest that the genetic variants of BRAP may contribute to a predisposition for an alcohol use disorder.
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Affiliation(s)
- Jee Wook Kim
- Department of Neuropsychiatry, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Gyeonggi Province, Republic of Korea.,Department of Psychiatry, Hallym University College of Medicine, Chuncheon, Republic of Korea,
| | - Young Min Choe
- Department of Neuropsychiatry, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Gyeonggi Province, Republic of Korea.,Department of Psychiatry, Hallym University College of Medicine, Chuncheon, Republic of Korea,
| | - Joong-Gon Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
| | - Hyung-Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea.,Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul, Republic of Korea
| | - Ihn-Geun Choi
- Department of Psychiatry, Hallym University College of Medicine, Chuncheon, Republic of Korea, .,Department of Neuropsychiatry, Hallym University Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
| | - Boung Chul Lee
- Department of Psychiatry, Hallym University College of Medicine, Chuncheon, Republic of Korea, .,Department of Neuropsychiatry, Hallym University Hangang Sacred Heart Hospital, Seoul, Republic of Korea,
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26
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Frankel A, Brown JI. Evaluation of kinetic data: What the numbers tell us about PRMTs. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:306-316. [PMID: 30342239 DOI: 10.1016/j.bbapap.2018.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/10/2018] [Accepted: 10/14/2018] [Indexed: 01/06/2023]
Abstract
Protein arginine N-methyltransferase (PRMT) kinetic parameters have been catalogued over the past fifteen years for eight of the nine mammalian enzyme family members. Like the majority of methyltransferases, these enzymes employ the highly ubiquitous cofactor S-adenosyl-l-methionine as a co-substrate to methylate arginine residues in peptidic substrates with an approximately 4-μM median KM. The median values for PRMT turnover number (kcat) and catalytic efficiency (kcat/KM) are 0.0051 s-1 and 708 M-1 s-1, respectively. When comparing PRMT metrics to entries found in the BRENDA database, we find that while PRMTs exhibit high substrate affinity relative to other enzyme-substrate pairs, PRMTs display largely lower kcat and kcat/KM values. We observe that kinetic parameters for PRMTs and arginine demethylase activity from dual-functioning lysine demethylases are statistically similar, paralleling what the broader enzyme families in which they belong reveal, and adding to the evidence in support of arginine methylation reversibility.
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Affiliation(s)
- Adam Frankel
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada.
| | - Jennifer I Brown
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
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27
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Weil LE, Shmidov Y, Kublanovsky M, Morgenstern D, Feldman M, Bitton R, Levy D. Oligomerization and Auto-methylation of the Human Lysine Methyltransferase SETD6. J Mol Biol 2018; 430:4359-4368. [PMID: 30189201 DOI: 10.1016/j.jmb.2018.08.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/31/2018] [Accepted: 08/23/2018] [Indexed: 02/06/2023]
Abstract
Signaling via lysine methylation by protein lysine methyltransferases (PKMTs), has been linked to diverse biological and disease processes. The mono-methyltransferase SETD6 (SET-domain-containing protein 6) is a member of the PKMT family and was previously shown to regulate essential cellular processes such as the NF-κB, WNT and the oxidative stress pathways. However, on the biochemical level, little is known about the enzymatic mode of action of SETD6. Here we provide evidence that SETD6 forms high-molecular-weight structures. Specifically, we demonstrate that SETD6 monomeric, dimeric and trimeric forms are stabilized by the methyl donor, S-adenosyl-l-methionine. We then show that SETD6 has auto-methylation activity at K39 and K179, which serves as the major auto-methylation sites with a moderate auto-methylation activity toward K372. A point mutation at K179 but not at K39 and K372, located at the SET domain of SETD6, impaired SETD6 ability to form a trimer, strongly implying a link between the auto-methylation and the oligomerization state. Finally, by radioactive in vitro methylation experiments and biochemical kinetics analysis, we show that the auto-methylation at K39 and K179 increases the catalytic rate of SETD6. Collectively, our data support a model by which SETD6 auto-methylation and self-interaction positively regulate its enzymatic activity in vitro and may suggest that other PKMTs are regulated in the same manner.
