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Rossi V, Nielson SE, Ortolano A, Lonardo I, Haroldsen E, Comer D, Price OM, Wallace N, Hevel JM. Oligomerization of protein arginine methyltransferase 1 and its effect on methyltransferase activity and substrate specificity. Protein Sci 2024; 33:e5118. [PMID: 39022984 PMCID: PMC11255602 DOI: 10.1002/pro.5118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
Proper protein arginine methylation by protein arginine methyltransferase 1 (PRMT1) is critical for maintaining cellular health, while dysregulation is often associated with disease. How the activity of PRMT1 is regulated is therefore paramount, but is not clearly understood. Several studies have observed higher order oligomeric species of PRMT1, but it is unclear if these exist at physiological concentrations and there is confusion in the literature about how oligomerization affects activity. We therefore sought to determine which oligomeric species of PRMT1 are physiologically relevant, and quantitatively correlate activity with specific oligomer forms. Through quantitative western blotting, we determined that concentrations of PRMT1 available in a variety of human cell lines are in the sub-micromolar to low micromolar range. Isothermal spectral shift binding data were modeled to a monomer/dimer/tetramer equilibrium with an EC50 for tetramer dissociation of ~20 nM. A combination of sedimentation velocity and Native polyacrylamide gel electrophoresis experiments directly confirmed that the major oligomeric species of PRMT1 at physiological concentrations would be dimers and tetramers. Surprisingly, the methyltransferase activity of a dimeric PRMT1 variant is similar to wild type, tetrameric PRMT1 with some purified substrates, but dimer and tetramer forms of PRMT1 show differences in catalytic efficiencies and substrate specificity for other substrates. Our results define an oligomerization paradigm for PRMT1, show that the biophysical characteristics of PRMT1 are poised to support a monomer/dimer/tetramer equilibrium in vivo, and suggest that the oligomeric state of PRMT1 could be used to regulate substrate specificity.
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Affiliation(s)
- Vincent Rossi
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Sarah E. Nielson
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Ariana Ortolano
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Isabella Lonardo
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Emeline Haroldsen
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Drake Comer
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | - Owen M Price
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
| | | | - Joan M. Hevel
- Department of Chemistry and BiochemistryUtah State UniversityLoganUtahUSA
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2
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Vijayakumar A, Majumder M, Yin S, Brobbey C, Karam J, Howley B, Howe P, Berto S, Madan L, Gan W, Palanisamy V. PRMT5-mediated arginine methylation of FXR1 is essential for RNA binding in cancer cells. Nucleic Acids Res 2024; 52:7225-7244. [PMID: 38709899 PMCID: PMC11229354 DOI: 10.1093/nar/gkae319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/29/2024] [Accepted: 04/11/2024] [Indexed: 05/08/2024] Open
Abstract
Emerging evidence indicates that arginine methylation promotes the stability of arginine-glycine-rich (RGG) motif-containing RNA-binding proteins (RBPs) and regulates gene expression. Here, we report that post-translational modification of FXR1 enhances the binding with mRNAs and is involved in cancer cell growth and proliferation. Independent point mutations in arginine residues of FXR1's nuclear export signal (R386 and R388) and RGG (R453, R455 and R459) domains prevent it from binding to RNAs that form G-quadruplex (G4) RNA structures. Disruption of G4-RNA structures by lithium chloride failed to bind with FXR1, indicating its preference for G4-RNA structure containing mRNAs. Furthermore, loss-of-function of PRMT5 inhibited FXR1 methylation both in vivo and in vitro, affecting FXR1 protein stability, inhibiting RNA-binding activity and cancer cell growth and proliferation. Finally, the enhanced crosslinking and immunoprecipitation (eCLIP) analyses reveal that FXR1 binds with the G4-enriched mRNA targets such as AHNAK, MAP1B, AHNAK2, HUWE1, DYNC1H1 and UBR4 and controls its mRNA expression in cancer cells. Our findings suggest that PRMT5-mediated FXR1 methylation is required for RNA/G4-RNA binding, which promotes gene expression in cancer cells. Thus, FXR1's structural characteristics and affinity for RNAs preferentially G4 regions provide new insights into the molecular mechanism of FXR1 in oral cancer cells.
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Affiliation(s)
- Anitha Vijayakumar
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Shasha Yin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Charles Brobbey
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joseph Karam
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Breege Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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3
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Zhang K, Mishra A, Jagannath C. New insight into arginine and tryptophan metabolism in macrophage activation during tuberculosis. Front Immunol 2024; 15:1363938. [PMID: 38605962 PMCID: PMC11008464 DOI: 10.3389/fimmu.2024.1363938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
Arginine and tryptophan are pivotal in orchestrating cytokine-driven macrophage polarization and immune activation. Specifically, interferon-gamma (IFN-γ) stimulates inducible nitric oxide synthase (iNOS) expression), leading to the conversion of arginine into citrulline and nitric oxide (NO), while Interleukin-4 (IL4) promotes arginase activation, shifting arginine metabolism toward ornithine. Concomitantly, IFN-γ triggers indoleamine 2,3-dioxygenase 1 (IDO1) and Interleukin-4 induced 1 (IL4i1), resulting in the conversion of tryptophan into kynurenine and indole-3-pyruvic acid. These metabolic pathways are tightly regulated by NAD+-dependent sirtuin proteins, with Sirt2 and Sirt5 playing integral roles. In this review, we present novel insights that augment our understanding of the metabolic pathways of arginine and tryptophan following Mycobacterium tuberculosis infection, particularly their relevance in macrophage responses. Additionally, we discuss arginine methylation and demethylation and the role of Sirt2 and Sirt5 in regulating tryptophan metabolism and arginine metabolism, potentially driving macrophage polarization.
