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Brown T, Nguyen T, Zhou B, Zheng YG. Chemical probes and methods for the study of protein arginine methylation. RSC Chem Biol 2023; 4:647-669. [PMID: 37654509 PMCID: PMC10467615 DOI: 10.1039/d3cb00018d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023] Open
Abstract
Protein arginine methylation is a widespread post-translational modification (PTM) in eukaryotic cells. This chemical modification in proteins functionally modulates diverse cellular processes from signal transduction, gene expression, and DNA damage repair to RNA splicing. The chemistry of arginine methylation entails the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet, SAM) onto a guanidino nitrogen atom of an arginine residue of a target protein. This reaction is catalyzed by about 10 members of protein arginine methyltransferases (PRMTs). With impacts on a variety of cellular processes, aberrant expression and activity of PRMTs have been shown in many disease conditions. Particularly in oncology, PRMTs are commonly overexpressed in many cancerous tissues and positively correlated with tumor initiation, development and progression. As such, targeting PRMTs is increasingly recognized as an appealing therapeutic strategy for new drug discovery. In the past decade, a great deal of research efforts has been invested in illuminating PRMT functions in diseases and developing chemical probes for the mechanistic study of PRMTs in biological systems. In this review, we provide a brief developmental history of arginine methylation along with some key updates in arginine methylation research, with a particular emphasis on the chemical aspects of arginine methylation. We highlight the research endeavors for the development and application of chemical approaches and chemical tools for the study of functions of PRMTs and arginine methylation in regulating biology and disease.
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Affiliation(s)
- Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Terry Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Bo Zhou
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia Athens GA 30602 USA +1-(706) 542-5358 +1-(706) 542-0277
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2
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Luo YY, Wu JJ, Li YM. Regulation of liquid-liquid phase separation with focus on post-translational modifications. Chem Commun (Camb) 2021; 57:13275-13287. [PMID: 34816836 DOI: 10.1039/d1cc05266g] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid-liquid phase separation (LLPS), a type of phase transition that is important in organisms, is a unique means of forming biomolecular condensates. LLPS plays a significant role in transcription, genome organisation, immune response and cell signaling, and its dysregulation may cause neurodegenerative diseases and cancers. Exploring the regulatory mechanism of LLPS contributes to the understanding of the pathogenic mechanism of abnormal phase transition and enables potential therapeutic targets to be proposed. Many factors have been found to regulate LLPS, of which post-translational modification (PTM) is among the most important. PTMs can change the structure, charge, hydrophobicity and other properties of the proteins involved in phase separation and thereby affect the phase transition behaviour. In this review, we discuss LLPS and the regulatory effects of PTMs, RNA and molecular chaperones in a phase separation system. We introduce several common PTMs (including phosphorylation, arginine methylation, arginine citrullination, acetylation, ubiquitination and poly(ADP-ribosyl)ation), highlight recent advances regarding their roles in LLPS and describe the regulatory mechanisms behind these features. This review provides a detailed overview of the field that will help further the understanding of and interventions in LLPS.
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Affiliation(s)
- Yun-Yi Luo
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
| | - Jun-Jun Wu
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China. .,Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, P. R. China
| | - Yan-Mei Li
- Key Lab of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China. .,Beijing Institute for Brain Disorders, Beijing 100069, P. R. China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, P. R. China
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3
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Aledo JC. The Role of Methionine Residues in the Regulation of Liquid-Liquid Phase Separation. Biomolecules 2021; 11:biom11081248. [PMID: 34439914 PMCID: PMC8394241 DOI: 10.3390/biom11081248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Membraneless organelles are non-stoichiometric supramolecular structures in the micron scale. These structures can be quickly assembled/disassembled in a regulated fashion in response to specific stimuli. Membraneless organelles contribute to the spatiotemporal compartmentalization of the cell, and they are involved in diverse cellular processes often, but not exclusively, related to RNA metabolism. Liquid-liquid phase separation, a reversible event involving demixing into two distinct liquid phases, provides a physical framework to gain insights concerning the molecular forces underlying the process and how they can be tuned according to the cellular needs. Proteins able to undergo phase separation usually present a modular architecture, which favors a multivalency-driven demixing. We discuss the role of low complexity regions in establishing networks of intra- and intermolecular interactions that collectively control the phase regime. Post-translational modifications of the residues present in these domains provide a convenient strategy to reshape the residue-residue interaction networks that determine the dynamics of phase separation. Focus will be placed on those proteins with low complexity domains exhibiting a biased composition towards the amino acid methionine and the prominent role that reversible methionine sulfoxidation plays in the assembly/disassembly of biomolecular condensates.
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Affiliation(s)
- Juan Carlos Aledo
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
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4
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Schisa JA, Elaswad MT. An Emerging Role for Post-translational Modifications in Regulating RNP Condensates in the Germ Line. Front Mol Biosci 2021; 8:658020. [PMID: 33898525 PMCID: PMC8060454 DOI: 10.3389/fmolb.2021.658020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins undergo regulated phase transitions in an array of cell types. The phase separation of RNA-binding proteins, and subsequent formation of RNP condensates or granules, occurs during physiological conditions and can also be induced by stress. Some RNP granules have roles in post-transcriptionally regulating mRNAs, and mutations that prevent the condensation of RNA-binding proteins can reduce an organism's fitness. The reversible and multivalent interactions among RNP granule components can result in RNP complexes that transition among diffuse and condensed states, the latter of which can be pathological; for example, in neurons solid RNP aggregates contribute to disease states such as amyotrophic lateral sclerosis (ALS), and the dysregulation of RNP granules in human germ cells may be involved in Fragile X-associated primary ovarian insufficiency. Thus, regulating the assembly of mRNAs and RNA-binding proteins into discrete granules appears to provide important functions at both cellular and physiological levels. Here we review our current understanding of the role of post-translational modifications (PTMs) in regulating the condensation of RNA-binding proteins in the germ line. We compare and contrast the in vitro evidence that methylation inhibits phase separation of RNA binding proteins, with the extent to which these results apply to the in vivo germ line environment of several model systems. We also focus on the role of phosphorylation in modulating the dynamics of RNP granules in the germ line. Finally, we consider the gaps that exist in our understanding of the role of PTMs in regulating germ line RNP granules.
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Affiliation(s)
- Jennifer A Schisa
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
| | - Mohamed T Elaswad
- Department of Biology, Central Michigan University, Mount Pleasant, MI, United States
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5
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S-adenosylmethionine upregulates the angiotensin receptor-binding protein ATRAP via the methylation of HuR in NAFLD. Cell Death Dis 2021; 12:306. [PMID: 33753727 PMCID: PMC7985363 DOI: 10.1038/s41419-021-03591-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) has emerged globally and is associated with inflammatory signaling. The underlying mechanisms remain poorly delineated, although NAFLD has attracted considerable attention and been extensively investigated. Recent publications have determined that angiotensin II (Ang II) plays an important role in stimulating NAFLD progression by causing lipid metabolism disorder and insulin resistance through its main receptor, Ang II type 1 receptor (AT1R). Herein, we explored the effect of supplementary S-adenosylmethionine (SAM), which is the main biological methyl donor in mammalian cells, in regulating AT1R-associated protein (ATRAP), which is the negative regulator of AT1R. We found that SAM was depleted in NAFLD and that SAM supplementation ameliorated steatosis. In addition, in both high-fat diet-fed C57BL/6 rats and L02 cells treated with oleic acid (OA), ATRAP expression was downregulated at lower SAM concentrations. Mechanistically, we found that the subcellular localization of human antigen R (HuR) was determined by the SAM concentration due to protein methylation modification. Moreover, HuR was demonstrated to directly bind ATRAP mRNA and control its nucleocytoplasmic shuttling. Thus, SAM was suggested to upregulate ATRAP protein expression by maintaining the export of its mRNA from the nucleus. Taken together, our findings suggest that SAM can positively regulate ATRAP in NAFLD and may have various potential benefits for the treatment of NAFLD.
