1
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Chen IP, Longbotham JE, McMahon S, Suryawanshi RK, Carlson-Stevermer J, Gupta M, Zhang MY, Soveg FW, Hayashi JM, Taha TY, Lam VL, Li Y, Yu Z, Titus EW, Diallo A, Oki J, Holden K, Krogan N, Galonić Fujimori D, Ott M. Viral E Protein Neutralizes BET Protein-Mediated Post-Entry Antagonism of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34816261 DOI: 10.1101/2021.11.14.468537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Inhibitors of Bromodomain and Extra-terminal domain (BET) proteins are possible anti-SARS-CoV-2 prophylactics as they downregulate angiotensin-converting enzyme 2 (ACE2). Here, we show that BET proteins should not be inactivated therapeutically as they are critical antiviral factors at the post-entry level. Knockouts of BRD3 or BRD4 in cells overexpressing ACE2 exacerbate SARS-CoV-2 infection; the same is observed when cells with endogenous ACE2 expression are treated with BET inhibitors during infection, and not before. Viral replication and mortality are also enhanced in BET inhibitor-treated mice overexpressing ACE2. BET inactivation suppresses interferon production induced by SARS-CoV-2, a process phenocopied by the envelope (E) protein previously identified as a possible "histone mimetic." E protein, in an acetylated form, directly binds the second bromodomain of BRD4. Our data support a model where SARS-CoV-2 E protein evolved to antagonize interferon responses via BET protein inhibition; this neutralization should not be further enhanced with BET inhibitor treatment.
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2
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Lee Yu K, Jung YM, Park SH, Lee SD, You JC. Human transcription factor YY1 could upregulate the HIV-1 gene expression. BMB Rep 2021. [PMID: 31818358 PMCID: PMC7262509 DOI: 10.5483/bmbrep.2020.53.5.222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Gene expression in HIV-1 is regulated by the promoters in 5’ long-terminal repeat (LTR) element, which contain multiple DNA regulatory elements that serve as binding sites for cellular transcription factors. YY1 could repress HIV-1 gene expression and latent infection. Here, however, we observed that virus production can be increased by YY1 over-expression and decreased under YY1 depleted condition by siRNA treatment. To identify functional domain(s) of YY1 activation, we constructed a number of YY1 truncated mutants. Our data show that full-length YY1 enhances the viral transcription both through U3 and U3RU5 promoters. Moreover, the C-terminal region (296-414 residues) of YY1 is responsible for the transcriptional upregulation, which could be enhanced further in the presence of the viral Tat protein. The central domain of YY1 (155-295 residues) does not affect LTR activity but has a negative effect on HIV-1 gene expression. Taken together, our study shows that YY1 could act as a transcriptional activator in HIV-1 replication, at least in the early stages of infection.
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Affiliation(s)
- Kyung Lee Yu
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
| | - Yu Mi Jung
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
| | - Seong Hyun Park
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
| | - Seong Deok Lee
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
| | - Ji Chang You
- National Research Laboratory of Molecular Virology, Department of Pathology, The Catholic University of Korea, Seoul 63071, Korea
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3
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Murray LA, Combs AN, Rekapalli P, Cristea IM. Methods for characterizing protein acetylation during viral infection. Methods Enzymol 2019; 626:587-620. [PMID: 31606092 DOI: 10.1016/bs.mie.2019.06.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lysine acetylation is a prevalent posttranslational modification that acts as a regulator of protein function, subcellular localization, and interactions. A growing body of work has highlighted the importance of temporal alterations in protein acetylation during infection with a range of human viruses. It has become clear that both cellular and viral proteins are decorated by lysine acetylations, and that these modifications contribute to core host defense and virus replication processes. Further defining the extent and dynamics of protein acetylation events during the progression of an infection can provide an important new perspective on the intricate mechanisms underlying the biology and pathogenesis of virus infections. Here, we provide protocols for identifying, quantifying, and probing the regulation of lysine acetylations during viral infection. We describe the use of acetyl-lysine immunoaffinity purification and quantitative mass spectrometry for assessing the cellular acetylome at different stages of an infection. As an alternative to traditional antibody-mediated western blotting, we discuss the benefits of targeted mass spectrometry approaches for detecting and quantifying site-specific acetylations on proteins of interest. Specifically, we provide a protocol using parallel reaction monitoring (PRM). We further discuss experimental considerations that are specific to studying viral infections. Finally, we provide a brief overview of the types of assays that can be employed to characterize the function of an acetylation event in the context of infection. As a method to interrogate the regulation of acetylation, we describe the Fluor de Lys assay for monitoring the enzymatic activities of deacetylases.
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Affiliation(s)
- Laura A Murray
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ, United States
| | - Ashton N Combs
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ, United States
| | - Pranav Rekapalli
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Princeton, NJ, United States.
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4
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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: 39] [Impact Index Per Article: 7.8] [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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5
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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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6
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Pervaiz M, Mishra P, Günther S. Bromodomain Drug Discovery - the Past, the Present, and the Future. CHEM REC 2018; 18:1808-1817. [PMID: 30289209 DOI: 10.1002/tcr.201800074] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/12/2018] [Indexed: 12/26/2022]
Abstract
With the bromodomain (BRD) inhibitor JQ1, a remarkable success story of BRD4 as a novel drug target has been set off that yielded many anti-cancer drugs that are now in clinical trials. But not all of the great prospects of BRDs as drug targets may become true. First evaluations of ongoing clinical trials revealed that treatment with BET-inhibitors can be accompanied with significant toxic side effects and the validation of the therapeutic benefit of BET-inhibitors compared to existing therapies is still pending. New strategies that may overcome possible obstacles in BRD drug discovery include combination therapies with other agents, dual target inhibitors, and proteolysis targeting chimeras (PROTACs). Furthermore, non-BET proteins seem promising drug targets as well. Most recently, BRDs have been identified as putative targets to treat parasitic diseases such as malaria. Milestones in BRD drug discovery are reviewed and promising new developments are evaluated.
