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Mamabolo K, Wadee R, Perner Y, Magangane P, Duze ST, Marimani M. Differential Epigenetic Regulation in Uninfected and Tuberculosis-Human Immunodeficiency Virus Co-Infected Patients. Microorganisms 2024; 12:1001. [PMID: 38792830 PMCID: PMC11123988 DOI: 10.3390/microorganisms12051001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
This study aimed to compare the degree of epigenetic modifications between a TB-HIV co-infected cohort and uninfected subjects. Formalin-fixed paraffin-embedded (FFPE) tissues were retrieved from 45 TB-HIV co-infected and 45 control individuals. Real-time PCR was applied to compare the level of expression of genes involved in epigenetic regulation. The protein multiplex assay was used to assess the degree of protein modification. DNA sequencing was used to determine the evolutionary relationships between the infecting HIV and Mtb strains. Our results indicated a significant increase in the expression of the five candidate genes in the patients with TB-HIV relative to the control cohort. A sharp increase in the degree of histone methylation, acetylation and phosphorylation was observed in TB-HIV co-infected patients. The phylogenetic analysis classified the strains into three distinct HIV clusters and five Mtb clusters. The disparities in the expression profiles of our candidate genes between the TB-HIV cohort and non-TB-HIV group highlights the important role played by various TB and HIV strains in regulating the host gene expression landscape.
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Affiliation(s)
- Katlego Mamabolo
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
| | - Reubina Wadee
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
| | - Yvonne Perner
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
| | - Pumza Magangane
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
| | - Sanelisiwe Thinasonke Duze
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
| | - Musa Marimani
- Anatomical Pathology, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa (R.W.)
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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3
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Jin J, Bai H, Yan H, Deng T, Li T, Xiao R, Fan L, Bai X, Ning H, Liu Z, Zhang K, Wu X, Liang K, Ma P, Gao X, Hu D. PRMT2 promotes HIV-1 latency by preventing nucleolar exit and phase separation of Tat into the Super Elongation Complex. Nat Commun 2023; 14:7274. [PMID: 37949879 PMCID: PMC10638354 DOI: 10.1038/s41467-023-43060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
The HIV-1 Tat protein hijacks the Super Elongation Complex (SEC) to stimulate viral transcription and replication. However, the mechanisms underlying Tat activation and inactivation, which mediate HIV-1 productive and latent infection, respectively, remain incompletely understood. Here, through a targeted complementary DNA (cDNA) expression screening, we identify PRMT2 as a key suppressor of Tat activation, thus contributing to proviral latency in multiple cell line latency models and in HIV-1-infected patient CD4+ T cells. Our data reveal that the transcriptional activity of Tat is oppositely regulated by NPM1-mediated nucleolar retention and AFF4-induced phase separation in the nucleoplasm. PRMT2 preferentially methylates Tat arginine 52 (R52) to reinforce its nucleolar sequestration while simultaneously counteracting its incorporation into the SEC droplets, thereby leading to its functional inactivation to promote proviral latency. Thus, our studies unveil a central and unappreciated role for Tat methylation by PRMT2 in connecting its subnuclear distribution, liquid droplet formation, and transactivating function, which could be therapeutically targeted to eradicate latent viral reservoirs.
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Affiliation(s)
- Jiaxing Jin
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China
| | - Hui Bai
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China
| | - Han Yan
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China
| | - Ting Deng
- Key Laboratory of Breast Cancer Prevention and Therapy of Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, 300060, Tianjin, China
| | - Tianyu Li
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, China
| | - Ruijing Xiao
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, China
| | - Lina Fan
- Department of Infectious Diseases, Tianjin Second People's Hospital, Nankai University, 300192, Tianjin, China
| | - Xue Bai
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Hanhan Ning
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China
| | - Zhe Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Kai Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Xudong Wu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, 300070, Tianjin, China
| | - Kaiwei Liang
- Department of Pathophysiology, School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, China
| | - Ping Ma
- Department of Infectious Diseases, Tianjin Second People's Hospital, Nankai University, 300192, Tianjin, China.
| | - Xin Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 300020, Tianjin, China.
- Tianjin Institutes of Health Science, 301600, Tianjin, China.
| | - Deqing Hu
- National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, State Key Laboratory of Experimental Hematology, Key Laboratory of Immune Microenvironment and Disease of Ministry of Education, Department of Cell Biology, School of Basic Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, 300070, Tianjin, China.
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4
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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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5
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Cao L, Wang M, Xu K. [Research Progress of Role and Mechanism of SETD7 in Tumor Occurrence
and Progression]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2023; 26:38-45. [PMID: 36792079 PMCID: PMC9987127 DOI: 10.3779/j.issn.1009-3419.2023.106.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The occurence and development of tumors is a complicated process, which not only depends on the mutation or deletion of genes, but also is affected by epigenetic regulation. Accumulating evidences have shown that epigenetic modifications play fundamental roles in transcriptional regulation, heterochromatin formation, X chromosome inactivation, DNA damage response and tumor development. SET domain containing lysine methyltransferase 7 (SETD7) was initially identified as an important lysine methyltransferase, which methylated histone and non-histone proteins. These modifications play fundamental roles. Once this modification disorders, it can directly lead to cell abnormalities and cause many diseases. Studies have shown that SETD7 is related to the occurence and development of various tumors, but the methylation sites of SETD7 and its regulatory mechanism have not been fully elucidated. This article summarizes the research progress of the role of SETD7 on histone and non-histone methylation modification in tumors and the molecular mechanism, in order to provide new therapeutic targets for tumor pathogenesis and diagnosis.
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Affiliation(s)
- Limin Cao
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute,
Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Min Wang
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute,
Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ke Xu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute,
Tianjin Medical University General Hospital, Tianjin 300052, China
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6
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Monteiro FL, Stepanauskaite L, Williams C, Helguero LA. SETD7 Expression Is Associated with Breast Cancer Survival Outcomes for Specific Molecular Subtypes: A Systematic Analysis of Publicly Available Datasets. Cancers (Basel) 2022; 14:cancers14246029. [PMID: 36551516 PMCID: PMC9775934 DOI: 10.3390/cancers14246029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
SETD7 is a lysine N-methyltransferase that targets many proteins important in breast cancer (BC). However, its role and clinical significance remain unclear. Here, we used online tools and multiple public datasets to explore the predictive potential of SETD7 expression (high or low quartile) considering BC subtype, grade, stage, and therapy. We also investigated overrepresented biological processes associated with its expression using TCGA-BRCA data. SETD7 expression was highest in the Her2 (ERBB2)-enriched molecular subtype and lowest in the basal-like subtype. For the basal-like subtype specifically, higher SETD7 was consistently correlated with worse recurrence-free survival (p < 0.009). High SETD7-expressing tumours further exhibited a higher rate of ERBB2 mutation (20% vs. 5%) along with a poorer response to anti-Her2 therapy. Overall, high SETD7-expressing tumours showed higher stromal and lower immune scores. This was specifically related to higher counts of cancer-associated fibroblasts and endothelial cells, but lower B and T cell signatures, especially in the luminal A subtype. Genes significantly associated with SETD7 expression were accordingly overrepresented in immune response processes, with distinct subtype characteristics. We conclude that the prognostic value of SETD7 depends on the BC subtype and that SETD7 may be further explored as a potential treatment-predictive marker for immune checkpoint inhibitors.
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Affiliation(s)
- Fátima Liliana Monteiro
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Lina Stepanauskaite
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, 114 28 Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Stockholm, Sweden
| | - Cecilia Williams
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, 114 28 Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institute, 141 83 Stockholm, Sweden
| | - Luisa A. Helguero
- SciLifeLab, Department of Protein Science, KTH Royal Institute of Technology, 114 28 Stockholm, Sweden
- Correspondence:
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7
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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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8
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Gao L, Yu W, Song P, Li Q. Non-histone methylation of SET7/9 and its biological functions. Recent Pat Anticancer Drug Discov 2021; 17:231-243. [PMID: 34856916 DOI: 10.2174/1574892816666211202160041] [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: 09/02/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND (su(var)-3-9,enhancer-of-zeste,trithorax) domain-containing protein 7/9 (SET7/9) is a member of the protein lysine methyltransferases (PLMTs or PKMTs) family. It contains a SET domain. Recent studies demonstrate that SET7/9 methylates both lysine 4 of histone 3 (H3-K4) and lysine(s) of non-histone proteins, including transcription factors, tumor suppressors, and membrane-associated receptors. OBJECTIVE This article mainly reviews the non-histone methylation effects of SET7/9 and its functions in tumorigenesis and development. METHODS PubMed was screened for this information. RESULTS SET7/9 plays a key regulatory role in various biological processes such as cell proliferation, transcription regulation, cell cycle, protein stability, cardiac morphogenesis, and development. In addition, SET7/9 is involved in the pathogenesis of hair loss, breast cancer progression, human carotid plaque atherosclerosis, chronic kidney disease, diabetes, obesity, ovarian cancer, prostate cancer, hepatocellular carcinoma, and pulmonary fibrosis. CONCLUSION SET7/9 is an important methyltransferase, which can catalyze the methylation of a variety of proteins. Its substrates are closely related to the occurrence and development of tumors.
