1
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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024:1-49. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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2
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Muraoka T, Okumura M, Saio T. Enzymatic and synthetic regulation of polypeptide folding. Chem Sci 2024; 15:2282-2299. [PMID: 38362427 PMCID: PMC10866363 DOI: 10.1039/d3sc05781j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 01/04/2024] [Indexed: 02/17/2024] Open
Abstract
Proper folding is essential for the biological functions of all proteins. The folding process is intrinsically error-prone, and the misfolding of a polypeptide chain can cause the formation of toxic aggregates related to pathological outcomes such as neurodegenerative disease and diabetes. Chaperones and some enzymes are involved in the cellular proteostasis systems that assist polypeptide folding to diminish the risk of aggregation. Elucidating the molecular mechanisms of chaperones and related enzymes is important for understanding proteostasis systems and protein misfolding- and aggregation-related pathophysiology. Furthermore, mechanistic studies of chaperones and related enzymes provide important clues to designing chemical mimics, or chemical chaperones, that are potentially useful for recovering proteostasis activities as therapeutic approaches for treating and preventing protein misfolding-related diseases. In this Perspective, we provide a comprehensive overview of the latest understanding of the folding-promotion mechanisms by chaperones and oxidoreductases and recent progress in the development of chemical mimics that possess activities comparable to enzymes, followed by a discussion of future directions.
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Affiliation(s)
- Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology Koganei Tokyo 184-8588 Japan
- Kanagawa Institute of Industrial Science and Technology (KISTEC) Kanagawa 243-0435 Japan
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University Sendai Miyagi 980-8578 Japan
| | - Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University Tokushima 770-8503 Japan
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3
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Deng Z, Richardson DR. The Myc Family and the Metastasis Suppressor NDRG1: Targeting Key Molecular Interactions with Innovative Therapeutics. Pharmacol Rev 2023; 75:1007-1035. [PMID: 37280098 DOI: 10.1124/pharmrev.122.000795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/07/2023] [Accepted: 05/01/2023] [Indexed: 06/08/2023] Open
Abstract
Cancer is a leading cause of death worldwide, resulting in ∼10 million deaths in 2020. Major oncogenic effectors are the Myc proto-oncogene family, which consists of three members including c-Myc, N-Myc, and L-Myc. As a pertinent example of the role of the Myc family in tumorigenesis, amplification of MYCN in childhood neuroblastoma strongly correlates with poor patient prognosis. Complexes between Myc oncoproteins and their partners such as hypoxia-inducible factor-1α and Myc-associated protein X (MAX) result in proliferation arrest and pro-proliferative effects, respectively. Interactions with other proteins are also important for N-Myc activity. For instance, the enhancer of zest homolog 2 (EZH2) binds directly to N-Myc to stabilize it by acting as a competitor against the ubiquitin ligase, SCFFBXW7, which prevents proteasomal degradation. Heat shock protein 90 may also be involved in N-Myc stabilization since it binds to EZH2 and prevents its degradation. N-Myc downstream-regulated gene 1 (NDRG1) is downregulated by N-Myc and participates in the regulation of cellular proliferation via associating with other proteins, such as glycogen synthase kinase-3β and low-density lipoprotein receptor-related protein 6. These molecular interactions provide a better understanding of the biologic roles of N-Myc and NDRG1, which can be potentially used as therapeutic targets. In addition to directly targeting these proteins, disrupting their key interactions may also be a promising strategy for anti-cancer drug development. This review examines the interactions between the Myc proteins and other molecules, with a special focus on the relationship between N-Myc and NDRG1 and possible therapeutic interventions. SIGNIFICANCE STATEMENT: Neuroblastoma is one of the most common childhood solid tumors, with a dismal five-year survival rate. This problem makes it imperative to discover new and more effective therapeutics. The molecular interactions between major oncogenic drivers of the Myc family and other key proteins; for example, the metastasis suppressor, NDRG1, may potentially be used as targets for anti-neuroblastoma drug development. In addition to directly targeting these proteins, disrupting their key molecular interactions may also be promising for drug discovery.
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Affiliation(s)
- Zhao Deng
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia (Z.D., D.R.R.), and Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan (D.R.R.)
| | - Des R Richardson
- Centre for Cancer Cell Biology and Drug Discovery, Griffith Institute for Drug Discovery, Griffith University, Nathan, Australia (Z.D., D.R.R.), and Department of Pathology and Biological Responses, Nagoya University Graduate School of Medicine, Nagoya, Japan (D.R.R.)
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4
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Zhou Y, Sharma S, Sun X, Guan X, Hou Y, Yang Z, Shi H, Zou MH, Song P, Zhou J, Wang S, Hu Z, Li C. SMYD2 regulates vascular smooth muscle cell phenotypic switching and intimal hyperplasia via interaction with myocardin. Cell Mol Life Sci 2023; 80:264. [PMID: 37615725 PMCID: PMC11071988 DOI: 10.1007/s00018-023-04883-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/14/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023]
Abstract
The SET and MYND domain-containing protein 2 (SMYD2) is a histone lysine methyltransferase that has been reported to regulate carcinogenesis and inflammation. However, its role in vascular smooth muscle cell (VSMC) homeostasis and vascular diseases has not been determined. Here, we investigated the role of SMYD2 in VSMC phenotypic modulation and vascular intimal hyperplasia and elucidated the underlying mechanism. We observed that SMYD2 expression was downregulated in injured carotid arteries in mice and phenotypically modulated VSMCs in vitro. Using an SMC-specific SMYD2 knockout mouse model, we found that SMYD2 ablation in VSMCs exacerbated neointima formation after vascular injury in vivo. Conversely, SMYD2 overexpression inhibited VSMC proliferation and migration in vitro and attenuated arterial narrowing in injured vessels in mice. SMYD2 downregulation promoted VSMC phenotypic switching accompanied with enhanced proliferation and migration. Mechanistically, genome-wide transcriptome analysis and loss/gain-of-function studies revealed that SMYD2 up-regulated VSMC contractile gene expression and suppressed VSMC proliferation and migration, in part, by promoting expression and transactivation of the master transcription cofactor myocardin. In addition, myocardin directly interacted with SMYD2, thereby facilitating SMYD2 recruitment to the CArG regions of SMC contractile gene promoters and leading to an open chromatin status around SMC contractile gene promoters via SMYD2-mediated H3K4 methylation. Hence, we conclude that SMYD2 is a novel regulator of VSMC contractile phenotype and intimal hyperplasia via a myocardin-dependent epigenetic regulatory mechanism.
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Affiliation(s)
- Yu Zhou
- Center for Molecular and Translational Medicine, Institute for Biomedical Sciences, Georgia State University, 157 Decatur St SE, Atlanta, GA, 30303, USA.
- Division of Vascular Surgery, National-Local Joint Engineering Laboratory of Vascular Disease Treatment, Engineering and Technology Center for Diagnosis and Treatment of Vascular Diseases, Guangdong Engineering Laboratory of Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, No 58, Zhongshan 2nd Street, Yuexiu District, Guangzhou, 510080, Guangdong, China.
| | - Shaligram Sharma
- Center for Molecular and Translational Medicine, Institute for Biomedical Sciences, Georgia State University, 157 Decatur St SE, Atlanta, GA, 30303, USA
| | - Xiaonan Sun
- Center for Molecular and Translational Medicine, Institute for Biomedical Sciences, Georgia State University, 157 Decatur St SE, Atlanta, GA, 30303, USA
| | - Xiaoqing Guan
- Center for Molecular and Translational Medicine, Institute for Biomedical Sciences, Georgia State University, 157 Decatur St SE, Atlanta, GA, 30303, USA
| | - Yuning Hou
- Center for Molecular and Translational Medicine, Institute for Biomedical Sciences, Georgia State University, 157 Decatur St SE, Atlanta, GA, 30303, USA
- Cancer Animal Models Shared Resource, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Zhe Yang
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Hang Shi
- Department of Biology, Center for Obesity Reversal, Georgia State University, Atlanta, GA, USA
| | - Ming-Hui Zou
- Center for Molecular and Translational Medicine, Institute for Biomedical Sciences, Georgia State University, 157 Decatur St SE, Atlanta, GA, 30303, USA
| | - Ping Song
- Center for Molecular and Translational Medicine, Institute for Biomedical Sciences, Georgia State University, 157 Decatur St SE, Atlanta, GA, 30303, USA
| | - Jiliang Zhou
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Shenming Wang
- Division of Vascular Surgery, National-Local Joint Engineering Laboratory of Vascular Disease Treatment, Engineering and Technology Center for Diagnosis and Treatment of Vascular Diseases, Guangdong Engineering Laboratory of Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, No 58, Zhongshan 2nd Street, Yuexiu District, Guangzhou, 510080, Guangdong, China
| | - Zuojun Hu
- Division of Vascular Surgery, National-Local Joint Engineering Laboratory of Vascular Disease Treatment, Engineering and Technology Center for Diagnosis and Treatment of Vascular Diseases, Guangdong Engineering Laboratory of Diagnosis and Treatment of Vascular Disease, The First Affiliated Hospital, Sun Yat-Sen University, No 58, Zhongshan 2nd Street, Yuexiu District, Guangzhou, 510080, Guangdong, China.
| | - Chunying Li
- Center for Molecular and Translational Medicine, Institute for Biomedical Sciences, Georgia State University, 157 Decatur St SE, Atlanta, GA, 30303, USA.
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Okada S, Matsumoto Y, Takahashi R, Arai K, Kanemura S, Okumura M, Muraoka T. Semi-enzymatic acceleration of oxidative protein folding by N-methylated heteroaromatic thiols. Chem Sci 2023; 14:7630-7636. [PMID: 37476727 PMCID: PMC10355094 DOI: 10.1039/d3sc01540h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/06/2023] [Indexed: 07/22/2023] Open
Abstract
We report the first example of a synthetic thiol-based compound that promotes oxidative protein folding upon 1-equivalent loading to the disulfide bonds in the client protein to afford the native form in over 70% yield. N-Methylation is a central post-translational processing of proteins in vivo for regulating functions including chaperone activities. Despite the universally observed biochemical reactions in nature, N-methylation has hardly been utilized in the design, functionalization, and switching of synthetic bioregulatory agents, particularly folding promotors. As a biomimetic approach, we developed pyridinylmethanethiols to investigate the effects of N-methylation on the promotion of oxidative protein folding. For a comprehensive study on the geometrical effects, constitutional isomers of pyridinylmethanethiols with ortho-, meta-, and para-substitutions have been synthesized. Among the constitutional isomers, para-substituted pyridinylmethanethiol showed the fastest disulfide-bond formation of the client proteins to afford the native forms most efficiently. N-Methylation drastically increased the acidity and enhanced the oxidizability of the thiol groups in the pyridinylmethanethiols to enhance the folding promotion efficiencies. Among the isomers, para-substituted N-methylated pyridinylmethanethiol accelerated the oxidative protein folding reactions with the highest efficiency, allowing for protein folding promotion by 1-equivalent loading as a semi-enzymatic activity. This study will offer a novel bioinspired molecular design of synthetic biofunctional agents that are semi-enzymatically effective for the promotion of oxidative protein folding including biopharmaceuticals such as insulin in vitro by minimum loading.