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Affiliation(s)
- Mehrosh Pervaiz
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 9, 79104, Freiburg, Germany
| | - Pankaj Mishra
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 9, 79104, Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 9, 79104, Freiburg, Germany
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7
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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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8
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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9
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Suryanarayanan V, Singh SK. Unravelling novel congeners from acetyllysine mimicking ligand targeting a lysine acetyltransferase PCAF bromodomain. J Biomol Struct Dyn 2018; 36:4303-4319. [DOI: 10.1080/07391102.2017.1415820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Venkatesan Suryanarayanan
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630004, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630004, India
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10
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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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11
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Abstract
Despite the success of cART, greater than 50% of HIV infected people develop cognitive and motor deficits termed HIV-associated neurocognitive disorders (HAND). Macrophages are the major cell type infected in the CNS. Unlike for T cells, the virus does not kill macrophages and these long-lived cells may become HIV reservoirs in the brain. They produce cytokines/chemokines and viral proteins that promote inflammation and neuronal damage, playing a key role in HIV neuropathogenesis. HIV Tat is the transactivator of transcription that is essential for replication and transcriptional regulation of the virus and is the first protein to be produced after HIV infection. Even with successful cART, Tat is produced by infected cells. In this study we examined the role of the HIV Tat protein in the regulation of gene expression in human macrophages. Using THP-1 cells, a human monocyte/macrophage cell line, and their infection with lentivirus, we generated stable cell lines that express Tat-Flag. We performed ChIP-seq analysis of these cells and found 66 association sites of Tat in promoter or coding regions. Among these are C5, CRLF2/TSLPR, BDNF, and APBA1/Mint1, genes associated with inflammation/damage. We confirmed the association of Tat with these sequences by ChIP assay and expression of these genes in our THP-1 cell lines by qRT-PCR. We found that HIV Tat increased expression of C5, APBA1, and BDNF, and decreased CRLF2. The K50A Tat-mutation dysregulated expression of these genes without affecting the binding of the Tat complex to their gene sequences. Our data suggest that HIV Tat, produced by macrophage HIV reservoirs in the brain despite successful cART, contributes to neuropathogenesis in HIV-infected people.
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12
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Humphreys PG, Bamborough P, Chung CW, Craggs PD, Gordon L, Grandi P, Hayhow TG, Hussain J, Jones KL, Lindon M, Michon AM, Renaux JF, Suckling CJ, Tough DF, Prinjha RK. Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe. J Med Chem 2017; 60:695-709. [DOI: 10.1021/acs.jmedchem.6b01566] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | | | | | - Paola Grandi
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | - Anne-Marie Michon
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Colin J. Suckling
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
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13
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Moustakim M, Clark PGK, Trulli L, Fuentes de Arriba AL, Ehebauer MT, Chaikuad A, Murphy EJ, Mendez-Johnson J, Daniels D, Hou CFD, Lin YH, Walker JR, Hui R, Yang H, Dorrell L, Rogers CM, Monteiro OP, Fedorov O, Huber KVM, Knapp S, Heer J, Dixon DJ, Brennan PE. Discovery of a PCAF Bromodomain Chemical Probe. Angew Chem Int Ed Engl 2016; 56:827-831. [PMID: 27966810 PMCID: PMC5412877 DOI: 10.1002/anie.201610816] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 11/28/2016] [Indexed: 12/14/2022]
Abstract
The p300/CBP‐associated factor (PCAF) and related GCN5 bromodomain‐containing lysine acetyl transferases are members of subfamily I of the bromodomain phylogenetic tree. Iterative cycles of rational inhibitor design and biophysical characterization led to the discovery of the triazolopthalazine‐based L‐45 (dubbed L‐Moses) as the first potent, selective, and cell‐active PCAF bromodomain (Brd) inhibitor. Synthesis from readily available (1R,2S)‐(−)‐norephedrine furnished L‐45 in enantiopure form. L‐45 was shown to disrupt PCAF‐Brd histone H3.3 interaction in cells using a nanoBRET assay, and a co‐crystal structure of L‐45 with the homologous Brd PfGCN5 from Plasmodium falciparum rationalizes the high selectivity for PCAF and GCN5 bromodomains. Compound L‐45 shows no observable cytotoxicity in peripheral blood mononuclear cells (PBMC), good cell‐permeability, and metabolic stability in human and mouse liver microsomes, supporting its potential for in vivo use.
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Affiliation(s)
- Moses Moustakim
- Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7DQ and OX3 7FZ, UK.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Peter G K Clark
- Department of Chemistry, Simon Fraser University, Burnaby, V5A 1S6, Canada
| | - Laura Trulli
- Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185, Roma, Italy
| | - Angel L Fuentes de Arriba
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Matthias T Ehebauer
- ARUK Oxford Drug Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - Apirat Chaikuad
- Johann Wolfgang Goethe-University, Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, 60438, Frankfurt am Main, Germany
| | - Emma J Murphy
- ARUK Oxford Drug Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | | | - Danette Daniels
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI, 153611, USA
| | - Chun-Feng D Hou
- Structural Genomics Consortium, MaRS South Tower, Suite 732, 101 College Street, Toronto, Ontario, M5G 1LZ, Canada
| | - Yu-Hui Lin
- Structural Genomics Consortium, MaRS South Tower, Suite 732, 101 College Street, Toronto, Ontario, M5G 1LZ, Canada
| | - John R Walker
- Structural Genomics Consortium, MaRS South Tower, Suite 732, 101 College Street, Toronto, Ontario, M5G 1LZ, Canada
| | - Raymond Hui
- Structural Genomics Consortium, MaRS South Tower, Suite 732, 101 College Street, Toronto, Ontario, M5G 1LZ, Canada
| | - Hongbing Yang
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 7FZ, UK
| | - Lucy Dorrell
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 7FZ, UK
| | - Catherine M Rogers
- Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7DQ and OX3 7FZ, UK
| | - Octovia P Monteiro
- Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7DQ and OX3 7FZ, UK
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7DQ and OX3 7FZ, UK
| | - Kilian V M Huber
- Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7DQ and OX3 7FZ, UK
| | - Stefan Knapp
- Johann Wolfgang Goethe-University, Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, 60438, Frankfurt am Main, Germany
| | - Jag Heer
- UCB Pharma Ltd, Slough, SL1 3WE, UK
| | - Darren J Dixon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Paul E Brennan
- Structural Genomics Consortium & Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7DQ and OX3 7FZ, UK.,ARUK Oxford Drug Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
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14
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Moustakim M, Clark PGK, Trulli L, Fuentes de Arriba AL, Ehebauer MT, Chaikuad A, Murphy EJ, Mendez‐Johnson J, Daniels D, Hou CD, Lin Y, Walker JR, Hui R, Yang H, Dorrell L, Rogers CM, Monteiro OP, Fedorov O, Huber KVM, Knapp S, Heer J, Dixon DJ, Brennan PE. Discovery of a PCAF Bromodomain Chemical Probe. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Moses Moustakim