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Affiliation(s)
- Lili Gao
- Department of Pathology, Pudong New Area People's Hospital, Shanghai 201299. China
| | - Weiping Yu
- Department of Pathophysiology, Medical school of Southeast University, Nanjing 210009, Jiangsu. China
| | - Peng Song
- Department of Pathology, Pudong New Area People's Hospital, Shanghai 201299. China
| | - Qing Li
- Department of Pathology, Pudong New Area People's Hospital, Shanghai 201299. China
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9
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Zhang XN, Wu LJ, Kong X, Zheng BY, Zhang Z, He ZW. Regulation of the expression of proinflammatory cytokines induced by SARS-CoV-2. World J Clin Cases 2021; 9:1513-1523. [PMID: 33728295 PMCID: PMC7942047 DOI: 10.12998/wjcc.v9.i7.1513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/08/2020] [Accepted: 12/25/2020] [Indexed: 02/06/2023] Open
Abstract
An outbreak of a novel coronavirus was reported in Wuhan, China, in late 2019. It has spread rapidly through China and many other countries, causing a global pandemic. Since February 2020, over 28 countries/regions have reported confirmed cases. Individuals with the infection known as coronavirus disease-19 (COVID-19) have similar clinical features as severe acute respiratory syndrome first encountered 17 years ago, with fever, cough, and upper airway congestion, along with high production of proinflammatory cytokines (PICs), which form a cytokine storm. PICs induced by COVID-19 include interleukin (IL)-6, IL-17, and monocyte chemoattractant protein-1. The production of cytokines is regulated by activated nuclear factor-kB and involves downstream pathways such as Janus kinase/signal transducers and activators transcription. Protein expression is also regulated by post-translational modification of chromosomal markers. Lysine residues in the peptide tails stretching out from the core of histones bind the sequence upstream of the coding portion of genomic DNA. Covalent modification, particularly methylation, activates or represses gene transcription. PICs have been reported to be induced by histone modification and stimulate exudation of hyaluronic acid, which is implicated in the occurrence of COVID-19. These findings indicate the impact of the expression of PICs on the pathogenesis and therapeutic targeting of COVID-19.
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Affiliation(s)
- Xiang-Ning Zhang
- Department of Pathophysiology, Guangdong Medical University, Dongguan 523808, Guangdong Province, China
| | - Long-Ji Wu
- Department of Pathophysiology, Guangdong Medical University, Dongguan 523808, Guangdong Province, China
| | - Xia Kong
- Department of Pathophysiology, Guangdong Medical University, Dongguan 523808, Guangdong Province, China
| | - Bi-Ying Zheng
- Department of Clinical Microbiology, Institute of Laboratory Medicine, Guangdong Medical University, Dongguan 523808, Guangdong Province, China
| | - Zhe Zhang
- Department of ENT and Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning 531000, Guangxi Zhuang Autonomous Region, China
| | - Zhi-Wei He
- Department of Pathophysiology, Guangdong Medical University, Dongguan 523808, Guangdong Province, China
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Identification of Modulators of HIV-1 Proviral Transcription from a Library of FDA-Approved Pharmaceuticals. Viruses 2020; 12:v12101067. [PMID: 32977702 PMCID: PMC7598649 DOI: 10.3390/v12101067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 12/21/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) is the most prevalent human retrovirus. Recent data show that 34 million people are living with HIV-1 worldwide. HIV-1 infections can lead to AIDS which still causes nearly 20,000 deaths annually in the USA alone. As this retrovirus leads to high morbidity and mortality conditions, more effective therapeutic regimens must be developed to treat these viral infections. A key target for intervention for which there are no current FDA-approved modulators is at the point of proviral transcription. One successful method for identifying novel therapeutics for treating infectious diseases is the repurposing of pharmaceuticals that are approved by the FDA for alternate indications. Major benefits of using FDA-approved drugs include the fact that the compounds have well established toxicity profiles, approved manufacturing processes, and immediate commercial availability to the patients. Here, we demonstrate that pharmaceuticals previously approved for other indications can be utilized to either activate or inhibit HIV-1 proviral transcription. Specifically, we found febuxostat, eltrombopag, and resveratrol to be activators of HIV-1 transcription, while mycophenolate was our lead inhibitor of HIV-1 transcription. Additionally, we observed that the infected cells of lymphoid and myeloid lineage responded differently to our lead transcriptional modulators. Finally, we demonstrated that the use of a multi-dose regimen allowed for enhanced activation with our transcriptional activators.
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11
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A Stronger Transcription Regulatory Circuit of HIV-1C Drives the Rapid Establishment of Latency with Implications for the Direct Involvement of Tat. J Virol 2020; 94:JVI.00503-20. [PMID: 32669338 DOI: 10.1128/jvi.00503-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/07/2020] [Indexed: 02/06/2023] Open
Abstract
The magnitude of transcription factor binding site variation emerging in HIV-1 subtype C (HIV-1C), especially the addition of NF-κB motifs by sequence duplication, makes the examination of transcriptional silence challenging. How can HIV-1 establish and maintain latency despite having a strong long terminal repeat (LTR)? We constructed panels of subgenomic reporter viral vectors with varying copy numbers of NF-κB motifs (0 to 4 copies) and examined the profile of latency establishment in Jurkat cells. Surprisingly, we found that the stronger the viral promoter, the faster the latency establishment. Importantly, at the time of commitment to latency and subsequent points, Tat levels in the cell were not limiting. Using highly sensitive strategies, we demonstrate the presence of Tat in the latent cell, recruited to the latent LTR. Our data allude, for the first time, to Tat establishing a negative feedback loop during the late phases of viral infection, leading to the rapid silencing of the viral promoter.IMPORTANCE Over the past 10 to 15 years, HIV-1 subtype C (HIV-1C) has been evolving rapidly toward gaining stronger transcriptional activity by sequence duplication of major transcription factor binding sites. The duplication of NF-κB motifs is unique and exclusive to HIV-1C, a property not shared with any of the other eight HIV-1 genetic families. What mechanism(s) does HIV-1C employ to establish and maintain transcriptional silence despite the presence of a strong promoter and concomitant strong, positive transcriptional feedback is the primary question that we attempted to address in the present manuscript. The role that Tat plays in latency reversal is well established. Our work with the most common HIV-1 subtype, HIV-1C, offers crucial leads toward Tat possessing a dual role in serving as both a transcriptional activator and repressor at different phases of viral infection of the cell. The leads that we offer through the present work have significant implications for HIV-1 cure research.
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12
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Hou Z, Min W, Zhang R, Niu A, Li Y, Cao L, Han J, Luo C, Yang P, Ding H. Lead discovery, chemical optimization, and biological evaluation studies of novel histone methyltransferase SET7 small-molecule inhibitors. Bioorg Med Chem Lett 2020; 30:127061. [PMID: 32173197 DOI: 10.1016/j.bmcl.2020.127061] [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: 11/25/2019] [Revised: 02/14/2020] [Accepted: 02/22/2020] [Indexed: 10/24/2022]
Abstract
The post-translational modifications of histones, including histone methylation and demethylation, control the expression switch of multiple genes. SET domain-containing lysine methyltransferase 7 (SET7) is the only methyltransferase, which can specifically monomethylate lysine-4 of histone H3 (H3K4me1) and play critical roles in various diseases, including breast cancer, hepatitis C virus (HCV), atherosclerotic vascular disease, diabetes, prostate cancer, hepatocellular carcinoma, and obesity. However, several known SET7 inhibitors exhibit weak activity or poor selectivity. Therefore, the development of novel SET7 inhibitors is highly desirable and of great clinical value. In this study, we identified 2-79 as a new hit compound by structure-based virtual screening and further AlphaLISA-based biochemical evaluation. Via chemical optimization, the synthesized compound DC21 was confirmed as a potent SET7 inhibitor with an IC50 value of 15.93 μM. The interaction between DC21 and SET7 was also validated through SPR experiment. Especially, DC21 retarded proliferation of MCF7 cells with an IC50 value of 25.84 μM in cellular level. In addition, DC21 has good selectivity for several other epigenetic targets, such as SUV39H1, G9a, NSD1, DOT1L and MOF. DC21 can serve as a lead compound to develop more potential SET7 inhibitors and as a chemical probe for SET7 biological function studies.
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Affiliation(s)
- Zeng Hou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Rukang Zhang
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ao Niu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Yuanqing Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Liyuan Cao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jie Han
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.