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The Role of Arginine in Disease Prevention, Gut Microbiota Modulation, Growth Performance and the Immune System of Broiler Chicken – A Review. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2019-0081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The effect of dietary arginine on disease prevention, immune system modulation, the gut micro-biota composition and growth of broiler chicken was reviewed. The main aim of poultry production is the maximization of profit at the least possible cost. This objective can mainly be achieved by ensuring that there is no interference in growth or disease outbreak and by feeding chicken with the best possible level of nutrients. With the ban on antibiotic growth promoters, attention is shifted towards other nutrition methods to prevent diseases and promote growth. More attention is therefore given to protein diets in animal nutrition due to their importance as essential part of active biological compounds in the body, assisting in the breakdown of body tissue and helping in the physiological processes of the animal. Arginine plays important function in serving as building blocks of proteins and polypeptides. It performs other roles during the regulation of important biochemical functions such as maintenance, growth, reproduction and immunity. Arginine cannot be synthesized by the body so it has to be supplemented in the diet. When arginine is supplemented above the recommended level, the gut mucosa is protected, immunosuppression is alleviated, diseases like necrotic enteritis, infectious bursal disease and coccidiosis in broiler chickens are prevented. There is an improvement in growth resulting from the increase in intestinal absorption, barrier function and microbiota composition.
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7
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Adamopoulos PG, Mavrogiannis AV, Kontos CK, Scorilas A. Novel alternative splice variants of the human protein arginine methyltransferase 1 (PRMT1) gene, discovered using next-generation sequencing. Gene 2019; 699:135-144. [PMID: 30849541 DOI: 10.1016/j.gene.2019.02.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/24/2019] [Accepted: 02/17/2019] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technology is highly expected to help researchers disclose the complexity of alternative splicing and understand its association with carcinogenesis. Alternative splicing alterations are firmly associated with multiple malignancies, in terms of functional roles in malignant transformation, motility, and/or metastasis of cancer cells. One perfect example illustrating the connection between alternative splicing and cancer is the human protein arginine methyltransferase 1 (PRMT1) gene, previously cloned from members of our research group and involved in a variety of processes including transcription, DNA repair, and signal transduction. Two splice variants of PRMT1 (variants v.1 and v.2) are downregulated in breast cancer. In addition, PRMT1 v.2 promotes the survival and invasiveness of breast cancer cells, while it could serve as a biomarker of unfavorable prognosis in colon cancer patients. The aim of this study was the molecular cloning of novel alternative splice variants of PRMT1 with the use of 3' RACE coupled with NGS technology. Extensive bioinformatics and computational analysis revealed a significant number of 19 novel alternative splicing events between annotated exons of PRMT1 as well as one novel exon, resulting in the discovery of multiple PRMT1 transcripts. In order to validate the full sequence of the novel transcripts, RT-PCR was carried out with the use of variant-specific primers. As a result, 58 novel PRMT1 transcripts were identified, 34 of which are mRNAs encoding new protein isoforms, whereas the rest 24 transcripts are candidates for nonsense-mediated mRNA decay (NMD).
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Adamantios V Mavrogiannis
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece.
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8
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Hofweber M, Dormann D. Friend or foe-Post-translational modifications as regulators of phase separation and RNP granule dynamics. J Biol Chem 2018; 294:7137-7150. [PMID: 30587571 DOI: 10.1074/jbc.tm118.001189] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membrane-less organelles consisting of RNA-binding proteins (RBPs) and RNA. RNA granules form through liquid-liquid phase separation (LLPS), whereby weak promiscuous interactions among RBPs and/or RNAs create a dense network of interacting macromolecules and drive the phase separation. Post-translational modifications (PTMs) of RBPs have emerged as important regulators of LLPS and RNP granule dynamics, as they can directly weaken or enhance the multivalent interactions between phase-separating macromolecules or can recruit or exclude certain macromolecules into or from condensates. Here, we review recent insights into how PTMs regulate phase separation and RNP granule dynamics, in particular arginine (Arg)-methylation and phosphorylation. We discuss how these PTMs regulate the phase behavior of prototypical RBPs and how, as "friend or foe," they might influence the assembly, disassembly, or material properties of cellular RNP granules, such as stress granules or amyloid-like condensates. We particularly highlight how PTMs control the phase separation and aggregation behavior of disease-linked RBPs. We also review how disruptions of PTMs might be involved in aberrant phase transitions and the formation of amyloid-like protein aggregates as observed in neurodegenerative diseases.
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Affiliation(s)
- Mario Hofweber
- From the BioMedical Center, Cell Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 9, 82152 Planegg-Martinsried.,the Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, and
| | - Dorothee Dormann
- From the BioMedical Center, Cell Biology, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 9, 82152 Planegg-Martinsried, .,the Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2, 82152 Planegg-Martinsried, and.,the Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
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9
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Janardhan A, Kathera C, Darsi A, Ali W, He L, Yang Y, Luo L, Guo Z. Prominent role of histone lysine demethylases in cancer epigenetics and therapy. Oncotarget 2018; 9:34429-34448. [PMID: 30344952 PMCID: PMC6188137 DOI: 10.18632/oncotarget.24319] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 12/04/2017] [Indexed: 12/14/2022] Open
Abstract
Protein methylation has an important role in the regulation of chromatin, gene expression and regulation. The protein methyl transferases are genetically altered in various human cancers. The enzymes that remove histone methylation have led to increased awareness of protein interactions as potential drug targets. Specifically, Lysine Specific Demethylases (LSD) removes methylated histone H3 lysine 4 (H3K4) and H3 lysine 9 (H3K9) through formaldehyde-generating oxidation. It has been reported that LSD1 and its downstream targets are involved in tumor-cell growth and metastasis. Functional studies of LSD1 indicate that it regulates activation and inhibition of gene transcription in the nucleus. Here we made a discussion about the summary of histone lysine demethylase and their functions in various human cancers.
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Affiliation(s)
- Avilala Janardhan
- The No. 7 People's Hospital of Changzhou, Changzhou, China.,Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chandrasekhar Kathera
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Amrutha Darsi
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wajid Ali
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanhua Yang
- The No. 7 People's Hospital of Changzhou, Changzhou, China
| | - Libo Luo
- The No. 7 People's Hospital of Changzhou, Changzhou, China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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10
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Elevated Levels of ADMA Are Associated with Lower DDAH2 and Higher PRMT1 in LPS-Induced Endometritis Rats. Inflammation 2017; 41:299-306. [DOI: 10.1007/s10753-017-0687-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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11
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Audagnotto M, Dal Peraro M. Protein post-translational modifications: In silico prediction tools and molecular modeling. Comput Struct Biotechnol J 2017; 15:307-319. [PMID: 28458782 PMCID: PMC5397102 DOI: 10.1016/j.csbj.2017.03.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 02/09/2023] Open
Abstract
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.
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Affiliation(s)
- Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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12
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Asymmetric Dimethylarginine and Hepatic Encephalopathy: Cause, Effect or Association? Neurochem Res 2016; 42:750-761. [PMID: 27885576 PMCID: PMC5357500 DOI: 10.1007/s11064-016-2111-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/07/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022]
Abstract
The methylated derivative of l-arginine, asymmetric dimethylarginine (ADMA) is synthesized in different mammalian tissues including the brain. ADMA acts as an endogenous, nonselective, competitive inhibitor of all three isoforms of nitric oxide synthase (NOS) and may limit l-arginine supply from the plasma to the enzyme via reducing its transport by cationic amino acid transporters. Hepatic encephalopathy (HE) is a relatively frequently diagnosed complex neuropsychiatric syndrome associated with acute or chronic liver failure, characterized by symptoms linked with impaired brain function leading to neurological disabilities. The l-arginine—nitric oxide (NO) pathway is crucially involved in the pathomechanism of HE via modulating important cerebral processes that are thought to contribute to the major HE symptoms. Specifically, activation of this pathway in acute HE leads to an increase in NO production and free radical formation, thus, contributing to astrocytic swelling and cerebral edema. Moreover, the NO-cGMP pathway seems to be involved in cerebral blood flow (CBF) regulation, altered in HE. For this reason, depressed NO-cGMP signaling accompanying chronic HE and ensuing cGMP deficit contributes to the cognitive and motor failure. However, it should be remembered that ADMA, a relatively little known element limiting NO synthesis in HE, may also influence the NO-cGMP pathway regulation. In this review, we will discuss the contribution of ADMA to the regulation of the NO-cGMP pathway in the brain, correlation of ADMA level with CBF and cognitive alterations observed during HE progression in patients and/or animal models of HE.
