1
|
D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2025; 437:168690. [PMID: 38936695 DOI: 10.1016/j.jmb.2024.168690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
A large body of work in the last four decades has revealed the key pillars of HIV-1 transcription control at the initiation and elongation steps. Here, I provide a recount of this collective knowledge starting with the genomic elements (DNA and nascent TAR RNA stem-loop) and transcription factors (cellular and the viral transactivator Tat), and later transitioning to the assembly and regulation of transcription initiation and elongation complexes, and the role of chromatin structure. Compelling evidence support a core HIV-1 transcriptional program regulated by the sequential and concerted action of cellular transcription factors and Tat to promote initiation and sustain elongation, highlighting the efficiency of a small virus to take over its host to produce the high levels of transcription required for viral replication. I summarize new advances including the use of CRISPR-Cas9, genetic tools for acute factor depletion, and imaging to study transcriptional dynamics, bursting and the progression through the multiple phases of the transcriptional cycle. Finally, I describe current challenges to future major advances and discuss areas that deserve more attention to both bolster our basic knowledge of the core HIV-1 transcriptional program and open up new therapeutic opportunities.
Collapse
Affiliation(s)
- Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
2
|
Asamitsu K, Hirokawa T, Okamoto T. Identification of a novel CDK9 inhibitor targeting the intramolecular hidden cavity of CDK9 induced by Tat binding. PLoS One 2022; 17:e0277024. [PMCID: PMC9665388 DOI: 10.1371/journal.pone.0277024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-1 transcription is specifically augmented by a transcriptional activator complex composed of Tat, an HIV-1-encoded activator, and the host transcription elongation factor P-TEFb, which is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1. Several observations suggest that P-TEFb is an attractive anti-HIV-1 drug target. However, the long-term cytotoxicity of CDK9 inhibitors hinders their widespread use in HIV-1 therapy. Thus, novel and safe inhibitors are sorely needed. By performing molecular dynamics simulations of the 3D structure of Tat/P-TEFb, we previously identified a unique cavity structure of CDK9, the CDK9 hidden cavity, that is specifically induced by Tat binding. Here, we attempted to identify compounds that fit this cavity and inhibit CDK9 activity by in silico screening. We identified compounds that could inhibit CDK9 activity. One of such compound, 127, showed the strongest inhibitory activity against CDK9. Interestingly, it also inhibited CDK6 to a similar extent. We inspected the amino acid sequence and structural properties of the CDK9 hidden cavity to determine whether it is conserved in other CDKs, such as CDK6. The Ile61, comprising the center of the CDK9 hidden cavity, appears to be crucial for its kinase activity, thus indicating that the identification of the CDK9 hidden cavity may provide vital information for the development of novel CDK9 inhibitors.
Collapse
Affiliation(s)
- Kaori Asamitsu
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
- * E-mail: (KA); (TH)
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaragi, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaragi, Japan
- * E-mail: (KA); (TH)
| | - Takashi Okamoto
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| |
Collapse
|
3
|
HIV-1 Latency and Viral Reservoirs: Existing Reversal Approaches and Potential Technologies, Targets, and Pathways Involved in HIV Latency Studies. Cells 2021; 10:cells10020475. [PMID: 33672138 PMCID: PMC7926981 DOI: 10.3390/cells10020475] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/14/2021] [Accepted: 02/20/2021] [Indexed: 02/07/2023] Open
Abstract
Eradication of latent human immunodeficiency virus (HIV) infection is a global health challenge. Reactivation of HIV latency and killing of virus-infected cells, the so-called "kick and kill" or "shock and kill" approaches, are a popular strategy for HIV cure. While antiretroviral therapy (ART) halts HIV replication by targeting multiple steps in the HIV life cycle, including viral entry, integration, replication, and production, it cannot get rid of the occult provirus incorporated into the host-cell genome. These latent proviruses are replication-competent and can rebound in cases of ART interruption or cessation. In general, a very small population of cells harbor provirus, serve as reservoirs in ART-controlled HIV subjects, and are capable of expressing little to no HIV RNA or proteins. Beyond the canonical resting memory CD4+ T cells, HIV reservoirs also exist within tissue macrophages, myeloid cells, brain microglial cells, gut epithelial cells, and hematopoietic stem cells (HSCs). Despite a lack of active viral production, latently HIV-infected subjects continue to exhibit aberrant cellular signaling and metabolic dysfunction, leading to minor to major cellular and systemic complications or comorbidities. These include genomic DNA damage; telomere attrition; mitochondrial dysfunction; premature aging; and lymphocytic, cardiac, renal, hepatic, or pulmonary dysfunctions. Therefore, the arcane machineries involved in HIV latency and its reversal warrant further studies to identify the cryptic mechanisms of HIV reservoir formation and clearance. In this review, we discuss several molecules and signaling pathways, some of which have dual roles in maintaining or reversing HIV latency and reservoirs, and describe some evolving strategies and possible approaches to eliminate viral reservoirs and, ultimately, cure/eradicate HIV infection.