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13
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Mahesh A, Khan MIK, Govindaraju G, Verma M, Awasthi S, Chavali PL, Chavali S, Rajavelu A, Dhayalan A. SET7/9 interacts and methylates the ribosomal protein, eL42 and regulates protein synthesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118611. [DOI: 10.1016/j.bbamcr.2019.118611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/21/2019] [Accepted: 11/13/2019] [Indexed: 12/14/2022]
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14
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Banga R, Rebecchini C, Procopio FA, Noto A, Munoz O, Ioannidou K, Fenwick C, Ohmiti K, Cavassini M, Corpataux JM, de Leval L, Pantaleo G, Perreau M. Lymph node migratory dendritic cells modulate HIV-1 transcription through PD-1 engagement. PLoS Pathog 2019; 15:e1007918. [PMID: 31329640 PMCID: PMC6675123 DOI: 10.1371/journal.ppat.1007918] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 08/01/2019] [Accepted: 06/14/2019] [Indexed: 12/29/2022] Open
Abstract
T-follicular helper (Tfh) cells, co-expressing PD-1 and TIGIT, serve as a major cell reservoir for HIV-1 and are responsible for active and persistent HIV-1 transcription after prolonged antiretroviral therapy (ART). However, the precise mechanisms regulating HIV-1 transcription in lymph nodes (LNs) remain unclear. In the present study, we investigated the potential role of immune checkpoint (IC)/IC-Ligand (IC-L) interactions on HIV-1 transcription in LN-microenvironment. We show that PD-L1 (PD-1-ligand) and CD155 (TIGIT-ligand) are predominantly co-expressed on LN migratory (CD1chighCCR7+CD127+) dendritic cells (DCs), that locate predominantly in extra-follicular areas in ART treated individuals. We demonstrate that TCR-mediated HIV production is suppressed in vitro in the presence of recombinant PD-L1 or CD155 and, more importantly, when LN migratory DCs are co-cultured with PD-1+/Tfh cells. These results indicate that LN migratory DCs expressing IC-Ls may more efficiently restrict HIV-1 transcription in the extra-follicular areas and explain the persistence of HIV transcription in PD-1+/Tfh cells after prolonged ART within germinal centers. Increasing number of evidences indicate that B-cell follicles might be anatomical sanctuaries for active transcription in both HIV/SIV viremic controllers and in ART treated aviremic HIV-infected individuals. While multiple mechanisms may be involved in the regulation of HIV transcription, recent studies suggested that immune checkpoint molecule (IC) signaling may contribute to maintain HIV-1 latency in infected CD4 T cells. These observations prompted us to investigate the involvement of IC/IC-L interactions in the regulation of HIV-1 transcription in lymph node (LN) tissues. In the present study, we show that T follicular helper (Tfh) cells predominantly co-expressed PD-1 and TIGIT, which were functionally active. An in-depth mass cytometry analysis revealed that PD-L1, PD-L2 (PD-1 ligands) and CD155 (TIGIT-ligand) were predominantly co-expressed on a specific LN dendritic cell (DC) subpopulation expressing markers of migratory DCs. We subsequently demonstrated that LN migratory DCs, locating predominantly in LN extra-follicular areas, could modulate HIV-1 transcription by a mechanism involving PD-L1/PD-1 interactions. Interestingly, the frequency of LN migratory DCs inversely correlated with HIV-1 transcription from LN memory CD4 T cells, suggesting that IC-L expressing migratory DCs might contribute to control HIV-1 transcription and maintain HIV-1 latency in extra-follicular areas. These findings represent a step forward in our understanding of potential mechanisms contributing to the regulation of HIV persistence in lymphoid tissues.
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Affiliation(s)
- Riddhima Banga
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Caterina Rebecchini
- Institute of Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Francesco Andrea Procopio
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alessandra Noto
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Olivia Munoz
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Kalliopi Ioannidou
- Institute of Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Craig Fenwick
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Khalid Ohmiti
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Matthias Cavassini
- Service of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jean-Marc Corpataux
- Service of Vascular Surgery, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Laurence de Leval
- Institute of Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Matthieu Perreau
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- * E-mail:
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15
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Loboda AP, Soond SM, Piacentini M, Barlev NA. Lysine-specific post-translational modifications of proteins in the life cycle of viruses. Cell Cycle 2019; 18:1995-2005. [PMID: 31291816 DOI: 10.1080/15384101.2019.1639305] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The process of protein post-translational modifications (PTM) is one of the critical mechanisms of regulation of many cellular processes, which makes it an attractive target for various viruses. Since viruses cannot replicate on their own, they have developed unique abilities to alter metabolic and signaling cell pathways, including protein PTMs, to ensure faithful replication of their genomes. This review describes several ways of how lysine-specific PTMs are used by various viruses to ensure its successful invasion and replication. Covalent modifications like acetylation, ubiquitination, and methylation form a complex system of reversible and often competing modifications, which adds an additional level of complexity to the system of regulation of the activity of host proteins involved in viral replication and propagation. In furthering these, we also describe the manner in which PTM pathways can also be accosted by various types of viruses to neutralize the host's cellular mechanisms for anti-viral protection and highlight key areas for future therapeutic targeting and design.
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Affiliation(s)
- Anna P Loboda
- a Laboratory of Intracellular Signaling, Moscow Institute of Physics and Technology , Dolgoprudny, Moscow Region , Russian Federation
| | - Surinder M Soond
- b Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University , Moscow , Russian Federation
| | - Mauro Piacentini
- c Laboratory of Molecular Medicine, Institute of Cytology of the Russian Academy of Science , St-Petersburg , Russian Federation
| | - Nickolai A Barlev
- a Laboratory of Intracellular Signaling, Moscow Institute of Physics and Technology , Dolgoprudny, Moscow Region , Russian Federation.,c Laboratory of Molecular Medicine, Institute of Cytology of the Russian Academy of Science , St-Petersburg , Russian Federation
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16
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Pinto DO, Scott TA, DeMarino C, Pleet ML, Vo TT, Saifuddin M, Kovalskyy D, Erickson J, Cowen M, Barclay RA, Zeng C, Weinberg MS, Kashanchi F. Effect of transcription inhibition and generation of suppressive viral non-coding RNAs. Retrovirology 2019; 16:13. [PMID: 31036006 PMCID: PMC6489247 DOI: 10.1186/s12977-019-0475-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 04/20/2019] [Indexed: 01/03/2023] Open
Abstract
Background HIV-1 patients receiving combination antiretroviral therapy (cART) survive infection but require life-long adherence at high expense. In chronic cART-treated patients with undetectable viral titers, cell-associated viral RNA is still detectable, pointing to low-level viral transcriptional leakiness. To date, there are no FDA-approved drugs against HIV-1 transcription. We have previously shown that F07#13, a third generation Tat peptide mimetic with competitive activity against Cdk9/T1-Tat binding sites, inhibits HIV-1 transcription in vitro and in vivo. Results Here, we demonstrate that increasing concentrations of F07#13 (0.01, 0.1, 1 µM) cause a decrease in Tat levels in a dose-dependent manner by inhibiting the Cdk9/T1-Tat complex formation and subsequent ubiquitin-mediated Tat sequestration and degradation. Our data indicate that complexes I and IV contain distinct patterns of ubiquitinated Tat and that transcriptional inhibition induced by F07#13 causes an overall reduction in Tat levels. This reduction may be triggered by F07#13 but ultimately is mediated by TAR-gag viral RNAs that bind suppressive transcription factors (similar to 7SK, NRON, HOTAIR, and Xist lncRNAs) to enhance transcriptional gene silencing and latency. These RNAs complex with PRC2, Sin3A, and Cul4B, resulting in epigenetic modifications. Finally, we observed an F07#13-mediated decrease of viral burden by targeting the R region of the long terminal repeat (HIV-1 promoter region, LTR), promoting both paused polymerases and increased efficiency of CRISPR/Cas9 editing in infected cells. This implies that gene editing may be best performed under a repressed transcriptional state. Conclusions Collectively, our results indicate that F07#13, which can terminate RNA Polymerase II at distinct sites, can generate scaffold RNAs, which may assemble into specific sets of “RNA Machines” that contribute to gene regulation. It remains to be seen whether these effects can also be seen in various clades that have varying promoter strength, mutant LTRs, and in patient samples. Electronic supplementary material The online version of this article (10.1186/s12977-019-0475-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel O Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Tristan A Scott
- Center for Gene Therapy, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Michelle L Pleet
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Thy T Vo
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Mohammed Saifuddin
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Dmytro Kovalskyy
- Protein Engineering Department, Institute of Molecular Biology and Genetics, UAS, Kiev, Ukraine
| | - James Erickson
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Robert A Barclay
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Chen Zeng
- Department of Physics, The George Washington University, Washington, DC, USA
| | - Marc S Weinberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Wits/SA MRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA. .,Laboratory of Molecular Virology, George Mason University, Discovery Hall Room 182, 10900 University Blvd., Manassas, VA, 20110, USA.
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17
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Spector C, Mele AR, Wigdahl B, Nonnemacher MR. Genetic variation and function of the HIV-1 Tat protein. Med Microbiol Immunol 2019; 208:131-169. [PMID: 30834965 DOI: 10.1007/s00430-019-00583-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/11/2019] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) encodes a transactivator of transcription (Tat) protein, which has several functions that promote viral replication, pathogenesis, and disease. Amino acid variation within Tat has been observed to alter the functional properties of Tat and, depending on the HIV-1 subtype, may produce Tat phenotypes differing from viruses' representative of each subtype and commonly used in in vivo and in vitro experimentation. The molecular properties of Tat allow for distinctive functional activities to be determined such as the subcellular localization and other intracellular and extracellular functional aspects of this important viral protein influenced by variation within the Tat sequence. Once Tat has been transported into the nucleus and becomes engaged in transactivation of the long terminal repeat (LTR), various Tat variants may differ in their capacity to activate viral transcription. Post-translational modification patterns based on these amino acid variations may alter interactions between Tat and host factors, which may positively or negatively affect this process. In addition, the ability of HIV-1 to utilize or not utilize the transactivation response (TAR) element within the LTR, based on genetic variation and cellular phenotype, adds a layer of complexity to the processes that govern Tat-mediated proviral DNA-driven transcription and replication. In contrast, cytoplasmic or extracellular localization of Tat may cause pathogenic effects in the form of altered cell activation, apoptosis, or neurotoxicity. Tat variants have been shown to differentially induce these processes, which may have implications for long-term HIV-1-infected patient care in the antiretroviral therapy era. Future studies concerning genetic variation of Tat with respect to function should focus on variants derived from HIV-1-infected individuals to efficiently guide Tat-targeted therapies and elucidate mechanisms of pathogenesis within the global patient population.