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Affiliation(s)
- Lital Estrella Weil
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Yulia Shmidov
- Department of Chemical Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Margarita Kublanovsky
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - David Morgenstern
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Ronit Bitton
- Department of Chemical Engineering, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, Be'er-Sheva 84105, Israel.
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28
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Biswas S, Rao CM. Epigenetic tools (The Writers, The Readers and The Erasers) and their implications in cancer therapy. Eur J Pharmacol 2018; 837:8-24. [PMID: 30125562 DOI: 10.1016/j.ejphar.2018.08.021] [Citation(s) in RCA: 206] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 02/08/2023]
Abstract
Addition of chemical tags on the DNA and modification of histone proteins impart a distinct feature on chromatin architecture. With the advancement in scientific research, the key players underlying these changes have been identified as epigenetic modifiers of the chromatin. Indeed, the plethora of enzymes catalyzing these modifications, portray the diversity of epigenetic space and the intricacy in regulating gene expression. These epigenetic players are categorized as writers: that introduce various chemical modifications on DNA and histones, readers: the specialized domain containing proteins that identify and interpret those modifications and erasers: the dedicated group of enzymes proficient in removing these chemical tags. Research over the past few decades has established that these epigenetic tools are associated with numerous disease conditions especially cancer. Besides, with the involvement of epigenetics in cancer, these enzymes and protein domains provide new targets for cancer drug development. This is certain from the volume of epigenetic research conducted in universities and R&D sector of pharmaceutical industry. Here we have highlighted the different types of epigenetic enzymes and protein domains with an emphasis on methylation and acetylation. This review also deals with the recent developments in small molecule inhibitors as potential anti-cancer drugs targeting the epigenetic space.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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29
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Cáceres TB, Thakur A, Price OM, Ippolito N, Li J, Qu J, Acevedo O, Hevel JM. Phe71 in Type III Trypanosomal Protein Arginine Methyltransferase 7 (TbPRMT7) Restricts the Enzyme to Monomethylation. Biochemistry 2018; 57:1349-1359. [PMID: 29378138 DOI: 10.1021/acs.biochem.7b01265] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Protein arginine methyltransferase 7 (PRMT7) is unique within the PRMT family as it is the only isoform known to exclusively make monomethylarginine (MMA). Given its role in epigenetics, the mechanistic basis for the strict monomethylation activity is under investigation. It is thought that PRMT7 enzymes are unable to add a second methyl group because of steric hindrance in the active site that restricts them to monomethylation. To test this, we probed the active site of trypanosomal PRMT7 (TbPRMT7) using accelerated molecular dynamics, site-directed mutagenesis, kinetic, binding, and product analyses. Both the dynamics simulations and experimental results show that the mutation of Phe71 to Ile converts the enzyme from a type III methyltransferase into a mixed type I/II, that is, an enzyme that can now perform dimethylation. In contrast, the serine and alanine mutants of Phe71 preserve the type III behavior of the native enzyme. These results are inconsistent with a sterics-only model to explain product specificity. Instead, molecular dynamics simulations of these variants bound to peptides show hydrogen bonding between would-be substrates and Glu172 of TbPRMT7. Only in the case of the Phe71 to Ile mutation is this interaction between MMA and the enzyme maintained, and the geometry for optimal SN2 methyl transfer is obtained. The results of these studies highlight the benefit of combined computational and experimental methods in providing a better understanding for how product specificity is dictated by PRMTs.
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Affiliation(s)
- Tamar B Cáceres
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Abhishek Thakur
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Owen M Price
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
| | - Nicole Ippolito
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York , Kapoor 318, North Campus, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York , Kapoor 318, North Campus, Buffalo, New York 14260, United States.,New York State Center of Excellence in Bioinformatics and Life Sciences , 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Orlando Acevedo
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Joan M Hevel
- Department of Chemistry and Biochemistry, Utah State University , 0300 Old Main Hill, Logan, Utah 84322, United States
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30
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Brown JI, Koopmans T, van Strien J, Martin NI, Frankel A. Kinetic Analysis of PRMT1 Reveals Multifactorial Processivity and a Sequential Ordered Mechanism. Chembiochem 2017; 19:85-99. [PMID: 29112789 DOI: 10.1002/cbic.201700521] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Indexed: 01/13/2023]
Abstract
Arginine methylation is a prevalent post-translational modification in eukaryotic cells. Two significant debates exist within the field: do these enzymes dimethylate their substrates in a processive or distributive manner, and do these enzymes operate using a random or sequential method of bisubstrate binding? We revealed that human protein arginine N-methyltransferase 1 (PRMT1) enzyme kinetics are dependent on substrate sequence. Further, peptides containing an Nη-hydroxyarginine generally demonstrated substrate inhibition and had improved KM values, which evoked a possible role in inhibitor design. We also revealed that the perceived degree of enzyme processivity is a function of both cofactor and enzyme concentration, suggesting that previous conclusions about PRMT sequential methyl transfer mechanisms require reassessment. Finally, we demonstrated a sequential ordered Bi-Bi kinetic mechanism for PRMT1, based on steady-state kinetic analysis. Together, our data indicate a PRMT1 mechanism of action and processivity that might also extend to other functionally and structurally conserved PRMTs.