Collapse
|
4
|
Eyvazi S, Hejazi MS, Kahroba H, Abasi M, Zamiri RE, Tarhriz V. CDK9 as an Appealing Target for Therapeutic Interventions. Curr Drug Targets 2020; 20:453-464. [PMID: 30362418 DOI: 10.2174/1389450119666181026152221] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 02/05/2023]
Abstract
Cyclin Dependent Kinase 9 (CDK9) as a serine/threonine kinase belongs to a great number of CDKs. CDK9 is the main core of PTEF-b complex and phosphorylates RNA polymerase (RNAP) II besides other transcription factors which regulate gene transcription elongation in numerous physiological processes. Multi-functional nature of CDK9 in diverse cellular pathways proposes that it is as an appealing target. In this review, we summarized the recent findings on the molecular interaction of CDK9 with critical participant molecules to modulate their activity in various diseases. Furthermore, the presented review provides a rationale supporting the use of CDK9 as a therapeutic target in clinical developments for crucial diseases; particularly cancers will be reviewed.
Collapse
Affiliation(s)
- Shirin Eyvazi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Homan Kahroba
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mozghan Abasi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Eghdam Zamiri
- Faculty of medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
5
|
Khan SZ, Gasperino S, Zeichner SL. Nuclear Transit and HIV LTR Binding of NF-κB Subunits Held by IκB Proteins: Implications for HIV-1 Activation. Viruses 2019; 11:v11121162. [PMID: 31888181 PMCID: PMC6949894 DOI: 10.3390/v11121162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
No effective therapy to eliminate the HIV latently infected cell reservoir has been developed. One approach, “shock and kill”, employs agents that activate HIV, subsequently killing the activated infected cells and/or virus. Shock and kill requires agents that safely and effectively activate HIV. One class of activation agents works through classical NF-κB pathways, but global NF-κB activators are non-specific and toxic. There exist two major IκBs: IκBα, and IκBε, which hold activating NF-κB subunits in the cytoplasm, releasing them for nuclear transit upon cell stimulation. IκBα was considered the main IκB responsible for gene expression regulation, including HIV activation. IκBε is expressed in cells constituting much of the latent HIV reservoir, and IκBε knockout mice have a minimal phenotype, suggesting that IκBε could be a valuable target for HIV activation and reservoir depletion. We previously showed that targeting IκBε yields substantial increases in HIV expression. Here, we show that IκBε holds c-Rel and p65 activating NF-κB subunits in the cytoplasm, and that targeting IκBε with siRNA produces a strong increase in HIV expression associated with enhanced c-Rel and p65 transit to the nucleus and binding to the HIV LTR of the activating NF-κBs, demonstrating a mechanism through which targeting IκBε increases HIV expression. The findings suggest that it may be helpful to develop HIV activation approaches, acting specifically to target IκBε and its interactions with the NF-κBs.
Collapse
Affiliation(s)
- Sohrab Z. Khan
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
| | - Sofia Gasperino
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
| | - Steven L. Zeichner
- Department of Pediatrics, Child Health Research Center, and the Pendleton Pediatric Infectious Disease Laboratory, University of Virginia, Charlottesville, VA 22908, USA; (S.Z.K.); (S.G.)
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
- Correspondence:
| |
Collapse
|
6
|
Chen L, Keppler OT, Schölz C. Post-translational Modification-Based Regulation of HIV Replication. Front Microbiol 2018; 9:2131. [PMID: 30254620 PMCID: PMC6141784 DOI: 10.3389/fmicb.2018.02131] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus (HIV) relies heavily on the host cellular machinery for production of viral progeny. To exploit cellular proteins for replication and to overcome host factors with antiviral activity, HIV has evolved a set of regulatory and accessory proteins to shape an optimized environment for its replication and to facilitate evasion from the immune system. Several cellular pathways are hijacked by the virus to modulate critical steps during the viral life cycle. Thereby, post-translational modifications (PTMs) of viral and cellular proteins gain increasingly attention as modifying enzymes regulate virtually every step of the viral replication cycle. This review summarizes the current knowledge of HIV-host interactions influenced by PTMs with a special focus on acetylation, ubiquitination, and phosphorylation of proteins linked to cellular signaling and viral replication. Insights into these interactions are surmised to aid development of new intervention strategies.