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Affiliation(s)
- Cassandra Spector
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Anthony R Mele
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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18
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Kurnaeva MA, Sheval EV, Musinova YR, Vassetzky YS. Tat basic domain: A "Swiss army knife" of HIV-1 Tat? Rev Med Virol 2019; 29:e2031. [PMID: 30609200 DOI: 10.1002/rmv.2031] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 01/16/2023]
Abstract
Tat (transactivator of transcription) regulates transcription from the HIV provirus. It plays a crucial role in disease progression, supporting efficient replication of the viral genome. Tat also modulates many functions in the host genome via its interaction with chromatin and proteins. Many of the functions of Tat are associated with its basic domain rich in arginine and lysine residues. It is still unknown why the basic domain exhibits so many diverse functions. However, the highly charged basic domain, coupled with the overall structural flexibility of Tat protein itself, makes the basic domain a key player in binding to or associating with cellular and viral components. In addition, the basic domain undergoes diverse posttranslational modifications, which further expand and modulate its functions. Here, we review the current knowledge of Tat basic domain and its versatile role in the interaction between the virus and the host cell.
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Affiliation(s)
- Margarita A Kurnaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, CNRS, Villejuif, France
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, CNRS, Villejuif, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yegor S Vassetzky
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, CNRS, Villejuif, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Nuclear Organization and Pathologies, CNRS, UMR8126, Université Paris-Sud, Institut Gustave Roussy, Villejuif, France
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19
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Tang B, Li B, Li B, Qin J, Zhao J, Xu J, Qiu Y, Wu Z, Fang M. Insights into the stereoselectivity of human SETD7 methyltransferase. RSC Adv 2019; 9:9218-9227. [PMID: 35517649 PMCID: PMC9062083 DOI: 10.1039/c9ra00190e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/04/2019] [Indexed: 12/31/2022] Open
Abstract
Human SETD7 methyltransferase (hSETD7) is involved in a wide range of physiological processes, and has been considered as a significant target to develop new drugs. (R)-PFI-2, one hSETD7 inhibitor, could bind to the pocket of substrates with potent (low nanomolar) activity and high selectivity, while its enantiomer (S)-PFI-2 showed 500-fold less activity in IC50 determination. Why do this pair of enantiomers, with nearly identical structures, exert tremendously different inhibitory activity? We performed a total of 900 ns long-timescale molecular dynamics (MD) simulations and 80 ps hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations to understand the molecular mechanism of the stereoselectivity of hSETD7. For each SAM/hSETD7/PFI-2 system, we characterized and compared the residual fluctuation of hSETD7, and generated molecular interaction fingerprints (IFP) to exemplify the propensities of SAM/hSETD7-inhibitor interactions. Based on the QM/MM MD, we accurately captured the difference of hydrogen bonds between the SAM/hSETD7/(R)-PFI-2 and SAM/hSETD7/(S)-PFI-2 systems. Especially the strength of the hydrogen bond between G336 and two inhibitors, which determines the stability of the post-SET loop. The energy barrier for (S)-PFI-2 was much bigger than (R)-PFI-2 from global minimum to bioactive conformation as the potential energy surface scanning (PES) showed. Moreover, by estimating the binding affinity and phylogenetic tree analysis, we discovered 16 hotspots were essential for binding both enantiomers but the specific mode of interaction between these hotspots and enantiomorphs is different. Our findings reveal the effect of chirality on the inhibition activity of hSETD7 in detail, and provide valuable information for hSETD7 structure-based drug development. This work clearly reveals the interaction of SAM/hSET7/(R/S)-PFI-2 systems, and confirms that the different bioactive energy barriers of (R)-PFI-2 and (S)-PFI-2 lead to the tremendously different inhibitory activities between these two antipodes.![]()
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Affiliation(s)
- Bowen Tang
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Baicun Li
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Boqun Li
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Jingbo Qin
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Junming Zhao
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Jianwenn Xu
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Yingkun Qiu
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Zhen Wu
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
| | - Meijuan Fang
- School of Pharmaceutical Sciences
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- Xiamen University
- Xiamen 361000
- China
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20
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Pham VV, Salguero C, Khan SN, Meagher JL, Brown WC, Humbert N, de Rocquigny H, Smith JL, D'Souza VM. HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry. Nat Commun 2018; 9:4266. [PMID: 30323330 PMCID: PMC6189040 DOI: 10.1038/s41467-018-06591-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 09/11/2018] [Indexed: 01/05/2023] Open
Abstract
The HIV Tat protein competes with the 7SK:HEXIM interaction to hijack pTEFb from 7SK snRNP and recruit it to the TAR motif on stalled viral transcripts. Here we solve structures of 7SK stemloop-1 and TAR in complex with Tat’s RNA binding domain (RBD) to gain insights into this process. We find that 7SK is peppered with arginine sandwich motifs (ASM)—three classical and one with a pseudo configuration. Despite having similar RBDs, the presence of an additional arginine, R52, confers Tat the ability to remodel the pseudo configuration, required for HEXIM binding, into a classical sandwich, thus displacing HEXIM. Tat also uses R52 to remodel the TAR bulge into an ASM whose structure is identical to that of the remodeled ASM in 7SK. Together, our structures reveal a dual structural mimicry wherein viral Tat and TAR have co-opted structural motifs present in cellular HEXIM and 7SK for productive transcription of its genome. The HIV Tat protein recruits a host elongation factor from the cellular 7SK complex to the viral TAR RNA to ensure transcriptional elongation. Here, Pham et al. solve the structures of both 7SK and TAR RNAs in complex with Tat’s RNA binding domain and gain mechanistic insights into the process.
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Affiliation(s)
- Vincent V Pham
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Carolina Salguero
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.,Vice Presidency of Research, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Shamsun Nahar Khan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Pharmacy, East West University, Dhaka, 1212, Bangladesh
| | - Jennifer L Meagher
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI, 48109, USA
| | - W Clay Brown
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI, 48109, USA
| | - Nicolas Humbert
- Faculté de Pharmacie, Laboratoire de Bioimagerie et Pathologies, UMR 7021 du CNRS, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France
| | - Hugues de Rocquigny
- Faculté de Pharmacie, Laboratoire de Bioimagerie et Pathologies, UMR 7021 du CNRS, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France.,Inserm - U1259 MAVIVH. Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, 10 boulevard Tonnelle - BP 3223, 37032, Tours Cedex 1, France
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave, Ann Arbor, MI, 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Victoria M D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA.
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21
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Hirano T, Mori S, Kagechika H. Recent Advances in Chemical Tools for the Regulation and Study of Protein Lysine Methyltransferases. CHEM REC 2018; 18:1745-1759. [DOI: 10.1002/tcr.201800034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Tomoya Hirano
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Shuichi Mori
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku Tokyo 101-0062 Japan
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22
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Biological processes and signal transduction pathways regulated by the protein methyltransferase SETD7 and their significance in cancer. Signal Transduct Target Ther 2018; 3:19. [PMID: 30013796 PMCID: PMC6043541 DOI: 10.1038/s41392-018-0017-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/05/2018] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Protein methyltransferases have been shown to methylate histone and non-histone proteins, leading to regulation of several biological processes that control cell homeostasis. Over the past few years, the histone-lysine N-methyltransferase SETD7 (SETD7; also known as SET7/9, KIAA1717, KMT7, SET7, SET9) has emerged as an important regulator of at least 30 non-histone proteins and a potential target for the treatment of several human diseases. This review discusses current knowledge of the structure and subcellular localization of SETD7, as well as its function as a histone and non-histone methyltransferase. This work also underlines the putative contribution of SETD7 to the regulation of gene expression, control of cell proliferation, differentiation and endoplasmic reticulum stress, which indicate that SETD7 is a candidate for novel targeted therapies with the aim of either stimulating or inhibiting its activity, depending on the cell signaling context.
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Hirano T, Fujiwara T, Niwa H, Hirano M, Ohira K, Okazaki Y, Sato S, Umehara T, Maemoto Y, Ito A, Yoshida M, Kagechika H. Development of Novel Inhibitors for Histone Methyltransferase SET7/9 based on Cyproheptadine. ChemMedChem 2018; 13:1530-1540. [PMID: 29882380 DOI: 10.1002/cmdc.201800233] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/04/2018] [Indexed: 12/19/2022]
Abstract
The histone methyltransferase SET7/9 methylates not only histone but also non-histone proteins as substrates, and therefore, SET7/9 inhibitors are considered candidates for the treatment of diseases. Previously, our group identified cyproheptadine, used clinically as a serotonin receptor antagonist and histamine receptor (H1) antagonist, as a novel scaffold of the SET7/9 inhibitor. In this work, we focused on dibenzosuberene as a substructure of cyproheptadine and synthesized derivatives with various functional groups. Among them, the compound bearing a 2-hydroxy group showed the most potent activity. On the other hand, a 3-hydroxy group or another hydrophilic functional group such as acetamide decreased the activity. Structural analysis clarified a rationale for the improved potency only by tightly restricted location and type of the hydrophilic group. In addition, a SET7/9 loop, which was only partially visible in the complex with cyproheptadine, became more clearly visible in the complex with 2-hydroxycyproheptadine. These results are expected to be helpful for further structure-based development of SET7/9 inhibitors.