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Affiliation(s)
- Jennifer I Brown
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Timo Koopmans
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Jolinde van Strien
- Leiden Institute for Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Nathaniel I Martin
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CG, Utrecht, The Netherlands
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
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31
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Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification. J Mol Biol 2017; 430:102-118. [PMID: 29183786 DOI: 10.1016/j.jmb.2017.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/07/2017] [Accepted: 11/22/2017] [Indexed: 01/24/2023]
Abstract
Protein methylation is one of the major post-translational modifications (PTMs) in the cell. In Saccharomyces cerevisiae, over 20 protein methyltransferases (MTases) and their respective substrates have been identified. However, the way in which these MTases are modified and potentially subject to regulation remains poorly understood. Here, we investigated six overexpressed S. cerevisiae protein MTases (Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1) to identify PTMs of potential functional relevance. We identified 48 PTM sites across the six MTases, including phosphorylation, acetylation and methylation. Forty-two sites are novel. We contextualized the PTM sites in structural models of the MTases and revealed that many fell in catalytic pockets or enzyme-substrate interfaces. These may regulate MTase activity. Finally, we compared PTMs on Hmt1 with those on its human homologs PRMT1, PRMT3, CARM1, PRMT6 and PRMT8. This revealed that several PTMs are conserved from yeast to human, whereas others are only found in Hmt1. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD006767.
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32
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Plett KL, Raposo AE, Bullivant S, Anderson IC, Piller SC, Plett JM. Root morphogenic pathways in Eucalyptus grandis are modified by the activity of protein arginine methyltransferases. BMC PLANT BIOLOGY 2017; 17:62. [PMID: 28279165 PMCID: PMC5345158 DOI: 10.1186/s12870-017-1010-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/01/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Methylation of proteins at arginine residues, catalysed by members of the protein arginine methyltransferase (PRMT) family, is crucial for the regulation of gene transcription and for protein function in eukaryotic organisms. Inhibition of the activity of PRMTs in annual model plants has demonstrated wide-ranging involvement of PRMTs in key plant developmental processes, however, PRMTs have not been characterised or studied in long-lived tree species. RESULTS Taking advantage of the recently available genome for Eucalyptus grandis, we demonstrate that most of the major plant PRMTs are conserved in E. grandis as compared to annual plants and that they are expressed in all major plant tissues. Proteomic and transcriptomic analysis in roots suggest that the PRMTs of E. grandis control a number of regulatory proteins and genes related to signalling during cellular/root growth and morphogenesis. We demonstrate here, using chemical inhibition of methylation and transgenic approaches, that plant type I PRMTs are necessary for normal root growth and branching in E. grandis. We further show that EgPRMT1 has a key role in root hair initiation and elongation and is involved in the methylation of β-tubulin, a key protein in cytoskeleton formation. CONCLUSIONS Together, our data demonstrate that PRMTs encoded by E. grandis methylate a number of key proteins and alter the transcription of a variety of genes involved in developmental processes. Appropriate levels of expression of type I PRMTs are necessary for the proper growth and development of E. grandis roots.