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Affiliation(s)
- Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, United States
| | - Abhishek Mishra
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Weill-Cornell Medicine, Houston, TX, United States
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4
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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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5
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Xie J, Sun Y, Cao Y, Han L, Li Y, Ding B, Gao C, Hao P, Jin X, Chang Y, Song J, Yin D, Ding J. Transcriptomic and Metabolomic Analyses Provide Insights into the Growth and Development Advantages of Triploid Apostichopus japonicus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:151-162. [PMID: 35122573 PMCID: PMC8940865 DOI: 10.1007/s10126-022-10093-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Polyploid breeding is widely used in aquaculture as an important area of new research. We have previously grown Apostichopus japonicus triploids with a growth advantage. The body length, body weight, and aestivation time of triploid and diploid A. japonicus were measured in this study, and the transcriptome and metabolome were used to examine the growth advantage of triploids A. japonicus. The results showed that the proportion of triploid A. japonicus with a body length of 6-12 cm and 12-18 cm was significantly higher than that of diploid A. japonicus, and triploid A. japonicus had a shorter aestivation time (39 days) than diploid (63 days). We discovered 3296 differentially expressed genes (DEGs); 13 DEGs (for example, cyclin-dependent kinase 2) related to growth advantage, immune regulation, and energy storage were screened as potential candidates. According to Gene Ontology (GO) enrichment analysis, DEGs were significantly enriched in the cytoplasm (cellular component), ATP binding process (molecular function), oxidation-reduction process (biological process), and other pathways. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment data, DEGs were significantly enriched in ribosome production and other areas. We discovered 414 significant differential metabolites (SDMs), with 11 important SDMs (for example, nocodazole) linked to a growth advantage. SDMs are significantly enriched in metabolic pathways, as well as other pathways, according to the KEGG enrichment results. According to a combined transcriptome and metabolome analysis, 6 DEGs have regulatory relationships with 11 SDMs, which act on 11 metabolic pathways together. Our results further enrich the biological data of triploid A. japonicus and provide useful resources for genetic improvement of this species.
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Affiliation(s)
- Jiahui Xie
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yi Sun
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yue Cao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Lingshu Han
- Ningbo University, Ningbo, Zhejiang, People's Republic of China, 315211
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Beichen Ding
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Chuang Gao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Donghong Yin
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023.
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6
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Maron MI, Lehman SM, Gayatri S, DeAngelo JD, Hegde S, Lorton BM, Sun Y, Bai DL, Sidoli S, Gupta V, Marunde MR, Bone JR, Sun ZW, Bedford MT, Shabanowitz J, Chen H, Hunt DF, Shechter D. Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases. iScience 2021; 24:102971. [PMID: 34505004 PMCID: PMC8417332 DOI: 10.1016/j.isci.2021.102971] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 06/21/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022] Open
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the post-translational monomethylation (Rme1), asymmetric (Rme2a), or symmetric (Rme2s) dimethylation of arginine. To determine the cellular consequences of type I (Rme2a) and II (Rme2s) PRMTs, we developed and integrated multiple approaches. First, we determined total cellular dimethylarginine levels, revealing that Rme2s was ∼3% of total Rme2 and that this percentage was dependent upon cell type and PRMT inhibition status. Second, we quantitatively characterized in vitro substrates of the major enzymes and expanded upon PRMT substrate recognition motifs. We also compiled our data with publicly available methylarginine-modified residues into a comprehensive database. Third, we inhibited type I and II PRMTs and performed proteomic and transcriptomic analyses to reveal their phenotypic consequences. These experiments revealed both overlapping and independent PRMT substrates and cellular functions. Overall, this study expands upon PRMT substrate diversity, the arginine methylome, and the complex interplay of type I and II PRMTs.
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Affiliation(s)
- Maxim I. Maron
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Stephanie M. Lehman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Sitaram Gayatri
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Graduate Program in Genetics and Epigenetics, The University of Texas MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Joseph D. DeAngelo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Subray Hegde
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Benjamin M. Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Yan Sun
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dina L. Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Varun Gupta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - James R. Bone
- EpiCypher, Inc., Research Triangle Park, NC 27709, USA
| | - Zu-Wen Sun
- EpiCypher, Inc., Research Triangle Park, NC 27709, USA
| | - Mark T. Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
- Graduate Program in Genetics and Epigenetics, The University of Texas MD Anderson UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Hongshan Chen
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Donald F. Hunt
- Departments of Chemistry and Pathology, University of Virginia, Charlottesville, VA 22904, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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7
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Zhang F, Kerbl-Knapp J, Rodriguez Colman MJ, Meinitzer A, Macher T, Vujić N, Fasching S, Jany-Luig E, Korbelius M, Kuentzel KB, Mack M, Akhmetshina A, Pirchheim A, Paar M, Rinner B, Hörl G, Steyrer E, Stelzl U, Burgering B, Eisenberg T, Pertschy B, Kratky D, Madl T. Global analysis of protein arginine methylation. CELL REPORTS METHODS 2021; 1:100016. [PMID: 35475236 PMCID: PMC9017121 DOI: 10.1016/j.crmeth.2021.100016] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/02/2021] [Accepted: 05/12/2021] [Indexed: 12/25/2022]
Abstract
Quantitative information about the levels and dynamics of post-translational modifications (PTMs) is critical for an understanding of cellular functions. Protein arginine methylation (ArgMet) is an important subclass of PTMs and is involved in a plethora of (patho)physiological processes. However, because of the lack of methods for global analysis of ArgMet, the link between ArgMet levels, dynamics, and (patho)physiology remains largely unknown. We utilized the high sensitivity and robustness of nuclear magnetic resonance (NMR) spectroscopy to develop a general method for the quantification of global protein ArgMet. Our NMR-based approach enables the detection of protein ArgMet in purified proteins, cells, organoids, and mouse tissues. We demonstrate that the process of ArgMet is a highly prevalent PTM and can be modulated by small-molecule inhibitors and metabolites and changes in cancer and during aging. Thus, our approach enables us to address a wide range of biological questions related to ArgMet in health and disease.