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Affiliation(s)
- Shunsuke Okada
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Yosuke Matsumoto
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
| | - Rikana Takahashi
- Department of Chemistry, School of Science, Tokai University Kitakaname Hiratsuka-shi Kanagawa 259-1292 Japan
| | - Kenta Arai
- Department of Chemistry, School of Science, Tokai University Kitakaname Hiratsuka-shi Kanagawa 259-1292 Japan
- Institute of Advanced Biosciences, Tokai University Kitakaname Hiratsuka-shi Kanagawa 259-1292 Japan
| | - Shingo Kanemura
- School of Science, Kwansei Gakuin University 1 Gakuen Uegahara Sanda Hyogo 669-1330 Japan
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University 6-3 Aramaki-Aza-Aoba, Aoba-ku Sendai 980-8578 Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology 2-24-16 Naka-cho Koganei Tokyo 184-8588 Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology 3-8-1 Harumi-cho Fuchu Tokyo 183-8538 Japan
- Kanagawa Institute of Industrial Science and Technology 3-2-1 Sakato, Takatsu-ku Kawasaki Kanagawa 213-0012 Japan
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6
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Zhu L, Brown MA, Sims RJ, Tiwari GR, Nie H, Mayfield RD, Tucker HO. Lysine Methyltransferase SMYD1 Regulates Myogenesis via skNAC Methylation. Cells 2023; 12:1695. [PMID: 37443729 PMCID: PMC10340688 DOI: 10.3390/cells12131695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
The SMYD family is a unique class of lysine methyltransferases (KMTases) whose catalytic SET domain is split by a MYND domain. Among these, Smyd1 was identified as a heart- and skeletal muscle-specific KMTase and is essential for cardiogenesis and skeletal muscle development. SMYD1 has been characterized as a histone methyltransferase (HMTase). Here we demonstrated that SMYD1 methylates is the Skeletal muscle-specific splice variant of the Nascent polypeptide-Associated Complex (skNAC) transcription factor. SMYD1-mediated methylation of skNAC targets K1975 within the carboxy-terminus region of skNAC. Catalysis requires physical interaction of SMYD1 and skNAC via the conserved MYND domain of SMYD1 and the PXLXP motif of skNAC. Our data indicated that skNAC methylation is required for the direct transcriptional activation of myoglobin (Mb), a heart- and skeletal muscle-specific hemoprotein that facilitates oxygen transport. Our study revealed that the skNAC, as a methylation target of SMYD1, illuminates the molecular mechanism by which SMYD1 cooperates with skNAC to regulate transcriptional activation of genes crucial for muscle functions and implicates the MYND domain of the SMYD-family KMTases as an adaptor to target substrates for methylation.
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Affiliation(s)
- Li Zhu
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA
- Department of Pathology, Lokey Stem Cell Research Building, 1291 Welch Rd Rm. G2035, Stanford, CA 94305, USA
| | - Mark A Brown
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA
- Department of Clinical Sciences and Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert J Sims
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA
- Flare Therapeutics, Cambridge, MA 02142, USA
| | - Gayatri R Tiwari
- Center for Biomedical Research Services, Department of Neuroscience, The University of Texas at Austin, 2500 Speedway A4800, Austin, TX 78712, USA
| | - Hui Nie
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA
- Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - R Dayne Mayfield
- Center for Biomedical Research Services, Department of Neuroscience, The University of Texas at Austin, 2500 Speedway A4800, Austin, TX 78712, USA
| | - Haley O Tucker
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA
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Boehm D, Lam V, Schnolzer M, Ott M. The lysine methyltransferase SMYD5 amplifies HIV-1 transcription and is post-transcriptionally upregulated by Tat and USP11. Cell Rep 2023; 42:112234. [PMID: 36897778 PMCID: PMC10124996 DOI: 10.1016/j.celrep.2023.112234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/22/2022] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
A successful HIV-1 cure strategy may require enhancing HIV-1 latency to silence HIV-1 transcription. Modulators of gene expression show promise as latency-promoting agents in vitro and in vivo. Here, we identify Su(var)3-9, enhancer-of-zeste, and trithorax (SET) and myeloid, Nervy, and DEAF-1 (MYND) domain-containing protein 5 (SMYD5) as a host factor required for HIV-1 transcription. SMYD5 is expressed in CD4+ T cells and activates the HIV-1 promoter with or without the viral Tat protein, while knockdown of SMYD5 decreases HIV-1 transcription in cell lines and primary T cells. SMYD5 associates in vivo with the HIV-1 promoter and binds the HIV trans-activation response (TAR) element RNA and Tat. Tat is methylated by SMYD5 in vitro, and in cells expressing Tat, SMYD5 protein levels are increased. The latter requires expression of the Tat cofactor and ubiquitin-specific peptidase 11 (USP11). We propose that SMYD5 is a host activator of HIV-1 transcription stabilized by Tat and USP11 and, together with USP11, a possible target for latency-promoting therapy.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Victor Lam
- Tetrad Graduate Program, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martina Schnolzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Melanie Ott
- Gladstone Institute of Virology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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8
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Padilla A, Manganaro JF, Huesgen L, Roess DA, Brown MA, Crans DC. Targeting Epigenetic Changes Mediated by Members of the SMYD Family of Lysine Methyltransferases. Molecules 2023; 28:molecules28042000. [PMID: 36838987 PMCID: PMC9967872 DOI: 10.3390/molecules28042000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
A comprehensive understanding of the mechanisms involved in epigenetic changes in gene expression is essential to the clinical management of diseases linked to the SMYD family of lysine methyltransferases. The five known SMYD enzymes catalyze the transfer of donor methyl groups from S-adenosylmethionine (SAM) to specific lysines on histones and non-histone substrates. SMYDs family members have distinct tissue distributions and tissue-specific functions, including regulation of development, cell differentiation, and embryogenesis. Diseases associated with SMYDs include the repressed transcription of SMYD1 genes needed for the formation of ion channels in the heart leading to heart failure, SMYD2 overexpression in esophageal squamous cell carcinoma (ESCC) or p53-related cancers, and poor prognosis associated with SMYD3 overexpression in more than 14 types of cancer including breast cancer, colon cancer, prostate cancer, lung cancer, and pancreatic cancer. Given the importance of epigenetics in various pathologies, the development of epigenetic inhibitors has attracted considerable attention from the pharmaceutical industry. The pharmacologic development of the inhibitors involves the identification of molecules regulating both functional SMYD SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) and MYND (Myeloid-Nervy-DEAF1) domains, a process facilitated by available X-ray structures for SMYD1, SMYD2, and SMYD3. Important leads for potential pharmaceutical agents have been reported for SMYD2 and SMYD3 enzymes, and six epigenetic inhibitors have been developed for drugs used to treat myelodysplastic syndrome (Vidaza, Dacogen), cutaneous T-cell lymphoma (Zoinza, Isrodax), and peripheral T-cell lymphoma (Beleodag, Epidaza). The recently demonstrated reversal of SMYD histone methylation suggests that reversing the epigenetic effects of SMYDs in cancerous tissues may be a desirable target for pharmacological development.
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Affiliation(s)
- Alyssa Padilla
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - John F. Manganaro
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
| | - Lydia Huesgen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - Deborah A. Roess
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - Mark A. Brown
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523-1678, USA
- Graduate Degree Program in Ecology, Department of Ethnic Studies, Global Health and Health Disparities, Colorado School of Public Health, Colorado State University, Fort Collins, CO 80523-1612, USA
- Correspondence: (M.A.B.); (D.C.C.)
| | - Debbie C. Crans
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA
- Correspondence: (M.A.B.); (D.C.C.)
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9
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Mao F, Shi YG. Targeting the LSD1/KDM1 Family of Lysine Demethylases in Cancer and Other Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:15-49. [PMID: 37751134 DOI: 10.1007/978-3-031-38176-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) was the first histone demethylase discovered and the founding member of the flavin-dependent lysine demethylase family (KDM1). The human KDM1 family includes KDM1A and KDM1B, which primarily catalyze demethylation of histone H3K4me1/2. The KDM1 family is involved in epigenetic gene regulation and plays important roles in various biological and disease pathogenesis processes, including cell differentiation, embryonic development, hormone signaling, and carcinogenesis. Malfunction of many epigenetic regulators results in complex human diseases, including cancers. Regulators such as KDM1 have become potential therapeutic targets because of the reversibility of epigenetic control of genome function. Indeed, several classes of KDM1-selective small molecule inhibitors have been developed, some of which are currently in clinical trials to treat various cancers. In this chapter, we review the discovery, biochemical, and molecular mechanisms, atomic structure, genetics, biology, and pathology of the KDM1 family of lysine demethylases. Focusing on cancer, we also provide a comprehensive summary of recently developed KDM1 inhibitors and related preclinical and clinical studies to provide a better understanding of the mechanisms of action and applications of these KDM1-specific inhibitors in therapeutic treatment.
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Affiliation(s)
- Fei Mao
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yujiang Geno Shi
- Longevity and Aging Institute (LAI), IBS and Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, P.R. China.
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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10
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Backe SJ, Woodford MR, Ahanin E, Sager RA, Bourboulia D, Mollapour M. Impact of Co-chaperones and Posttranslational Modifications Toward Hsp90 Drug Sensitivity. Subcell Biochem 2023; 101:319-350. [PMID: 36520312 PMCID: PMC10077965 DOI: 10.1007/978-3-031-14740-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Posttranslational modifications (PTMs) regulate myriad cellular processes by modulating protein function and protein-protein interaction. Heat shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone whose activity is responsible for the stabilization and maturation of more than 300 client proteins. Hsp90 is a substrate for numerous PTMs, which have diverse effects on Hsp90 function. Interestingly, many Hsp90 clients are enzymes that catalyze PTM, demonstrating one of the several modes of regulation of Hsp90 activity. Approximately 25 co-chaperone regulatory proteins of Hsp90 impact structural rearrangements, ATP hydrolysis, and client interaction, representing a second layer of influence on Hsp90 activity. A growing body of literature has also established that PTM of these co-chaperones fine-tune their activity toward Hsp90; however, many of the identified PTMs remain uncharacterized. Given the critical role of Hsp90 in supporting signaling in cancer, clinical evaluation of Hsp90 inhibitors is an area of great interest. Interestingly, differential PTM and co-chaperone interaction have been shown to impact Hsp90 binding to its inhibitors. Therefore, understanding these layers of Hsp90 regulation will provide a more complete understanding of the chaperone code, facilitating the development of new biomarkers and combination therapies.
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Affiliation(s)
- Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Elham Ahanin
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, USA. .,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA. .,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, USA.