- Structural Genomics Consortium & Target Discovery Institute University of Oxford NDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
- Department of Chemistry Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Peter G. K. Clark
- Department of Chemistry Simon Fraser University Burnaby V5A 1S6 Canada
| | - Laura Trulli
- Dipartimento di Chimica Università degli Studi di Roma “La Sapienza” Piazzale Aldo Moro 5 00185 Roma Italy
| | - Angel L. Fuentes de Arriba
- Department of Chemistry Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | | | - Apirat Chaikuad
- Johann Wolfgang Goethe-University Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences 60438 Frankfurt am Main Germany
| | - Emma J. Murphy
- ARUK Oxford Drug Discovery Institute University of Oxford Oxford OX3 7FZ UK
| | | | - Danette Daniels
- Promega Corporation 2800 Woods Hollow Road Madison WI 153611 USA
| | - Chun‐Feng D. Hou
- Structural Genomics Consortium MaRS South Tower, Suite 732 101 College Street Toronto Ontario M5G 1LZ Canada
| | - Yu‐Hui Lin
- Structural Genomics Consortium MaRS South Tower, Suite 732 101 College Street Toronto Ontario M5G 1LZ Canada
| | - John R. Walker
- Structural Genomics Consortium MaRS South Tower, Suite 732 101 College Street Toronto Ontario M5G 1LZ Canada
| | - Raymond Hui
- Structural Genomics Consortium MaRS South Tower, Suite 732 101 College Street Toronto Ontario M5G 1LZ Canada
| | - Hongbing Yang
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre University of Oxford Oxford OX3 7FZ UK
| | - Lucy Dorrell
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre University of Oxford Oxford OX3 7FZ UK
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery Institute University of Oxford NDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Octovia P. Monteiro
- Structural Genomics Consortium & Target Discovery Institute University of Oxford NDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery Institute University of Oxford NDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery Institute University of Oxford NDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
| | - Stefan Knapp
- Johann Wolfgang Goethe-University Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences 60438 Frankfurt am Main Germany
| | - Jag Heer
- UCB Pharma Ltd Slough SL1 3WE UK
| | - Darren J. Dixon
- Department of Chemistry Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery Institute University of Oxford NDM Research Building Roosevelt Drive Oxford OX3 7DQ and OX3 7FZ UK
- ARUK Oxford Drug Discovery Institute University of Oxford Oxford OX3 7FZ UK
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15
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The Multifaceted Contributions of Chromatin to HIV-1 Integration, Transcription, and Latency. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 328:197-252. [PMID: 28069134 DOI: 10.1016/bs.ircmb.2016.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood. Transcription from the HIV-1 genome occurs in the context of chromatin and is subjected to the same regulatory mechanisms that drive cellular gene expression. Much like in eukaryotic genes, the nucleosomal landscape of the HIV-1 promoter and its position within genomic chromatin are determinants of its transcriptional activity. Understanding the multilayered chromatin-mediated mechanisms that underpin HIV-1 integration and expression is of utmost importance for the development of therapeutic strategies aimed at reducing the pool of latently infected cells. In this review, we discuss the impact of chromatin structure on viral integration, transcriptional regulation and latency, and the host factors that influence HIV-1 replication by regulating chromatin organization. Finally, we describe therapeutic strategies under development to target the chromatin-HIV-1 interplay.
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16
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Moustakim M, Clark PGK, Hay DA, Dixon DJ, Brennan PE. Chemical probes and inhibitors of bromodomains outside the BET family. MEDCHEMCOMM 2016; 7:2246-2264. [PMID: 29170712 PMCID: PMC5644722 DOI: 10.1039/c6md00373g] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/06/2016] [Indexed: 01/03/2023]
Abstract
Significant progress has been made in discovering inhibitors and chemical probes of bromodomains, epigenetic readers of lysine acetylation.
In the last five years, the development of inhibitors of bromodomains has emerged as an area of intensive worldwide research. Emerging evidence has implicated a number of non-BET bromodomains in the onset and progression of diseases such as cancer, HIV infection and inflammation. The development and use of small molecule chemical probes has been fundamental to pre-clinical evaluation of bromodomains as targets. Recent efforts are described highlighting the development of potent, selective and cell active non-BET bromodomain inhibitors and their therapeutic potential. Over half of typical bromodomains now have reported ligands, but those with atypical binding site residues remain resistant to chemical probe discovery efforts.
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Affiliation(s)
- Moses Moustakim
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK. .,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
| | - Peter G K Clark
- Department of Chemistry, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Duncan A Hay
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Darren J Dixon
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK. .,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
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17
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Conrad RJ, Ott M. Therapeutics Targeting Protein Acetylation Perturb Latency of Human Viruses. ACS Chem Biol 2016; 11:669-80. [PMID: 26845514 DOI: 10.1021/acschembio.5b00999] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Persistent viral infections are widespread and represent significant public health burdens. Some viruses endure in a latent state by co-opting the host epigenetic machinery to manipulate viral gene expression. Small molecules targeting epigenetic pathways are now in the clinic for certain cancers and are considered as potential treatment strategies to reverse latency in HIV-infected individuals. In this review, we discuss how drugs interfering with one epigenetic pathway, protein acetylation, perturb latency of three families of pathogenic human viruses-retroviruses, herpesviruses, and papillomaviruses.
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Affiliation(s)
- Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- Graduate
Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, California 94158, United States
- Department
of Medicine, University of California, San Francisco, California 94158, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- Graduate
Program in Pharmaceutical Sciences and Pharmacogenomics, University of California, San Francisco, California 94158, United States
- Department
of Medicine, University of California, San Francisco, California 94158, United States
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18
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Chaikuad A, Lang S, Brennan PE, Temperini C, Fedorov O, Hollander J, Nachane R, Abell C, Müller S, Siegal G, Knapp S. Structure-Based Identification of Inhibitory Fragments Targeting the p300/CBP-Associated Factor Bromodomain. J Med Chem 2016; 59:1648-53. [PMID: 26731131 PMCID: PMC4770306 DOI: 10.1021/acs.jmedchem.5b01719] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
The
P300/CBP-associated factor plays a central role in retroviral
infection and cancer development, and the C-terminal bromodomain provides
an opportunity for selective targeting. Here, we report several new
classes of acetyl-lysine mimetic ligands ranging from mM to low micromolar
affinity that were identified using fragment screening approaches.
The binding modes of the most attractive fragments were determined
using high resolution crystal structures providing chemical starting
points and structural models for the development of potent and selective
PCAF inhibitors.