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13
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Madreiter-Sokolowski CT, Klec C, Parichatikanond W, Stryeck S, Gottschalk B, Pulido S, Rost R, Eroglu E, Hofmann NA, Bondarenko AI, Madl T, Waldeck-Weiermair M, Malli R, Graier WF. PRMT1-mediated methylation of MICU1 determines the UCP2/3 dependency of mitochondrial Ca(2+) uptake in immortalized cells. Nat Commun 2016; 7:12897. [PMID: 27642082 PMCID: PMC5031806 DOI: 10.1038/ncomms12897] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/12/2016] [Indexed: 12/18/2022] Open
Abstract
Recent studies revealed that mitochondrial Ca2+ channels, which control energy flow, cell signalling and death, are macromolecular complexes that basically consist of the pore-forming mitochondrial Ca2+ uniporter (MCU) protein, the essential MCU regulator (EMRE), and the mitochondrial Ca2+ uptake 1 (MICU1). MICU1 is a regulatory subunit that shields mitochondria from Ca2+ overload. Before the identification of these core elements, the novel uncoupling proteins 2 and 3 (UCP2/3) have been shown to be fundamental for mitochondrial Ca2+ uptake. Here we clarify the molecular mechanism that determines the UCP2/3 dependency of mitochondrial Ca2+ uptake. Our data demonstrate that mitochondrial Ca2+ uptake is controlled by protein arginine methyl transferase 1 (PRMT1) that asymmetrically methylates MICU1, resulting in decreased Ca2+ sensitivity. UCP2/3 normalize Ca2+ sensitivity of methylated MICU1 and, thus, re-establish mitochondrial Ca2+ uptake activity. These data provide novel insights in the complex regulation of the mitochondrial Ca2+ uniporter by PRMT1 and UCP2/3. MICU1 is a regulatory subunit of mitochondrial Ca2+ channels that shields mitochondria from Ca2+ overload. Here the authors show that MICU1 methylation by PRMT1 reduces Ca2+ sensitivity, which is normalized by UCP2/3, re-establishing mitochondrial Ca2+ uptake activity.
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Affiliation(s)
- Corina T Madreiter-Sokolowski
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Christiane Klec
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Warisara Parichatikanond
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Sarah Stryeck
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Benjamin Gottschalk
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Sergio Pulido
- Institute of Chemistry, University of Graz, Graz 8010, Austria
| | - Rene Rost
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Emrah Eroglu
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Nicole A Hofmann
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Alexander I Bondarenko
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Tobias Madl
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria.,Center for Integrated Protein Science, Department Chemistry, Technical University Munich, Garching 85748, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Markus Waldeck-Weiermair
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Roland Malli
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
| | - Wolfgang F Graier
- Center for Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, Graz 8010, Austria
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14
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Xu Q, Xu F, Liu L, Chen Y. Compositional Analysis of Asymmetric and Symmetric Dimethylated H3R2 Using Liquid Chromatography–Tandem Mass Spectrometry-Based Targeted Proteomics. Anal Chem 2016; 88:8441-9. [DOI: 10.1021/acs.analchem.6b00076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Qingqing Xu
- School of Pharmacy, Nanjing Medical University, 818
Tian Yuan East Road, Nanjing, 211166, China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University, 818
Tian Yuan East Road, Nanjing, 211166, China
| | - Liang Liu
- School of Pharmacy, Nanjing Medical University, 818
Tian Yuan East Road, Nanjing, 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, 818
Tian Yuan East Road, Nanjing, 211166, China
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15
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Grammatikakis I, Abdelmohsen K, Gorospe M. Posttranslational control of HuR function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27307117 DOI: 10.1002/wrna.1372] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 12/28/2022]
Abstract
The RNA-binding protein HuR (human antigen R) associates with numerous transcripts, coding and noncoding, and controls their splicing, localization, stability, and translation. Through its regulation of target transcripts, HuR has been implicated in cellular events including proliferation, senescence, differentiation, apoptosis, and the stress and immune responses. In turn, HuR influences processes such as cancer and inflammation. HuR function is primarily regulated through posttranslational modifications that alter its subcellular localization and its ability to bind target RNAs; such modifications include phosphorylation, methylation, ubiquitination, NEDDylation, and proteolytic cleavage. In this review, we describe the modifications that impact upon HuR function on gene expression programs and disease states. WIREs RNA 2017, 8:e1372. doi: 10.1002/wrna.1372 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ioannis Grammatikakis
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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16
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Basso M, Pennuto M. Serine phosphorylation and arginine methylation at the crossroads to neurodegeneration. Exp Neurol 2015; 271:77-83. [DOI: 10.1016/j.expneurol.2015.05.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/29/2015] [Accepted: 05/02/2015] [Indexed: 12/13/2022]
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17
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Bekpinar S, Vardagli D, Unlucerci Y, Can A, Uysal M, Gurdol F. Effect of rosiglitazone on asymmetric dimethylarginine metabolism in thioacetamide-induced acute liver injury. ACTA ACUST UNITED AC 2015. [PMID: 26224212 DOI: 10.1016/j.pathophys.2015.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Asymmetric dimethylarginine (ADMA), an endogenous nitric oxide synthase inhibitor, is metabolized in the liver by dimethylarginine dimethylaminohydrolase (DDAH). We aimed to investigate the effect of rosiglitazone, a peroxysome proliferator-activated receptor-gamma (PPAR-γ) agonist, on ADMA metabolism in acute liver injury. Male Sprague Dawley rats were injected thioacetamide (TAA; 500mgkg(-1)) intraperitoneally in order to induce acute liver injury. ADMA, SDMA and arginine levels were determined in plasma by the HPLC. Liver DDAH activity and malondialdehyde (MDA) levels were measured by spectrophotometric procedures. TAA injection caused marked increases in ALT and AST activities. Plasma ADMA levels were increased, while arginine levels and arginine/ADMA ratio were decreased. Liver DDAH activity was significantly diminished and MDA levels were elevated. In another group of animals which were treated with a PPAR-γ agonist (rosiglitazone, 5mgkg(-1)) daily via gastric intubation for a week prior to TAA injection, significant recoveries in DDAH activity and antioxidant status were observed when compared with solely TAA-injected animals. Rosiglitazone pretreatment improved the plasma arginine/ADMA ratio. Our findings indicated that PPAR-γ agonist rosiglitazone beneficially influenced hepatic metabolism of ADMA in TAA-induced acute liver damage.
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Affiliation(s)
- Seldag Bekpinar
- Department of Biochemistry, Istanbul Faculty of Medicine, Istanbul University, Capa, 34093, Istanbul, Turkey.
| | - Duygu Vardagli
- Department of Biochemistry, Istanbul Faculty of Medicine, Istanbul University, Capa, 34093, Istanbul, Turkey
| | - Yesim Unlucerci
- Department of Biochemistry, Istanbul Faculty of Medicine, Istanbul University, Capa, 34093, Istanbul, Turkey
| | - Ayten Can
- Department of Biochemistry, Istanbul Faculty of Medicine, Istanbul University, Capa, 34093, Istanbul, Turkey
| | - Mujdat Uysal
- Department of Biochemistry, Istanbul Faculty of Medicine, Istanbul University, Capa, 34093, Istanbul, Turkey
| | - Figen Gurdol
- Department of Biochemistry, Istanbul Faculty of Medicine, Istanbul University, Capa, 34093, Istanbul, Turkey
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18
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Milewski K, Hilgier W, Albrecht J, Zielińska M. The dimethylarginine (ADMA)/nitric oxide pathway in the brain and periphery of rats with thioacetamide-induced acute liver failure: Modulation by histidine. Neurochem Int 2014; 88:26-31. [PMID: 25523831 DOI: 10.1016/j.neuint.2014.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/25/2014] [Accepted: 12/04/2014] [Indexed: 12/12/2022]
Abstract
Hepatic encephalopathy (HE) is related to variations in the nitric oxide (NO) synthesis and oxidative/nitrosative stress (ONS), and asymmetric dimethylarginine (ADMA) is an endogenous inhibitor of nitric oxide synthases (NOSs). In the present study we compared the effects of acute liver failure (ALF) in the rat TAA model on ADMA concentration in plasma and cerebral cortex, and on the activity and expression of the ADMA degrading enzyme, dimethylarginine dimethylaminohydrolase (DDAH), in brain and liver. ALF increased blood and brain ADMA, and the increase was correlated with decreased DDAH activity in both brain and liver. An i.p. administration of histidine (His), an amino acid reported to alleviate oxidative stress associated with HE (100 mg/kg b.w.), reversed the increase of brain ADMA, which was accompanied by the recovery of brain DDAH activity (determined ex vivo), and with an increase of the total NOS activity. His also activated DDAH ex vivo in brain homogenates derived from control and TAA rats. ALF in this model was also accompanied by increases of blood cyclooxygenase activity and blood and brain TNF-α content, markers of the inflammatory response in the periphery, but these changes were not affected by His, except for the reduction of TNF-α mRNA transcript in the brain. His increased the total antioxidant capacity of the brain cortex, but not of the blood, further documenting its direct neuroprotective power.