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11
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Zheng Q, Zhang W, Rao GW. Protein Lysine Methyltransferase SMYD2: A Promising Small Molecule Target for Cancer Therapy. J Med Chem 2022; 65:10119-10132. [PMID: 35914250 DOI: 10.1021/acs.jmedchem.2c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In epigenetic research, the abnormality of protein methylation modification is closely related to the occurrence and development of tumors, which stimulates the interest of researchers in protein methyltransferase research and the efforts to develop corresponding specific small molecule inhibitors. Currently, the protein lysine methyltransferase SMYD2 has been identified as a promising new small molecule target for cancer therapy. But its biological functions have not been fully studied and relatively few inhibitors have been reported, thus this field needs to be further explored. This perspective provides a comprehensive and systematic review of the available resources in this field, including its research status, biological structure, related substrates and methylation mechanisms, and research status of inhibitors. In addition, this perspective elaborates in detail the current challenges in this field, our insights into what needs to be done next, rational drug design of novel SMYD2 inhibitors, and foreseeable development directions in the future.
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Affiliation(s)
- Quan Zheng
- College of Pharmaceutical Science, Zhejiang University of Technology, and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Wen Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Guo-Wu Rao
- College of Pharmaceutical Science, Zhejiang University of Technology, and Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou 310014, China
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12
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SMYD5 acts as a potential biomarker for hepatocellular carcinoma. Exp Cell Res 2022; 414:113076. [PMID: 35218722 DOI: 10.1016/j.yexcr.2022.113076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/24/2022]
Abstract
Determining the prognosis of patients remains a challenge due to the phenotypic and molecular diversities of hepatocellular carcinomas (HCC). We aimed to evaluate the role of SMYD5 in HCC. Wilcoxon signed-rank test and logistic regression analyzed the relationship between clinical pathologic features and SMYD5. We found that increased expression of SMYD5 in HCC was closely associated with high histologic grade, stage, T stage and nodal stage. Kaplan-Meier method, Cox regression, univariate analysis and multivariate analysis detected overall survival of TCGA-HCC patients. It turned out that high expression of SMYD5 predicted a worse prognosis in HCC. Gene Set Enrichment Analysis (GSEA) was applied via TCGA data set, which indicated that complement and coagulation cascades, fatty acid metabolism, primary bile acid biosynthesis, drug metabolism cytochrome P450, PPAR signaling pathway and retinol metabolism were differentially enriched in SMYD5 high expression phenotype. Interestingly, we proved that SMYD5 upregulation in HCC cells was induced by promoter hypo-methylation. Moreover, functional experiments demonstrated that SMYD5 silencing abrogated cell proliferation, migration and invasion and enhanced paclitaxel sensitivity in HCC. All findings implied that SMYD5 might be an underlying biomarker for prognosis and treatment of HCC.
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13
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Malbeteau L, Pham HT, Eve L, Stallcup MR, Poulard C, Le Romancer M. How Protein Methylation Regulates Steroid Receptor Function. Endocr Rev 2022; 43:160-197. [PMID: 33955470 PMCID: PMC8755998 DOI: 10.1210/endrev/bnab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Indexed: 02/06/2023]
Abstract
Steroid receptors (SRs) are members of the nuclear hormonal receptor family, many of which are transcription factors regulated by ligand binding. SRs regulate various human physiological functions essential for maintenance of vital biological pathways, including development, reproduction, and metabolic homeostasis. In addition, aberrant expression of SRs or dysregulation of their signaling has been observed in a wide variety of pathologies. SR activity is tightly and finely controlled by post-translational modifications (PTMs) targeting the receptors and/or their coregulators. Whereas major attention has been focused on phosphorylation, growing evidence shows that methylation is also an important regulator of SRs. Interestingly, the protein methyltransferases depositing methyl marks are involved in many functions, from development to adult life. They have also been associated with pathologies such as inflammation, as well as cardiovascular and neuronal disorders, and cancer. This article provides an overview of SR methylation/demethylation events, along with their functional effects and biological consequences. An in-depth understanding of the landscape of these methylation events could provide new information on SR regulation in physiology, as well as promising perspectives for the development of new therapeutic strategies, illustrated by the specific inhibitors of protein methyltransferases that are currently available.
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Affiliation(s)
- Lucie Malbeteau
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Ha Thuy Pham
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Louisane Eve
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Michael R Stallcup
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Coralie Poulard
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
| | - Muriel Le Romancer
- Université de Lyon, F-69000 Lyon, France.,Inserm U1052, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, F-69000 Lyon, France
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14
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LSD1: Expanding Functions in Stem Cells and Differentiation. Cells 2021; 10:cells10113252. [PMID: 34831474 PMCID: PMC8624367 DOI: 10.3390/cells10113252] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 12/23/2022] Open
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSC) provide a powerful model system to uncover fundamental mechanisms that control cellular identity during mammalian development. Histone methylation governs gene expression programs that play a key role in the regulation of the balance between self-renewal and differentiation of ESCs. Lysine-specific demethylase 1 (LSD1, also known as KDM1A), the first identified histone lysine demethylase, demethylates H3K4me1/2 and H3K9me1/2 at target loci in a context-dependent manner. Moreover, it has also been shown to demethylate non-histone substrates playing a central role in the regulation of numerous cellular processes. In this review, we summarize current knowledge about LSD1 and the molecular mechanism by which LSD1 influences the stem cells state, including the regulatory circuitry underlying self-renewal and pluripotency.
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15
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Circular RNA Expression: Its Potential Regulation and Function in Abdominal Aortic Aneurysms. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:9934951. [PMID: 34306317 PMCID: PMC8263248 DOI: 10.1155/2021/9934951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/30/2021] [Indexed: 12/18/2022]
Abstract
Abdominal aortic aneurysms (AAAs) have posed a great threat to human life, and the necessity of its monitoring and treatment is decided by symptomatology and/or the aneurysm size. Accumulating evidence suggests that circular RNAs (circRNAs) contribute a part to the pathogenesis of AAAs. circRNAs are novel single-stranded RNAs with a closed loop structure and high stability, having become the candidate biomarkers for numerous kinds of human disorders. Besides, circRNAs act as molecular "sponge" in organisms, capable of regulating the transcription level. Here, we characterize that the molecular mechanisms underlying the role of circRNAs in AAA development were further elucidated. In the present work, studies on the biosynthesis, bibliometrics, and mechanisms of action of circRNAs were aims comprehensively reviewed, the role of circRNAs in the AAA pathogenic mechanism was illustrated, and their potential in diagnosing AAAs was examined. Moreover, the current evidence about the effects of circRNAs on AAA development through modulating endothelial cells (ECs), macrophages, and vascular smooth muscle cells (VSMCs) was summarized. Through thorough investigation, the molecular mechanisms underlying the role of circRNAs in AAA development were further elucidated. The results demonstrated that circRNAs had the application potential in the diagnosis and prevention of AAAs in clinical practice. The study of circRNA regulatory pathways would be of great assistance to the etiologic research of AAAs.
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16
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Khan MIK, Charles RCM, Ramachandran R, Gupta S, Govindaraju G, Mishra R, Rajavelu A, Coumar MS, Chavali S, Dhayalan A. The ribosomal protein eL21 interacts with the protein lysine methyltransferase SMYD2 and regulates its steady state levels. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119079. [PMID: 34147559 DOI: 10.1016/j.bbamcr.2021.119079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/24/2021] [Accepted: 06/13/2021] [Indexed: 01/23/2023]
Abstract
The protein lysine methyltransferase, SMYD2 is involved in diverse cellular events by regulating protein functions through lysine methylation. Though several substrate proteins of SMYD2 are well-studied, only a limited number of its interaction partners have been identified and characterized. Here, we performed a yeast two-hybrid screening of SMYD2 and found that the ribosomal protein, eL21 could interact with SMYD2. SMYD2-eL21 interaction in the human cells was confirmed by immunoprecipitation methods. In vitro pull-down assays revealed that SMYD2 interacts with eL21 directly through its SET and MYND domain. Computational mapping, followed by experimental studies identified that Lys81 and Lys83 residues of eL21 are important for the SMYD2-eL21 interaction. Evolutionary analysis showed that these residues might have co-evolved with the emergence of SMYD2. We found that eL21 regulates the steady state levels of SMYD2 by promoting its transcription and inhibiting its proteasomal degradation. Importantly, SMYD2-eL21 interaction plays an important role in regulating cell proliferation and its dysregulation might lead to tumorigenesis. Our findings highlight a novel extra-ribosomal function of eL21 on regulating SMYD2 levels and imply that ribosomal proteins might regulate wide range of cellular functions through protein-protein interactions in addition to their core function in translation.
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Affiliation(s)
- Mohd Imran K Khan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | | | - Reshma Ramachandran
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517 507, India
| | - Somlee Gupta
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Gayathri Govindaraju
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | - Rashmi Mishra
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India
| | - Arumugam Rajavelu
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | | | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517 507, India.
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry 605 014, India.
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17
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Wang Y, Li S, Rentfrow G, Chen J, Zhu H, Suman SP. Myoglobin Post-Translational Modifications Influence Color Stability of Beef Longissimus Lumborum. MEAT AND MUSCLE BIOLOGY 2021. [DOI: 10.22175/mmb.11689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Post-translational modifications (PTM) of proteins play critical roles in biological processes. PTM of muscle proteins influence meat quality. Nonetheless, myoglobin (Mb) PTM and their impact on fresh beef color stability have not been characterized yet. Therefore, our objectives were to identify Mb PTM in beef longissimus lumborum muscle during postmortem aging and to characterize their influence on color stability. The longissimus lumborum muscles from 9 (n = 9) beef carcasses (24 h postmortem) were subjected to wet aging for 0, 7, 14, and 21 d. At the end of each wet-aging period, steaks were fabricated. One steak for analyses of PTM was immediately frozen at −80°C, whereas other steaks were assigned to refrigerated storage in the darkness under aerobic packaging. Instrumental color and biochemical attributes were evaluated on day 0, 3, or 6 of storage. Mb PTM were analyzed using two-dimensional electrophoresis and tandem mass spectrometry. Surface redness (a* value), color stability, and Mb concentration decreased (P < 0.05) upon aging. Gel image analyses identified 6 Mb spots with similar molecular weight (17 kDa) but different isoelectric pH. Tandem mass spectrometry identified multiple PTM (phosphorylation, methylation, carboxymethylation, acetylation, and 4-hydroxynonenal alkylation) in these 6 isoforms. The amino acids susceptible to phosphorylation were serine (S), threonine (T), and tyrosine, whereas other PTM were detected in lysine (K), arginine (R), and histidine residues. Additionally, distal histidine (position 64), critical to heme stability, was found to be alkylated. Overall, Mb PTM increased with aging. The aging-induced PTM, especially those occurring close to hydrophobic heme pocket, could disrupt Mb tertiary structure, influence heme affinity, and compromise oxygen binding capacity, leading to decreased color stability of fresh beef. Furthermore, PTM at K45, K47, and K87 were unique to Mb from non-aged beef, whereas PTM at R31, T51, K96, K98, S121, R139, and K147 were unique to Mb from aged counterparts, indicating that these Mb PTM could be used as novel biomarkers for fresh beef color stability.