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Affiliation(s)
- Apirat Chaikuad
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, U.K
| | - Steffen Lang
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Paul E Brennan
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, U.K
| | - Claudia Temperini
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, U.K
| | | | - Ruta Nachane
- ZoBio , Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Chris Abell
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, U.K
| | - Gregg Siegal
- ZoBio , Einsteinweg 55, 2333 CC Leiden, Netherlands
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, U.K.,Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University and Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
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19
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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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20
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Jeng MY, Ali I, Ott M. Manipulation of the host protein acetylation network by human immunodeficiency virus type 1. Crit Rev Biochem Mol Biol 2015; 50:314-25. [PMID: 26329395 PMCID: PMC4816045 DOI: 10.3109/10409238.2015.1061973] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Over the past 15 years, protein acetylation has emerged as a globally important post-translational modification that fine-tunes major cellular processes in many life forms. This dynamic regulatory system is critical both for complex eukaryotic cells and for the viruses that infect them. HIV-1 accesses the host acetylation network by interacting with several key enzymes, thereby promoting infection at multiple steps during the viral life cycle. Inhibitors of host histone deacetylases and bromodomain-containing proteins are now being pursued as therapeutic strategies to enhance current antiretroviral treatment. As more acetylation-targeting compounds are reaching clinical trials, it is time to review the role of reversible protein acetylation in HIV-infected CD4(+) T cells.
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Affiliation(s)
- Mark Y. Jeng
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94158, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94158, USA
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21
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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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22
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BET bromodomain inhibition suppresses graft-versus-host disease after allogeneic bone marrow transplantation in mice. Blood 2015; 125:2724-8. [PMID: 25778533 DOI: 10.1182/blood-2014-08-598037] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 03/05/2015] [Indexed: 02/06/2023] Open
Abstract
Acute graft-versus-host disease (GVHD) is the major obstacle of allogeneic bone marrow transplantation (BMT). Bromodomain and extra-terminal (BET) protein inhibitors selectively block acetyl-binding pockets of the bromodomains and modulate histone acetylation. Here, we report that inhibition of BET bromodomain (BRD) proteins with I-BET151 alters cytokine expression in dendritic cells (DCs) and T cells, including surface costimulatory molecules, in vitro and in vivo cytokine secretion, and expansion. Mechanistic studies with I-BET151 and JQ1, another inhibitor, demonstrate that these effects could be from disruption of association between BRD4 and acetyl-310 RelA of nuclear factor kappa B. Short-term administration early during BMT reduced GVHD severity and improved mortality in two different allogeneic BMT models but retained sufficient graft-versus-tumor effect. Thus inhibiting BRD proteins may serve as a novel approach for preventing GVHD.
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23
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Tough DF, Lewis HD, Rioja I, Lindon MJ, Prinjha RK. Epigenetic pathway targets for the treatment of disease: accelerating progress in the development of pharmacological tools: IUPHAR Review 11. Br J Pharmacol 2014; 171:4981-5010. [PMID: 25060293 PMCID: PMC4253452 DOI: 10.1111/bph.12848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 05/22/2014] [Accepted: 06/13/2014] [Indexed: 02/06/2023] Open
Abstract
The properties of a cell are determined both genetically by the DNA sequence of its genes and epigenetically through processes that regulate the pattern, timing and magnitude of expression of its genes. While the genetic basis of disease has been a topic of intense study for decades, recent years have seen a dramatic increase in the understanding of epigenetic regulatory mechanisms and a growing appreciation that epigenetic misregulation makes a significant contribution to human disease. Several large protein families have been identified that act in different ways to control the expression of genes through epigenetic mechanisms. Many of these protein families are finally proving tractable for the development of small molecules that modulate their function and represent new target classes for drug discovery. Here, we provide an overview of some of the key epigenetic regulatory proteins and discuss progress towards the development of pharmacological tools for use in research and therapy.
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Affiliation(s)
- David F Tough
- Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Epinova DPU, Stevenage, UK
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24
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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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25
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The growing landscape of lysine acetylation links metabolism and cell signalling. Nat Rev Mol Cell Biol 2014; 15:536-50. [PMID: 25053359 DOI: 10.1038/nrm3841] [Citation(s) in RCA: 978] [Impact Index Per Article: 97.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lysine acetylation is a conserved protein post-translational modification that links acetyl-coenzyme A metabolism and cellular signalling. Recent advances in the identification and quantification of lysine acetylation by mass spectrometry have increased our understanding of lysine acetylation, implicating it in many biological processes through the regulation of protein interactions, activity and localization. In addition, proteins are frequently modified by other types of acylations, such as formylation, butyrylation, propionylation, succinylation, malonylation, myristoylation, glutarylation and crotonylation. The intricate link between lysine acylation and cellular metabolism has been clarified by the occurrence of several such metabolite-sensitive acylations and their selective removal by sirtuin deacylases. These emerging findings point to new functions for different lysine acylations and deacylating enzymes and also highlight the mechanisms by which acetylation regulates various cellular processes.
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26
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Marmorstein R, Zhou MM. Writers and readers of histone acetylation: structure, mechanism, and inhibition. Cold Spring Harb Perspect Biol 2014; 6:a018762. [PMID: 24984779 DOI: 10.1101/cshperspect.a018762] [Citation(s) in RCA: 371] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone acetylation marks are written by histone acetyltransferases (HATs) and read by bromodomains (BrDs), and less commonly by other protein modules. These proteins regulate many transcription-mediated biological processes, and their aberrant activities are correlated with several human diseases. Consequently, small molecule HAT and BrD inhibitors with therapeutic potential have been developed. Structural and biochemical studies of HATs and BrDs have revealed that HATs fall into distinct subfamilies containing a structurally related core for cofactor binding, but divergent flanking regions for substrate-specific binding, catalysis, and autoregulation. BrDs adopt a conserved left-handed four-helix bundle to recognize acetyllysine; divergent loop residues contribute to substrate-specific acetyllysine recognition.