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Affiliation(s)
- Krzysztof Milewski
- Department of Neurotoxicology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawińskiego 5 Str, 02-106 Warsaw, Poland
| | - Wojciech Hilgier
- Department of Neurotoxicology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawińskiego 5 Str, 02-106 Warsaw, Poland
| | - Jan Albrecht
- Department of Neurotoxicology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawińskiego 5 Str, 02-106 Warsaw, Poland
| | - Magdalena Zielińska
- Department of Neurotoxicology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawińskiego 5 Str, 02-106 Warsaw, Poland.
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Casci I, Pandey UB. A fruitful endeavor: modeling ALS in the fruit fly. Brain Res 2014; 1607:47-74. [PMID: 25289585 DOI: 10.1016/j.brainres.2014.09.064] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 09/26/2014] [Accepted: 09/27/2014] [Indexed: 12/11/2022]
Abstract
For over a century Drosophila melanogaster, commonly known as the fruit fly, has been instrumental in genetics research and disease modeling. In more recent years, it has been a powerful tool for modeling and studying neurodegenerative diseases, including the devastating and fatal amyotrophic lateral sclerosis (ALS). The success of this model organism in ALS research comes from the availability of tools to manipulate gene/protein expression in a number of desired cell-types, and the subsequent recapitulation of cellular and molecular phenotypic features of the disease. Several Drosophila models have now been developed for studying the roles of ALS-associated genes in disease pathogenesis that allowed us to understand the molecular pathways that lead to motor neuron degeneration in ALS patients. Our primary goal in this review is to highlight the lessons we have learned using Drosophila models pertaining to ALS research. This article is part of a Special Issue entitled ALS complex pathogenesis.
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Affiliation(s)
- Ian Casci
- Department of Pediatrics, Child Neurology and Neurobiology, Children׳s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA; Human Genetics Graduate Program, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Child Neurology and Neurobiology, Children׳s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA.
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20
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Suchánková J, Legartová S, Sehnalová P, Kozubek S, Valente S, Labella D, Mai A, Eckerich C, Fackelmayer FO, Sorokin DV, Bartova E. PRMT1 arginine methyltransferase accumulates in cytoplasmic bodies that respond to selective inhibition and DNA damage. Eur J Histochem 2014; 58:2389. [PMID: 24998928 PMCID: PMC4083328 DOI: 10.4081/ejh.2014.2389] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 12/18/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) are responsible for symmetric and asymmetric methylation of arginine residues of nuclear and cytoplasmic proteins. In the nucleus, PRMTs belong to important chromatin modifying enzymes of immense functional significance that affect gene expression, splicing and DNA repair. By time-lapse microscopy we have studied the sub-cellular localization and kinetics of PRMT1 after inhibition of PRMT1 and after irradiation. Both transiently expressed and endogenous PRMT1 accumulated in cytoplasmic bodies that were located in the proximity of the cell nucleus. The shape and number of these bodies were stable in untreated cells. However, when cell nuclei were microirradiated by UV-A, the mobility of PRMT1 cytoplasmic bodies increased their, size was reduced, and they disappeared within approximately 20 min. The same response occurred after γ-irradiation of the whole cell population, but with delayed kinetics. Treatment with PRMT1 inhibitors induced disintegration of these PRMT1 cytoplasmic bodies and prevented formation of 53BP1 nuclear bodies (NBs) that play a role during DNA damage repair. The formation of 53BP1 NBs was not influenced by PRMT1 over-expression. Taken together, we show that PRMT1 concentrates in cytoplasmic bodies, which respond to DNA injury in the cell nucleus, and to treatment with various PRMT1 inhibitors.
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Abstract
The last one and half a decade witnessed an outstanding re-emergence of attention and remarkable progress in the field of protein methylation. In the present article, we describe the early discoveries in research and review the role protein methylation played in the biological function of the antiproliferative gene, BTG2/TIS21/PC3.
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Affiliation(s)
- Woon Ki Paik
- Professor Emeritus, Temple University School of Medicine, Philadelphia, PA, USA
| | - Sangduk Kim
- Professor Emeritus, Temple University School of Medicine, Philadelphia, PA, USA
| | - In Kyoung Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Korea
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22
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Christodoulou MS, Thomas A, Poulain S, Vidakovic M, Lahtela-Kakkonen M, Matulis D, Bertrand P, Bartova E, Blanquart C, Mikros E, Fokialakis N, Passarella D, Benhida R, Martinet N. Can we use the epigenetic bioactivity of caloric restriction and phytochemicals to promote healthy ageing? MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00268g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Why is it relevant to propose epigenetic “Nutricures” to prevent diseases linked with ageing?
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23
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Scaramuzzino C, Monaghan J, Milioto C, Lanson NA, Maltare A, Aggarwal T, Casci I, Fackelmayer FO, Pennuto M, Pandey UB. Protein arginine methyltransferase 1 and 8 interact with FUS to modify its sub-cellular distribution and toxicity in vitro and in vivo. PLoS One 2013; 8:e61576. [PMID: 23620769 PMCID: PMC3631215 DOI: 10.1371/journal.pone.0061576] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 03/11/2013] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a late onset and progressive motor neuron disease. Mutations in the gene coding for fused in sarcoma/translocated in liposarcoma (FUS) are responsible for some cases of both familial and sporadic forms of ALS. The mechanism through which mutations of FUS result in motor neuron degeneration and loss is not known. FUS belongs to the family of TET proteins, which are regulated at the post-translational level by arginine methylation. Here, we investigated the impact of arginine methylation in the pathogenesis of FUS-related ALS. We found that wild type FUS (FUS-WT) specifically interacts with protein arginine methyltransferases 1 and 8 (PRMT1 and PRMT8) and undergoes asymmetric dimethylation in cultured cells. ALS-causing FUS mutants retained the ability to interact with both PRMT1 and PRMT8 and undergo asymmetric dimethylation similar to FUS-WT. Importantly, PRMT1 and PRMT8 localized to mutant FUS-positive inclusion bodies. Pharmacologic inhibition of PRMT1 and PRMT8 activity reduced both the nuclear and cytoplasmic accumulation of FUS-WT and ALS-associated FUS mutants in motor neuron-derived cells and in cells obtained from an ALS patient carrying the R518G mutation. Genetic ablation of the fly homologue of human PRMT1 (DART1) exacerbated the neurodegeneration induced by overexpression of FUS-WT and R521H FUS mutant in a Drosophila model of FUS-related ALS. These results support a role for arginine methylation in the pathogenesis of FUS-related ALS.