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Affiliation(s)
- Fangrong Zhang
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Jakob Kerbl-Knapp
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Maria J. Rodriguez Colman
- Oncode Institute and Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Andreas Meinitzer
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, 8010 Graz, Austria
| | - Therese Macher
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Nemanja Vujić
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Sandra Fasching
- Institute of Pharmaceutical Sciences, University of Graz, 8010 Graz, Austria
| | - Evelyne Jany-Luig
- Institute of Pharmaceutical Sciences, University of Graz, 8010 Graz, Austria
| | - Melanie Korbelius
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Katharina B. Kuentzel
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Maximilian Mack
- BioTechMed-Graz, 8010 Graz, Austria
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Alena Akhmetshina
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Anita Pirchheim
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Margret Paar
- Otto-Loewi Research Center, Physiological Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Beate Rinner
- Division of Biomedical Research, Medical University of Graz, 8036 Graz, Austria
| | - Gerd Hörl
- Otto-Loewi Research Center, Physiological Chemistry, Medical University of Graz, 8010 Graz, Austria
| | - Ernst Steyrer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
| | - Ulrich Stelzl
- BioTechMed-Graz, 8010 Graz, Austria
- Institute of Pharmaceutical Sciences, University of Graz, 8010 Graz, Austria
| | - Boudewijn Burgering
- Oncode Institute and Department of Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Tobias Eisenberg
- BioTechMed-Graz, 8010 Graz, Austria
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
- Field of Excellence BioHealth – University of Graz, Graz, Austria
| | - Brigitte Pertschy
- BioTechMed-Graz, 8010 Graz, Austria
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
- Field of Excellence BioHealth – University of Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
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8
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Tao Y, Yang Y, Zhang Y, Dai X. Current status and future trends in methylation detection approaches. Epigenomics 2021; 13:335-339. [PMID: 33661022 DOI: 10.2217/epi-2020-0418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Ying Tao
- The Fourth People's Hospital of Zhenjiang, Prenatal diagnosis center, Zhenjiang, Jiangsu 212000, China
| | - Yan Yang
- The Fourth People's Hospital of Zhenjiang, Prenatal diagnosis center, Zhenjiang, Jiangsu 212000, China
| | - Yuxin Zhang
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
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9
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Musiani D, Massignani E, Cuomo A, Yadav A, Bonaldi T. Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass Spectrometry. Curr Protein Pept Sci 2021; 21:725-739. [PMID: 32338214 DOI: 10.2174/1389203721666200426232531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/20/2019] [Accepted: 12/24/2019] [Indexed: 12/27/2022]
Abstract
The absence of efficient mass spectrometry-based approaches for the large-scale analysis of protein arginine methylation has hindered the understanding of its biological role, beyond the transcriptional regulation occurring through histone modification. In the last decade, however, several technological advances of both the biochemical methods for methylated polypeptide enrichment and the computational pipelines for MS data analysis have considerably boosted this research field, generating novel insights about the extent and role of this post-translational modification. Here, we offer an overview of state-of-the-art approaches for the high-confidence identification and accurate quantification of protein arginine methylation by high-resolution mass spectrometry methods, which comprise the development of both biochemical and bioinformatics methods. The further optimization and systematic application of these analytical solutions will lead to ground-breaking discoveries on the role of protein methylation in biological processes.
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Affiliation(s)
- Daniele Musiani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Avinash Yadav
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan 20139, Italy
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10
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Urulangodi M, Mohanty A. DNA damage response and repair pathway modulation by non-histone protein methylation: implications in neurodegeneration. J Cell Commun Signal 2020; 14:31-45. [PMID: 31749026 PMCID: PMC7176765 DOI: 10.1007/s12079-019-00538-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
Protein post-translational modifications (PTMs) have emerged to be combinatorial, essential mechanisms used by eukaryotic cells to regulate local chromatin structure, diversify and extend their protein functions and dynamically coordinate complex intracellular signalling processes. Most common types of PTMs include enzymatic addition of small chemical groups resulting in phosphorylation, glycosylation, poly(ADP-ribosyl)ation, nitrosylation, methylation, acetylation or covalent attachment of complete proteins such as ubiquitin and SUMO. Protein arginine methyltransferases (PRMTs) and protein lysine methyltransferases (PKMTs) enzymes catalyse the methylation of arginine and lysine residues in target proteins, respectively. Rapid progress in quantitative proteomic analysis and functional assays have not only documented the methylation of histone proteins post-translationally but also identified their occurrence in non-histone proteins which dynamically regulate a plethora of cellular functions including DNA damage response and repair. Emerging advances have now revealed the role of both histone and non-histone methylations in the regulating the DNA damage response (DDR) proteins, thereby modulating the DNA repair pathways both in proliferating and post-mitotic neuronal cells. Defects in many cellular DNA repair processes have been found primarily manifested in neuronal tissues. Moreover, fine tuning of the dynamicity of methylation of non-histone proteins as well as the perturbations in this dynamic methylation processes have recently been implicated in neuronal genomic stability maintenance. Considering the impact of methylation on chromatin associated pathways, in this review we attempt to link the evidences in non-histone protein methylation and DDR with neurodegenerative research.
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Affiliation(s)
- Madhusoodanan Urulangodi
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, PIN-695011, India.
| | - Abhishek Mohanty
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, PIN-110085, India.
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11
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Rakow S, Pullamsetti SS, Bauer UM, Bouchard C. Assaying epigenome functions of PRMTs and their substrates. Methods 2019; 175:53-65. [PMID: 31542509 DOI: 10.1016/j.ymeth.2019.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Among the widespread and increasing number of identified post-translational modifications (PTMs), arginine methylation is catalyzed by the protein arginine methyltransferases (PRMTs) and regulates fundamental processes in cells, such as gene regulation, RNA processing, translation, and signal transduction. As epigenetic regulators, PRMTs play key roles in pluripotency, differentiation, proliferation, survival, and apoptosis, which are essential biological programs leading to development, adult homeostasis but also pathological conditions including cancer. A full understanding of the molecular mechanisms that underlie PRMT-mediated gene regulation requires the genome wide mapping of each player, i.e., PRMTs, their substrates and epigenetic marks, methyl-marks readers as well as interaction partners, in a thorough and unambiguous manner. However, despite the tremendous advances in high throughput sequencing technologies and the numerous efforts from the scientific community, the epigenomic profiling of PRMTs as well as their histone and non-histone substrates still remains a big challenge owing to obvious limitations in tools and methodologies. This review will summarize the present knowledge about the genome wide mapping of PRMTs and their substrates as well as the technical approaches currently in use. The limitations and pitfalls of the technical tools along with conventional approaches will be then discussed in detail. Finally, potential new strategies for chromatin profiling of PRMTs and histone substrates will be proposed and described.