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Affiliation(s)
- Ronen Marmorstein
- Program in Gene Expression and Regulation, Wistar Institute, and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10065
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27
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Liu M, Li D, Sun L, Chen J, Sun X, Zhang L, Huo L, Zhou J. Modulation of Eg5 activity contributes to mitotic spindle checkpoint activation and Tat-mediated apoptosis in CD4-positive T-lymphocytes. J Pathol 2014; 233:138-47. [PMID: 24488929 DOI: 10.1002/path.4333] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 01/12/2014] [Accepted: 01/26/2014] [Indexed: 12/20/2022]
Abstract
Tat, the transactivation factor of human immunodeficiency virus type 1 (HIV-1), represents one of the major players mediating the loss of CD4-positive T-lymphocytes in HIV-1-infected patients, primarily due to the ability of Tat to trigger apoptosis. However, the molecular events underlying this process remain elusive. In this study, we provide evidence that Tat interacts with Eg5, a microtubule-associated motor protein, and allosterically modulates the ATPase activity of Eg5 by affecting ADP release from the enzyme's active centre. This action of Tat impairs the formation of the mitotic spindle and activates the spindle checkpoint, thereby blocking cell cycle progression at mitosis and leading to apoptosis. Further studies reveal that lysine 85 in the carboxyl terminus of Tat is critical for its interaction with Eg5 and hence its effects on Eg5 activity, mitotic progression, and apoptosis. These findings identify Tat as a viral regulator of Eg5 and provide novel insights into the mechanisms of action of Tat in mediating the reduction of CD4-positive T-lymphocytes.
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Affiliation(s)
- Min Liu
- Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
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28
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Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell 2013; 52:314-24. [PMID: 24207025 PMCID: PMC3936344 DOI: 10.1016/j.molcel.2013.10.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/26/2013] [Accepted: 09/27/2013] [Indexed: 11/17/2022]
Abstract
Lysine acetylation regulates transcription by targeting histones and nonhistone proteins. Here we report that the central regulator of transcription, RNA polymerase II, is subject to acetylation in mammalian cells. Acetylation occurs at eight lysines within the C-terminal domain (CTD) of the largest polymerase subunit and is mediated by p300/KAT3B. CTD acetylation is specifically enriched downstream of the transcription start sites of polymerase-occupied genes genome-wide, indicating a role in early stages of transcription initiation or elongation. Mutation of lysines or p300 inhibitor treatment causes the loss of epidermal growth-factor-induced expression of c-Fos and Egr2, immediate-early genes with promoter-proximally paused polymerases, but does not affect expression or polymerase occupancy at housekeeping genes. Our studies identify acetylation as a new modification of the mammalian RNA polymerase II required for the induction of growth factor response genes.
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Affiliation(s)
- Sebastian Schröder
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eva Herker
- Gladstone Institutes, San Francisco, CA 94158, USA
- Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, 20251 Hamburg, Germany
| | - Friederike Itzen
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Daniel He
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sean Thomas
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel A. Gilchrist
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Katrin Kaehlcke
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sungyoo Cho
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - John A. Capra
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Matthias Geyer
- Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
- Research Center Caesar, 53175 Bonn, Germany
| | - Benoit G. Bruneau
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karen Adelman
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
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29
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Systematic Analysis of the Functions of Lysine Acetylation in the Regulation of Tat Activity. PLoS One 2013; 8:e67186. [PMID: 23826228 PMCID: PMC3695041 DOI: 10.1371/journal.pone.0067186] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Accepted: 05/15/2013] [Indexed: 11/28/2022] Open
Abstract
The Tat protein of HIV-1 has several well-known properties, such as nucleocytoplasmic trafficking, transactivation of transcription, interaction with tubulin, regulation of mitotic progression, and induction of apoptosis. Previous studies have identified a couple of lysine residues in Tat that are essential for its functions. In order to analyze the functions of all the lysine residues in Tat, we mutated them individually to alanine, glutamine, and arginine. Through systematic analysis of the lysine mutants, we discovered several previously unidentified characteristics of Tat. We found that lysine acetylation could modulate the subcellular localization of Tat, in addition to the regulation of its transactivation activity. Our data also revealed that lysine mutations had distinct effects on microtubule assembly and Tat binding to bromodomain proteins. By correlation analysis, we further found that the effects of Tat on apoptosis and mitotic progression were not entirely attributed to its effect on microtubule assembly. Our findings suggest that Tat may regulate diverse cellular activities through binding to different proteins and that the acetylation of distinct lysine residues in Tat may modulate its interaction with various partners.
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30
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Van Lint C, Bouchat S, Marcello A. HIV-1 transcription and latency: an update. Retrovirology 2013; 10:67. [PMID: 23803414 PMCID: PMC3699421 DOI: 10.1186/1742-4690-10-67] [Citation(s) in RCA: 246] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 05/29/2013] [Indexed: 12/11/2022] Open
Abstract
Combination antiretroviral therapy, despite being potent and life-prolonging, is not curative and does not eradicate HIV-1 infection since interruption of treatment inevitably results in a rapid rebound of viremia. Reactivation of latently infected cells harboring transcriptionally silent but replication-competent proviruses is a potential source of persistent residual viremia in cART-treated patients. Although multiple reservoirs may exist, the persistence of resting CD4+ T cells carrying a latent infection represents a major barrier to eradication. In this review, we will discuss the latest reports on the molecular mechanisms that may regulate HIV-1 latency at the transcriptional level, including transcriptional interference, the role of cellular factors, chromatin organization and epigenetic modifications, the viral Tat trans-activator and its cellular cofactors. Since latency mechanisms may also operate at the post-transcriptional level, we will consider inhibition of nuclear RNA export and inhibition of translation by microRNAs as potential barriers to HIV-1 gene expression. Finally, we will review the therapeutic approaches and clinical studies aimed at achieving either a sterilizing cure or a functional cure of HIV-1 infection, with a special emphasis on the most recent pharmacological strategies to reactivate the latent viruses and decrease the pool of viral reservoirs.
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Affiliation(s)
- Carine Van Lint
- Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute of Molecular Biology and Medicine, 12, Rue des Profs Jeener et Brachet, 6041, Gosselies, Belgium.
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31
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Lu H, Li Z, Xue Y, Zhou Q. Viral-host interactions that control HIV-1 transcriptional elongation. Chem Rev 2013; 113:8567-82. [PMID: 23795863 DOI: 10.1021/cr400120z] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Huasong Lu
- School of Pharmaceutical Sciences, Xiamen University , Xiamen, Fujian 361005, China
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32
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Bromodomain proteins in HIV infection. Viruses 2013; 5:1571-86. [PMID: 23793227 PMCID: PMC3717722 DOI: 10.3390/v5061571] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/09/2013] [Accepted: 06/13/2013] [Indexed: 02/06/2023] Open
Abstract
Bromodomains are conserved protein modules of ~110 amino acids that bind acetylated lysine residues in histone and non-histone proteins. Bromodomains are present in many chromatin-associated transcriptional regulators and have been linked to diverse aspects of the HIV life cycle, including transcription and integration. Here, we review the role of bromodomain-containing proteins in HIV infection. We begin with a focus on acetylated viral factors, followed by a discussion of structural and biological studies defining the involvement of bromodomain proteins in the HIV life cycle. We end with an overview of promising new studies of bromodomain inhibitory compounds for the treatment of HIV latency.