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Affiliation(s)
- Chiara Scaramuzzino
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - John Monaghan
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Carmelo Milioto
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Nicholas A. Lanson
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Astha Maltare
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Tanya Aggarwal
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
| | - Ian Casci
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Frank O. Fackelmayer
- Laboratory of Epigenetics and Chromosome Biology, Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (IMBB-FORTH), University Campus, Ioannina, Greece
| | - Maria Pennuto
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genova, Italy
- * E-mail: (MP); (UBP)
| | - Udai Bhan Pandey
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
- * E-mail: (MP); (UBP)
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24
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Low JKK, Wilkins MR. Protein arginine methylation in Saccharomyces cerevisiae. FEBS J 2012; 279:4423-43. [PMID: 23094907 DOI: 10.1111/febs.12039] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/10/2012] [Accepted: 10/19/2012] [Indexed: 11/27/2022]
Abstract
Recent research has implicated arginine methylation as a major regulator of cellular processes, including transcription, translation, nucleocytoplasmic transport, signalling, DNA repair, RNA processing and splicing. Arginine methylation is evolutionarily conserved, and it is now thought that it may rival other post-translational modifications such as phosphorylation in terms of its occurrence in the proteome. In addition, multiple recent examples demonstrate an exciting new theme: the interplay between methylation and other post-translational modifications such as phosphorylation. In this review, we summarize our current understanding of arginine methylation and the recent advances made, with a focus on the lower eukaryote Saccharomyces cerevisiae. We cover the types of methylated proteins, their responsible methyltransferases, where and how the effects of arginine methylation are seen in the cell, and, finally, discuss the conservation of the biological function of methylarginines between S. cerevisiae and mammals.
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Affiliation(s)
- Jason K K Low
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
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25
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Arginylation and methylation double up to regulate nuclear proteins and nuclear architecture in vivo. ACTA ACUST UNITED AC 2012; 18:1369-78. [PMID: 22118671 DOI: 10.1016/j.chembiol.2011.08.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 08/08/2011] [Accepted: 08/24/2011] [Indexed: 02/04/2023]
Abstract
Protein arginylation and arginine methylation are two posttranslational modifications of emerging importance that involve Arg residues and their modifications. To test a hypothesis that posttranslationally added arginines can be methylated, we used high-precision mass spectrometry and metabolic labeling to find whether posttranslationally added arginines can serve as methylation sites. We identified a number of proteins in vivo, on which posttranslationally added Arg have undergone mono- and dimethylation. This double modification predominantly affects the chromatin-containing nuclear fraction and likely plays an important regulatory role in chromatin-associated proteins. Moreover, inhibition of arginylation and Arg methylation results in a significant reduction of the nucleus size in cultured cells, suggesting changes in chromatin compaction and nuclear architecture. Our findings suggest a functional link between protein regulation by arginylation and methylation that affects nuclear structure in vivo.
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26
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Martinet N, Bertrand P. Interpreting clinical assays for histone deacetylase inhibitors. Cancer Manag Res 2011; 3:117-41. [PMID: 21625397 PMCID: PMC3101110 DOI: 10.2147/cmr.s9661] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Indexed: 12/14/2022] Open
Abstract
As opposed to genetics, dealing with gene expressions by direct DNA sequence modifications, the term epigenetics applies to all the external influences that target the chromatin structure of cells with impact on gene expression unrelated to the sequence coding of DNA itself. In normal cells, epigenetics modulates gene expression through all development steps. When "imprinted" early by the environment, epigenetic changes influence the organism at an early stage and can be transmitted to the progeny. Together with DNA sequence alterations, DNA aberrant cytosine methylation and microRNA deregulation, epigenetic modifications participate in the malignant transformation of cells. Their reversible nature has led to the emergence of the promising field of epigenetic therapy. The efforts made to inhibit in particular the epigenetic enzyme family called histone deacetylases (HDACs) are described. HDAC inhibitors (HDACi) have been proposed as a viable clinical therapeutic approach for the treatment of leukemia and solid tumors, but also to a lesser degree for noncancerous diseases. Three epigenetic drugs are already arriving at the patient's bedside, and more than 100 clinical assays for HDACi are registered on the National Cancer Institute website. They explore the eventual additive benefits of combined therapies. In the context of the pleiotropic effects of HDAC isoforms, more specific HDACi and more informative screening tests are being developed for the benefit of the patients.
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Affiliation(s)
- Nadine Martinet
- Laboratory of Bioactive Molecules, Institute of Chemistry, University of Nice – Sophia Antipolis, Parc Valrose, Nice, France
| | - Philippe Bertrand
- Laboratory of Synthesis and Reactivity of Natural Substances, University of Poitiers, Poitiers, France
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Blifernez O, Wobbe L, Niehaus K, Kruse O. Protein arginine methylation modulates light-harvesting antenna translation in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:119-130. [PMID: 21175895 DOI: 10.1111/j.1365-313x.2010.04406.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Methylation of protein arginines represents an important post-translational modification mechanism, which has so far primarily been characterized in mammalian cells. In this work, we successfully identified and characterized arginine methylation as a crucial type of post-translational modification in the activity regulation of the cytosolic translation repressor protein NAB1 in the plant model organism Chlamydomonas reinhardtii. NAB1 represses the cytosolic translation of light-harvesting protein encoding mRNAs by sequestration into translationally silent messenger ribonucleoprotein complexes (mRNPs). Protein arginine methylation of NAB1 could be demonstrated by PRMT1 catalyzed methylation of recombinant NAB1 in vitro, and by immunodetection of methylated NAB1 arginines in vivo. Mass spectrometric analyses of NAB1 purified from C. reinhardtii revealed the asymmetric dimethylation of Arg90 and Arg92 within GAR motif I. Inhibition of arginine methylation by either adenosine-2'-3'-dialdehyde (AdOx) or 7,7'-carbonylbis(azanediyl)bis(4-hydroxynaphthalene-2-sulfonic acid) sodium salt hydrate (AMI-1) caused a dark-green phenotype characterized by the increased accumulation of light-harvesting complex proteins, and indicating a reduced translation repressor activity of NAB1. The extent of NAB1 arginine methylation depends on the growth conditions, with phototrophic growth causing a high methylation state and heterotrophic growth resulting in lowered methylation of the protein. In addition, we could show that NAB1 activity regulation by arginine methylation operates independently from cysteine-based redox control, which has previously been shown to control the activity of NAB1.
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Affiliation(s)
- Olga Blifernez
- Department of Algae Biotechnology & Bioenergy, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, GermanyDepartment of Proteome & Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Lutz Wobbe
- Department of Algae Biotechnology & Bioenergy, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, GermanyDepartment of Proteome & Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Karsten Niehaus
- Department of Algae Biotechnology & Bioenergy, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, GermanyDepartment of Proteome & Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Olaf Kruse
- Department of Algae Biotechnology & Bioenergy, Faculty of Biology, Bielefeld University, D-33615 Bielefeld, GermanyDepartment of Proteome & Metabolome Research, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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28
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Friend of Prmt1, a novel chromatin target of protein arginine methyltransferases. Mol Cell Biol 2010; 30:260-72. [PMID: 19858291 DOI: 10.1128/mcb.00645-09] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We describe the isolation and characterization of Friend of Prmt1 (Fop), a novel chromatin target of protein arginine methyltransferases. Human Fop is encoded by C1orf77, a gene of previously unknown function. We show that Fop is tightly associated with chromatin, and that it is modified by both asymmetric and symmetric arginine methylation in vivo. Furthermore, Fop plays an important role in the ligand-dependent activation of estrogen receptor target genes, including TFF1 (pS2). Fop depletion results in an almost complete block of estradiol-induced promoter occupancy by the estrogen receptor. Our data indicate that Fop recruitment to the promoter is an early critical event in the activation of estradiol-dependent transcription.
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Yu J, Shin B, Park ES, Yang S, Choi S, Kang M, Rho J. Protein arginine methyltransferase 1 regulates herpes simplex virus replication through ICP27 RGG-box methylation. Biochem Biophys Res Commun 2009; 391:322-8. [PMID: 19913501 DOI: 10.1016/j.bbrc.2009.11.057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 11/09/2009] [Indexed: 11/26/2022]
Abstract
Protein arginine methylation is involved in viral infection and replication through the modulation of diverse cellular processes including RNA metabolism, cytokine signaling, and subcellular localization. It has been suggested previously that the protein arginine methylation of the RGG-box of ICP27 is required for herpes simplex virus type-1 (HSV-1) viral replication and gene expression in vivo. However, a cellular mediator for this process has not yet been identified. In our current study, we show that the protein arginine methyltransferase 1 (PRMT1) is a cellular mediator of the arginine methylation of ICP27 RGG-box. We generated arginine substitution mutants in this domain and examined which arginine residues are required for methylation by PRMT1. R138, R148 and R150 were found to be the major sites of this methylation but additional arginine residues serving as minor methylation sites are still required to sustain the fully methylated form of ICP27 RGG. We also demonstrate that the nuclear foci-like structure formation, SRPK interactions, and RNA-binding activity of ICP27 are modulated by the arginine methylation of the ICP27 RGG-box. Furthermore, HSV-1 replication is inhibited by hypomethylation of this domain resulting from the use of general PRMT inhibitors or arginine mutations. Our data thus suggest that the PRMT1 plays a key role as a cellular regulator of HSV-1 replication through ICP27 RGG-box methylation.