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Affiliation(s)
- Tomoya Hirano
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Takashi Fujiwara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Hideaki Niwa
- Epigenetics Drug Discovery Unit, RIKEN Center for Life Science Technologies (CLST), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Michitake Hirano
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Kasumi Ohira
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Yusuke Okazaki
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Shin Sato
- Epigenetics Drug Discovery Unit, RIKEN Center for Life Science Technologies (CLST), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Takashi Umehara
- Epigenetics Drug Discovery Unit, RIKEN Center for Life Science Technologies (CLST), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yuki Maemoto
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Akihiro Ito
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.,Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Drug Discovery Platforms Cooperation Division, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
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24
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Abstract
BACKGROUND The viral transactivator Tat protein is a key modulator of HIV-1 replication, as it regulates transcriptional elongation from the integrated proviral genome. Tat recruits the human transcription elongation factor b, and other host proteins, such as the super elongation complex, to activate the cellular RNA polymerase II, normally stalled shortly after transcription initiation at the HIV promoter. By means of a complex set of interactions with host cellular factors, Tat determines the fate of viral activity within the infected cell. The virus will either actively replicate to promote dissemination in blood and tissues, or become dormant mostly in memory CD4+ T cells, as part of a small but long-living latent reservoir, the main obstacle for HIV eradication. OBJECTIVE In this review, we summarize recent advances in the understanding of the multi-step mechanism that regulates Tat-mediated HIV-1 transcription and RNA polymerase II release, to promote viral transcription elongation. Early events of the human transcription elongation factor b release from the inhibitory 7SK small nuclear ribonucleoprotein complex and its recruitment to the HIV promoter will be discussed. Specific roles of the super elongation complex subunits during transcription elongation, and insight on recently identified cellular factors and mechanisms regulating HIV latency will be detailed. CONCLUSION Understanding the complexity of HIV transcriptional regulation by host factors may open the door for development of novel strategies to eradicate the resilient latent reservoir.
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Affiliation(s)
- Guillaume Mousseau
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
| | - Susana T Valente
- The Scripps Research Institute, Department of Immunology and Microbiology, 130 Scripps Way, Jupiter, FL 33458. United States
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25
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Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, Yates JR, Jones KA. SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy. PLoS Pathog 2018; 14:e1007071. [PMID: 29791506 PMCID: PMC5988312 DOI: 10.1371/journal.ppat.1007071] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 06/05/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
HIV-1 Tat is a key regulator of viral transcription, however little is known about the mechanisms that control its turnover in T cells. Here we use a novel proteomics technique, called DiffPOP, to identify the molecular target of JIB-04, a small molecule compound that potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines. Mass-spectrometry analysis of whole-cell extracts from 2D10 Jurkat T cells revealed that JIB-04 targets Serine Hydroxymethyltransferase 2 (SHMT2), a regulator of glycine biosynthesis and an adaptor for the BRCC36 K63Ub-specific deubiquitinase in the BRISC complex. Importantly, knockdown of SHMT1,2 or BRCC36, or exposure of cells to JIB-04, strongly increased Tat K63Ub-dependent destruction via autophagy. Moreover, point mutation of multiple lysines in Tat, or knockdown of BRCC36 or SHMT1,2, was sufficient to prevent destruction of Tat by JIB-04. We conclude that HIV-1 Tat levels are regulated through K63Ub-selective autophagy mediated through SHMT1,2 and the BRCC36 deubiquitinase.
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Affiliation(s)
- Muyu Xu
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - James J. Moresco
- Mass Spectrometry Core for Proteomics and Metabolomics, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Max Chang
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
| | - Amey Mukim
- Division of Infectious Diseases, University of California San Diego School of Medicine, La Jolla, CA, United States of America
| | - Davey Smith
- Division of Infectious Diseases, University of California San Diego School of Medicine, La Jolla, CA, United States of America
| | - Jolene K. Diedrich
- Mass Spectrometry Core for Proteomics and Metabolomics, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, United States of America
| | - John R. Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, United States of America
| | - Katherine A. Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, United States of America
- * E-mail:
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26
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Khoury G, Mota TM, Li S, Tumpach C, Lee MY, Jacobson J, Harty L, Anderson JL, Lewin SR, Purcell DFJ. HIV latency reversing agents act through Tat post translational modifications. Retrovirology 2018; 15:36. [PMID: 29751762 PMCID: PMC5948896 DOI: 10.1186/s12977-018-0421-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 05/05/2018] [Indexed: 12/18/2022] Open
Abstract
Background Different classes of latency reversing agents (LRAs) are being evaluated to measure their effects in reactivating HIV replication from latently infected cells. A limited number of studies have demonstrated additive effects of LRAs with the viral protein Tat in initiating transcription, but less is known about how LRAs interact with Tat, particularly through basic residues that may be post-translationally modified to alter the behaviour of Tat for processive transcription and co-transcriptional RNA processing. Results Here we show that various lysine and arginine mutations reduce the capacity of Tat to induce both transcription and mRNA splicing. The lysine 28 and lysine 50 residues of Tat, or the acetylation and methylation modifications of these basic amino acids, were essential for Tat transcriptional control, and also for the proviral expression effects elicited by histone deacetylase inhibitors (HDACi) or the bromodomain inhibitor JQ1. We also found that JQ1 was the only LRA tested that could induce HIV mRNA splicing in the absence of Tat, or rescue splicing for Tat lysine mutants in a BRD4-dependent manner. Conclusions Our data provide evidence that Tat activities in both co-transcriptional RNA processing together with transcriptional initiation and processivity are crucial during reactivation of latent HIV infection. The HDACi and JQ1 LRAs act with Tat to increase transcription, but JQ1 also enables post-transcriptional mRNA splicing. Tat residues K28 and K50, or their modifications through acetylation or methylation, are critical for LRAs that function in conjunction with Tat. Electronic supplementary material The online version of this article (10.1186/s12977-018-0421-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Georges Khoury
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Talia M Mota
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Shuang Li
- School of Life Sciences, Peking University, Beijing, China
| | - Carolin Tumpach
- The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Michelle Y Lee
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Jonathan Jacobson
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Leigh Harty
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Jenny L Anderson
- The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia.,Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.
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27
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Ding H, Lu WC, Hu JC, Liu YC, Zhang CH, Lian FL, Zhang NX, Meng FW, Luo C, Chen KX. Identification and Characterizations of Novel, Selective Histone Methyltransferase SET7 Inhibitors by Scaffold Hopping- and 2D-Molecular Fingerprint-Based Similarity Search. Molecules 2018; 23:molecules23030567. [PMID: 29498708 PMCID: PMC6017732 DOI: 10.3390/molecules23030567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 02/23/2018] [Accepted: 02/28/2018] [Indexed: 12/17/2022] Open
Abstract
SET7, serving as the only histone methyltransferase that monomethylates 'Lys-4' of histone H3, has been proved to function as a key regulator in diverse biological processes, such as cell proliferation, transcriptional network regulation in embryonic stem cell, cell cycle control, protein stability, heart morphogenesis and development. What's more, SET7 is involved inthe pathogenesis of alopecia aerate, breast cancer, tumor and cancer progression, atherosclerosis in human carotid plaques, chronic renal diseases, diabetes, obesity, ovarian cancer, prostate cancer, hepatocellular carcinoma, and pulmonary fibrosis. Therefore, there is urgent need to develop novel SET7 inhibitors. In this paper, based on DC-S239 which has been previously reported in our group, we employed scaffold hopping- and 2D fingerprint-based similarity searches and identified DC-S285 as the new hit compound targeting SET7 (IC50 = 9.3 μM). Both radioactive tracing and NMR experiments validated the interactions between DC-S285 and SET7 followed by the second-round similarity search leading to the identification ofDC-S303 with the IC50 value of 1.1 μM. In cellular level, DC-S285 retarded tumor cell proliferation and showed selectivity against MCF7 (IC50 = 21.4 μM), Jurkat (IC50 = 2.2 μM), THP1 (IC50 = 3.5 μM), U937 (IC50 = 3.9 μM) cell lines. Docking calculations suggested that DC-S303 share similar binding mode with the parent compoundDC-S239. What's more, it presented good selectivity against other epigenetic targets, including SETD1B, SETD8, G9a, SMYD2 and EZH2. DC-S303 can serve as a drug-like scaffold which may need further optimization for drug development, and can be used as chemical probe to help the community to better understand the SET7 biology.