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33
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Guillaume-Gentil O, Potthoff E, Ossola D, Dörig P, Zambelli T, Vorholt JA. Force-controlled fluidic injection into single cell nuclei. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:1904-7. [PMID: 23166090 DOI: 10.1002/smll.201202276] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Indexed: 05/03/2023]
Affiliation(s)
- Orane Guillaume-Gentil
- ETH Zurich, Institute of Microbiology, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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34
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Taube R, Peterlin BM. Lost in transcription: molecular mechanisms that control HIV latency. Viruses 2013; 5:902-27. [PMID: 23518577 PMCID: PMC3705304 DOI: 10.3390/v5030902] [Citation(s) in RCA: 53] [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: 02/27/2013] [Revised: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 02/06/2023] Open
Abstract
Highly active antiretroviral therapy (HAART) has limited the replication and spread of the human immunodeficiency virus (HIV). However, despite treatment, HIV infection persists in latently infected reservoirs, and once therapy is interrupted, viral replication rebounds quickly. Extensive efforts are being directed at eliminating these cell reservoirs. This feat can be achieved by reactivating latent HIV while administering drugs that prevent new rounds of infection and allow the immune system to clear the virus. However, current approaches to HIV eradication have not been effective. Moreover, as HIV latency is multifactorial, the significance of each of its molecular mechanisms is still under debate. Among these, transcriptional repression as a result of reduced levels and activity of the positive transcription elongation factor b (P-TEFb: CDK9/cyclin T) plays a significant role. Therefore, increasing levels of P-TEFb expression and activity is an excellent strategy to stimulate viral gene expression. This review summarizes the multiple steps that cause HIV to enter into latency. It positions the interplay between transcriptionally active and inactive host transcriptional activators and their viral partner Tat as valid targets for the development of new strategies to reactivate latent viral gene expression and eradicate HIV.
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Affiliation(s)
- Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva, 84105, Israel
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +972-8-6479858; Fax: +972-8-6479953
| | - Boris Matija Peterlin
- Department of Medicine, Microbiology and Immunology, Rosalind Russell Medical Research Center, University of California at San Francisco, San Francisco, CA 94143, USA; E-Mail:
- Department of Virology, Haartman Institute, University of Helsinki, 00014 Helsinki, Finland
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35
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Knipe DM, Lieberman PM, Jung JU, McBride AA, Morris KV, Ott M, Margolis D, Nieto A, Nevels M, Parks RJ, Kristie TM. Snapshots: chromatin control of viral infection. Virology 2013; 435:141-56. [PMID: 23217624 DOI: 10.1016/j.virol.2012.09.023] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 09/20/2012] [Accepted: 09/22/2012] [Indexed: 12/11/2022]
Abstract
Like their cellular host counterparts, many invading viral pathogens must contend with, modulate, and utilize the host cell's chromatin machinery to promote efficient lytic infection or control persistent-latent states. While not intended to be comprehensive, this review represents a compilation of conceptual snapshots of the dynamic interplay of viruses with the chromatin environment. Contributions focus on chromatin dynamics during infection, viral circumvention of cellular chromatin repression, chromatin organization of large DNA viruses, tethering and persistence, viral interactions with cellular chromatin modulation machinery, and control of viral latency-reactivation cycles.
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Affiliation(s)
- David M Knipe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
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36
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Wang Q, Wang R, Zhang B, Zhang S, Zheng Y, Wang Z. Small organic molecules targeting PCAF bromodomain as potent inhibitors of HIV-1 replication. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md20376j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Dhamija N, Rawat P, Mitra D. Epigenetic regulation of HIV-1 persistence and evolving strategies for virus eradication. Subcell Biochem 2013; 61:479-505. [PMID: 23150264 DOI: 10.1007/978-94-007-4525-4_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the intense effort put by researchers globally to understand Human Immunodeficiency Virus (HIV-1) pathogenesis since its discovery 30 years ago, the acquired knowledge till date is not good enough to eradicate HIV-1 from an infected individual. HIV-1 infects cells of the human immune system and integrates into the host cell genome thereby leading to persistent infection in these cells. Based on the activation status of the cells, the infection could be productive or result in latent infection. The current regimen used to treat HIV-1 infection in an AIDS patient includes combination of antiretroviral drugs called Highly Active Anti-Retroviral Therapy (HAART). A major challenge for the success of HAART has been these latent reservoirs of HIV which remain hidden and pose major hurdle for the eradication of virus. Combination of HAART therapy with simultaneous activation of latent reservoirs of HIV-1 seems to be the future of anti-retroviral therapy; however, this will require a much better understanding of the mechanisms and regulation of HIV-1 latency. In this chapter, we have tried to elaborate on HIV-1 latency, highlighting the strategies employed by the virus to ensure persistence in the host with specific focus on epigenetic regulation of latency. A complete understanding of HIV-1 latency will be extremely essential for ultimate eradication of HIV-1 from the human host.
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Affiliation(s)
- Neeru Dhamija
- National Centre for Cell Science, NCCS Complex, Pune University Campus, Ganeshkhind, Pune, 411007, India
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38
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Strategies to Block HIV Transcription: Focus on Small Molecule Tat Inhibitors. BIOLOGY 2012; 1:668-97. [PMID: 24832514 PMCID: PMC4009808 DOI: 10.3390/biology1030668] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 01/29/2023]
Abstract
After entry into the target cell, the human immunodeficiency virus type I (HIV) integrates into the host genome and becomes a proviral eukaryotic transcriptional unit. Transcriptional regulation of provirus gene expression is critical for HIV replication. Basal transcription from the integrated HIV promoter is very low in the absence of the HIV transactivator of transcription (Tat) protein and is solely dependent on cellular transcription factors. The 5' terminal region (+1 to +59) of all HIV mRNAs forms an identical stem-bulge-loop structure called the Transactivation Responsive (TAR) element. Once Tat is made, it binds to TAR and drastically activates transcription from the HIV LTR promoter. Mutations in either the Tat protein or TAR sequence usually affect HIV replication, indicating a strong requirement for their conservation. The necessity of the Tat-mediated transactivation cascade for robust HIV replication renders Tat one of the most desirable targets for transcriptional therapy against HIV replication. Screening based on inhibition of the Tat-TAR interaction has identified a number of potential compounds, but none of them are currently used as therapeutics, partly because these agents are not easily delivered for an efficient therapy, emphasizing the need for small molecule compounds. Here we will give an overview of the different strategies used to inhibit HIV transcription and review the current repertoire of small molecular weight compounds that target HIV transcription.