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Affiliation(s)
- Jungeun Yu
- Department of Microbiology, Chungnam National University, Yuseong-gu, Daejon 305-764, Republic of Korea
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30
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Hung CJ, Lee YJ, Chen DH, Li C. Proteomic analysis of methylarginine-containing proteins in HeLa cells by two-dimensional gel electrophoresis and immunoblotting with a methylarginine-specific antibody. Protein J 2009; 28:139-47. [PMID: 19365714 DOI: 10.1007/s10930-009-9174-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Protein arginine methylation is found in many nucleic acid binding proteins affecting numerous cellular functions. In this study we identified methylarginine-containing proteins in HeLa cell extracts by two-dimensional electrophoresis and immunoblotting with a methylarginine-specific antibody. Protein spots with matched protein stain and blotting signals were analyzed by mass spectrometry. The identities of 12 protein spots as 11 different proteins were suggested. Known methylarginine-containing proteins such as hnRNP A2/B1, hnRNP A1, hnRNP G and FUS were identified, indicating the feasibility of our approach. However, four highly abundant metabolic enzymes that might co-electrophorese with methylarginine-containing proteins were also identified. Other nucleic acid binding proteins hnRNP M, hnRNP I and NonO protein were identified. Recombinant hnRNP M and a peptide with the RGG sequence in hnRNP M could be further methylated in vitro. The immunoblotting results of immunoprecipitated hnRNP I and NonO protein are consistent with arginine methylation in both proteins. In this study we identified methylarginine-containing proteins in HeLa cells through proteomic approaches and the method is fast and robust for further applications.
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Affiliation(s)
- Chien-Jen Hung
- Department of Biomedical Sciences, Chung Shan Medical University, 110 Sec. 1, Taichung, Taiwan, ROC
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31
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An S, Yun M, Park YG, Park GH. Proteomic identification of cytosolic proteins that undergo arginine methylation during rat liver regeneration. Electrophoresis 2009; 30:2412-21. [DOI: 10.1002/elps.200800772] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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32
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Arginine methylation of human adenovirus type 5 L4 100-kilodalton protein is required for efficient virus production. J Virol 2009; 83:4778-90. [PMID: 19264777 DOI: 10.1128/jvi.02493-08] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The adenovirus type 5 (Ad5) late region 4 (L4) 100-kDa nonstructural protein (L4-100K) mediates inhibition of cellular protein synthesis and selective translation of tripartite leader (TL)-containing viral late mRNAs via ribosome shunting. In addition, L4-100K has been implicated in the trimerization and nuclear localization of hexon protein. We previously proved that L4-100K is a substrate of the protein arginine methylation machinery, an emergent posttranslational modification system involved in a growing list of cellular processes, including transcriptional regulation, cell signaling, RNA processing, and DNA repair. As understood at present, L4-100K arginine methylation involves protein arginine methyltransferase 1 (PRMT1), which asymmetrically dimethylates arginines embedded in arginine-glycine-glycine (RGG) or glycine-arginine-rich (GAR) domains. To identify the methylated arginine residues and assess the role of L4-100K arginine methylation, we generated amino acid substitution mutations in the RGG and GAR motifs to examine their effects in Ad-infected and plasmid-transfected cells. Arginine-to-glycine exchanges in the RGG boxes significantly diminished L4-100K methylation in the course of an infection and substantially reduced virus growth, demonstrating that L4-100K methylation in RGG motifs is an important host cell function required for efficient Ad replication. Our data further indicate that PRMT1-catalyzed arginine methylation in the RGG boxes regulates the binding of L4-100K to hexon and promotes the capsid assembly of the structural protein as well as modulating TL-mRNA interaction. Furthermore, substitutions in GAR, but not RGG, regions affected L4-100K nuclear import, implying that the nuclear localization signal of L4-100K is located within the GAR sequence.
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Herrmann F, Pably P, Eckerich C, Bedford MT, Fackelmayer FO. Human protein arginine methyltransferases in vivo--distinct properties of eight canonical members of the PRMT family. J Cell Sci 2009; 122:667-77. [PMID: 19208762 DOI: 10.1242/jcs.039933] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Methylation of arginine residues is a widespread post-translational modification of proteins catalyzed by a small family of protein arginine methyltransferases (PRMTs). Functionally, the modification appears to regulate protein functions and interactions that affect gene regulation, signalling and subcellular localization of proteins and nucleic acids. All members have been, to different degrees, characterized individually and their implication in cellular processes has been inferred from characterizing substrates and interactions. Here, we report the first comprehensive comparison of all eight canonical members of the human PRMT family with respect to subcellular localization and dynamics in living cells. We show that the individual family members differ significantly in their properties, as well as in their substrate specificities, suggesting that they fulfil distinctive, non-redundant functions in vivo. In addition, certain PRMTs display different subcellular localization in different cell types, implicating cell- and tissue-specific mechanisms for regulating PRMT functions.
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Affiliation(s)
- Frank Herrmann
- EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), c/Dr. Aiguader 88, 08003 Barcelona, Spain
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Herrmann F, Fackelmayer FO. Nucleo-cytoplasmic shuttling of protein arginine methyltransferase 1 (PRMT1) requires enzymatic activity. Genes Cells 2009; 14:309-17. [PMID: 19170758 DOI: 10.1111/j.1365-2443.2008.01266.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Methylation of arginine residues is a widespread post-translational modification of proteins catalyzed by a family of protein arginine methyltransferases (PRMT), of which PRMT1 is the predominant member in human cells. We have previously described the localization and mobility of PRMT1 in live cells, and found that it shuttles between the nucleus and the cytoplasm depending on the methylation status of substrate proteins. Recently, amino-terminal splicing isoforms of PRMT1 were shown to differ significantly in intracellular localization, the most interesting being splice variant 2 that carries a nuclear export signal in its amino terminus, and is expressed in increased levels in breast cancer cells. We show here that enzymatic activity is required for nucleo-cytoplasmic shuttling of PRMT1v2, as a catalytically inactive mutant highly accumulates in the nucleus and displays altered intranuclear mobility as determined by fluorescence recovery after photobleaching experiments. Our results indicate that nuclear export of PRMT1v2 is dominant over activity-independent nuclear import, but can only occur after activity-dependent release of the enzyme from substrates, suggesting that shuttling of the enzyme provides a dynamic mechanism for the regulation of substrate methylation.
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Affiliation(s)
- Frank Herrmann
- EMBL-CRG Systems Biology, c/Doctor Aiguader 88, 08003 Barcelona, Spain
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35
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Hyun S, Jeong S, Yu J. Effects of asymmetric arginine dimethylation on RNA-binding peptides. Chembiochem 2009; 9:2790-2. [PMID: 18924194 DOI: 10.1002/cbic.200800544] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Soonsil Hyun
- Department of Chemistry and Education, Seoul National University, Seoul 151-742, Korea
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36
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Hahn P, Böse J, Edler S, Lengeling A. Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins. BMC Genomics 2008; 9:293. [PMID: 18564434 PMCID: PMC2453528 DOI: 10.1186/1471-2164-9-293] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 06/18/2008] [Indexed: 12/24/2022] Open
Abstract
Background The jumonji C (JmjC) domain containing gene 6 (Jmjd6, previously known as phosphatidylserine receptor) has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Given the importance of JmjC domain containing proteins in controlling a wide range of diverse biological functions, we undertook a comparative genomic analysis to gain further insights in Jmjd6 gene organisation, evolution, and protein function. Results We describe here a semiautomated computational pipeline to identify and annotate JmjC domain containing proteins. Using a sequence segment N-terminal of the Jmjd6 JmjC domain as query for a reciprocal BLAST search, we identified homologous sequences in 62 species across all major phyla. Retrieved Jmjd6 sequences were used to phylogenetically analyse corresponding loci and their genomic neighbourhood. This analysis let to the identification and characterisation of a bi-directional transcriptional unit compromising the Jmjd6 and 1110005A03Rik genes and to the recognition of a new, before overseen Jmjd6 exon in mammals. Using expression studies, two novel Jmjd6 splice variants were identified and validated in vivo. Analysis of the Jmjd6 neighbouring gene 1110005A03Rik revealed an incident deletion of this gene in two out of three earlier reported Jmjd6 knockout mice, which might affect previously described conflicting phenotypes. To determine potentially important residues for Jmjd6 function a structural model of the Jmjd6 protein was calculated based on sequence conservation. This approach identified a conserved double-stranded β-helix (DSBH) fold and a HxDxnH facial triad as structural motifs. Moreover, our systematic annotation in nine species identified 313 DSBH fold-containing proteins that split into 25 highly conserved subgroups. Conclusion We give further evidence that Jmjd6 most likely has a function as a nonheme-Fe(II)-2-oxoglutarate-dependent dioxygenase as previously suggested. Further, we provide novel insights into the evolution of Jmjd6 and other related members of the superfamily of JmjC domain containing proteins. Finally, we discuss possibilities of the involvement of Jmjd6 and 1110005A03Rik in an antagonistic biochemical pathway.