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Affiliation(s)
- Sinja Rakow
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Soni Savai Pullamsetti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Uta-Maria Bauer
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Caroline Bouchard
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany.
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12
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Lorton BM, Shechter D. Cellular consequences of arginine methylation. Cell Mol Life Sci 2019; 76:2933-2956. [PMID: 31101937 PMCID: PMC6642692 DOI: 10.1007/s00018-019-03140-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/22/2019] [Accepted: 05/10/2019] [Indexed: 02/07/2023]
Abstract
Arginine methylation is a ubiquitous post-translational modification. Three predominant types of arginine-guanidino methylation occur in Eukarya: mono (Rme1/MMA), symmetric (Rme2s/SDMA), and asymmetric (Rme2a/ADMA). Arginine methylation frequently occurs at sites of protein-protein and protein-nucleic acid interactions, providing specificity for binding partners and stabilization of important biological interactions in diverse cellular processes. Each methylarginine isoform-catalyzed by members of the protein arginine methyltransferase family, Type I (PRMT1-4,6,8) and Type II (PRMT5,9)-has unique downstream consequences. Methylarginines are found in ordered domains, domains of low complexity, and in intrinsically disordered regions of proteins-the latter two of which are intimately connected with biological liquid-liquid phase separation. This review highlights discoveries illuminating how arginine methylation affects genome integrity, gene transcription, mRNA splicing and mRNP biology, protein translation and stability, and phase separation. As more proteins and processes are found to be regulated by arginine methylation, its importance for understanding cellular physiology will continue to grow.
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Affiliation(s)
- Benjamin M Lorton
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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13
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Fulton MD, Brown T, Zheng YG. The Biological Axis of Protein Arginine Methylation and Asymmetric Dimethylarginine. Int J Mol Sci 2019; 20:ijms20133322. [PMID: 31284549 PMCID: PMC6651691 DOI: 10.3390/ijms20133322] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 12/20/2022] Open
Abstract
Protein post-translational modifications (PTMs) in eukaryotic cells play important roles in the regulation of functionalities of the proteome and in the tempo-spatial control of cellular processes. Most PTMs enact their regulatory functions by affecting the biochemical properties of substrate proteins such as altering structural conformation, protein-protein interaction, and protein-nucleic acid interaction. Amid various PTMs, arginine methylation is widespread in all eukaryotic organisms, from yeasts to humans. Arginine methylation in many situations can drastically or subtly affect the interactions of substrate proteins with their partnering proteins or nucleic acids, thus impacting major cellular programs. Recently, arginine methylation has become an important regulator of the formation of membrane-less organelles inside cells, a phenomenon of liquid-liquid phase separation (LLPS), through altering π-cation interactions. Another unique feature of arginine methylation lies in its impact on cellular physiology through its downstream amino acid product, asymmetric dimethylarginine (ADMA). Accumulation of ADMA in cells and in the circulating bloodstream is connected with endothelial dysfunction and a variety of syndromes of cardiovascular diseases. Herein, we review the current knowledge and understanding of protein arginine methylation in regards to its canonical function in direct protein regulation, as well as the biological axis of protein arginine methylation and ADMA biology.
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Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA.
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14
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Ning Z, Star AT, Mierzwa A, Lanouette S, Mayne J, Couture JF, Figeys D. A charge-suppressing strategy for probing protein methylation. Chem Commun (Camb) 2016; 52:5474-7. [PMID: 27021271 DOI: 10.1039/c6cc00814c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Methylation of arginine and lysine (RK) residues play essential roles in epigenetics and the regulation of gene expression. However, research in this area is often hindered by the lack of effective tools for probing the protein methylation. Here, we present an antibody-free strategy to capture protein methylation on RK residues by using chemical reactions to eliminate the charges on un-modified RK residues and peptide N-termini. Peptides containing methylated RK residues remain positively charged and are then enriched by strong cation exchange chromatography, followed by high-resolution mass spectrometry identification.
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Affiliation(s)
- Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Alexandra Therese Star
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Anna Mierzwa
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Janice Mayne
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Jean-Francois Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, Faculty of Medicine, University of Ottawa, Ontario, Canada.