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Affiliation(s)
- Krista L. Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753 Australia
| | - Anita E. Raposo
- School of Science and Health, Western Sydney University, Penrith, NSW 2751 Australia
| | - Stephen Bullivant
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753 Australia
| | - Ian C. Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753 Australia
| | - Sabine C. Piller
- School of Science and Health, Western Sydney University, Penrith, NSW 2751 Australia
| | - Jonathan M. Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753 Australia
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33
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Discovery and characterisation of the automethylation properties of PRDM9. Biochem J 2017; 474:971-982. [PMID: 28126738 DOI: 10.1042/bcj20161067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 11/17/2022]
Abstract
We have previously characterised the histone lysine methyltransferase properties of PRDM9, a member of the PRDM family of putative transcriptional regulators. PRDM9 displays broad substrate recognition and methylates a range of histone substrates, including octamers, core histone proteins, and peptides. In the present study, we show that PRDM9 performs intramolecular automethylation on multiple lysine residues localised to a lysine-rich region on the post-SET (suppressor of variegation 3-9, enhancer of zeste and trithorax) domain. PRDM9 automethylation is abolished by a single active-site mutation, C321P, also known to disrupt interactions with S-adenosylmethionine. We have taken an initial step towards tool compound generation through rational design of a substrate-mimic, peptidic inhibitor of PRDM9 automethylation. The discovery of automethylation in PRDM9 adds a new dimension to our understanding of PRDM9 enzymology.
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34
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Geng P, Zhang Y, Liu X, Zhang N, Liu Y, Liu X, Lin C, Yan X, Li Z, Wang G, Li Y, Tan J, Liu DX, Huang B, Lu J. Automethylation of protein arginine methyltransferase 7 and its impact on breast cancer progression. FASEB J 2017; 31:2287-2300. [PMID: 28188177 DOI: 10.1096/fj.201601196r] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze protein arginine methylation and are linked to carcinogenesis and metastasis. Some members of PRMTs have been found to undergo automethylation; however, the biologic significance of this self-modification is not entirely clear. In this report, we demonstrate that R531 of PRMT7 is self-methylated, both in vitro and in vivo Automethylation of PRMT7 plays a key role in inducing the epithelial-mesenchymal transition (EMT) program and in promoting the migratory and invasive behavior of breast cancer cells. We also prove in a nude mouse model that expression of wild-type PRMT7 in MCF7 breast cancer cells promotes metastasis in vivo, in contrast to the PRMT7 R531K mutant (a mimic of the unmethylated status). Moreover, our immunohistochemical data unravel a close link between PRMT7 automethylation and the clinical outcome of breast carcinomas. Mechanistically, we determine that loss of PRMT7 automethylation leads to the reduction of its recruitment to the E-cadherin promoter by YY1, which consequently derepresses the E-cadherin expression through decreasing the H4R3me2s level. The findings in this work define a novel post-translational modification of PRMT7 that has a promoting impact on breast cancer metastasis.-Geng, P., Zhang, Y., Liu, X., Zhang, N., Liu, Y., Liu, X., Lin, C., Yan, X., Li, Z., Wang, G., Li, Y., Tan, J., Liu, D.-X., Huang, B., Lu, J. Automethylation of protein arginine methyltransferase 7 and its impact on breast cancer progression.
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Affiliation(s)
- Pengyu Geng
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yu Zhang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiaoqing Liu
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Na Zhang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Yingqi Liu
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Xin Liu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Cong Lin
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Xu Yan
- Pathological Diagnostic Center, The First Hospital of Jilin University, Changchun, China
| | - Zhongwei Li
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Guannan Wang
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, China; and
| | - Yuxin Li
- National Engineering Laboratory for Druggable Gene and Protein Screening, Northeast Normal University, Changchun, China; and
| | - Jiang Tan
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Dong-Xu Liu
- School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Baiqu Huang
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China;
| | - Jun Lu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China;
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35
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Solari C, Echegaray CV, Luzzani C, Cosentino MS, Waisman A, Petrone MV, Francia M, Sassone A, Canizo J, Sevlever G, Barañao L, Miriuka S, Guberman A. Protein arginine Methyltransferase 8 gene is expressed in pluripotent stem cells and its expression is modulated by the transcription factor Sox2. Biochem Biophys Res Commun 2016; 473:194-199. [DOI: 10.1016/j.bbrc.2016.03.077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 03/17/2016] [Indexed: 01/08/2023]
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36
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Novel helical assembly in arginine methyltransferase 8. J Mol Biol 2016; 428:1197-1208. [DOI: 10.1016/j.jmb.2016.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/03/2016] [Accepted: 02/03/2016] [Indexed: 12/18/2022]
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37