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Affiliation(s)
- Phillip Hahn
- Research Group Infection Genetics, Department of Experimental Mouse Genetics, Helmholtz Centre for Infection Research, D-31824 Braunschweig, Germany.
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37
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Goulet I, Gauvin G, Boisvenue S, Côté J. Alternative Splicing Yields Protein Arginine Methyltransferase 1 Isoforms with Distinct Activity, Substrate Specificity, and Subcellular Localization. J Biol Chem 2007; 282:33009-21. [PMID: 17848568 DOI: 10.1074/jbc.m704349200] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PRMT1 is the predominant member of a family of protein arginine methyltransferases (PRMTs) that have been implicated in various cellular processes, including transcription, RNA processing, and signal transduction. It was previously reported that the human PRMT1 pre-mRNA was alternatively spliced to yield three isoforms with distinct N-terminal sequences. Close inspection of the genomic organization in the 5'-end of the PRMT1 gene revealed that it can produce up to seven protein isoforms, all varying in their N-terminal domain. A detailed biochemical characterization of these variants revealed that unique N-terminal sequences can influence catalytic activity as well as substrate specificity. In addition, our results uncovered the presence of a functional nuclear export sequence in PRMT1v2. Finally, we find that the relative balance of PRMT1 isoforms is altered in breast cancer.
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Affiliation(s)
- Isabelle Goulet
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada
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38
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Iwasaki H, Yada T. Protein arginine methylation regulates insulin signaling in L6 skeletal muscle cells. Biochem Biophys Res Commun 2007; 364:1015-21. [PMID: 17971302 DOI: 10.1016/j.bbrc.2007.10.113] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Accepted: 10/22/2007] [Indexed: 10/22/2022]
Abstract
Protein N-arginine methyltransferase (PRMT)1 catalyzes arginine methylation in a variety of substrates, although the potential role of PRMT1 in insulin action has not been defined. We therefore investigated the effect of PRMT1-mediated methylation on insulin signaling and glucose uptake in skeletal L6 myotubes. Exposure of L6 myotubes to insulin rapidly induced translocation of PRMT1 and increased its catalytic activity in membrane fraction. Several proteins in the membrane fraction were arginine-methylated after insulin treatment, which were inhibited by pretreatment with an inhibitor of methyltransferase, 5'-deoxy-5'-(methylthio)adenosine (MTA), or a small interfering RNA against PRMT1 (PRMT1-siRNA). Inhibition of arginine methylation with MTA or PRMT1-siRNA diminished later phase of insulin-stimulated tyrosine phosphorylation of insulin receptor (IR) beta and IRS-1, association of IRS-1 with p85alpha subunit of PI3-K, and glucose uptake. Our results suggest that PRMT1-mediated methylation serves as a positive modulator of IR/IRS-1/PI3-K pathway and subsequent glucose uptake in skeletal muscle cells.
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Affiliation(s)
- Hiroaki Iwasaki
- Division of Integrative Physiology, Department of Physiology, Jichi Medical University, School of Medicine, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
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Sayegh J, Webb K, Cheng D, Bedford MT, Clarke SG. Regulation of protein arginine methyltransferase 8 (PRMT8) activity by its N-terminal domain. J Biol Chem 2007; 282:36444-53. [PMID: 17925405 DOI: 10.1074/jbc.m704650200] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human protein arginine methyltransferase PRMT8 has been recently described as a type I enzyme in brain that is localized to the plasma membrane by N-terminal myristoylation. The amino acid sequence of human PRMT8 is almost 80% identical to human PRMT1, the major protein arginine methyltransferase activity in mammalian cells. However, the activity of a recombinant PRMT8 GST fusion protein toward methyl-accepting substrates is much lower than that of a GST fusion of PRMT1. We show here that both His-tagged and GST fusion species lacking the initial 60 amino acid residues of PRMT8 have enhanced enzymatic activity, suggesting that the N-terminal domain may regulate PRMT8 activity. This conclusion is supported by limited proteolysis experiments showing an increase in the activity of the digested full-length protein, consistent with the loss of the N-terminal domain. In contrast, the activity of the N-terminal truncated protein was slightly diminished by limited proteolysis. Significantly, we detect automethylation at two sites in the N-terminal domain, as well as binding sites for SH3 domain-containing proteins. We suggest that the N-terminal domain may function as an autoregulator that may be displaced by interaction with one or more physiological inducers.
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Affiliation(s)
- Joyce Sayegh
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
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40
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Scebba F, De Bastiani M, Bernacchia G, Andreucci A, Galli A, Pitto L. PRMT11: a new Arabidopsis MBD7 protein partner with arginine methyltransferase activity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 52:210-22. [PMID: 17711414 DOI: 10.1111/j.1365-313x.2007.03238.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Plant methyl-DNA-binding proteins (MBDs), discovered by sequence homology to their animal counterparts, have not been well characterized at the physiological and functional levels. In order better to characterize the Arabidopsis AtMBD7 protein, unique in bearing three MBD domains, we used a yeast two-hybrid system to identify its partners. One of the interacting proteins we cloned is the Arabidopsis arginine methyltransferase 11 (AtPRMT11). Glutathione S-transferase pull-down and co-immunoprecipitation assays confirmed that the two proteins interact with each other and can be co-isolated. Using GFP fluorescence, we show that both AtMBD7 and AtPRMT11 are present in the nucleus. Further analyses revealed that AtPRMT11 acts as an arginine methyltransferase active on both histones and proteins of cellular extracts. The analysis of a T-DNA mutant line lacking AtPRMT11 mRNA revealed reduced levels of proteins with asymmetrically dimethylated arginines, suggesting that AtPRMT11, which is highly similar to mammalian PRMT1, is indeed a type I arginine methyltransferase. Further, AtMBD7 is a substrate for AtPRMT11, which post-translationally modifies the portion of the protein-containing C-terminal methylated DNA-binding domain. These results suggest the existence of a link between DNA methylation and arginine methylation.
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Affiliation(s)
- Francesca Scebba
- Laboratorio di Terapia Genica e Molecolare, Istituto di Fisiologia Clinica, Area della Ricerca CNR, via Moruzzi 1, 56100 Pisa, Italy
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Abstract
Although the field of protein methylation enjoys widespread interest in the scientific literature of today, this is a recent phenomenon. Papers on 'protein methylation' were first published in the 1960s. By the early 1980s, it was known that lysine, arginine, histidine and dicarboxylic amino acids were post-translationally methylated by highly specific methyltransferases. However, despite these early advances, the biological importance of these reactions remained largely unproven. With the introduction of modern molecular biology techniques in the mid-1990s, an enormous surge of interest in protein methylation occurred. It is now clear that protein methylation carries many important biological functions, including gene regulation and signal transduction. Thus, the story of protein-methylation research is a testament to both modern molecular biology and the importance of continuing to pursue lines of research in which the precise biological function might not be currently known.