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15
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Nonaka S, Sekine M, Tsunoda M, Ozeki Y, Fujii K, Akiyama K, Shimoda K, Furuchi T, Katane M, Saitoh Y, Homma H. Simultaneous determination of N
G
-monomethyl-l
-arginine, N
G
,N
G
-dimethyl-l
-arginine, N
G
,N
G′
-dimethyl-l
-arginine, and l
-arginine using monolithic silica disk-packed spin columns and a monolithic silica column. J Sep Sci 2014; 37:2087-94. [DOI: 10.1002/jssc.201400240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/26/2014] [Accepted: 05/26/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Satoko Nonaka
- Faculty of Pharmaceutical Life Sciences; Kitasato University; Tokyo Japan
- Pfizer Worldwide Research & Development; Tokyo Laboratories; Tokyo Japan
| | - Masae Sekine
- Faculty of Pharmaceutical Life Sciences; Kitasato University; Tokyo Japan
| | - Makoto Tsunoda
- Graduate School of Pharmaceutical Sciences; University of Tokyo; Tokyo Japan
| | - Yuji Ozeki
- Department of Psychiatry; Dokkyo Medical University School of Medicine; Tochigi Japan
| | - Kumiko Fujii
- Department of Psychiatry; Dokkyo Medical University School of Medicine; Tochigi Japan
| | - Kazufumi Akiyama
- Department of Biological Psychiatry and Neuroscience; Dokkyo Medical University School of Medicine; Tochigi Japan
| | - Kazutaka Shimoda
- Department of Psychiatry; Dokkyo Medical University School of Medicine; Tochigi Japan
| | - Takemitsu Furuchi
- Faculty of Pharmaceutical Life Sciences; Kitasato University; Tokyo Japan
| | - Masumi Katane
- Faculty of Pharmaceutical Life Sciences; Kitasato University; Tokyo Japan
| | - Yasuaki Saitoh
- Faculty of Pharmaceutical Life Sciences; Kitasato University; Tokyo Japan
| | - Hiroshi Homma
- Faculty of Pharmaceutical Life Sciences; Kitasato University; Tokyo Japan
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16
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Emerging technologies to map the protein methylome. J Mol Biol 2014; 426:3350-62. [PMID: 24805349 DOI: 10.1016/j.jmb.2014.04.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/26/2023]
Abstract
Protein methylation plays an integral role in cellular signaling, most notably by modulating proteins bound at chromatin and increasingly through regulation of non-histone proteins. One central challenge in understanding how methylation acts in signaling is identifying and measuring protein methylation. This includes locus-specific modification of histones, on individual non-histone proteins, and globally across the proteome. Protein methylation has been studied traditionally using candidate approaches such as methylation-specific antibodies, mapping of post-translational modifications by mass spectrometry, and radioactive labeling to characterize methylation on target proteins. Recent developments have provided new approaches to identify methylated proteins, measure methylation levels, identify substrates of methyltransferase enzymes, and match methylated proteins to methyl-specific reader domains. Methyl-binding protein domains and improved antibodies with broad specificity for methylated proteins are being used to characterize the "protein methylome". They also have the potential to be used in high-throughput assays for inhibitor screens and drug development. These tools are often coupled to improvements in mass spectrometry to quickly identify methylated residues, as well as to protein microarrays, where they can be used to screen for methylated proteins. Finally, new chemical biology strategies are being used to probe the function of methyltransferases, demethylases, and methyl-binding "reader" domains. These tools create a "system-level" understanding of protein methylation and integrate protein methylation into broader signaling processes.
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17
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Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T. Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. MOLECULAR BIOSYSTEMS 2014; 9:2231-47. [PMID: 23748837 DOI: 10.1039/c3mb00009e] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein methylation is a post-translational modification (PTM) by which a variable number of methyl groups are transferred to lysine and arginine residues within proteins. Despite increased interest in this modification due to its reversible nature and its emerging role in a diverse set of biological pathways beyond chromatin, global identification of protein methylation has remained an unachieved goal. To characterise sites of lysine and arginine methylation beyond histones, we employed an approach that combines heavy methyl stable isotope labelling by amino acids in cell culture (hmSILAC) with high-resolution mass spectrometry-based proteomics. Through a broad evaluation of immuno-affinity enrichment and the application of two classical protein separation techniques prior to mass spectrometry, to nucleosolic and cytosolic fractions separately, we identified a total of 501 different methylation types, on 397 distinct lysine and arginine sites, present on 139 unique proteins. Our results considerably extend the number of known in vivo methylation sites and indicate their significant presence on several protein complexes involved at all stages of gene expression, from chromatin remodelling and transcription to splicing and translation. In addition, we describe the potential of the hmSILAC approach for accurate relative quantification of methylation levels between distinct functional states.
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Affiliation(s)
- Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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18
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Lau HT, Lewis KA, Ong SE. Quantifying in vivo, site-specific changes in protein methylation with SILAC. Methods Mol Biol 2014; 1188:161-175. [PMID: 25059611 DOI: 10.1007/978-1-4939-1142-4_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Interest in protein methylation has grown rapidly in recent years. Mass spectrometry-based proteomics is ideally suited to characterize protein modifications, but the multiplicity of methylated residues and the lack of efficient methods to enrich methylated proteins have limited the proteomic identification of protein methylation sites. In this protocol, we compare two metabolic labeling approaches, stable isotope labeling by amino acids in cell culture (SILAC) and its variant heavy methyl SILAC, for studying protein methylation. Instead of heavy lysine and arginine in the typical SILAC experiment, heavy methyl SILAC uses (13)C, (2)H methionine as the labeling amino acid. As cells convert methionine to S-adenosylmethionine, heavy methyl SILAC encodes a 4 Da mass tag for each methyl group, distinguishing between degrees of methylation is possible from mass difference alone. We provide a protocol for SILAC-based analyses of protein methylation and highlight the strengths and weaknesses of each method for targeted and proteomic analyses.
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Affiliation(s)
- Ho-Tak Lau
- Department of Pharmacology, University of Washington, 1959 NE Pacific Street, 357280, Seattle, WA, 98195, USA
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19
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Hui Y, Wong M, Kim JO, Love J, Ansley DM, Chen DDY. A new derivatization method coupled with LC-MS/MS to enable baseline separation and quantification of dimethylarginines in human plasma from patients to receive on-pump CABG surgery. Electrophoresis 2012; 33:1911-20. [PMID: 22740479 DOI: 10.1002/elps.201100536] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Asymmetric dimethylarginine (ADMA) is an inhibitor of nitric oxide synthase and a risk factor for cardiovascular events. We have developed a new derivatization method to enable baseline separation of the regio-isomers, ADMA, and symmetric dimethylarginine (SDMA), within 15 min on a C18 reverse phase column. Reacting naphthalene-2,3-dicarboxaldehyde with ADMA and SDMA in the presence of 2-mercaptoethanol produces corresponding 2,3-dihydro-benzo[f]isoindol-1-ones that are more stable than previously reported ortho-phthaldialdehyde and 2-mercaptoethanol derivatives. LC-MS/MS quantitation of these derivatives can be used to determine ADMA and SDMA concentrations in the plasma of patients to receive on-pump coronary artery bypass grafting (CABG) surgery. The LOD, LOQ and lower LOQ (LLOQ) of this method were determined to be 2.6, 8.7, and 25 nM for ADMA, and 2.5, 8.3, and 25 nM for SDMA, respectively, with consumption of only 50 μL of plasma. The relative standard deviations and relative errors of the intraday and interday determinations, as measurements of reproducibility and accuracy, are all within 15%. The ADMA and SDMA concentrations in patient plasma are 298.1 ± 11.2 nM (mean ± S.E.M., n = 123) and 457.7 ± 19.8 nM (mean ± S.E.M., n = 123), respectively. Upon unblinding of our clinical trial, these predetermined values might explain patient clinical outcomes associated with on-pump CABG surgery, as ADMA is known to inhibit nitric oxide production. Furthermore, this derivatization reaction in conjunction with LC-MS/MS analysis may open a venue to explore alternative chemical labeling modes for LC-MS/MS applications, such as analysis of other amino acids, metabolites, and peptides containing primary amine group(s).