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Affiliation(s)
- Hong Ding
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Wen Chao Lu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Jun Chi Hu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Yu-Chih Liu
- Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China.
| | - Chen Hua Zhang
- Shanghai ChemPartner Co., Ltd., #5 Building, 998 Halei Road, Shanghai 201203, China.
| | - Fu Lin Lian
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Nai Xia Zhang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Fan Wang Meng
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada.
| | - Cheng Luo
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Kai Xian Chen
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
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28
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Ne E, Palstra RJ, Mahmoudi T. Transcription: Insights From the HIV-1 Promoter. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:191-243. [DOI: 10.1016/bs.ircmb.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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29
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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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30
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Boehm D, Ott M. Host Methyltransferases and Demethylases: Potential New Epigenetic Targets for HIV Cure Strategies and Beyond. AIDS Res Hum Retroviruses 2017; 33:S8-S22. [PMID: 29140109 DOI: 10.1089/aid.2017.0180] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A successful HIV cure strategy may require reversing HIV latency to purge hidden viral reservoirs or enhancing HIV latency to permanently silence HIV transcription. Epigenetic modifying agents show promise as antilatency therapeutics in vitro and ex vivo, but also affect other steps in the viral life cycle. In this review, we summarize what we know about cellular DNA and protein methyltransferases (PMTs) as well as demethylases involved in HIV infection. We describe the biology and function of DNA methyltransferases, and their controversial role in HIV infection. We further explain the biology of PMTs and their effects on lysine and arginine methylation of histone and nonhistone proteins. We end with a focus on protein demethylases, their unique modes of action and their emerging influence on HIV infection. An outlook on the use of methylation-modifying agents in investigational HIV cure strategies is provided.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
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31
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Chen M, Gan X, Yoshino KI, Kitakawa M, Shoji I, Deng L, Hotta H. Hepatitis C virus NS5A protein interacts with lysine methyltransferase SET and MYND domain-containing 3 and induces activator protein 1 activation. Microbiol Immunol 2017; 60:407-17. [PMID: 27080060 DOI: 10.1111/1348-0421.12383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/01/2016] [Accepted: 04/10/2016] [Indexed: 12/27/2022]
Abstract
Hepatitis C virus (HCV) non-structural protein 5A (NS5A) is a multifunctional protein that is involved in the HCV life cycle and pathogenesis. In this study, a host protein(s) interacting with NS5A by tandem affinity purification were searched for with the aim of elucidating the role of NS5A. An NS5A-interacting protein, SET and MYND domain-containing 3 (SMYD3), a lysine methyltransferase reportedly involved in the development of cancer, was identified. The interaction between NS5A and SMYD3 was confirmed in ectopically expressing, HCV RNA replicon-harboring and HCV-infected cells. The other HCV proteins did not bind to SMYD3. SMYD3 bound to NS5A of HCV genotypes 1b and 2a. Deletion mutational analysis revealed that domains II and III of NS5A (amino acids [aa] 250 to 447) and the MYND and N-SET domains of SMYD3 (aa 1 to 87) are involved in the full extent of NS5A-SMYD3 interaction. NS5A co-localized with SMYD3 exclusively in the cytoplasm, thereby inhibiting nuclear localization of SMYD3. Moreover, NS5A formed a complex with SMYD3 and heat shock protein 90 (HSP90), which is a positive regulator of SMYD3. The intensity of binding between SMYD3 and HSP90 was enhanced by NS5A. Luciferase reporter assay demonstrated that NS5A significantly induces activator protein 1 (AP-1) activity, this being potentiated by co-expression of SMYD3 with NS5A. Taken together, the present results suggest that NS5A interacts with SMYD3 and induces AP-1 activation, possibly by facilitating binding between HSP90 and SMYD3. This may be a novel mechanism of AP-1 activation in HCV-infected cells.
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Affiliation(s)
- Ming Chen
- Division of Microbiology.,Division of Infectious Disease Control, Kobe University Graduate School of Medicine
| | - Xiang Gan
- Division of Microbiology.,Institute of Biochemistry and Molecular Biology, Hubei University, Wuhan, China
| | | | | | - Ikuo Shoji
- Division of Infectious Disease Control, Kobe University Graduate School of Medicine
| | - Lin Deng
- Division of Microbiology.,Division of Infectious Disease Control, Kobe University Graduate School of Medicine
| | - Hak Hotta
- Division of Microbiology.,Department of Oral Vaccine and Drug Development, Kobe University Graduate School of Health Sciences, Kobe, Japan
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32
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Current perspectives in Set7 mediated stem cell differentiation. Noncoding RNA 2016; 2:ncrna2040014. [PMID: 29657272 PMCID: PMC5831927 DOI: 10.3390/ncrna2040014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 12/14/2022] Open
Abstract
Set7 is a key regulatory enzyme involved in the methylation of lysine residues of histone and non-histone proteins. This lysine methyltransferase is induced during stem cell differentiation and regulates lineage specific gene transcription and cell fate. In this article we discuss recent experimental evidence identifying regulatory targets under the control of Set7 as well as emerging evidence of regulation in stem cell differentiation. Furthermore, we discuss the function of non-coding RNAs regulated by Set7 implicated in cell plasticity.
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Liu MC, Chen CY, Chiang CH, Wang WM, Cheng RP. Effect of lysine methylation and acetylation on the RNA recognition and cellular uptake of Tat-derived peptides. Bioorg Med Chem 2016; 24:5047-5051. [DOI: 10.1016/j.bmc.2016.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/09/2016] [Accepted: 08/11/2016] [Indexed: 11/25/2022]
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Papeta N, Patel A, D’Agati VD, Gharavi AG. Refinement of the HIVAN1 Susceptibility Locus on Chr. 3A1-A3 via Generation of Sub-Congenic Strains. PLoS One 2016; 11:e0163860. [PMID: 27736906 PMCID: PMC5063463 DOI: 10.1371/journal.pone.0163860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/15/2016] [Indexed: 01/19/2023] Open
Abstract
HIV-1 transgenic mice on the FVB/NJ background (TgFVB) represent a validated model of HIV-associated nephropathy (HIVAN). A major susceptibility locus, HIVAN1, was previously mapped to chromosome 3A1-A3 in a cross between TgFVB and CAST/EiJ (CAST) strains, and introgression of a 51.9 Mb segment encompassing HIVAN1 from CAST into TgFVB resulted in accelerated development of nephropathy. We generated three sub-congenic strains carrying CAST alleles in the proximal or distal regions of the HIVAN1 locus (Sub-II, 3.02–38.93 Mb; Sub-III, 38.45–55.1 Mb and Sub-IV, 47.7–55.1 Mb, build 38). At 5–10 weeks of age, histologic injury and proteinuria did not differ between HIV-1 transgenic Sub-II and TgFVB mice. In contrast, HIV-1 transgenic Sub-III and Sub-IV mice displayed up to 4.4 fold more histopathologic injury and 6-fold more albuminuria compared to TgFVB mice, similar in severity to the full-length congenic mice. The Sub-IV segment defines a maximal 7.4 Mb interval for HIVAN1, and encodes 31 protein coding genes: 15 genes have missense variants differentiating CAST from FVB, and 14 genes show differential renal expression. Of these, Frem1, Foxo1, and Setd7 have been implicated in the pathogenesis of nephropathy. HIVAN1 congenic kidneys are histologically normal without the HIV-1 transgene, yet their global transcriptome is enriched for molecular signatures of apoptosis, adenoviral infection, as well as genes repressed by histone H3 lysine 27 trimethylation, a histone modification associated with HIV-1 life cycle. These data refine HIVAN1to 7.4 Mb and identify latent molecular derangements that may predispose to nephropathy upon exposure to HIV-1.
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Affiliation(s)
- Natalia Papeta
- Department of Medicine, Columbia University, New York, New York, United States of America
| | - Ami Patel
- Department of Medicine, Columbia University, New York, New York, United States of America
| | - Vivette D. D’Agati
- Department of Pathology, Columbia University, New York, New York, United States of America
| | - Ali G. Gharavi
- Department of Medicine, Columbia University, New York, New York, United States of America
- * E-mail:
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Kudithipudi S, Jeltsch A. Approaches and Guidelines for the Identification of Novel Substrates of Protein Lysine Methyltransferases. Cell Chem Biol 2016; 23:1049-1055. [PMID: 27569752 DOI: 10.1016/j.chembiol.2016.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 06/11/2016] [Accepted: 07/03/2016] [Indexed: 12/18/2022]
Abstract
Protein lysine methylation is emerging as a general post-translational modification (PTM) with essential functions regulating protein stability, activity, and protein-protein interactions. One of the outstanding challenges in this field is linking protein lysine methyltransferases (PKMTs) with specific substrates and lysine methylation events in a systematic manner. Inability to validate reported PKMT substrates delayed progress in the field and cast unnecessary doubt about protein lysine methylation as a truly general PTM. Here, we aim to provide a concise guide to help avoid some of the most common pitfalls in studies searching for new PKMT substrates and propose a set of seven basic biochemical rules: (1) include positive controls; (2) use target lysine mutations of substrate proteins as negative controls; (3) use inactive enzyme variants as negative controls; (4) report quantitative methylation data; (5) consider PKMT specificity; (6) validate methyl lysine antibodies; and (7) connect cellular and in vitro results. We explain the logic behind them and discuss how they should be implemented in the experimental work.
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Affiliation(s)
- Srikanth Kudithipudi
- Faculty of Chemistry, Institute of Biochemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Faculty of Chemistry, Institute of Biochemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
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Fujiwara T, Ohira K, Urushibara K, Ito A, Yoshida M, Kanai M, Tanatani A, Kagechika H, Hirano T. Steric structure-activity relationship of cyproheptadine derivatives as inhibitors of histone methyltransferase Set7/9. Bioorg Med Chem 2016; 24:4318-4323. [PMID: 27448773 DOI: 10.1016/j.bmc.2016.07.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 12/20/2022]
Abstract
Set7/9 is a histone lysine methyltransferase, but it is also thought to be involved in a wide variety of pathophysiological functions. We previously identified cyproheptadine, which has a characteristic butterfly-like molecular conformation with bent tricyclic dibenzosuberene and chair-form N-methylpiperidine moieties, as a Set7/9 inhibitor. In this work, we synthesized several derivatives in order to examine the steric structure-inhibitory activity relationship. We found that even a small change of molecular shape due to reduction or replacement of the 10,11-olefinic bond of the tricyclic ring generally resulted in a drastic decrease of the inhibitory activity. Our results should be useful not only for development of more potent and selective inhibitors, but also for the construction of novel inhibitor scaffolds.