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Affiliation(s)
- Yifei Wang
- University of Kentucky Department of Animal and Food Sciences
| | - Shuting Li
- University of Kentucky Department of Animal and Food Sciences
| | - Gregg Rentfrow
- University of Kentucky Department of Animal and Food Sciences
| | - Jing Chen
- University of Kentucky Proteomics Core Facility
| | - Haining Zhu
- University of Kentucky Proteomics Core Facility
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18
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Arifuzzaman S, Khatun MR, Khatun R. Emerging of lysine demethylases (KDMs): From pathophysiological insights to novel therapeutic opportunities. Biomed Pharmacother 2020; 129:110392. [PMID: 32574968 DOI: 10.1016/j.biopha.2020.110392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, there have been remarkable scientific advancements in the understanding of lysine demethylases (KDMs) because of their demethylation of diverse substrates, including nucleic acids and proteins. Novel structural architectures, physiological roles in the gene expression regulation, and ability to modify protein functions made KDMs the topic of interest in biomedical research. These structural diversities allow them to exert their function either alone or in complex with numerous other bio-macromolecules. Impressive number of studies have demonstrated that KDMs are localized dynamically across the cellular and tissue microenvironment. Their dysregulation is often associated with human diseases, such as cancer, immune disorders, neurological disorders, and developmental abnormalities. Advancements in the knowledge of the underlying biochemistry and disease associations have led to the development of a series of modulators and technical compounds. Given the distinct biophysical and biochemical properties of KDMs, in this review we have focused on advances related to the structure, function, disease association, and therapeutic targeting of KDMs highlighting improvements in both the specificity and efficacy of KDM modulation.
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Affiliation(s)
- Sarder Arifuzzaman
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh; Everest Pharmaceuticals Ltd., Dhaka-1208, Bangladesh.
| | - Mst Reshma Khatun
- Department of Pharmacy, Jahangirnagar University, Dhaka-1342, Bangladesh
| | - Rabeya Khatun
- Department of Pediatrics, TMSS Medical College and Rafatullah Community Hospital, Gokul, Bogura, 5800, Bangladesh
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19
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Backe SJ, Sager RA, Woodford MR, Makedon AM, Mollapour M. Post-translational modifications of Hsp90 and translating the chaperone code. J Biol Chem 2020; 295:11099-11117. [PMID: 32527727 DOI: 10.1074/jbc.rev120.011833] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Cells have a remarkable ability to synthesize large amounts of protein in a very short period of time. Under these conditions, many hydrophobic surfaces on proteins may be transiently exposed, and the likelihood of deleterious interactions is quite high. To counter this threat to cell viability, molecular chaperones have evolved to help nascent polypeptides fold correctly and multimeric protein complexes assemble productively, while minimizing the danger of protein aggregation. Heat shock protein 90 (Hsp90) is an evolutionarily conserved molecular chaperone that is involved in the stability and activation of at least 300 proteins, also known as clients, under normal cellular conditions. The Hsp90 clients participate in the full breadth of cellular processes, including cell growth and cell cycle control, signal transduction, DNA repair, transcription, and many others. Hsp90 chaperone function is coupled to its ability to bind and hydrolyze ATP, which is tightly regulated both by co-chaperone proteins and post-translational modifications (PTMs). Many reported PTMs of Hsp90 alter chaperone function and consequently affect myriad cellular processes. Here, we review the contributions of PTMs, such as phosphorylation, acetylation, SUMOylation, methylation, O-GlcNAcylation, ubiquitination, and others, toward regulation of Hsp90 function. We also discuss how the Hsp90 modification state affects cellular sensitivity to Hsp90-targeted therapeutics that specifically bind and inhibit its chaperone activity. The ultimate challenge is to decipher the comprehensive and combinatorial array of PTMs that modulate Hsp90 chaperone function, a phenomenon termed the "chaperone code."
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Affiliation(s)
- Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, USA.,College of Medicine, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, USA.,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Alan M Makedon
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, New York, USA .,Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA.,Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, New York, USA
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20
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A methylated lysine is a switch point for conformational communication in the chaperone Hsp90. Nat Commun 2020; 11:1219. [PMID: 32139682 PMCID: PMC7057950 DOI: 10.1038/s41467-020-15048-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 02/15/2020] [Indexed: 02/06/2023] Open
Abstract
Methylation of a conserved lysine in C-terminal domain of the molecular chaperone Hsp90 was shown previously to affect its in vivo function. However, the underlying mechanism remained elusive. Through a combined experimental and computational approach, this study shows that this site is very sensitive to sidechain modifications and crucial for Hsp90 activity in vitro and in vivo. Our results demonstrate that this particular lysine serves as a switch point for the regulation of Hsp90 functions by influencing its conformational cycle, ATPase activity, co-chaperone regulation, and client activation of yeast and human Hsp90. Incorporation of the methylated lysine via genetic code expansion specifically shows that upon modification, the conformational cycle of Hsp90 is altered. Molecular dynamics simulations including the methylated lysine suggest specific conformational changes that are propagated through Hsp90. Thus, methylation of the C-terminal lysine allows a precise allosteric tuning of Hsp90 activity via long distances. Methylation of a lysine residue in Hsp90 is a recently discovered post-translational modification but the mechanistic effects of this modification have remained unknown so far. Here the authors combine biochemical and biophysical approaches, molecular dynamics (MD) simulations and functional experiments with yeast and show that this lysine is a switch point, which specifically modulates conserved Hsp90 functions including co-chaperone regulation and client activation.
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21
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Function of the MYND Domain and C-Terminal Region in Regulating the Subcellular Localization and Catalytic Activity of the SMYD Family Lysine Methyltransferase Set5. Mol Cell Biol 2020; 40:MCB.00341-19. [PMID: 31685550 DOI: 10.1128/mcb.00341-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/01/2019] [Indexed: 11/20/2022] Open
Abstract
SMYD lysine methyltransferases target histones and nonhistone proteins for methylation and are critical regulators of muscle development and implicated in neoplastic transformation. They are characterized by a split catalytic SET domain and an intervening MYND zinc finger domain, as well as an extended C-terminal domain. Saccharomyces cerevisiae contains two SMYD proteins, Set5 and Set6, which share structural elements with the mammalian SMYD enzymes. Set5 is a histone H4 lysine 5, 8, and 12 methyltransferase, implicated in the regulation of stress responses and genome stability. While the SMYD proteins have diverse roles in cells, there are many gaps in our understanding of how these enzymes are regulated. Here, we performed mutational analysis of Set5, combined with phosphoproteomics, to identify regulatory mechanisms for its enzymatic activity and subcellular localization. Our results indicate that the MYND domain promotes Set5 chromatin association in cells and is required for its role in repressing subtelomeric genes. Phosphoproteomics revealed extensive phosphorylation of Set5, and phosphomimetic mutations enhance Set5 catalytic activity but diminish its ability to interact with chromatin in cells. These studies uncover multiple regions within Set5 that regulate its localization and activity and highlight potential avenues for understanding mechanisms controlling the diverse roles of SMYD enzymes.
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22
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Li X. Epigenetics and cell cycle regulation in cystogenesis. Cell Signal 2019; 68:109509. [PMID: 31874209 DOI: 10.1016/j.cellsig.2019.109509] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022]
Abstract
The role of genetic mutations in the development of polycystic kidney disease (PKD), such as alterations in PKD1 and PKD2 genes in autosomal dominant PKD (ADPKD), is well understood. However, the significance of epigenetic mechanisms in the progression of PKD remains unclear and is increasingly being investigated. The term of epigenetics describes a range of mechanisms in genome function that do not solely result from the DNA sequence itself. Epigenetic information can be inherited during mammalian cell division to sustain phenotype specifically and physiologically responsive gene expression in the progeny cells. A multitude of functional studies of epigenetic modifiers and systematic genome-wide mapping of epigenetic marks reveal the importance of epigenomic mechanisms, including DNA methylation, histone/chromatin modifications and non-coding RNAs, in PKD pathologies. Deregulated proliferation is a characteristic feature of cystic renal epithelial cells. Moreover, defects in many of the molecules that regulate the cell cycle have been implicated in cyst formation and progression. Recent evidence suggests that alterations of DNA methylation and histone modifications on specific genes and the whole genome involved in cell cycle regulation and contribute to the pathogenesis of PKD. This review summarizes the recent advances of epigenetic mechanisms in PKD, which helps us to define the term of "PKD epigenetics" and group PKD epigenetic changes in three categories. In particularly, this review focuses on the interplay of epigenetic mechanisms with cell cycle regulation during normal cell cycle progression and cystic cell proliferation, and discusses the potential to detect and quantify DNA methylation from body fluids as diagnostic/prognostic biomarkers. Collectively, this review provides concepts and examples of epigenetics in cell cycle regulation to reveal a broad view of different aspects of epigenetics in biology and PKD, which may facilitate to identify possible novel therapeutic intervention points and to explore epigenetic biomarkers in PKD.
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Affiliation(s)
- Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States of America; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, United States of America.
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23
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Sun J, Shi F, Yang N. Exploration of the Substrate Preference of Lysine Methyltransferase SMYD3 by Molecular Dynamics Simulations. ACS OMEGA 2019; 4:19573-19581. [PMID: 31788587 PMCID: PMC6881823 DOI: 10.1021/acsomega.9b01842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
SMYD3, a SET and MYND domain containing lysine methyltransferase, catalyzes the transfer of the methyl group from a methyl donor onto the Nε group of a lysine residue in the substrate protein. Methylation of MAP3 kinase kinase (MAP3K2) by SMYD3 has been implicated in Ras-driven tumorigenesis. The crystal structure of SMYD3 in complex with MAP3K2 peptide reveals a shallow hydrophobic pocket (P-2), which accommodates the binding of a phenylalanine residue at the -2 position of the substrate (F258) is a crucial determinant of substrate specificity of SMYD3. To better understand the substrate preference of SMYD3 at the -2 position, molecular dynamics (MD) simulations and the MM/GBSA method were performed on the crystal structure of SMYD3-MAP3K2 complex (PDB: 5EX0) after substitution of F258 residue of MAP3K2 to each of the other 19 natural residues, respectively. Binding free energy calculations reveal that the P-2 pocket prefers an aromatic hydrophobic group and none of the substitutions behave better than the wild-type phenylalanine residue does. Furthermore, we investigated the structure-activity relationships (SAR) of a series of non-natural phenylalanine derivative substitutions at the -2 position and found that quite a few modifications on the sidechain of F258 residue could strengthen its binding to the P-2 pocket of SMYD3. These explorations provide insights into developing novel SMYD3 inhibitors with high potency and high selectivity against MAP3K2 and cancer.