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Affiliation(s)
- Yu Hui
- Department of Chemistry, University of British Colombia, Vancouver, BC, Canada
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20
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Protein Arginine Methyltransferases (PRMTs): promising targets for the treatment of pulmonary disorders. Int J Mol Sci 2012. [PMID: 23202904 PMCID: PMC3497278 DOI: 10.3390/ijms131012383] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Protein arginine methylation is a novel posttranslational modification that plays a pivotal role in a variety of intracellular events, such as signal transduction, protein-protein interaction and transcriptional regulation, either by the direct regulation of protein function or by metabolic products originating from protein arginine methylation that influence nitric oxide (NO)-dependent processes. A growing body of evidence suggests that both mechanisms are implicated in cardiovascular and pulmonary diseases. This review will present and discuss recent research on PRMTs and the methylation of non-histone proteins and its consequences for the pathogenesis of various lung disorders, including lung cancer, pulmonary fibrosis, pulmonary hypertension, chronic obstructive pulmonary disease and asthma. This article will also highlight novel directions for possible future investigations to evaluate the functional contribution of arginine methylation in lung homeostasis and disease.
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21
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Uhlmann T, Geoghegan VL, Thomas B, Ridlova G, Trudgian DC, Acuto O. A method for large-scale identification of protein arginine methylation. Mol Cell Proteomics 2012; 11:1489-99. [PMID: 22865923 PMCID: PMC3494207 DOI: 10.1074/mcp.m112.020743] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The lack of methods for proteome-scale detection of arginine methylation restricts our knowledge of its relevance in physiological and pathological processes. Here we show that most tryptic peptides containing methylated arginine(s) are highly basic and hydrophilic. Consequently, they could be considerably enriched from total cell extracts by simple protocols using either one of strong cation exchange chromatography, isoelectric focusing, or hydrophilic interaction liquid chromatography, the latter being by far the most effective of all. These methods, coupled with heavy methyl-stable isotope labeling by amino acids in cell culture and mass spectrometry, enabled in T cells the identification of 249 arginine methylation sites in 131 proteins, including 190 new sites and 93 proteins not previously known to be arginine methylated. By extending considerably the number of known arginine methylation sites, our data reveal a novel proline-rich consensus motif and identify for the first time arginine methylation in proteins involved in cytoskeleton rearrangement at the immunological synapse and in endosomal trafficking.
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Affiliation(s)
- Thomas Uhlmann
- T Cell Signalling Laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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22
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Dalloneau E, Lopes Pereira P, Brault V, Nabel EG, Hérault Y. Prmt2 Regulates the Lipopolysaccharide-Induced Responses in Lungs and Macrophages. THE JOURNAL OF IMMUNOLOGY 2011; 187:4826-34. [DOI: 10.4049/jimmunol.1101087] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Zakrzewicz D, Zakrzewicz A, Wilker S, Boedeker RH, Padberg W, Eickelberg O, Grau V. Dimethylarginine metabolism during acute and chronic rejection of rat renal allografts. Nephrol Dial Transplant 2010; 26:124-35. [PMID: 20647192 PMCID: PMC3006445 DOI: 10.1093/ndt/gfq392] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background. Dimethylarginines are inhibitors of NO synthesis and are involved in the pathogenesis of vascular diseases. In this study, we ask the question if asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA) levels change during fatal and reversible acute rejection, and contribute to the pathogenesis of chronic vasculopathy. Methods. The Dark Agouti to Lewis rat strain combination was used to investigate fatal acute rejection. Fischer 344 kidneys were transplanted to Lewis rats to study reversible acute rejection episode and the process of chronic rejection. Isograft recipients and untreated Lewis rats were used as controls. l-arginine derivatives were determined by HPLC, and ADMA-metabolizing enzymes were studied by quantitative RT–PCR and western blotting. Results. Renal transplantation transiently increased dimethylarginine levels independent of acute rejection. ADMA plasma levels did not importantly differ between recipients undergoing fatal or reversible acute rejection, whereas SDMA was even lower in recipients of Fisher 344 grafts. In comparison to isograft recipients, ADMA and SDMA levels were slightly elevated during reversible, but not during the process of chronic rejection. Increased dimethylarginine levels, however, did not block NO synthesis. Interestingly, protein methylation, but not ADMA degradation, was increased in allografts. Conclusions. Our data do not support the concept that renal allografts are protected from fatal rejection by dimethylarginines. Dimethylarginines may play a role in triggering chronic rejection, but a contribution to vascular remodelling itself is improbable. In contrast, differential arginine methylation of yet unknown proteins by PRMT1 may be involved in the pathogenesis of acute and chronic rejection.