Collapse
Affiliation(s)
- Lin Chen
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Oliver T Keppler
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Christian Schölz
- Max von Pettenkofer-Institute and Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| |
Collapse
|
7
|
Sardo L, Lin A, Khakhina S, Beckman L, Ricon L, Elbezanti W, Jaison T, Vishwasrao H, Shroff H, Janetopoulos C, Klase ZA. Real-time visualization of chromatin modification in isolated nuclei. J Cell Sci 2017; 130:2926-2940. [PMID: 28743737 PMCID: PMC5612227 DOI: 10.1242/jcs.205823] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/13/2017] [Indexed: 12/31/2022] Open
Abstract
Chromatin modification is traditionally assessed in biochemical assays that provide average measurements of static events given that the analysis requires components from many cells. Microscopy can visualize single cells, but the cell body and organelles can hamper staining and visualization of the nucleus. Normally, chromatin is visualized by immunostaining a fixed sample or by expressing exogenous fluorescently tagged proteins in a live cell. Alternative microscopy tools to observe changes of endogenous chromatin in real-time are needed. Here, we isolated transcriptionally competent nuclei from cells and used antibody staining without fixation to visualize changes in endogenous chromatin. This method allows the real-time addition of drugs and fluorescent probes to one or more nuclei while under microscopy observation. A high-resolution map of 11 endogenous nuclear markers of the histone code, transcription machinery and architecture was obtained in transcriptionally active nuclei by performing confocal and structured illumination microscopy. We detected changes in chromatin modification and localization at the single-nucleus level after inhibition of histone deacetylation. Applications in the study of RNA transcription, viral protein function and nuclear architecture are presented. This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Luca Sardo
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Angel Lin
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Svetlana Khakhina
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Lucas Beckman
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Luis Ricon
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Weam Elbezanti
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Tara Jaison
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Harshad Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD 28092, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 28092, USA
| | - Christopher Janetopoulos
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| | - Zachary A Klase
- Department of Biological Sciences, McNeil Science and Technology Center, University of the Sciences, 600 S 43rd Street, Philadelphia, PA 19104, USA
| |
Collapse
|
8
|
Asamitsu K, Hirokawa T, Okamoto T. MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding. PLoS One 2017; 12:e0171727. [PMID: 28178316 PMCID: PMC5298246 DOI: 10.1371/journal.pone.0171727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/24/2017] [Indexed: 02/02/2023] Open
Abstract
In this study, we applied molecular dynamics (MD) simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs), lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.
Collapse
Grants
- Ministry of Education, Culture, Sports, Science, and Technology "The Platform Project for Supporting Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science)"
- Ministry of Education, Culture, Sports, Science, and Technology
- Asahi Grass Foundation
- Japan Agency for Medical Research and Development
- Junwakai Foundation
Collapse
Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail: (TH); (TO)
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
- * E-mail: (TH); (TO)
| |
Collapse
|
9
|
Bowman EA, Kelly WG. RNA polymerase II transcription elongation and Pol II CTD Ser2 phosphorylation: A tail of two kinases. Nucleus 2014; 5:224-36. [PMID: 24879308 DOI: 10.4161/nucl.29347] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The transition between initiation and productive elongation during RNA Polymerase II (Pol II) transcription is a well-appreciated point of regulation across many eukaryotes. Elongating Pol II is modified by phosphorylation of serine 2 (Ser2) on its carboxy terminal domain (CTD) by two kinases, Bur1/Ctk1 in yeast and Cdk9/Cdk12 in metazoans. Here, we discuss the roles and regulation of these kinases and their relationship to Pol II elongation control, and focus on recent data from work in C. elegans that point out gaps in our current understand of transcription elongation.