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Lee WC, Lin WL, Matsui T, Chen ESW, Wei TYW, Lin WH, Hu H, Zheng YG, Tsai MD, Ho MC. Protein Arginine Methyltransferase 8: Tetrameric Structure and Protein Substrate Specificity. Biochemistry 2015; 54:7514-23. [PMID: 26529540 DOI: 10.1021/acs.biochem.5b00995] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Type I protein arginine methyltransferases (PRMTs) catalyze asymmetric dimethylation of various proteins, and their dysregulations often correlate with tumorigenesis or developmental deficiency. Recent studies have focused on the in vivo substrate identification and the enzyme mechanism with peptide substrates. However, how PRMTs recognize substrates at the protein level remains unknown. PRMT8 is one of the least characterized type I PRMTs, and its crystal structure has not been reported. Here, we report the crystal structure of the PRMT8:SAH complex, identify a new non-histone protein substrate NIFK, and uncover a previously unknown regulatory region specifically required for recognizing NIFK. Instead of the canonical dimeric structure for other type I PRMTs, PRMT8 exists as a tetramer in solution. Using X-ray crystallography in combination with small-angle X-ray scattering experiments, the dimer of dimers architecture in which two PRMT8 dimers are held together mainly by β strand interactions was proposed. Mutation of PRMT8-β15 impedes the methylation of NIFK but still allows methylation of the histone H2A/H2B dimer or a peptide substrate, suggesting a possible structural basis for recognition of protein substrates. Lastly, we observed two PRMT8 dimer orientations resulting in open (without SAH) and closed (with SAH bound) conformations. The comparison between open and closed conformations may provide useful information for PRMT1/8 inhibitor design.
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Affiliation(s)
- Wei-Chao Lee
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wen-Ling Lin
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University , Menlo Park, California 94025, United States
| | - Eric S-W Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Tong-You Wade Wei
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wen-Hsuan Lin
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Hao Hu
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, Georgia 30602, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, Georgia 30602, United States
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
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38
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Morales Y, Cáceres T, May K, Hevel JM. Biochemistry and regulation of the protein arginine methyltransferases (PRMTs). Arch Biochem Biophys 2015; 590:138-152. [PMID: 26612103 DOI: 10.1016/j.abb.2015.11.030] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/14/2015] [Accepted: 11/15/2015] [Indexed: 12/27/2022]
Abstract
Many key cellular processes can be regulated by the seemingly simple addition of one, or two, methyl groups to arginine residues by the nine known mammalian protein arginine methyltransferases (PRMTs). The impact that arginine methylation has on cellular well-being is highlighted by the ever growing evidence linking PRMT dysregulation to disease states, which has marked the PRMTs as prominent pharmacological targets. This review is meant to orient the reader with respect to the structural features of the PRMTs that account for catalytic activity, as well as provide a framework for understanding how these enzymes are regulated. An overview of what we understand about substrate recognition and binding is provided. Control of product specificity and enzyme processivity are introduced as necessary but flexible features of the PRMTs. Precise control of PRMT activity is a critical component to eukaryotic cell health, especially given that an arginine demethylase has not been identified. We therefore conclude the review with a comprehensive discussion of how protein arginine methylation is regulated.
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Affiliation(s)
- Yalemi Morales
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Tamar Cáceres
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Kyle May
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States
| | - Joan M Hevel
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT 84322, United States.
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39
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Kim JD, Park KE, Ishida J, Kako K, Hamada J, Kani S, Takeuchi M, Namiki K, Fukui H, Fukuhara S, Hibi M, Kobayashi M, Kanaho Y, Kasuya Y, Mochizuki N, Fukamizu A. PRMT8 as a phospholipase regulates Purkinje cell dendritic arborization and motor coordination. SCIENCE ADVANCES 2015; 1:e1500615. [PMID: 26665171 PMCID: PMC4672763 DOI: 10.1126/sciadv.1500615] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/21/2015] [Indexed: 06/02/2023]
Abstract
The development of vertebrate neurons requires a change in membrane phosphatidylcholine (PC) metabolism. Although PC hydrolysis is essential for enhanced axonal outgrowth mediated by phospholipase D (PLD), less is known about the determinants of PC metabolism on dendritic arborization. We show that protein arginine methyltransferase 8 (PRMT8) acts as a phospholipase that directly hydrolyzes PC, generating choline and phosphatidic acid. We found that PRMT8 knockout mice (prmt8 (-/-)) displayed abnormal motor behaviors, including hindlimb clasping and hyperactivity. Moreover, prmt8 (-/-) mice and TALEN-induced zebrafish prmt8 mutants and morphants showed abnormal phenotypes, including the development of dendritic trees in Purkinje cells and altered cerebellar structure. Choline and acetylcholine levels were significantly decreased, whereas PC levels were increased, in the cerebellum of prmt8 (-/-) mice. Our findings suggest that PRMT8 acts both as an arginine methyltransferase and as a PC-hydrolyzing PLD that is essential for proper neurological functions.