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Affiliation(s)
- Dariusz Zakrzewicz
- Department of Medicine II, University of Giessen Lung Center, Aulweg 123, D-35392 Giessen, Germany
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24
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Effect of acute variations of insulin and glucose on plasma concentrations of asymmetric dimethylarginine in young people with Type 1 diabetes. Clin Sci (Lond) 2008; 115:361-9. [DOI: 10.1042/cs20080079] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
ADMA (asymmetric dimethylarginine), an endogenous inhibitor of nitric oxide synthase, is considered a major risk factor for cardiovascular disease and progression of renal disease. In the present study we aim to investigate the effect of acute variations in plasma glucose and insulin on plasma ADMA levels in young people with T1D (Type 1 diabetes). Fifteen young patients (ten males) with T1D, median age 18.3 (13.2–24.4) years, HbA1c (glycated haemoglobin) 9% (6.4–13.6%), underwent an overnight (18:00–08:00 hours) variable insulin infusion for euglycaemia, followed by a hyperinsulinaemic–euglycaemic clamp (08:00–12:00 hours). Blood samples were collected every 15 min for determination of ADMA, SDMA (symmetric dimethylarginine), valine, phenylalanine, arginine, creatinine and glucose. Insulin levels were assessed every 30 min. During the overnight period, glucose levels increased following the evening meal. In response to the protein intake there was a significant increase in ADMA, arginine, valine, phenylalanine and creatinine. For the remaining part of the night, glucose levels progressively decreased reaching 5 mmol/l by 04:00 hours. ADMA and SDMA did not change significantly. During the hyperinsulinaemic clamp, a significant fall in ADMA was observed, from 0.468±0.056 to 0.364±0.050 μmol/l (P<0.001). A significant fall was also found in SDMA, valine, phenylalanine, arginine and the ADMA/SDMA ratio (all P<0.001), but not in creatinine levels. No correlation was found between insulin sensitivity and ADMA. We conclude that acute changes in glycaemia do not significantly affect plasma ADMA levels whereas infusion of insulin significantly reduces ADMA, suggesting an important role for insulin in the regulation of this cardiovascular risk factor.
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25
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Zinellu A, Sotgia S, Scanu B, Deiana L, Carru C. Determination of protein-incorporated methylated arginine reference values in healthy subjects whole blood and evaluation of factors affecting protein methylation. Clin Biochem 2008; 41:1218-23. [DOI: 10.1016/j.clinbiochem.2008.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Revised: 07/18/2008] [Accepted: 07/18/2008] [Indexed: 11/17/2022]
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26
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Zinellu A, Sotgia S, Scanu B, Formato M, Deiana L, Carru C. Assessment of protein-incorporated arginine methylation in biological specimens by CZE UV-detection. Electrophoresis 2007; 28:4452-8. [DOI: 10.1002/elps.200700153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Kitowska K, Zakrzewicz D, Königshoff M, Chrobak I, Grimminger F, Seeger W, Bulau P, Eickelberg O. Functional role and species-specific contribution of arginases in pulmonary fibrosis. Am J Physiol Lung Cell Mol Physiol 2007; 294:L34-45. [PMID: 17934065 DOI: 10.1152/ajplung.00007.2007] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lung fibrosis is characterized by increased deposition of ECM, especially collagens, and enhanced proliferation of fibroblasts. l-arginine is a key precursor of nitric oxide, asymmetric dimethylarginine, and proline, an amino acid enriched in collagen. We hypothesized that l-arginine metabolism is altered in pulmonary fibrosis, ultimately affecting collagen synthesis. Expression analysis of key enzymes in the arginine pathway, protein arginine methyltransferases (Prmt), arginine transporters, and arginases by quantitative (q) RT-PCR and Western blot revealed significant upregulation of arginase-1 and -2, but not Prmt or arginine transporters, during bleomycin-induced pulmonary fibrosis in mice. HPLC revealed a concomitant, time-dependent decrease in pulmonary l-arginine levels. Arginase-1 and -2 mRNA and protein expression was increased in primary fibroblasts isolated from bleomycin-treated mice, compared with controls, and assessed by qRT-PCR and Western blot analysis. TGF-beta1, a key profibrotic mediator, induced arginase-1 and -2 mRNA expression in primary and NIH/3T3 fibroblasts. Treatment of fibroblasts with the arginase inhibitor, NG-hydroxy-l-arginine, attenuated TGF-beta1-stimulated collagen deposition, but not collagen mRNA expression or Smad signaling, in fibroblasts. In human lungs derived from patients with idiopathic pulmonary fibrosis, arginase activity was unchanged, but arginase-1 expression significantly decreased when compared with donor lungs. Our results thus demonstrate that arginase-1 is expressed and functionally important for collagen deposition in lung fibroblasts. TGF-beta1-induced upregulation of arginase-1 suggests an interplay between profibrotic agents and l-arginine metabolism during the course of lung fibrosis in the mouse, whereas species-specific regulatory mechanisms may account for the differences observed in mouse and human.
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Affiliation(s)
- Kamila Kitowska
- Department of Medicine II, Univ. of Giessen School of Medicine, Aulweg 123, D-35392 Giessen, Germany
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PRMT6 diminishes HIV-1 Rev binding to and export of viral RNA. Retrovirology 2006; 3:93. [PMID: 17176473 PMCID: PMC1779295 DOI: 10.1186/1742-4690-3-93] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Accepted: 12/18/2006] [Indexed: 11/10/2022] Open
Abstract
Background The HIV-1 Rev protein mediates nuclear export of unspliced and partially spliced viral RNA through interaction with the Rev response element (RRE) by means of an arginine rich motif that is similar to the one found in Tat. Since Tat is known to be asymmetrically arginine dimethylated by protein arginine methyltransferase 6 (PRMT6) in its arginine rich motif, we investigated whether the Rev protein could act as a substrate for this enzyme. Results Here, we report the methylation of Rev due to a single arginine dimethylation in the N-terminal portion of its arginine rich motif and the association of Rev with PRMT6 in vivo. Further analysis demonstrated that the presence of increasing amounts of wild-type PRMT6, as well as a methylation-inactive mutant PRMT6, dramatically down-regulated Rev protein levels in concentration-dependent fashion, which was not dependent on the methyltransferase activity of PRMT6. Quantification of Rev mRNA revealed that attenuation of Rev protein levels was due to a posttranslational event, carried out by a not yet defined activity of PRMT6. However, no relevant protein attenuation was observed in subsequent chloramphenicol acetyltransferase (CAT) expression experiments that screened for RNA export and interaction with the RRE. Binding of the Rev arginine rich motif to the RRE was reduced in the presence of wild-type PRMT6, whereas mutant PRMT6 did not exert this negative effect. In addition, diminished interactions between viral RNA and mutant Rev proteins were observed, due to the introduction of single arginine to lysine substitutions in the Rev arginine rich motif. More importantly, wild-type PRMT6, but not mutant methyltransferase, significantly decreased Rev-mediated viral RNA export from the nucleus to the cytoplasm in a dose-dependent manner. Conclusion These findings indicate that PRMT6 severely impairs the function of HIV-1 Rev.