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Affiliation(s)
- Woon Ki Paik
- Graduate School of Biomedical Sciences, Korea University Medical School, Seoul 136-705, Korea
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42
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Raijmakers R, Zendman AJW, Egberts WV, Vossenaar ER, Raats J, Soede-Huijbregts C, Rutjes FPJT, van Veelen PA, Drijfhout JW, Pruijn GJM. Methylation of arginine residues interferes with citrullination by peptidylarginine deiminases in vitro. J Mol Biol 2007; 367:1118-29. [PMID: 17303166 DOI: 10.1016/j.jmb.2007.01.054] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 12/19/2006] [Accepted: 01/20/2007] [Indexed: 10/23/2022]
Abstract
Peptidylarginine deiminase (PAD) enzymes catalyze the conversion of arginine residues in proteins to citrulline residues. Citrulline is a non-standard amino acid that is not incorporated in proteins during translation, but can be generated post-translationally by the PAD enzymes. Although the existence of citrulline residues in proteins has been known for a long time, only a few proteins have been reported to contain this amino acid under normal conditions. These include the nuclear histones, which also contain a wide variety of other post-translational modifications, as for instance methylation of arginine residues. It has been suggested that citrullination and methylation of arginine residues are competing processes and that PAD enzymes might "reverse" the methylation of arginine residues by converting monomethylated arginine into citrulline. However, conflicting data have been reported on the capacity of PADs to citrullinate monomethylated peptidylarginine. Using synthetic peptides that contain either arginine or methylated arginine residues, we show that the human PAD2, PAD3 and PAD4 enzymes and PAD enzyme present in several mouse tissues in vitro can only convert non-methylated peptidylarginine into peptidylcitrulline and that hPAD6 does not show any deiminating activity at all. A comparison of bovine histones either treated or untreated with PAD by amino acid analysis also supported the interference of deimination by arginine methylation. Taken together, these data indicate that it is unlikely that methyl groups at the guanidino position of peptidylarginine can be removed by peptidylarginine deiminases, which has important implications for the recently reported role of these enzymes in gene regulation.
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Affiliation(s)
- Reinout Raijmakers
- Department of Biomolecular Chemistry, Nijmegen Center for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands.
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43
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Ong S, Mann M. Identifying and Quantifying Sites of Protein Methylation by Heavy Methyl SILAC. ACTA ACUST UNITED AC 2006; Chapter 14:14.9.1-14.9.12. [DOI: 10.1002/0471140864.ps1409s46] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shao‐En Ong
- The Broad Institute of MIT and Harvard Cambridge Massachusetts
| | - Matthias Mann
- Max Planck Institute for Biochemistry Martinsried Germany
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44
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Schöneich C. Protein modification in aging: an update. Exp Gerontol 2006; 41:807-12. [PMID: 17008045 DOI: 10.1016/j.exger.2006.07.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2006] [Revised: 07/14/2006] [Accepted: 07/17/2006] [Indexed: 10/24/2022]
Abstract
Post-translational modifications of proteins are an important biologic tool for the production of various protein species from a single gene, which may vary in conformation, function, biologic half-life and complex formation with other proteins. The present minireview summarizes a few selected research observations important for the role of post-translational modifications in biologic aging and age-related diseases, including farnesylation, methylglyoxal-derivatization, transglutaminase pathways and the formation of 3-nitrotyrosine and 2-oxo-histidine in vivo.
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Affiliation(s)
- Christian Schöneich
- Department of Pharmaceutical Chemistry, The University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, USA.
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45
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Chen H, Xue Y, Huang N, Yao X, Sun Z. MeMo: a web tool for prediction of protein methylation modifications. Nucleic Acids Res 2006; 34:W249-53. [PMID: 16845004 PMCID: PMC1538891 DOI: 10.1093/nar/gkl233] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Protein methylation is an important and reversible post-translational modification of proteins (PTMs), which governs cellular dynamics and plasticity. Experimental identification of the methylation site is labor-intensive and often limited by the availability of reagents, such as methyl-specific antibodies and optimization of enzymatic reaction. Computational analysis may facilitate the identification of potential methylation sites with ease and provide insight for further experimentation. Here we present a novel protein methylation prediction web server named MeMo, protein methylation modification prediction, implemented in Support Vector Machines (SVMs). Our present analysis is primarily focused on methylation on lysine and arginine, two major protein methylation sites. However, our computational platform can be easily extended into the analyses of other amino acids. The accuracies for prediction of protein methylation on lysine and arginine have reached 67.1 and 86.7%, respectively. Thus, the MeMo system is a novel tool for predicting protein methylation and may prove useful in the study of protein methylation function and dynamics. The MeMo web server is available at: http://www.bioinfo.tsinghua.edu.cn/~tigerchen/memo.html.
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Affiliation(s)
| | - Yu Xue
- Laboratory of Cellular Dynamics, Hefei National Laboratory for Physical Sciences, and the University of Science and Technology of ChinaHefei, China 230027
| | | | - Xuebiao Yao
- Laboratory of Cellular Dynamics, Hefei National Laboratory for Physical Sciences, and the University of Science and Technology of ChinaHefei, China 230027
- To whom correspondence should be addressed. Tel: +86 551 3606294; Fax: +86 551 3607141;
| | - Zhirong Sun
- Correspondence may also be addressed to Zhirong Sun. Tel: +86 10 62772237; Fax: +86 10 62772237;
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46
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Pahlich S, Zakaryan RP, Gehring H. Protein arginine methylation: Cellular functions and methods of analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1890-903. [PMID: 17010682 DOI: 10.1016/j.bbapap.2006.08.008] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2006] [Revised: 08/10/2006] [Accepted: 08/21/2006] [Indexed: 02/01/2023]
Abstract
During the last few years, new members of the growing family of protein arginine methyltransferases (PRMTs) have been identified and the role of arginine methylation in manifold cellular processes like signaling, RNA processing, transcription, and subcellular transport has been extensively investigated. In this review, we describe recent methods and findings that have yielded new insights into the cellular functions of arginine-methylated proteins, and we evaluate the currently used procedures for the detection and analysis of arginine methylation.
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Affiliation(s)
- Steffen Pahlich
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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47
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Thompson PR, Fast W. Histone citrullination by protein arginine deiminase: is arginine methylation a green light or a roadblock? ACS Chem Biol 2006; 1:433-41. [PMID: 17168521 DOI: 10.1021/cb6002306] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein citrullination, a once-obscure post-translational modification (PTM) of peptidylarginine, has recently become an area of significant interest because of its suspected role in human disease states, including rheumatoid arthritis and multiple sclerosis, and also because of its newfound role in gene regulation. One protein isozyme responsible for this modification, protein arginine deiminase 4 (PAD4), has also been proposed to "reverse" epigenetic histone modifications made by the protein arginine methyltransferases. Here, we review the in vivo and in vitro studies of transcriptional regulation by PAD4, evaluate conflicting evidence for its ability to use methylated peptidylarginine as a substrate, and highlight promising areas of future work. Understanding the interplay of multiple arginine PTMs is an emerging area of importance in health and disease and is a topic best addressed by novel tools in proteomics and chemical biology.
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Affiliation(s)
- Paul R Thompson
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.
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48
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Harauz G, Musse AA. A Tale of Two Citrullines—Structural and Functional Aspects of Myelin Basic Protein Deimination in Health and Disease. Neurochem Res 2006; 32:137-58. [PMID: 16900293 DOI: 10.1007/s11064-006-9108-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2006] [Indexed: 02/03/2023]
Abstract
Myelin basic protein (MBP) binds to negatively charged lipids on the cytosolic surface of oligodendrocyte membranes and is responsible for adhesion of these surfaces in the multilayered myelin sheath. The pattern of extensive post-translational modifications of MBP is dynamic during normal central nervous system (CNS) development and during myelin degeneration in multiple sclerosis (MS), affecting its interactions with the myelin membranes and with other molecules. In particular, the degree of deimination (or citrullination) of MBP is correlated with the severity of MS, and may represent a primary defect that precedes neurodegeneration due to autoimmune attack. That the degree of MBP deimination is also high in early CNS development indicates that this modification plays major physiological roles in myelin assembly. In this review, we describe the structural and functional consequences of MBP deimination in healthy and diseased myelin.
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Affiliation(s)
- George Harauz
- Department of Molecular and Cellular Biology, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G 2W1.
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