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Affiliation(s)
| | | | - Na Yang
- E-mail: . Tel/Fax: + 8622 85358193
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24
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Meng X, Zhao Y, Liu J, Wang L, Dong Z, Zhang T, Gu X, Zheng Z. Comprehensive analysis of histone modification-associated genes on differential gene expression and prognosis in gastric cancer. Exp Ther Med 2019; 18:2219-2230. [PMID: 31452712 DOI: 10.3892/etm.2019.7808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/27/2019] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence suggests that the epigenetic alterations caused by histone modifications have important roles in the genesis of gastric cancer (GC), particularly the well-studied acetylation and methylation modifications. In the present study, a Bioinformatics analysis of the expression of histone modification-associated genes in GC and normal tissues was performed by using datasets from Oncomine, the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). The clinical data of GC patients were downloaded from TCGA to determine the association between histone modification-associated gene expression and clinicopathological parameters or survival of GC. Finally, lysine acetyltransferase 2A (KAT2A), nuclear receptor coactivator 1 (NCOA1), SMYD family member 5 (SMYD5), protein arginine methyltransferase 1 (PRMT1) and PRDF1-RIZ (PR)/Su(var)3-9, enhancer-of-zeste and trithorax (SET) domain 16 (PRDM16) were screened; KAT2A, SMYD5 and PRMT1 were upregulated, while PRDM16 expression was downregulated in GC. Analysis of the GEO and Oncomine datasets revealed that NCOA1 was upregulated, which was contrary to the result obtained with the TCGA stomach adenocarcinoma dataset. Aberrant expression of KAT2A, NCOA1, SMYD5 and PRMT1 was more obvious in gastric intestinal-type adenocarcinoma; low NCOA1 expression was associated with better overall survival of GC patients [hazard ratio (HR)=0.690, 95% CI=0.570-0.840, P<0.001] and was an independent predictor for patients diagnosed with GC (HR=0.639, 95% CI=0.437-0.933, P=0.020). Correlation analysis and protein-protein interaction network analysis indicated a close association between ATAD2 and estrogen receptor 1 (ESR1), PRMT1, NCOA1 and KAT2A. In conclusion, differential expression of KAT2A, NCOA1, SMYD5, PRMT1 and PRDM16 was identified in GC vs. normal tissues, low NCOA1 expression was associated with poor survival of GC and ATAD2 may interact with ESR1 to regulate NCOA1 and PRMT1 in GC.
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Affiliation(s)
- Xiangyu Meng
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Yan Zhao
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Jingwei Liu
- Department of Anorectal Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Lu Wang
- Department of Ultrasonography, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Zhe Dong
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Tao Zhang
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Xiaohu Gu
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
| | - Zhichao Zheng
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital and Institute, Shenyang, Liaoning 110042, P.R. China
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25
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Lee A, Borrello MT, Ganesan A. LSD
(Lysine‐Specific Demethylase): A Decade‐Long Trip from Discovery to Clinical Trials. ACTA ACUST UNITED AC 2019. [DOI: 10.1002/9783527809257.ch10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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26
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Heat-shock protein 90α is involved in maintaining the stability of VP16 and VP16-mediated transactivation of α genes from herpes simplex virus-1. Mol Med 2018; 24:65. [PMID: 30577726 PMCID: PMC6303900 DOI: 10.1186/s10020-018-0066-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/05/2018] [Indexed: 01/24/2023] Open
Abstract
Background Numerous host cellular factors are exploited by viruses to facilitate infection. Our previous studies and those of others have shown heat-shock protein 90 (Hsp90), a cellular molecular chaperone, is involved in herpes simplex virus (HSV)-1 infection. However, the function of the dominant Hsp90 isoform and the relationship between Hsp90 and HSV-1 α genes remain unclear. Methods and results Hsp90α knockdown or inhibition significantly inhibited the promoter activity of HSV-1 α genes and downregulated virion protein 16(VP16) expression from virus and plasmids. The Hsp90α knockdown-induced suppression of α genes promoter activity and downregulation of α genes was reversed by VP16 overexpression, indicating that Hsp90α is involved in VP16-mediated transcription of HSV-1 α genes. Co-immunoprecipitation experiments indicated that VP16 interacted with Hsp90α through the conserved core domain within VP16. Based on using autophagy inhibitors and the presence of Hsp90 inhibitors in ATG7−/− (autophagy-deficient) cells, Hsp90 inhibition-induced degradation of VP16 is dependent on macroautophagy-mediated degradation but not chaperone-mediated autophagy (CMA) pathway. In vivo studies demonstrated that treatment with gels containing Hsp90 inhibitor effectively reduced the level of VP16 and α genes, which may contribute to the amelioration of the skin lesions in an HSV-1 infection mediated zosteriform model. Conclusion Our study provides new insights into the mechanisms by which Hsp90α facilitates the transactivation of HSV-1 α genes and viral infection, and highlights the importance of developing selective inhibitors targeting the interaction between Hsp90α and VP16 to reduce toxicity, a major challenge in the clinical use of Hsp90 inhibitors. Electronic supplementary material The online version of this article (10.1186/s10020-018-0066-x) contains supplementary material, which is available to authorized users.
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27
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Obermann WMJ. A motif in HSP90 and P23 that links molecular chaperones to efficient estrogen receptor α methylation by the lysine methyltransferase SMYD2. J Biol Chem 2018; 293:16479-16487. [PMID: 30190324 DOI: 10.1074/jbc.ra118.003578] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/31/2018] [Indexed: 11/06/2022] Open
Abstract
Heat shock protein 90 (HSP90) is a molecular chaperone that supervises folding of cellular signaling proteins such as steroid receptors and many protein kinases. HSP90 relies on ATP hydrolysis for powering a conformational circuit that helps fold the client protein. To that end, HSP90 binds to co-chaperone proteins that regulate ATP hydrolysis rate or interaction with client proteins. Co-chaperones such as P23, cell division cycle 37 (CDC37), or activator of HSP90 ATPase activity 1 (AHA1) interact with the N-terminal or middle domain of HSP90, whereas others, such as HSP70/HSP90-organizing protein (HOP), use tetratricopeptide repeat (TPR) domains to bind the EEVD motif at the very C-terminal end of HSP90. Recently, the lysine methyltransferase SET and MYND domain-containing 2 (SMYD2) has been proposed as an HSP90-binding partner, and interaction analyses indicate that SMYD2 binding to HSP90 is independent of the EEVD motif. Using the amplified luminescence proximity homogeneous assay (Alpha) technique, I identified a new (M/I/L/V)PXL motif at the C termini of HSP90 and P23 that mediates an interaction with SMYD2, and synthetic peptides harboring this motif dissociated this complex. Of note, the HSP90- and P23-dependent client estrogen receptor α (ERα), was a major methylation target of SMYD2. In a reconstituted system in bacteria, I analyzed HSP90/P23-associated, SMYD2-mediated ERα methylation and found that when SMYD2 binds to the molecular chaperones, it considerably increases methylation of Lys-266 in ERα. Because methylation represses ERα activity, the observed complex formation between SMYD2 and HSP90/P23 may contribute to ERα regulation.
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Affiliation(s)
- Wolfgang M J Obermann
- From the Department of Systems Physiology, Ruhr-University Bochum, Universitätsstrasse 150, 44801 Bochum, Germany
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28
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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29
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Regulation of the Hsp90 system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:889-897. [PMID: 29563055 DOI: 10.1016/j.bbamcr.2018.03.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 01/01/2023]
Abstract
Hsp90 is a highly conserved and abundant chaperone. It participates in essential cellular activities by supporting the maturation process of its client proteins, many of which are protein kinases and steroid receptors. Client processing is achieved via extensive conformational changes within the dimeric chaperone. This requires an ATP hydrolysis activity that is controlled by auto-inhibitory mechanisms and several structurally diverse cofactors. Especially the client-specificity of Hsp90 depends on client-specific cofactors, which can adapt Hsp90's activities to the client requirements at different conditions and in different cell types. Additionally, post-translational modifications can influence almost every aspect of Hsp90's interactions and activities. In this review, we present these regulatory principles, discuss the factors that have an impact on Hsp90's function and elaborate the mechanisms that are responsible for regulating the Hsp90 machinery.
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30
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Boehm D, Jeng M, Camus G, Gramatica A, Schwarzer R, Johnson JR, Hull PA, Montano M, Sakane N, Pagans S, Godin R, Deeks SG, Krogan NJ, Greene WC, Ott M. SMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency. Cell Host Microbe 2017; 21:569-579.e6. [PMID: 28494238 DOI: 10.1016/j.chom.2017.04.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 03/07/2017] [Accepted: 04/24/2017] [Indexed: 12/28/2022]
Abstract
Transcriptional latency of HIV is a last barrier to viral eradication. Chromatin-remodeling complexes and post-translational histone modifications likely play key roles in HIV-1 reactivation, but the underlying mechanisms are incompletely understood. We performed an RNAi-based screen of human lysine methyltransferases and identified the SET and MYND domain-containing protein 2 (SMYD2) as an enzyme that regulates HIV-1 latency. Knockdown of SMYD2 or its pharmacological inhibition reactivated latent HIV-1 in T cell lines and in primary CD4+ T cells. SMYD2 associated with latent HIV-1 promoter chromatin, which was enriched in monomethylated lysine 20 at histone H4 (H4K20me1), a mark lost in cells lacking SMYD2. Further, we find that lethal 3 malignant brain tumor 1 (L3MBTL1), a reader protein with chromatin-compacting properties that recognizes H4K20me1, was recruited to the latent HIV-1 promoter in a SMYD2-dependent manner. We propose that a SMYD2-H4K20me1-L3MBTL1 axis contributes to HIV-1 latency and can be targeted with small-molecule SMYD2 inhibitors.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark Jeng
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gregory Camus
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrea Gramatica
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Roland Schwarzer
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey R Johnson
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Philip A Hull
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mauricio Montano
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Naoki Sakane
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Pharmaceutical Frontier Research Laboratory, JT, 1-13-2 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Sara Pagans
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Warner C Greene
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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31
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Tracy C, Warren JS, Szulik M, Wang L, Garcia J, Makaju A, Russell K, Miller M, Franklin S. The Smyd Family of Methyltransferases: Role in Cardiac and Skeletal Muscle Physiology and Pathology. CURRENT OPINION IN PHYSIOLOGY 2017; 1:140-152. [PMID: 29435515 DOI: 10.1016/j.cophys.2017.10.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein methylation plays a pivotal role in the regulation of various cellular processes including chromatin remodeling and gene expression. SET and MYND domain-containing proteins (Smyd) are a special class of lysine methyltransferases whose catalytic SET domain is split by an MYND domain. The hallmark feature of this family was thought to be the methylation of histone H3 (on lysine 4). However, several studies suggest that the role of the Smyd family is dynamic, targeting unique histone residues associated with both transcriptional activation and repression. Smyd proteins also methylate several non-histone proteins to regulate various cellular processes. Although we are only beginning to understand their specific molecular functions and role in chromatin remodeling, recent studies have advanced our understanding of this relatively uncharacterized family, highlighting their involvement in development, cell growth and differentiation and during disease in various animal models. This review summarizes our current knowledge of the structure, function and methylation targets of the Smyd family and provides a compilation of data emphasizing their prominent role in cardiac and skeletal muscle physiology and pathology.