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Affiliation(s)
- Takashi Fujiwara
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Kasumi Ohira
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Ko Urushibara
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Akihiro Ito
- Chemical Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Chemical Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Drug Discovery Platforms Cooperation Division, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Misae Kanai
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Tomoya Hirano
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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Ali I, Ramage H, Boehm D, Dirk LMA, Sakane N, Hanada K, Pagans S, Kaehlcke K, Aull K, Weinberger L, Trievel R, Schnoelzer M, Kamada M, Houtz R, Ott M. The HIV-1 Tat Protein Is Monomethylated at Lysine 71 by the Lysine Methyltransferase KMT7. J Biol Chem 2016; 291:16240-8. [PMID: 27235396 DOI: 10.1074/jbc.m116.735415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/06/2022] Open
Abstract
The HIV-1 transactivator protein Tat is a critical regulator of HIV transcription primarily enabling efficient elongation of viral transcripts. Its interactions with RNA and various host factors are regulated by ordered, transient post-translational modifications. Here, we report a novel Tat modification, monomethylation at lysine 71 (K71). We found that Lys-71 monomethylation (K71me) is catalyzed by KMT7, a methyltransferase that also targets lysine 51 (K51) in Tat. Using mass spectrometry, in vitro enzymology, and modification-specific antibodies, we found that KMT7 monomethylates both Lys-71 and Lys-51 in Tat. K71me is important for full Tat transactivation, as KMT7 knockdown impaired the transcriptional activity of wild type (WT) Tat but not a Tat K71R mutant. These findings underscore the role of KMT7 as an important monomethyltransferase regulating HIV transcription through Tat.
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Affiliation(s)
- Ibraheem Ali
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Departments of Medicine and
| | - Holly Ramage
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Daniela Boehm
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Lynnette M A Dirk
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40508
| | - Naoki Sakane
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Kazuki Hanada
- Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Sara Pagans
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Katrin Kaehlcke
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Katherine Aull
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158
| | - Leor Weinberger
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158
| | - Raymond Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and
| | | | - Masafumi Kamada
- Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Robert Houtz
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40508
| | - Melanie Ott
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Departments of Medicine and
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Cohen DO, Duchin S, Feldman M, Zarivach R, Aharoni A, Levy D. Engineering of Methylation State Specific 3xMBT Domain Using ELISA Screening. PLoS One 2016; 11:e0154207. [PMID: 27111853 PMCID: PMC4844143 DOI: 10.1371/journal.pone.0154207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/10/2016] [Indexed: 01/08/2023] Open
Abstract
The ε-amino group of lysine residues may be mono-, di- or tri-methylated by protein lysine methyltransferases. In the past few years it has been highly considered that methylation of both histone and non-histone proteins has fundamental role in development and progression of various human diseases. Thus, the establishment of tools to study lysine methylation that will distinguish between the different states of methylation is required to elucidate their cellular functions. The 3X malignant brain tumor domain (3XMBT) repeats of the Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1) have been utilized in the past as an affinity reagent for the identification of mono- and di-methylated lysine residues on individual proteins and on a proteomic scale. Here, we have utilized the 3XMBT domain to develop an enzyme-linked immunosorbent assay (ELISA) that allows the high-throughput detection of 3XMBT binding to methylated lysines. We demonstrated that this system allows the detection of methylated peptides, methylated proteins and PKMT activity on both peptides and proteins. We also optimized the assay to detect 3XMBT binding in crude E. coli lysates which facilitated the high throughput screening of 3XMBT mutant libraries. We have utilized protein engineering tools and generated a double site saturation 3XMBT library of residues 361 and 411 that were shown before to be important for binding mono and di-methylated substrates and identified variants that can exclusively recognize only di-methylated peptides. Together, our results demonstrate a powerful new approach that will contribute to deeper understanding of lysine methylation biology and that can be utilized for the engineering of domains for specific binders of other post-translational modifications.
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Affiliation(s)
- Dan Od Cohen
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Shai Duchin
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Michal Feldman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
- * E-mail: (DL); (AA)
| | - Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- The National Institute for Biotechnology in the Negev (NIBN), Ben-Gurion University of the Negev, Be’er Sheva, Israel
- * E-mail: (DL); (AA)
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Recent advances in the identification of Tat-mediated transactivation inhibitors: progressing toward a functional cure of HIV. Future Med Chem 2016; 8:421-42. [PMID: 26933891 DOI: 10.4155/fmc.16.3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The current anti-HIV combination therapy does not eradicate the virus that persists mainly in quiescent infected CD4(+) T cells as a latent integrated provirus that resumes after therapy interruption. The Tat-mediated transactivation (TMT) is a critical step in the HIV replication cycle that could give the opportunity to reduce the size of latent reservoirs. More than two decades of research led to the identification of various TMT inhibitors. While none of them met the criteria to reach the market, the search for a suitable TMT inhibitor is still actively pursued. Really promising compounds, including one in a Phase III clinical trial, have been recently identified, thus warranting an update.
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40
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Liu C, Ma X, Liu B, Chen C, Zhang H. HIV-1 functional cure: will the dream come true? BMC Med 2015; 13:284. [PMID: 26588898 PMCID: PMC4654816 DOI: 10.1186/s12916-015-0517-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/03/2015] [Indexed: 02/07/2023] Open
Abstract
The reservoir of human immunodeficiency virus type 1 (HIV-1), a long-lived pool of latently infected cells harboring replication-competent viruses, is the major obstacle to curing acquired immune deficiency syndrome (AIDS). Although the combination antiretroviral therapy (cART) can successfully suppress HIV-1 viremia and significantly delay the progression of the disease, it cannot eliminate the viral reservoir and the patient must continue to take anti-viral medicines for life. Currently, the appearance of the 'Berlin patient', the 'Boston patients', and the 'Mississippi baby' have inspired many therapeutic strategies for HIV-1 aimed at curing efforts. However, the specific eradication of viral latency and the recovery and optimization of the HIV-1-specific immune surveillance are major challenges to achieving such a cure. Here, we summarize recent studies addressing the mechanisms underlying the viral latency and define two categories of viral reservoir: 'shallow' and 'deep'. We also present the current strategies and recent advances in the development of a functional cure for HIV-1, focusing on full/partial replacement of the immune system, 'shock and kill', and 'permanent silencing' approaches.
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Affiliation(s)
- Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Xiancai Ma
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Bingfeng Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Cancan Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
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41
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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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42
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Meng F, Cheng S, Ding H, Liu S, Liu Y, Zhu K, Chen S, Lu J, Xie Y, Li L, Liu R, Shi Z, Zhou Y, Liu YC, Zheng M, Jiang H, Lu W, Liu H, Luo C. Discovery and Optimization of Novel, Selective Histone Methyltransferase SET7 Inhibitors by Pharmacophore- and Docking-Based Virtual Screening. J Med Chem 2015; 58:8166-81. [DOI: 10.1021/acs.jmedchem.5b01154] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fanwang Meng
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Sufang Cheng
- Chinese Academy of Sciences Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hong Ding
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shien Liu
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yan Liu
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kongkai Zhu
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shijie Chen
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Junyan Lu
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yiqian Xie
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Linjuan Li
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Rongfeng Liu
- Shanghai ChemPartner
Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Zhe Shi
- Shanghai ChemPartner
Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Yu Zhou
- Chinese Academy of Sciences Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yu-Chih Liu
- Shanghai ChemPartner
Co., Ltd., Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - Mingyue Zheng
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Wencong Lu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Hong Liu
- Chinese Academy of Sciences Key Laboratory of Receptor Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Drug Discovery
and Design Center, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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43
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Bose D, Gagnon J, Chebloune Y. Comparative Analysis of Tat-Dependent and Tat-Deficient Natural Lentiviruses. Vet Sci 2015; 2:293-348. [PMID: 29061947 PMCID: PMC5644649 DOI: 10.3390/vetsci2040293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 01/10/2023] Open
Abstract
The emergence of human immunodeficiency virus (HIV) causing acquired immunodeficiency syndrome (AIDS) in infected humans has resulted in a global pandemic that has killed millions. HIV-1 and HIV-2 belong to the lentivirus genus of the Retroviridae family. This genus also includes viruses that infect other vertebrate animals, among them caprine arthritis-encephalitis virus (CAEV) and Maedi-Visna virus (MVV), the prototypes of a heterogeneous group of viruses known as small ruminant lentiviruses (SRLVs), affecting both goat and sheep worldwide. Despite their long host-SRLV natural history, SRLVs were never found to be responsible for immunodeficiency in contrast to primate lentiviruses. SRLVs only replicate productively in monocytes/macrophages in infected animals but not in CD4+ T cells. The focus of this review is to examine and compare the biological and pathological properties of SRLVs as prototypic Tat-independent lentiviruses with HIV-1 as prototypic Tat-dependent lentiviruses. Results from this analysis will help to improve the understanding of why and how these two prototypic lentiviruses evolved in opposite directions in term of virulence and pathogenicity. Results may also help develop new strategies based on the attenuation of SRLVs to control the highly pathogenic HIV-1 in humans.