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Affiliation(s)
- Jun-Dal Kim
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577, Japan
| | - Kyung-Eui Park
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8572, Japan
| | - Junji Ishida
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577, Japan
| | - Koichiro Kako
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8572, Japan
| | - Juri Hamada
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577, Japan
| | - Shuichi Kani
- Laboratory for Vertebrate Axis Formation, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan
| | - Miki Takeuchi
- Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8575, Japan
| | - Kana Namiki
- Department of Biochemistry and Molecular Pharmacology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba 260-8670, Japan
| | - Hajime Fukui
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Fujishirodai 5-7-1, Suita, Osaka 565-8565, Japan
| | - Shigetomo Fukuhara
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Fujishirodai 5-7-1, Suita, Osaka 565-8565, Japan
| | - Masahiko Hibi
- Laboratory for Vertebrate Axis Formation, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan
- Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Makoto Kobayashi
- Department of Molecular and Developmental Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8575, Japan
| | - Yasunori Kanaho
- Department of Physiological Chemistry, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8575, Japan
| | - Yoshitoshi Kasuya
- Department of Biochemistry and Molecular Pharmacology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chiba 260-8670, Japan
| | - Naoki Mochizuki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Fujishirodai 5-7-1, Suita, Osaka 565-8565, Japan
- AMED-CREST, National Cerebral and Cardiovascular Center Research Institute, Fujishirodai 5-7-1, Suita, Osaka 565-8565, Japan
| | - Akiyoshi Fukamizu
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8572, Japan
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8575, Japan
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40
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Zhou R, Xie Y, Hu H, Hu G, Patel VS, Zhang J, Yu K, Huang Y, Jiang H, Liang Z, Zheng YG, Luo C. Molecular Mechanism underlying PRMT1 Dimerization for SAM Binding and Methylase Activity. J Chem Inf Model 2015; 55:2623-32. [PMID: 26562720 DOI: 10.1021/acs.jcim.5b00454] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the posttranslational methylation of arginine, which is important in a range of biological processes, including epigenetic regulation, signal transduction, and cancer progression. Although previous studies of PRMT1 mutants suggest that the dimerization arm and the N-terminal region of PRMT1 are important for activity, the contributions of these regions to the structural architecture of the protein and its catalytic methylation activity remain elusive. Molecular dynamics (MD) simulations performed in this study showed that both the dimerization arm and the N-terminal region undergo conformational changes upon dimerization. Because a correlation was found between the two regions despite their physical distance, an allosteric pathway mechanism was proposed based on a network topological analysis. The mutation of residues along the allosteric pathways markedly reduced the methylation activity of PRMT1, which may be attributable to the destruction of dimer formation and accordingly reduced S-adenosyl-L-methionine (SAM) binding. This study provides the first demonstration of the use of a combination of MD simulations, network topological analysis, and biochemical assays for the exploration of allosteric regulation upon PRMT1 dimerization. These findings illuminate the results of mechanistic studies of PRMT1, which have revealed that dimer formation facilitates SAM binding and catalytic methylation, and provided direction for further allosteric studies of the PRMT family.