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Affiliation(s)
- Christopher Tracy
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Junco S Warren
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Marta Szulik
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Li Wang
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - June Garcia
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Aman Makaju
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Kristi Russell
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Mickey Miller
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Sarah Franklin
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
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32
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Zipin-Roitman A, Aqaqe N, Yassin M, Biechonski S, Amar M, van Delft MF, Gan OI, McDermott SP, Buzina A, Ketela T, Shlush L, Xie S, Voisin V, Moffat J, Minden MD, Dick JE, Milyavsky M. SMYD2 lysine methyltransferase regulates leukemia cell growth and regeneration after genotoxic stress. Oncotarget 2017; 8:16712-16727. [PMID: 28187429 PMCID: PMC5369996 DOI: 10.18632/oncotarget.15147] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/24/2017] [Indexed: 12/12/2022] Open
Abstract
The molecular determinants governing escape of Acute Myeloid Leukemia (AML) cells from DNA damaging therapy remain poorly defined and account for therapy failures. To isolate genes responsible for leukemia cells regeneration following multiple challenges with irradiation we performed a genome-wide shRNA screen. Some of the isolated hits are known players in the DNA damage response (e.g. p53, CHK2), whereas other, e.g. SMYD2 lysine methyltransferase (KMT), remains uncharacterized in the AML context. Here we report that SMYD2 knockdown confers relative resistance to human AML cells against multiple classes of DNA damaging agents. Induction of the transient quiescence state upon SMYD2 downregulation correlated with the resistance. We revealed that diminished SMYD2 expression resulted in the upregulation of the related methyltransferase SET7/9, suggesting compensatory relationships. Indeed, pharmacological targeting of SET7/9 with (R)-PFI2 inhibitor preferentially inhibited the growth of cells expressing low levels of SMYD2. Finally, decreased expression of SMYD2 in AML patients correlated with the reduced sensitivity to therapy and lower probability to achieve complete remission. We propose that the interplay between SMYD2 and SET7/9 levels shifts leukemia cells from growth to quiescence state that is associated with the higher resistance to DNA damaging agents and rationalize SET7/9 pharmacological targeting in AML.
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Affiliation(s)
- Adi Zipin-Roitman
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nasma Aqaqe
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Muhammad Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Biechonski
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mariam Amar
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mark F van Delft
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Sean P McDermott
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Leidos Biomedical Research, Washington D.C., USA
| | - Alla Buzina
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Troy Ketela
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Liran Shlush
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Stephanie Xie
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Veronique Voisin
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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33
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Chen YJ, Tsai CH, Wang PY, Teng SC. SMYD3 Promotes Homologous Recombination via Regulation of H3K4-mediated Gene Expression. Sci Rep 2017. [PMID: 28630472 PMCID: PMC5476597 DOI: 10.1038/s41598-017-03385-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SMYD3 is a methyltransferase highly expressed in many types of cancer. It usually functions as an oncogenic protein to promote cell cycle, cell proliferation, and metastasis. Here, we show that SMYD3 modulates another hallmark of cancer, DNA repair, by stimulating transcription of genes involved in multiple steps of homologous recombination. Deficiency of SMYD3 induces DNA-damage hypersensitivity, decreases levels of repair foci, and leads to impairment of homologous recombination. Moreover, the regulation of homologous recombination-related genes is via the methylation of H3K4 at the target gene promoters. These data imply that, besides its reported oncogenic abilities, SMYD3 may maintain genome integrity by ensuring expression levels of HR proteins to cope with the high demand of restart of stalled replication forks in cancers.
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Affiliation(s)
- Yun-Ju Chen
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Cheng-Hui Tsai
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Pin-Yu Wang
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan. .,Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, 10051, Taiwan.
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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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35
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Carlson SM, Gozani O. Nonhistone Lysine Methylation in the Regulation of Cancer Pathways. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026435. [PMID: 27580749 DOI: 10.1101/cshperspect.a026435] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Proteins are regulated by an incredible array of posttranslational modifications (PTMs). Methylation of lysine residues on histone proteins is a PTM with well-established roles in regulating chromatin and epigenetic processes. The recent discovery that hundreds and likely thousands of nonhistone proteins are also methylated at lysine has opened a tremendous new area of research. Major cellular pathways involved in cancer, such as growth signaling and the DNA damage response, are regulated by lysine methylation. Although the field has developed quickly in recent years many fundamental questions remain to be addressed. We review the history and molecular functions of lysine methylation. We then discuss the enzymes that catalyze methylation of lysine residues, the enzymes that remove lysine methylation, and the cancer pathways known to be regulated by lysine methylation. The rest of the article focuses on two open questions that we suggest as a roadmap for future research. First is understanding the large number of candidate methyltransferase and demethylation enzymes whose enzymatic activity is not yet defined and which are potentially associated with cancer through genetic studies. Second is investigating the biological processes and cancer mechanisms potentially regulated by the multitude of lysine methylation sites that have been recently discovered.
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Affiliation(s)
- Scott M Carlson
- Department of Biology, Stanford University, Stanford, California 94305
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, California 94305
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36
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H3K36 methyltransferases as cancer drug targets: rationale and perspectives for inhibitor development. Future Med Chem 2016; 8:1589-607. [PMID: 27548565 DOI: 10.4155/fmc-2016-0071] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Methylation at histone 3, lysine 36 (H3K36) is a conserved epigenetic mark regulating gene transcription, alternative splicing and DNA repair. Genes encoding H3K36 methyltransferases (KMTases) are commonly overexpressed, mutated or involved in chromosomal translocations in cancer. Molecular biology studies have demonstrated that H3K36 KMTases regulate oncogenic transcriptional programs. Structural studies of the catalytic SET domain of H3K36 KMTases have revealed intriguing opportunities for design of small molecule inhibitors. Nevertheless, potent inhibitors for most H3K36 KMTases have not yet been developed, underlining the challenges associated with this target class. As we now have strong evidence linking H3K36 KMTases to cancer, drug development efforts are predicted to yield novel compounds in the near future.
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37
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Al-Shar'i NA, Alnabulsi SM. Explaining the autoinhibition of the SMYD enzyme family: A theoretical study. J Mol Graph Model 2016; 68:147-157. [PMID: 27447830 DOI: 10.1016/j.jmgm.2016.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/09/2016] [Accepted: 07/11/2016] [Indexed: 10/21/2022]
Abstract
The SMYD enzymes (SMYD1-5) are lysine methyltransferases that have diverse biological functions including gene expression and regulation of skeletal and cardiac muscle development and function. Recently, they have gained more attention as potential drug targets because of their involvement in cardiovascular diseases and in the progression of different cancer types. Their activity has been suggested to be regulated by a posttranslational mechanism and by autoinhibition. The later relies on a hinge-like movement of the N- and C-lobes to adopt an open or closed conformation, consequently, determining the accessibility of the active site and substrate specificity. In this study we aim to investigate and explain the possibility of the regulatory autoinhibition process of the SMYD enzymes by a thorough computational exploration of their dynamic, energetic, and structural changes by using extended molecular dynamics simulations; normal mode analysis (NMA); and energy correlations. Three SMYD models (SMYD1-3) were used in this study. Our results showed an obvious hinge-like motion between the N- and C-lobes. Also, we identified interaction energy pathways within the 3D structures of the proteins, and hot spots on their surfaces that could be of particular importance for the regulation of their activities via allosteric means. These results can help in a better understanding of the nature of these promising drug targets; and in designing selective drugs that can interfere with (inhibit) the function of a specific SMYD member by disrupting its dynamical and conformational behaviour without disrupting the function of the entire SMYD proteins.
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Affiliation(s)
- Nizar A Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan.
| | - Soraya M Alnabulsi
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan.
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38
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Fujii T, Tsunesumi SI, Sagara H, Munakata M, Hisaki Y, Sekiya T, Furukawa Y, Sakamoto K, Watanabe S. Smyd5 plays pivotal roles in both primitive and definitive hematopoiesis during zebrafish embryogenesis. Sci Rep 2016; 6:29157. [PMID: 27377701 PMCID: PMC4932602 DOI: 10.1038/srep29157] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 06/15/2016] [Indexed: 12/24/2022] Open
Abstract
Methylation of histone tails plays a pivotal role in the regulation of a wide range of biological processes. SET and MYND domain-containing protein (SMYD) is a methyltransferase, five family members of which have been identified in humans. SMYD1, SMYD2, SMYD3, and SMYD4 have been found to play critical roles in carcinogenesis and/or the development of heart and skeletal muscle. However, the physiological functions of SMYD5 remain unknown. To investigate the function of Smyd5 in vivo, zebrafish were utilised as a model system. We first examined smyd5 expression patterns in developing zebrafish embryos. Smyd5 transcripts were abundantly expressed at early developmental stages and then gradually decreased. Smyd5 was expressed in all adult tissues examined. Loss-of-function analysis of Smyd5 was then performed in zebrafish embryos using smyd5 morpholino oligonucleotide (MO). Embryos injected with smyd5-MO showed normal gross morphological development, including of heart and skeletal muscle. However, increased expression of both primitive and definitive hematopoietic markers, including pu.1, mpx, l-plastin, and cmyb, were observed. These phenotypes of smyd5-MO zebrafish embryos were also observed when we introduced mutations in smyd5 gene with the CRISPR/Cas9 system. As the expression of myeloid markers was elevated in smyd5 loss-of-function zebrafish, we propose that Smyd5 plays critical roles in hematopoiesis.
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Affiliation(s)
- Tomoaki Fujii
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Tokyo 101-0062, Japan.,Department of Coloproctological Surgery, Juntendo University, Faculty of Medicine, Tokyo 113-8421, Japan.,Division of Molecular and Developmental Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Shin-Ichiro Tsunesumi
- Division of Clinical Genome Research, Advanced Clinical Research Center, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroshi Sagara
- Fine Morphological Analysis Group Medical Proteomics Laboratory Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Miyo Munakata
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Tokyo 101-0062, Japan
| | - Yoshihiro Hisaki
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Tokyo 101-0062, Japan.,Division of Molecular and Developmental Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takao Sekiya
- Department of Cancer Genome Research, Sasaki Institute, Sasaki Foundation, Tokyo 101-0062, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, Advanced Clinical Research Center, The University of Tokyo, Tokyo 108-8639, Japan
| | - Kazuhiro Sakamoto
- Department of Coloproctological Surgery, Juntendo University, Faculty of Medicine, Tokyo 113-8421, Japan
| | - Sumiko Watanabe
- Division of Molecular and Developmental Biology, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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39
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Ahmed H, Duan S, Arrowsmith CH, Barsyte-Lovejoy D, Schapira M. An Integrative Proteomic Approach Identifies Novel Cellular SMYD2 Substrates. J Proteome Res 2016; 15:2052-9. [DOI: 10.1021/acs.jproteome.6b00220] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hazem Ahmed
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre and Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
- Princess Margaret Cancer Centre and Department
of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University of Toronto; 1 King’s
College Circle, Toronto, Ontario M5S 1A8, Canada
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40
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Eggert E, Hillig RC, Koehr S, Stöckigt D, Weiske J, Barak N, Mowat J, Brumby T, Christ CD, Ter Laak A, Lang T, Fernandez-Montalvan AE, Badock V, Weinmann H, Hartung IV, Barsyte-Lovejoy D, Szewczyk M, Kennedy S, Li F, Vedadi M, Brown PJ, Santhakumar V, Arrowsmith CH, Stellfeld T, Stresemann C. Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (BAY-598) for the Protein Lysine Methyltransferase SMYD2. J Med Chem 2016; 59:4578-600. [PMID: 27075367 PMCID: PMC4917279 DOI: 10.1021/acs.jmedchem.5b01890] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Protein
lysine methyltransferases have recently emerged as a new target class
for the development of inhibitors that modulate gene transcription
or signaling pathways. SET and MYND domain containing protein 2 (SMYD2)
is a catalytic SET domain containing methyltransferase reported to
monomethylate lysine residues on histone and nonhistone proteins.