Collapse
Affiliation(s)
- Elizabeth A Bowman
- National Institute of Environmental Health Sciences; Research Triangle Park, NC USA
| | | |
Collapse
|
10
|
Role of noncoding RNAs in the regulation of P-TEFb availability and enzymatic activity. BIOMED RESEARCH INTERNATIONAL 2014; 2014:643805. [PMID: 24701579 PMCID: PMC3950470 DOI: 10.1155/2014/643805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/13/2014] [Indexed: 11/23/2022]
Abstract
P-TEFb is a transcriptional factor that specifically regulates the elongation step of RNA polymerase II-dependent transcription and its activity strictly required for Human Immunodeficiency Virus (HIV) infection and during cardiac differentiation. P-TEFb role has emerged as a crucial regulator of transcription elongation and its activity found finely tuned in vivo at transcriptional level as well as posttranscriptionally by dynamic association with different multisubunit molecular particles. Both physiological and pathological cellular signals rapidly converge on P-TEFb regulation by modifying expression and activity of the complex to allow cells to properly respond to different stimuli. In this review we will give a panoramic view on P-TEFb regulation by noncoding RNAs in both physiological and pathological conditions.
Collapse
|
11
|
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: 4.4] [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.
Collapse
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
| |
Collapse
|
12
|
Hong P, Chen K, Huang B, Liu M, Cui M, Rozenberg I, Chaqour B, Pan X, Barton ER, Jiang XC, Siddiqui MAQ. HEXIM1 controls satellite cell expansion after injury to regulate skeletal muscle regeneration. J Clin Invest 2013; 122:3873-87. [PMID: 23023707 DOI: 10.1172/jci62818] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 08/02/2012] [Indexed: 01/07/2023] Open
Abstract
The native capacity of adult skeletal muscles to regenerate is vital to the recovery from physical injuries and dystrophic diseases. Currently, the development of therapeutic interventions has been hindered by the complex regulatory network underlying the process of muscle regeneration. Using a mouse model of skeletal muscle regeneration after injury, we identified hexamethylene bisacetamide inducible 1 (HEXIM1, also referred to as CLP-1), the inhibitory component of the positive transcription elongation factor b (P-TEFb) complex, as a pivotal regulator of skeletal muscle regeneration. Hexim1-haplodeficient muscles exhibited greater mass and preserved function compared with those of WT muscles after injury, as a result of enhanced expansion of satellite cells. Transplanted Hexim1-haplodeficient satellite cells expanded and improved muscle regeneration more effectively than WT satellite cells. Conversely, HEXIM1 overexpression restrained satellite cell proliferation and impeded muscle regeneration. Mechanistically, dissociation of HEXIM1 from P-TEFb and subsequent activation of P-TEFb are required for satellite cell proliferation and the prevention of early myogenic differentiation. These findings suggest a crucial role for the HEXIM1/P-TEFb pathway in the regulation of satellite cell–mediated muscle regeneration and identify HEXIM1 as a potential therapeutic target for degenerative muscular diseases.
Collapse
Affiliation(s)
- Peng Hong
- Department of Cell Biology, State University of New York Downstate Medical Center,New York, New York, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Ramakrishnan R, Rice AP. Cdk9 T-loop phosphorylation is regulated by the calcium signaling pathway. J Cell Physiol 2012; 227:609-17. [PMID: 21448926 DOI: 10.1002/jcp.22760] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Eukaryotic RNA polymerase II transcriptional elongation is a tightly regulated process and is dependent upon positive transcription elongation factor-b (P-TEFb). The core P-TEFb complex is composed of Cdk9 and Cyclin T and is essential for the expression of most protein coding genes. Cdk9 kinase function is dependent upon phosphorylation of Thr186 in its T-loop. In this study, we examined kinases and signaling pathways that influence Cdk9 T-loop phosphorylation. Using an RNAi screen in HeLa cells, we found that Cdk9 T-loop phosphorylation is regulated by Ca(2+)/calmodulin-dependent kinase 1D (CaMK1D). Using small molecules inhibitors in HeLa cells and primary CD4(+) T lymphocytes, we found that the Ca(2+) signaling pathway is required for Cdk9 T-loop phosphorylation. Inhibition of Ca(2+) signaling led to dephosphorylation of Thr186 on Cdk9. In reporter plasmid assays, inhibition of the Ca(2+) signaling pathway repressed the PCNA promoter and HIV-1 Tat transactivation of the HIV-1 LTR, but not HTLV-1 Tax transactivation of the HTLV-1 LTR, suggesting that perturbation of the Ca(2+) pathway and reduction of Cdk9 T-loop phosphorylation inhibits transcription units that have a rigorous requirement for P-TEFb function.