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Affiliation(s)
- Ran Zhou
- Center for Systems Biology, Soochow University , Jiangsu 215006, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Yiqian Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Hao Hu
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, Georgia 30602, United States
| | - Guang Hu
- Center for Systems Biology, Soochow University , Jiangsu 215006, China
| | - Viral Sanjay Patel
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, Georgia 30602, United States
| | - Jin Zhang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai 201203, China
| | - Kunqian Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Yiran Huang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University , Shanghai 201203, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
| | - Zhongjie Liang
- Center for Systems Biology, Soochow University , Jiangsu 215006, China
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia , Athens, Georgia 30602, United States
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China
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41
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Weirich S, Kusevic D, Kudithipudi S, Jeltsch A. Investigation of the methylation of Numb by the SET8 protein lysine methyltransferase. Sci Rep 2015; 5:13813. [PMID: 26391684 PMCID: PMC4585732 DOI: 10.1038/srep13813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 08/06/2015] [Indexed: 01/22/2023] Open
Abstract
It has been reported that the Numb protein is methylated at lysine 158 and 163 and that this methylation is introduced by the SET8 protein lysine methyltransferase [Dhami et al., (2013) Molecular Cell 50, 565-576]. We studied this methylation in vitro using peptide arrays and recombinant Numb protein as substrates. Numb peptides and protein were incubated with recombinant SET8 purified after expression in E. coli or human HEK293 cells. However, no methylation of Numb by SET8 was detectable. SET8 methylation of Histone H4 and p53 peptides and proteins, which were used as positive controls, was readily observed. While SET8 methylation of Numb in cells cannot be ruled out, based on our findings, more evidence is needed to support this claim. It appears likely that another not yet identified PKMT is responsible for the reported methylation of Numb in cells.
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Affiliation(s)
- Sara Weirich
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Denis Kusevic
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Srikanth Kudithipudi
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Stuttgart University, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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42
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Bonnefond L, Stojko J, Mailliot J, Troffer-Charlier N, Cura V, Wurtz JM, Cianférani S, Cavarelli J. Functional insights from high resolution structures of mouse protein arginine methyltransferase 6. J Struct Biol 2015; 191:175-83. [PMID: 26094878 DOI: 10.1016/j.jsb.2015.06.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 03/19/2015] [Accepted: 06/18/2015] [Indexed: 01/15/2023]
Abstract
PRMT6 is a protein arginine methyltransferase involved in transcriptional regulation, human immunodeficiency virus pathogenesis, DNA base excision repair, and cell cycle progression. Like other PRMTs, PRMT6 is overexpressed in several cancer types and is therefore considered as a potential anti-cancer drug target. In the present study, we described six crystal structures of PRMT6 from Mus musculus, solved and refined at 1.34 Å for the highest resolution structure. The crystal structures revealed that the folding of the helix αX is required to stabilize a productive active site before methylation of the bound peptide can occur. In the absence of cofactor, metal cations can be found in the catalytic pocket at the expected position of the guanidinium moiety of the target arginine substrate. Using mass spectrometry under native conditions, we show that PRMT6 dimer binds two cofactor and a single H4 peptide molecules. Finally, we characterized a new site of in vitro automethylation of mouse PRMT6 at position 7.
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Affiliation(s)
- Luc Bonnefond
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Johann Stojko
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg, CNRS, UMR7178, 25 rue Becquerel, Strasbourg 67087, France
| | - Justine Mailliot
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Nathalie Troffer-Charlier
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Vincent Cura
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Jean-Marie Wurtz
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC-DSA, Université de Strasbourg, CNRS, UMR7178, 25 rue Becquerel, Strasbourg 67087, France
| | - Jean Cavarelli
- Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, CNRS UMR7104, INSERM U964, 1 rue Laurent Fries, Illkirch, F-67404, France.
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43
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Lott K, Mukhopadhyay S, Li J, Wang J, Yao J, Sun Y, Qu J, Read LK. Arginine methylation of DRBD18 differentially impacts its opposing effects on the trypanosome transcriptome. Nucleic Acids Res 2015; 43:5501-23. [PMID: 25940618 PMCID: PMC4477658 DOI: 10.1093/nar/gkv428] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/22/2015] [Indexed: 12/30/2022] Open
Abstract
Arginine methylation is a posttranslational modification that impacts wide-ranging cellular functions, including transcription, mRNA splicing and translation. RNA binding proteins (RBPs) represent one of the largest classes of arginine methylated proteins in both mammals and the early diverging parasitic protozoan, Trypanosoma brucei. Here, we report the effects of arginine methylation on the functions of the essential and previously uncharacterized T. brucei RBP, DRBD18. RNAseq analysis shows that DRBD18 depletion causes extensive rearrangement of the T. brucei transcriptome, with increases and decreases in hundreds of mRNAs. DRBD18 contains three methylated arginines, and we used complementation of DRBD18 knockdown cells with methylmimic or hypomethylated DRBD18 to assess the functions of these methylmarks. Methylmimic and hypomethylated DRBD18 associate with different ribonucleoprotein complexes. These altered macromolecular interactions translate into differential impacts on the T. brucei transcriptome. Methylmimic DRBD18 preferentially stabilizes target RNAs, while hypomethylated DRBD18 is more efficient at destabilizing RNA. The protein arginine methyltransferase, TbPRMT1, interacts with DRBD18 and knockdown of TbPRMT1 recapitulates the effects of hypomethylated DRBD18 on mRNA levels. Together, these data support a model in which arginine methylation acts as a switch that regulates T. brucei gene expression.