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Affiliation(s)
- Deepanwita Bose
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Jean Gagnon
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Yahia Chebloune
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
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Burg JM, Link JE, Morgan BS, Heller FJ, Hargrove AE, McCafferty DG. KDM1 class flavin-dependent protein lysine demethylases. Biopolymers 2015; 104:213-46. [PMID: 25787087 PMCID: PMC4747437 DOI: 10.1002/bip.22643] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 12/11/2022]
Abstract
Flavin-dependent, lysine-specific protein demethylases (KDM1s) are a subfamily of amine oxidases that catalyze the selective posttranslational oxidative demethylation of methyllysine side chains within protein and peptide substrates. KDM1s participate in the widespread epigenetic regulation of both normal and disease state transcriptional programs. Their activities are central to various cellular functions, such as hematopoietic and neuronal differentiation, cancer proliferation and metastasis, and viral lytic replication and establishment of latency. Interestingly, KDM1s function as catalytic subunits within complexes with coregulatory molecules that modulate enzymatic activity of the demethylases and coordinate their access to specific substrates at distinct sites within the cell and chromatin. Although several classes of KDM1-selective small molecule inhibitors have been recently developed, these pan-active site inhibition strategies lack the ability to selectively discriminate between KDM1 activity in specific, and occasionally opposing, functional contexts within these complexes. Here we review the discovery of this class of demethylases, their structures, chemical mechanisms, and specificity. Additionally, we review inhibition of this class of enzymes as well as emerging interactions with coregulatory molecules that regulate demethylase activity in highly specific functional contexts of biological and potential therapeutic importance.
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Blum G, Islam K, Luo M. Bioorthogonal profiling of protein methylation (BPPM) using an azido analog of S-adenosyl-L-methionine. ACTA ACUST UNITED AC 2015; 5:45-66. [PMID: 23667794 DOI: 10.1002/9780470559277.ch120240] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein methyltransferases (PMTs) utilize S-adenosyl-L-methionine (SAM) as a cofactor and transfer its sulfonium methyl moiety to diverse substrates. These methylation events can lead to meaningful biological outcomes, from transcriptional activation/silencing to cell cycle regulation. This article describes recently developed technology based on protein engineering in tandem with SAM analog cofactors and bioorthogonal click chemistry to unambiguously profile the substrates of a specific PMT. The protocols encapsulate the logic and methods of selectively profiling the substrates of a candidate PMT by (1) engineering the selected PMT to accommodate a bulky SAM analog; (2) generating a proteome containing the engineered PMT; (3) visualizing the proteome-wide substrates of the designated PMT via bioorthogonal labeling with a fluorescent tag; and finally (4) pulling down the proteome-wide substrates for mass spectrometric analysis.
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Affiliation(s)
- Gil Blum
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
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Han T, Wan Y, Wang J, Zhao P, Yuan Y, Wang L, She Y, Broering R, Lu M, Ye L, Zhu Y. Set7 facilitates hepatitis C virus replication via enzymatic activity-dependent attenuation of the IFN-related pathway. THE JOURNAL OF IMMUNOLOGY 2015; 194:2757-68. [PMID: 25681344 DOI: 10.4049/jimmunol.1400583] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hepatitis C virus (HCV) infection is a major cause of chronic liver disease, usually resulting in persistent infection involving hepatic steatosis, cirrhosis, and hepatocellular carcinoma via escape of the host's immune response. Set7 is a lysine-specific methyltransferase that is involved in gene regulation and virus replication. However, the mechanism underlying the immune evasion between HCV and Set7 is not well understood. In this study, we observed that the expression of Set7 in Huh7.5.1 cells was upregulated by HCV infection, and high levels of Set7 expression were also found in the sera, PBMCs, and liver tissue of HCV patients relative to healthy individuals. Further investigation showed that Set7 enhanced HCV replication in an enzymatic activity-dependent manner. Moreover, our data showed that Set7 decreased the expression of virus-induced IFN and IFN-related effectors, such as dsRNA-activated protein kinase and 2',5'-oligoadenylate synthetase. Further investigation suggested that Set7 suppressed the endogenous IFN expression by reducing the nuclear translocation of IFN regulatory factor 3/7 and the p65 subunit of NF-κB and reduced IFN-induced dsRNA-activated protein kinase and 2',5'-oligoadenylate synthetase via attenuation of the phosphorylation of STAT1 and STAT2. Additionally, IFN receptors, including IFNAR1 and IFNAR2, which are located upstream of the JAK/STAT pathway, were reduced by Set7. Taken together, our results reveal that Set7 facilitates HCV replication through the attenuation of IFN signaling pathways and IFN-related effectors.
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Affiliation(s)
- Tao Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yushun Wan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Jun Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Peng Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yue Yuan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Li Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yinglong She
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Ruth Broering
- Medical Faculty, Department of Gastroenterology and Hepatology, University of Duisburg-Essen, 45127 Essen, Germany; and
| | - Mengji Lu
- Institute of Virology, University of Duisburg-Essen, 45127 Essen, Germany
| | - Linbai Ye
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Ying Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei 430072, China;
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Zhang L, Qin J, Li Y, Wang J, He Q, Zhou J, Liu M, Li D. Modulation of the stability and activities of HIV-1 Tat by its ubiquitination and carboxyl-terminal region. Cell Biosci 2014; 4:61. [PMID: 25328666 PMCID: PMC4201738 DOI: 10.1186/2045-3701-4-61] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/27/2014] [Indexed: 11/28/2022] Open
Abstract
Background The transactivator of transcription (Tat) protein of human immunodeficiency virus type 1 (HIV-1) is known to undergo ubiquitination. However, the roles of ubiquitination in regulating Tat stability and activities are unclear. In addition, although the 72- and 86-residue forms are commonly used for in vitro studies, the 101-residue form is predominant in the clinical isolates of HIV-1. The influence of the carboxyl-terminal region of Tat on its functions remains unclear. Results In this study, we find that Tat undergoes lysine 48-linked ubiquitination and is targeted to proteasome-dependent degradation. Expression of various ubiquitin mutants modulates Tat activities, including the transactivation of transcription, induction of apoptosis, interaction with tubulin, and stabilization of microtubules. Moreover, the 72-, 86- and 101-residue forms of Tat also exhibit different stability and aforementioned activities. Conclusions Our findings demonstrate that the ubiquitination and carboxyl-terminal region of Tat are critical determinants of its stability and activities.
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Affiliation(s)
- Linlin Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Juan Qin
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Yuanyuan Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Jian Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Qianqian He
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Jun Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Min Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
| | - Dengwen Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071 China
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(R)-PFI-2 is a potent and selective inhibitor of SETD7 methyltransferase activity in cells. Proc Natl Acad Sci U S A 2014; 111:12853-8. [PMID: 25136132 DOI: 10.1073/pnas.1407358111] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
SET domain containing (lysine methyltransferase) 7 (SETD7) is implicated in multiple signaling and disease related pathways with a broad diversity of reported substrates. Here, we report the discovery of (R)-PFI-2-a first-in-class, potent (Ki (app) = 0.33 nM), selective, and cell-active inhibitor of the methyltransferase activity of human SETD7-and its 500-fold less active enantiomer, (S)-PFI-2. (R)-PFI-2 exhibits an unusual cofactor-dependent and substrate-competitive inhibitory mechanism by occupying the substrate peptide binding groove of SETD7, including the catalytic lysine-binding channel, and by making direct contact with the donor methyl group of the cofactor, S-adenosylmethionine. Chemoproteomics experiments using a biotinylated derivative of (R)-PFI-2 demonstrated dose-dependent competition for binding to endogenous SETD7 in MCF7 cells pretreated with (R)-PFI-2. In murine embryonic fibroblasts, (R)-PFI-2 treatment phenocopied the effects of Setd7 deficiency on Hippo pathway signaling, via modulation of the transcriptional coactivator Yes-associated protein (YAP) and regulation of YAP target genes. In confluent MCF7 cells, (R)-PFI-2 rapidly altered YAP localization, suggesting continuous and dynamic regulation of YAP by the methyltransferase activity of SETD7. These data establish (R)-PFI-2 and related compounds as a valuable tool-kit for the study of the diverse roles of SETD7 in cells and further validate protein methyltransferases as a druggable target class.
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Guitot K, Scarabelli S, Drujon T, Bolbach G, Amoura M, Burlina F, Jeltsch A, Sagan S, Guianvarc’h D. Label-free measurement of histone lysine methyltransferases activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2014; 456:25-31. [DOI: 10.1016/j.ab.2014.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/02/2014] [Accepted: 04/07/2014] [Indexed: 11/28/2022]
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Lanouette S, Mongeon V, Figeys D, Couture JF. The functional diversity of protein lysine methylation. Mol Syst Biol 2014; 10:724. [PMID: 24714364 PMCID: PMC4023394 DOI: 10.1002/msb.134974] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Large‐scale characterization of post‐translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high‐throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine‐methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε‐amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non‐histone lysine‐methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.
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Affiliation(s)
- Sylvain Lanouette
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
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