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Yildirim AO, Bulau P, Zakrzewicz D, Kitowska KE, Weissmann N, Grimminger F, Morty RE, Eickelberg O. Increased Protein Arginine Methylation in Chronic Hypoxia. Am J Respir Cell Mol Biol 2006; 35:436-43. [PMID: 16690984 DOI: 10.1165/rcmb.2006-0097oc] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Asymmetric dimethylarginine (ADMA) is an endogenous inhibitor of nitric oxide synthesis. ADMA is generated by catabolism of proteins containing methylated arginine residues, and its levels are correlated with endothelial dysfunction in systemic cardiovascular diseases. Arginine methylation of cellular proteins is catalyzed by protein arginine methyltransferases (PRMT). The expression and localization of PRMT in the lung has not been addressed. Here, we sought to analyze the expression of PRMT isoforms in the lung and to determine whether PRMT expression is altered during exposure to chronic hypoxia (10% oxygen). Adult mice were exposed to hypoxia for up to 3 wk, and lung tissues were harvested and processed for RT-PCR, Western blotting, immunohistochemistry, and determination of tissue ADMA levels. All PRMT isoforms investigated were detected at the mRNA and protein level in mouse lung, and were localized primarily to the bronchial and alveolar epithelium. In lungs of mice subjected to chronic hypoxia, PRMT2 mRNA and protein levels were up-regulated, whereas the expression of all other PRMT isoforms remained unchanged. This was mainly due to increased expression of PRMT2 in alveolar type II cells, which did not express detectable levels of PRMT2 under normoxic conditions. Consistent with these observations, lung ADMA levels and ADMA/l-Arginine ratios were increased under hypoxic conditions. These results demonstrate that PRMTs are expressed and functional in the lung, and that hypoxia is a potent regulator of PRMT2 expression and lung ADMA concentrations. These data suggest that structural and functional changes caused by hypoxia may be linked to ADMA metabolism.
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Affiliation(s)
- Ali O Yildirim
- Department of Medicine II, University of Giessen Lung Center, Justus-Liebig University Giessen, Aulweg 123, Room 6-11, D-35392 Giessen, Germany
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Martens-Lobenhoffer J, Bode-Böger SM. Chromatographic-mass spectrometric methods for the quantification of L-arginine and its methylated metabolites in biological fluids. J Chromatogr B Analyt Technol Biomed Life Sci 2006; 851:30-41. [PMID: 16949893 DOI: 10.1016/j.jchromb.2006.07.038] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 07/17/2006] [Accepted: 07/20/2006] [Indexed: 01/22/2023]
Abstract
L-Arginine (Arg) and its methylated metabolites play a major role in the synthesis of the cell signaling molecule nitric oxide (NO). Arg serves as a substrate for the enzyme NO synthase (NOS), which produces NO, whereas monomethylarginine (L-NMMA) and asymmetric dimethylarginine (ADMA) act as competitive inhibitors of NOS. Symmetric dimethylarginine (SDMA) has virtually no inhibitory effect on NOS activity, but shares the pathway for cell entry and transport with Arg and ADMA. Accurate and reliable quantification of these substances in various biological fluids is essential for scientific research in this field. In this review, chromatographic-mass spectrometric methods for Arg and its methylated metabolites ADMA and SDMA are discussed. Mass spectrometric detection provides an intrinsic higher selectivity than detection by means of UV absorbance or fluorescence. Taking advantage of the high selectivity, approaches involving mass spectrometric detection require less laborious sample preparation and produce reliable results. A consensus emerges that the concentration values in plasma of young healthy volunteers are about 65 microM for Arg, 0.4 microM for ADMA and 0.5 microM for SDMA.
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Affiliation(s)
- Jens Martens-Lobenhoffer
- Institute of Clinical Pharmacology, University Hospital Magdeburg, Leipziger Strasse 44, 39120 Magdeburg, Germany.
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Bulau P, Zakrzewicz D, Kitowska K, Leiper J, Gunther A, Grimminger F, Eickelberg O. Analysis of methylarginine metabolism in the cardiovascular system identifies the lung as a major source of ADMA. Am J Physiol Lung Cell Mol Physiol 2006; 292:L18-24. [PMID: 16891395 DOI: 10.1152/ajplung.00076.2006] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Protein arginine methylation is catalyzed by a family of enzymes called protein arginine methyltransferases (PRMTs). Three forms of methylarginine have been identified in eukaryotes: monomethylarginine (l-NMMA), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA), all characterized by methylation of one or both guanidine nitrogen atoms of arginine. l-NMMA and ADMA, but not SDMA, are competitive inhibitors of all nitric oxide synthase isoforms. SDMA is eliminated almost entirely by renal excretion, whereas l-NMMA and ADMA are further metabolized by dimethylarginine dimethylaminohydrolase (DDAH). To explore the interplay between methylarginine synthesis and degradation in vivo, we determined PRMT expression and DDAH activity in mouse lung, heart, liver, and kidney homogenates. In addition, we employed HPLC-based quantification of protein-incorporated and free methylarginine, combined with immunoblotting for the assessment of tissue-specific patterns of arginine methylation. The salient findings of the present investigation can be summarized as follows: 1) pulmonary expression of type I PRMTs was correlated with enhanced protein arginine methylation; 2) pulmonary ADMA degradation was undertaken by DDAH1; 3) bronchoalveolar lavage fluid and serum exhibited almost identical ADMA/SDMA ratios, and 4) kidney and liver provide complementary routes for clearance and metabolic conversion of circulating ADMA. Together, these observations suggest that methylarginine metabolism by the pulmonary system significantly contributes to circulating ADMA and SDMA levels.
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Affiliation(s)
- Patrick Bulau
- Lung Center, University of Giessen School of Medicine, Aulweg 123, D-35329 Giessen, Germany.
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