Although several studies have uncovered an important role of SMYD2
in promoting cancer by protein methylation, the biology of SMYD2 is
far from being fully understood. Utilization of highly potent and
selective chemical probes for target validation has emerged as a concept
which circumvents possible limitations of knockdown experiments and,
in particular, could result in an improved exploration of drug targets
with a complex underlying biology. Here, we report the development
of a potent, selective, and cell-active, substrate-competitive inhibitor
of SMYD2, which is the first reported inhibitor suitable for in vivo
target validation studies in rodents.
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Affiliation(s)
- Erik Eggert
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Roman C Hillig
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Silke Koehr
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Detlef Stöckigt
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Jörg Weiske
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Naomi Barak
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Jeffrey Mowat
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Thomas Brumby
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Clara D Christ
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Antonius Ter Laak
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Tina Lang
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | | | - Volker Badock
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Hilmar Weinmann
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Ingo V Hartung
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Steven Kennedy
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | | | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5G 2M9, Canada
| | - Timo Stellfeld
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
| | - Carlo Stresemann
- Drug Discovery, BAYER Pharma AG , Muellerstrasse 178, 13353 Berlin, Germany
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41
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Borbolla-Vázquez J, Orozco E, Medina-Gómez C, Martínez-Higuera A, Javier-Reyna R, Chávez B, Betanzos A, Rodríguez MA. Identification and functional characterization of lysine methyltransferases of Entamoeba histolytica. Mol Microbiol 2016; 101:351-65. [PMID: 27062489 DOI: 10.1111/mmi.13394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2016] [Indexed: 02/07/2023]
Abstract
Lysine methylation of histones, a posttranslational modification catalyzed by lysine methyltransferases (HKMTs), plays an important role in the epigenetic regulation of transcription. Lysine methylation of non-histone proteins also impacts the biological function of proteins. Previously it has been shown that lysine methylation of histones of Entamoeba histolytica, the protozoan parasite that infects 50 million people worldwide each year and causing up to 100,000 deaths annually, is implicated in the epigenetic machinery of this microorganism. However, the identification and characterization of HKMTs in this parasite had not yet been determined. In this work we identified four HKMTs in E. histolytica (EhHKMT1 to EhHKMT4) that are expressed by trophozoites. Enzymatic assays indicated that all of them are able to transfer methyl groups to commercial histones. EhHKMT1, EhHKMT2 and EhHKMT4 were detected in nucleus and cytoplasm of trophozoites. In addition EhHKMT2 and EhHKMT4 were located in vesicles containing ingested cells during phagocytosis, and they co-immunoprecipitated with EhADH, a protein involved in the phagocytosis of this parasite. Results suggest that E. histolytica uses its HKMTs to regulate transcription by epigenetic mechanisms, and at least two of them could also be implicated in methylation of proteins that participate in phagocytosis.
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Affiliation(s)
- Jessica Borbolla-Vázquez
- Departamento de Infectómica y Patogénesis Molecular. CINVESTAV-IPN. AP. 14-740 México, D.F. México
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular. CINVESTAV-IPN. AP. 14-740 México, D.F. México
| | - Christian Medina-Gómez
- Departamento de Infectómica y Patogénesis Molecular. CINVESTAV-IPN. AP. 14-740 México, D.F. México
| | - Aarón Martínez-Higuera
- Departamento de Infectómica y Patogénesis Molecular. CINVESTAV-IPN. AP. 14-740 México, D.F. México
| | - Rosario Javier-Reyna
- Departamento de Infectómica y Patogénesis Molecular. CINVESTAV-IPN. AP. 14-740 México, D.F. México
| | - Bibiana Chávez
- Departamento de Infectómica y Patogénesis Molecular. CINVESTAV-IPN. AP. 14-740 México, D.F. México
| | - Abigail Betanzos
- Departamento de Infectómica y Patogénesis Molecular. CINVESTAV-IPN. AP. 14-740 México, D.F. México
| | - Mario A Rodríguez
- Departamento de Infectómica y Patogénesis Molecular. CINVESTAV-IPN. AP. 14-740 México, D.F. México
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42
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Reynoird N, Mazur PK, Stellfeld T, Flores NM, Lofgren SM, Carlson SM, Brambilla E, Hainaut P, Kaznowska EB, Arrowsmith CH, Khatri P, Stresemann C, Gozani O, Sage J. Coordination of stress signals by the lysine methyltransferase SMYD2 promotes pancreatic cancer. Genes Dev 2016; 30:772-85. [PMID: 26988419 PMCID: PMC4826394 DOI: 10.1101/gad.275529.115] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/01/2016] [Indexed: 12/13/2022]
Abstract
Here, Reynoird et al. identify the protein lysine methyltransferase SMYD2 as a key regulator of pancreatic cancer. They demonstrate that SMYD2 levels are increased in PDAC, genetic and pharmacological inhibition of SMYD2 restricts PDAC growth, and the stress response kinase MAPKAPK3 (MK3) is a substrate of SMYD2 in PDAC cells. Pancreatic ductal adenocarcinoma (PDAC) is a lethal form of cancer with few therapeutic options. We found that levels of the lysine methyltransferase SMYD2 (SET and MYND domain 2) are elevated in PDAC and that genetic and pharmacological inhibition of SMYD2 restricts PDAC growth. We further identified the stress response kinase MAPKAPK3 (MK3) as a new physiologic substrate of SMYD2 in PDAC cells. Inhibition of MAPKAPK3 impedes PDAC growth, identifying a potential new kinase target in PDAC. Finally, we show that inhibition of SMYD2 cooperates with standard chemotherapy to treat PDAC cells and tumors. These findings uncover a pivotal role for SMYD2 in promoting pancreatic cancer.
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Affiliation(s)
- Nicolas Reynoird
- Department of Biology, Stanford University, Stanford, California 94305, USA; Institut Albert Bonniot, U1209, Institut National de la Santé et de la Recherche Médicale, UMR5309, Centre National de la Recherche Scientifique, Université Grenoble-Alpes, F-38700 Grenoble, France
| | - Pawel K Mazur
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Timo Stellfeld
- Global Drug Discovery, Bayer Pharma AG, 13353 Berlin, Germany
| | - Natasha M Flores
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Shane M Lofgren
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Scott M Carlson
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Elisabeth Brambilla
- Institut Albert Bonniot, U1209, Institut National de la Santé et de la Recherche Médicale, UMR5309, Centre National de la Recherche Scientifique, Université Grenoble-Alpes, F-38700 Grenoble, France
| | - Pierre Hainaut
- Institut Albert Bonniot, U1209, Institut National de la Santé et de la Recherche Médicale, UMR5309, Centre National de la Recherche Scientifique, Université Grenoble-Alpes, F-38700 Grenoble, France
| | - Ewa B Kaznowska
- Faculty of Medicine, Centre for Innovative Research in Medical and Natural Sciences, University of Rzeszów, 35959 Rzeszów, Poland
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Purvesh Khatri
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Or Gozani
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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43
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Ohtomo-Oda R, Komatsu S, Mori T, Sekine S, Hirajima S, Yoshimoto S, Kanai Y, Otsuji E, Ikeda E, Tsuda H. SMYD2 overexpression is associated with tumor cell proliferation and a worse outcome in human papillomavirus–unrelated nonmultiple head and neck carcinomas. Hum Pathol 2016; 49:145-55. [DOI: 10.1016/j.humpath.2015.08.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/17/2015] [Accepted: 08/21/2015] [Indexed: 12/13/2022]
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44
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Liu S, Luo J, Chai J, Ren L, Zhou Y, Huang F, Liu X, Chen Y, Zhang C, Tao M, Lu B, Zhou W, Lin G, Mai C, Yuan S, Wang J, Li T, Qin Q, Feng H, Luo K, Xiao J, Zhong H, Zhao R, Duan W, Song Z, Wang Y, Wang J, Zhong L, Wang L, Ding Z, Du Z, Lu X, Gao Y, Murphy RW, Liu Y, Meyer A, Zhang YP. Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross. Proc Natl Acad Sci U S A 2016; 113:1327-32. [PMID: 26768847 PMCID: PMC4747765 DOI: 10.1073/pnas.1512955113] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Polyploidy is much rarer in animals than in plants but it is not known why. The outcome of combining two genomes in vertebrates remains unpredictable, especially because polyploidization seldom shows positive effects and more often results in lethal consequences because viable gametes fail to form during meiosis. Fortunately, the goldfish (maternal) × common carp (paternal) hybrids have reproduced successfully up to generation 22, and this hybrid lineage permits an investigation into the genomics of hybridization and tetraploidization. The first two generations of these hybrids are diploids, and subsequent generations are tetraploids. Liver transcriptomes from four generations and their progenitors reveal chimeric genes (>9%) and mutations of orthologous genes. Characterizations of 18 randomly chosen genes from genomic DNA and cDNA confirm the chimera. Some of the chimeric and differentially expressed genes relate to mutagenesis, repair, and cancer-related pathways in 2nF1. Erroneous DNA excision between homologous parental genes may drive the high percentage of chimeric genes, or even more potential mechanisms may result in this phenomenon. Meanwhile, diploid offspring show paternal-biased expression, yet tetraploids show maternal-biased expression. These discoveries reveal that fast and unstable changes are mainly deleterious at the level of transcriptomes although some offspring still survive their genomic abnormalities. In addition, the synthetic effect of genome shock might have resulted in greatly reduced viability of 2nF2 hybrid offspring. The goldfish × common carp hybrids constitute an ideal system for unveiling the consequences of intergenomic interactions in hybrid vertebrate genomes and their fertility.