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Affiliation(s)
- Kaylen Lott
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Shreya Mukhopadhyay
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jun Li
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jie Wang
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jin Yao
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
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44
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PRMT4-mediated arginine methylation negatively regulates retinoblastoma tumor suppressor protein and promotes E2F-1 dissociation. Mol Cell Biol 2014; 35:238-48. [PMID: 25348716 DOI: 10.1128/mcb.00945-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The retinoblastoma protein (pRb/p105) tumor suppressor plays a pivotal role in cell cycle regulation by blockage of the G1-to-S-phase transition. pRb tumor suppressor activity is governed by a variety of posttranslational modifications, most notably phosphorylation by cyclin-dependent kinase (Cdk) complexes. Here we report a novel regulation of pRb through protein arginine methyltransferase 4 (PRMT4)-mediated arginine methylation, which parallels phosphorylation. PRMT4 specifically methylates pRb at the pRb C-terminal domain (pRb C(term)) on arginine (R) residues R775, R787, and R798 in vitro and R787 in vivo. Arginine methylation is important for efficient pRb C(term) phosphorylation, as manifested by the reduced phosphorylation of a methylation-impaired mutant, pRb (R3K). A methylmimetic form of pRb, pRb (R3F), disrupts the formation of the E2F-1/DP1-pRb complex in cells as well as in an isolated system. Finally, studies using a Gal4-E2F-1 reporter system show that pRb (R3F) expression reduces the ability of pRb to repress E2F-1 transcriptional activation, while pRb (R3K) expression further represses E2F-1 transcriptional activation relative to that for cells expressing wild-type pRb. Together, our results suggest that arginine methylation negatively regulates the tumor suppressor function of pRb during cell cycle control, in part by creating a better substrate for Cdk complex phosphorylation and disrupting the interaction of pRb with E2F-1.
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45
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Feng Y, Maity R, Whitelegge JP, Hadjikyriacou A, Li Z, Zurita-Lopez C, Al-Hadid Q, Clark AT, Bedford MT, Masson JY, Clarke SG. Mammalian protein arginine methyltransferase 7 (PRMT7) specifically targets RXR sites in lysine- and arginine-rich regions. J Biol Chem 2013; 288:37010-25. [PMID: 24247247 DOI: 10.1074/jbc.m113.525345] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian protein arginine methyltransferase 7 (PRMT7) has been implicated in roles of transcriptional regulation, DNA damage repair, RNA splicing, cell differentiation, and metastasis. However, the type of reaction that it catalyzes and its substrate specificity remain controversial. In this study, we purified a recombinant mouse PRMT7 expressed in insect cells that demonstrates a robust methyltransferase activity. Using a variety of substrates, we demonstrate that the enzyme only catalyzes the formation of ω-monomethylarginine residues, and we confirm its activity as the prototype type III protein arginine methyltransferase. This enzyme is active on all recombinant human core histones, but histone H2B is a highly preferred substrate. Analysis of the specific methylation sites within intact histone H2B and within H2B and H4 peptides revealed novel post-translational modification sites and a unique specificity of PRMT7 for methylating arginine residues in lysine- and arginine-rich regions. We demonstrate that a prominent substrate recognition motif consists of a pair of arginine residues separated by one residue (RXR motif). These findings will significantly accelerate substrate profile analysis, biological function study, and inhibitor discovery for PRMT7.
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Affiliation(s)
- You Feng
- From the Departments of Chemistry and Biochemistry and
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