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39
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Grishina I, Debus K, García-Limones C, Schneider C, Shresta A, García C, Calzado MA, Schmitz ML. SIAH-mediated ubiquitination and degradation of acetyl-transferases regulate the p53 response and protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:2287-96. [PMID: 23044042 DOI: 10.1016/j.bbamcr.2012.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/26/2012] [Accepted: 09/30/2012] [Indexed: 12/01/2022]
Abstract
Posttranslational modification of proteins by lysine acetylation regulates many biological processes ranging from signal transduction to chromatin compaction. Here we identify the acetyl-transferases CBP/p300, Tip60 and PCAF as new substrates for the ubiquitin E3 ligases SIAH1 and SIAH2. While CBP/p300 can undergo ubiquitin/proteasome-dependent degradation by SIAH1 and SIAH2, the two other acetyl-transferases are exclusively degraded by SIAH2. Accordingly, SIAH-deficient cells show enhanced protein acetylation, thus revealing SIAH proteins as indirect regulators of the cellular acetylation status. Functional experiments show that Tip60/PCAF-mediated acetylation of the tumor suppressor p53 is antagonized by the p53 target gene SIAH2 which mediates ubiquitin/proteasome-mediated degradation of both acetyl-transferases and consequently diminishes p53 acetylation and transcriptional activity. The p53 kinase HIPK2 mediates hierarchical phosphorylation of SIAH2 at 5 sites, which further boosts its activity as a ubiquitin E3 ligase for several substrates and therefore dampens the late p53 response.
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Affiliation(s)
- Inna Grishina
- Department of Biochemistry, Medical Faculty, Friedrichstrasse 24, Justus Liebig University, Member of the German Center for Lung Research, 35392 Giessen, Germany
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40
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Hewings DS, Rooney TPC, Jennings LE, Hay DA, Schofield CJ, Brennan PE, Knapp S, Conway SJ. Progress in the development and application of small molecule inhibitors of bromodomain-acetyl-lysine interactions. J Med Chem 2012; 55:9393-413. [PMID: 22924434 DOI: 10.1021/jm300915b] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains, protein modules that recognize and bind to acetylated lysine, are emerging as important components of cellular machinery. These acetyl-lysine (KAc) "reader" domains are part of the write-read-erase concept that has been linked with the transfer of epigenetic information. By reading KAc marks on histones, bromodomains mediate protein-protein interactions between a diverse array of partners. There has been intense activity in developing potent and selective small molecule probes that disrupt the interaction between a given bromodomain and KAc. Rapid success has been achieved with the BET family of bromodomains, and a number of potent and selective probes have been reported. These compounds have enabled linking of the BET bromodomains with diseases, including cancer and inflammation, suggesting that bromodomains are druggable targets. Herein, we review the biology of the bromodomains and discuss the SAR for the existing small molecule probes. The biology that has been enabled by these compounds is summarized.
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Affiliation(s)
- David S Hewings
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
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41
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Brennan P, Filippakopoulos P, Knapp S. The therapeutic potential of acetyl-lysine and methyl-lysine effector domains. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.ddstr.2012.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
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43
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Sampey GC, Guendel I, Das R, Jaworski E, Klase Z, Narayanan A, Kehn-Hall K, Kashanchi F. Transcriptional Gene Silencing (TGS) via the RNAi Machinery in HIV-1 Infections. BIOLOGY 2012; 1:339-69. [PMID: 24832229 PMCID: PMC4009781 DOI: 10.3390/biology1020339] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 08/03/2012] [Accepted: 08/13/2012] [Indexed: 12/21/2022]
Abstract
Gene silencing via non-coding RNA, such as siRNA and miRNA, can occur at the transcriptional, post-transcriptional, and translational stages of expression. Transcriptional gene silencing (TGS) involving the RNAi machinery generally occurs through DNA methylation, as well as histone post-translational modifications, and corresponding remodeling of chromatin around the target gene into a heterochromatic state. The mechanism by which mammalian TGS occurs includes the recruitment of RNA-induced initiation of transcriptional gene silencing (RITS) complexes, DNA methyltransferases (DNMTs), and other chromatin remodelers. Additionally, virally infected cells encoding miRNAs have also been shown to manipulate the host cell RNAi machinery to induce TGS at the viral genome, thereby establishing latency. Furthermore, the introduction of exogenous siRNA and shRNA into infected cells that target integrated viral promoters can greatly suppress viral transcription via TGS. Here we examine the latest findings regarding mammalian TGS, specifically focusing on HIV-1 infected cells, and discuss future avenues of exploration in this field.
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Affiliation(s)
- Gavin C Sampey
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Irene Guendel
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Ravi Das
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Elizabeth Jaworski
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Zachary Klase
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, 9000 Rockville Pike, Bethesda, MD 20810, USA.
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Kylene Kehn-Hall
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
| | - Fatah Kashanchi
- National Center for Biodefense and Infectious Disease, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20108, USA.
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44
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Quy VC, Pantano S, Rossetti G, Giacca M, Carloni P. HIV-1 Tat Binding to PCAF Bromodomain: Structural Determinants from Computational Methods. BIOLOGY 2012; 1:277-96. [PMID: 24832227 PMCID: PMC4009784 DOI: 10.3390/biology1020277] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/09/2012] [Accepted: 07/26/2012] [Indexed: 12/13/2022]
Abstract
The binding between the HIV-1 trans-activator of transcription (Tat) and p300/(CREB-binding protein)-associated factor (PCAF) bromodomain is a crucial step in the HIV-1 life cycle. However, the structure of the full length acetylated Tat bound to PCAF has not been yet determined experimentally. Acetylation of Tat residues can play a critical role in enhancing HIV-1 transcriptional activation. Here, we have combined a fully flexible protein-protein docking approach with molecular dynamics simulations to predict the structural determinants of the complex for the common HIV-1BRU variant. This model reproduces all the crucial contacts between the Tat peptide 46SYGR(AcK)KRRQRC56 and the PCAF bromodomain previously reported by NMR spectroscopy. Additionally, inclusion of the entire Tat protein results in additional contact points at the protein-protein interface. The model is consistent with the available experimental data reported and adds novel information to our previous structural predictions of the PCAF bromodomain in complex with the rare HIVZ2 variant, which was obtained with a less accurate computational method. This improved characterization of Tat.PCAF bromodomain binding may help in defining the structural determinants of other protein interactions involving lysine acetylation.