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Affiliation(s)
- Shaojun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China;
| | - Jing Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jing Chai
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650204, China
| | - Li Ren
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yi Zhou
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Feng Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Xiaochuan Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Yubao Chen
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Chun Zhang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Min Tao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Bin Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Wei Zhou
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Guoliang Lin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Chao Mai
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Shuo Yuan
- School of Software, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jun Wang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Tao Li
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Qinbo Qin
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Hao Feng
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Kaikun Luo
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Jun Xiao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Huan Zhong
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Rurong Zhao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Wei Duan
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Zhenyan Song
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Yanqin Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jing Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Li Zhong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Zhaoli Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhenglin Du
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yun Gao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China; Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada M5S 2C6
| | - Yun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, Yunnan, China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China;
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Olsen JB, Cao XJ, Han B, Chen LH, Horvath A, Richardson TI, Campbell RM, Garcia BA, Nguyen H. Quantitative Profiling of the Activity of Protein Lysine Methyltransferase SMYD2 Using SILAC-Based Proteomics. Mol Cell Proteomics 2016; 15:892-905. [PMID: 26750096 DOI: 10.1074/mcp.m115.053280] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 12/13/2022] Open
Abstract
The significance of non-histone lysine methylation in cell biology and human disease is an emerging area of research exploration. The development of small molecule inhibitors that selectively and potently target enzymes that catalyze the addition of methyl-groups to lysine residues, such as the protein lysine mono-methyltransferase SMYD2, is an active area of drug discovery. Critical to the accurate assessment of biological function is the ability to identify target enzyme substrates and to define enzyme substrate specificity within the context of the cell. Here, using stable isotopic labeling with amino acids in cell culture (SILAC) coupled with immunoaffinity enrichment of mono-methyl-lysine (Kme1) peptides and mass spectrometry, we report a comprehensive, large-scale proteomic study of lysine mono-methylation, comprising a total of 1032 Kme1 sites in esophageal squamous cell carcinoma (ESCC) cells and 1861 Kme1 sites in ESCC cells overexpressing SMYD2. Among these Kme1 sites is a subset of 35 found to be potently down-regulated by both shRNA-mediated knockdown of SMYD2 and LLY-507, a selective small molecule inhibitor of SMYD2. In addition, we report specific protein sequence motifs enriched in Kme1 sites that are directly regulated by endogenous SMYD2 activity, revealing that SMYD2 substrate specificity is more diverse than expected. We further show direct activity of SMYD2 toward BTF3-K2, PDAP1-K126 as well as numerous sites within the repetitive units of two unique and exceptionally large proteins, AHNAK and AHNAK2. Collectively, our findings provide quantitative insights into the cellular activity and substrate recognition of SMYD2 as well as the global landscape and regulation of protein mono-methylation.
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Affiliation(s)
- Jonathan B Olsen
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285
| | - Xing-Jun Cao
- §Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Pennsylvania 19104
| | - Bomie Han
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285
| | - Lisa Hong Chen
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285
| | | | | | - Robert M Campbell
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285
| | - Benjamin A Garcia
- §Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Pennsylvania 19104;
| | - Hannah Nguyen
- From the ‡Lilly USA, Lilly Research Laboratories, Indianapolis, Indiana 46285;
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Spellmon N, Sun X, Sirinupong N, Edwards B, Li C, Yang Z. Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2. PLoS One 2015; 10:e0145758. [PMID: 26717235 PMCID: PMC4696779 DOI: 10.1371/journal.pone.0145758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/08/2015] [Indexed: 01/10/2023] Open
Abstract
SMYD proteins are an exciting field of study as they are linked to many types of cancer-related pathways. Cardiac and skeletal muscle development and function also depend on SMYD proteins opening a possible avenue for cardiac-related treatment. Previous crystal structure studies have revealed that this special class of protein lysine methyltransferases have a bilobal structure, and an open–closed motion may regulate substrate specificity. Here we use the molecular dynamics simulation to investigate the still-poorly-understood SMYD2 dynamics. Cross-correlation analysis reveals that SMYD2 exhibits a negative correlated inter-lobe motion. Principle component analysis suggests that this correlated dynamic is contributed to by a twisting motion of the C-lobe with respect to the N-lobe and a clamshell-like motion between the lobes. Dynamical network analysis defines possible allosteric paths for the correlated dynamics. There are nine communities in the dynamical network with six in the N-lobe and three in the C-lobe, and the communication between the lobes is mediated by a lobe-bridging β hairpin. This study provides insight into the dynamical nature of SMYD2 and could facilitate better understanding of SMYD2 substrate specificity.
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Affiliation(s)
- Nicholas Spellmon
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Xiaonan Sun
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Nualpun Sirinupong
- Nutraceuticals and Functional Food Research and Development Center, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
| | - Brian Edwards
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Chunying Li
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail: (ZY); (CL)
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail: (ZY); (CL)
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Hsp90 as a "Chaperone" of the Epigenome: Insights and Opportunities for Cancer Therapy. Adv Cancer Res 2015; 129:107-40. [PMID: 26916003 DOI: 10.1016/bs.acr.2015.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The cellular functions of Hsp90 have historically been attributed to its ability to chaperone client proteins involved in signal transduction. Although numerous stimuli and the signaling cascades they activate contribute to cancer progression, many of these pathways ultimately require transcriptional effectors to elicit tumor-promoting effects. Despite this obvious connection, the majority of studies evaluating Hsp90 function in malignancy have focused upon its regulation of cytosolic client proteins, and particularly members of receptor and/or kinase families. However, in recent years, Hsp90 has emerged as a pivotal orchestrator of nuclear events. Discovery of an expanding repertoire of Hsp90 clients has illuminated a vital role for Hsp90 in overseeing nuclear events and influencing gene transcription. Hence, this chapter will cast a spotlight upon several regulatory themes involving Hsp90-dependent nuclear functions. Highlighted topics include a summary of chaperone-dependent regulation of key transcription factors (TFs) and epigenetic effectors in malignancy, as well as a discussion of how the complex interplay among a subset of these TFs and epigenetic regulators may generate feed-forward loops that further support cancer progression. This chapter will also highlight less recognized indirect mechanisms whereby Hsp90-supported signaling may impinge upon epigenetic regulation. Finally, the relevance of these nuclear events is discussed within the framework of Hsp90's capacity to enable phenotypic variation and drug resistance. These newly acquired insights expanding our understanding of Hsp90 function support the collective notion that nuclear clients are major beneficiaries of Hsp90 action, and their impairment is likely responsible for many of the anticancer effects elicited by Hsp90-targeted approaches.
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He Q, Liu K, Tian Z, Du SJ. The Effects of Hsp90α1 Mutations on Myosin Thick Filament Organization. PLoS One 2015; 10:e0142573. [PMID: 26562659 PMCID: PMC4642942 DOI: 10.1371/journal.pone.0142573] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 10/24/2015] [Indexed: 01/08/2023] Open
Abstract
Heat shock protein 90α plays a key role in myosin folding and thick filament assembly in muscle cells. To assess the structure and function of Hsp90α and its potential regulation by post-translational modification, we developed a combined knockdown and rescue assay in zebrafish embryos to systematically analyze the effects of various mutations on Hsp90α function in myosin thick filament organization. DNA constructs expressing the Hsp90α1 mutants with altered putative ATP binding, phosphorylation, acetylation or methylation sites were co-injected with Hsp90α1 specific morpholino into zebrafish embryos. Myosin thick filament organization was analyzed in skeletal muscles of the injected embryos by immunostaining. The results showed that mutating the conserved D90 residue in the Hsp90α1 ATP binding domain abolished its function in thick filament organization. In addition, phosphorylation mimicking mutations of T33D, T33E and T87E compromised Hsp90α1 function in myosin thick filament organization. Similarly, K287Q acetylation mimicking mutation repressed Hsp90α1 function in myosin thick filament organization. In contrast, K206R and K608R hypomethylation mimicking mutations had not effect on Hsp90α1 function in thick filament organization. Given that T33 and T87 are highly conserved residues involved post-translational modification (PTM) in yeast, mouse and human Hsp90 proteins, data from this study could indicate that Hsp90α1 function in myosin thick filament organization is potentially regulated by PTMs involving phosphorylation and acetylation.
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Affiliation(s)
- Qiuxia He
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21202, United States of America
- Biology Institute of Shandong Academy of Sciences, Jinan, Shandong, 250014, P. R. China
| | - Kechun Liu
- Biology Institute of Shandong Academy of Sciences, Jinan, Shandong, 250014, P. R. China
| | - Zhenjun Tian
- Institute of Sports and Exercise Biology, Shaanxi Normal University, Xi’an, Shaanxi, 710062, P. R. China
| | - Shao Jun Du
- Institute of Marine and Environmental Technology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, 21202, United States of America
- * E-mail:
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Zhang X, Huang Y, Shi X. Emerging roles of lysine methylation on non-histone proteins. Cell Mol Life Sci 2015; 72:4257-72. [PMID: 26227335 PMCID: PMC11114002 DOI: 10.1007/s00018-015-2001-4] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 06/27/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Lysine methylation is a common posttranslational modification (PTM) of histones that is important for the epigenetic regulation of transcription and chromatin in eukaryotes. Increasing evidence demonstrates that in addition to histones, lysine methylation also occurs on various non-histone proteins, especially transcription- and chromatin-regulating proteins. In this review, we will briefly describe the histone lysine methyltransferases (KMTs) that have a broad spectrum of non-histone substrates. We will use p53 and nuclear receptors, especially estrogen receptor alpha, as examples to discuss the dynamic nature of non-histone protein lysine methylation, the writers, erasers, and readers of these modifications, and the crosstalk between lysine methylation and other PTMs in regulating the functions of the modified proteins. Understanding the roles of lysine methylation in normal cells and during development will shed light on the complex biology of diseases associated with the dysregulation of lysine methylation on both histones and non-histone proteins.
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Affiliation(s)
- Xi Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yaling Huang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The Genes and Development and the Epigenetics and Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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50
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Liu T, Wu C, Jain MR, Nagarajan N, Yan L, Dai H, Cui C, Baykal A, Pan S, Ago T, Sadoshima J, Li H. Master redox regulator Trx1 upregulates SMYD1 & modulates lysine methylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1816-1822. [PMID: 26410624 DOI: 10.1016/j.bbapap.2015.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 09/02/2015] [Accepted: 09/23/2015] [Indexed: 02/07/2023]
Abstract
Thioredoxin 1 (Trx1) is а antioxidant protein that regulates protein disulfide bond reduction, transnitrosylation, denitrosylation and other redox post-translational modifications. In order to better understand how Trx1 modulates downstream protective cellular signaling events following cardiac ischemia, we conducted an expression proteomics study of left ventricles (LVs) after thoracic aortic constriction stress treatment of transgenic mice with cardiac-specific over-expression of Trx1, an animal model that has been proven to withstand more stress than its non-transgenic littermates. Although previous redox post-translational modifications proteomics studies found that several cellular protein networks are regulated by Trx1-mediated disulfide reduction and transnitrosylation, we found that Trx1 regulates the expression of a limited number of proteins. Among the proteins found to be upregulated in this study was SET and MYND domain-containing protein 1 (SMYD1), a lysine methyltransferase highly expressed in cardiac and other muscle tissues and an important regulator of cardiac development. The observation of SMYD1 induction by Trx1 following thoracic aortic constriction stress is consistent with the retrograde fetal gene cardiac protection hypothesis. The results presented here suggest for the first time that, in addition to being a master redox regulator of protein disulfide bonds and nitrosation, Trx1 may also modulate lysine methylation, a non-redox post-translational modification, via the regulation of SMYD1 expression. Such crosstalk between redox signaling and a non-redox PTM regulation may provide novel insights into the functions of Trx1 that are independent from its immediate function as a protein reductase.
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Affiliation(s)
- Tong Liu
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Changgong Wu
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Mohit Raja Jain
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Narayani Nagarajan
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States
| | - Lin Yan
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Huacheng Dai
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Chuanlong Cui
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Ahmet Baykal
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Stacey Pan
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States
| | - Tetsuro Ago
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States
| | - Junichi Sadoshima
- Cardiovascular Research Institute, Department of Cell Biology and Molecular Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103, United States
| | - Hong Li
- Center for Advanced Proteomics Research, Department of Biochemistry and Molecular Biology, Rutgers University-New Jersey Medical School Cancer Center, Newark, NJ 07103, United States.
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