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Affiliation(s)
- Vo Cam Quy
- Computational Biophysics, German Research School for Simulation Sciences, Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich D-52425, Germany.
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo CP 11400, Uruguay.
| | - Giulia Rossetti
- Computational Biophysics, German Research School for Simulation Sciences, Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich D-52425, Germany.
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology, Trieste 34149, Italy.
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, Computational Biomedicine, Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich D-52425, Germany.
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45
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Impact of Tat Genetic Variation on HIV-1 Disease. Adv Virol 2012; 2012:123605. [PMID: 22899925 PMCID: PMC3414192 DOI: 10.1155/2012/123605] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 05/14/2012] [Indexed: 01/08/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) promoter or long-terminal repeat (LTR) regulates viral gene expression by interacting with multiple viral and host factors. The viral transactivator protein Tat plays an important role in transcriptional activation of HIV-1 gene expression. Functional domains of Tat and its interaction with transactivation response element RNA and cellular transcription factors have been examined. Genetic variation within tat of different HIV-1 subtypes has been shown to affect the interaction of the viral transactivator with cellular and/or viral proteins, influencing the overall level of transcriptional activation as well as its action as a neurotoxic protein. Consequently, the genetic variability within tat may impact the molecular architecture of functional domains of the Tat protein that may impact HIV pathogenesis and disease. Tat as a therapeutic target for anti-HIV drugs has also been discussed.
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46
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Abstract
The introduction of highly active antiretroviral therapy (HAART) has been an important breakthrough in the treatment of HIV-1 infection and has also a powerful tool to upset the equilibrium of viral production and HIV-1 pathogenesis. Despite the advent of potent combinations of this therapy, the long-lived HIV-1 reservoirs like cells from monocyte-macrophage lineage and resting memory CD4+ T cells which are established early during primary infection constitute a major obstacle to virus eradication. Further HAART interruption leads to immediate rebound viremia from latent reservoirs. This paper focuses on the essentials of the molecular mechanisms for the establishment of HIV-1 latency with special concern to present and future possible treatment strategies to completely purge and target viral persistence in the reservoirs.
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47
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Abstract
Thirteen years ago, human cyclin T1 was identified as part of the positive transcription elongation factor b (P-TEFb) and the long-sought host cofactor for the HIV-1 transactivator Tat. Recent years have brought new insights into the intricate regulation of P-TEFb function and its relationship with Tat, revealing novel mechanisms for controlling HIV transcription and fueling new efforts to overcome the barrier of transcriptional latency in eradicating HIV. Moreover, the improved understanding of HIV and Tat forms a basis for studying transcription elongation control in general. Here, we review advances in HIV transcription research with a focus on the growing family of cellular P-TEFb complexes, structural insights into the interactions between Tat, P-TEFb, and TAR RNA, and the multifaceted regulation of these interactions by posttranscriptional modifications of Tat.
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48
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Boehm D, Calvanese V, Dar RD, Xing S, Schroeder S, Martins L, Aull K, Li PC, Planelles V, Bradner JE, Zhou MM, Siliciano RF, Weinberger L, Verdin E, Ott M. BET bromodomain-targeting compounds reactivate HIV from latency via a Tat-independent mechanism. Cell Cycle 2012; 12:452-62. [PMID: 23255218 DOI: 10.4161/cc.23309] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The therapeutic potential of pharmacologic inhibition of bromodomain and extraterminal (BET) proteins has recently emerged in hematological malignancies and chronic inflammation. We find that BET inhibitor compounds (JQ1, I-Bet, I-Bet151 and MS417) reactivate HIV from latency. This is evident in polyclonal Jurkat cell populations containing latent infectious HIV, as well as in a primary T-cell model of HIV latency. Importantly, we show that this activation is dependent on the positive transcription elongation factor p-TEFb but independent from the viral Tat protein, arguing against the possibility that removal of the BET protein BRD4, which functions as a cellular competitor for Tat, serves as a primary mechanism for BET inhibitor action. Instead, we find that the related BET protein, BRD2, enforces HIV latency in the absence of Tat, pointing to a new target for BET inhibitor treatment in HIV infection. In shRNA-mediated knockdown experiments, knockdown of BRD2 activates HIV transcription to the same extent as JQ1 treatment, while a lesser effect is observed with BRD4. In single-cell time-lapse fluorescence microscopy, quantitative analyses across ~2,000 viral integration sites confirm the Tat-independent effect of JQ1 and point to positive effects of JQ1 on transcription elongation, while delaying re-initiation of the polymerase complex at the viral promoter. Collectively, our results identify BRD2 as a new Tat-independent suppressor of HIV transcription in latently infected cells and underscore the therapeutic potential of BET inhibitors in the reversal of HIV latency.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
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49
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Furdas SD, Carlino L, Sippl W, Jung M. Inhibition of bromodomain-mediated protein–protein interactions as a novel therapeutic strategy. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00201e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small molecule inhibitors of acetyl lysine–bromodomain interactions emerge as novel epigenetic tools with potential for therapeutic approaches.
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Affiliation(s)
- Silviya D. Furdas
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-University of Freiburg
- Freiburg
- Germany
| | - Luca Carlino
- Department of Pharmaceutical Chemistry
- Martin-Luther University of Halle-Wittenberg
- Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry
- Martin-Luther University of Halle-Wittenberg
- Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-University of Freiburg
- Freiburg
- Germany
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Chung CW, Witherington J. Progress in the discovery of small-molecule inhibitors of bromodomain--histone interactions. ACTA ACUST UNITED AC 2011; 16:1170-85. [PMID: 21956175 DOI: 10.1177/1087057111421372] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bromodomains are structurally conserved protein modules present in a large number of chromatin-associated proteins and in many nuclear histone acetyltransferases. The bromodomain functions as an acetyl-lysine binding domain and has been shown to be pivotal in regulating protein-protein interactions in chromatin-mediated cellular gene transcription, cell proliferation, and viral transcriptional activation. Structural analyses of these modules in complex with acetyl-lysine peptide ligands provide insights into the molecular basis for recognition and ligand selectivity within this epigenetic reader family. However, there are significant challenges in configuring assays to identify inhibitors of these proteins. This review focuses on the progress made in developing methods to identify peptidic and small-molecule ligands using biophysical label-free and biochemical approaches. The advantage of each technique and the results reported are summarized, highlighting the potential applicably to other reader domains and the caveats in translation from simple in vitro systems to a biological context.
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