Collapse
Affiliation(s)
- Rajesh Ramakrishnan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | |
Collapse
|
14
|
Ramakrishnan R, Yu W, Rice AP. Limited redundancy in genes regulated by Cyclin T2 and Cyclin T1. BMC Res Notes 2011; 4:260. [PMID: 21791050 PMCID: PMC3160394 DOI: 10.1186/1756-0500-4-260] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 07/26/2011] [Indexed: 12/04/2022] Open
Abstract
Background The elongation phase, like other steps of transcription by RNA Polymerase II, is subject to regulation. The positive transcription elongation factor b (P-TEFb) complex allows for the transition of mRNA synthesis to the productive elongation phase. P-TEFb contains Cdk9 (Cyclin-dependent kinase 9) as its catalytic subunit and is regulated by its Cyclin partners, Cyclin T1 and Cyclin T2. The HIV-1 Tat transactivator protein enhances viral gene expression by exclusively recruiting the Cdk9-Cyclin T1 P-TEFb complex to a RNA element in nascent viral transcripts called TAR. The expression patterns of Cyclin T1 and Cyclin T2 in primary monocytes and CD4+ T cells suggests that Cyclin T2 may be generally involved in expression of constitutively expressed genes in quiescent cells, while Cyclin T1 may be involved in expression of genes up-regulated during macrophage differentiation, T cell activation, and conditions of increased metabolic activity To investigate this issue, we wished to identify the sets of genes whose levels are regulated by either Cyclin T2 or Cyclin T1. Findings We used shRNA lentiviral vectors to stably deplete either Cyclin T2 or Cyclin T1 in HeLa cells. Total RNA extracted from these cells was subjected to cDNA microarray analysis. We found that 292 genes were down- regulated by depletion of Cyclin T2 and 631 genes were down-regulated by depletion of Cyclin T1 compared to cells transduced with a control lentivirus. Expression of 100 genes was commonly reduced in either knockdown. Additionally, 111 and 287 genes were up-regulated when either Cyclin T2 or Cyclin T1 was depleted, respectively, with 45 genes in common. Conclusions These results suggest that there is limited redundancy in genes regulated by Cyclin T1 or Cyclin T2.
Collapse
Affiliation(s)
- Rajesh Ramakrishnan
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | | | | |
Collapse
|
15
|
Johri MK, Mishra R, Chhatbar C, Unni SK, Singh SK. Tits and bits of HIV Tat protein. Expert Opin Biol Ther 2011; 11:269-83. [PMID: 21204735 DOI: 10.1517/14712598.2011.546339] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION HIV-Tat protein displays an array of functions that are essential for HIV replication. The structural flexibility of Tat protein has been regarded as one of the unique features responsible for sustaining diverse functions, from facilitated membrane-crossing ability to strong affinity for RNA binding. AREAS COVERED RNA binding ability and presence of multiple interacting domains in the same protein are very important properties of HIV-Tat protein. Tat protein has shown great ability to influence cellular and viral gene expression. We discuss the functions of HIV Tat protein, describing its structural significance, secretion and uptake of HIV Tat protein by immune cells, post-translational modifications and role of HIV Tat protein in HIV pathogenesis. EXPERT OPINION Perturbation in expression of many cytokines and chemokines by HIV-Tat protein exhibits downstream immune suppressive function as well as activation of several apoptotic genes. This explains the massive death of immune cells due to bystander effect of HIV Tat protein among HIV-infected patients.
Collapse
Affiliation(s)
- Manish K Johri
- Laboratory of Neurovirology & Inflammation Biology, Section of Infectious Diseases, Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad-500007, (A.P), India
| | | | | | | | | |
Collapse
|
16
|
Gautier VW, Gu L, O'Donoghue N, Pennington S, Sheehy N, Hall WW. In vitro nuclear interactome of the HIV-1 Tat protein. Retrovirology 2009; 6:47. [PMID: 19454010 PMCID: PMC2702331 DOI: 10.1186/1742-4690-6-47] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 05/19/2009] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND One facet of the complexity underlying the biology of HIV-1 resides not only in its limited number of viral proteins, but in the extensive repertoire of cellular proteins they interact with and their higher-order assembly. HIV-1 encodes the regulatory protein Tat (86-101aa), which is essential for HIV-1 replication and primarily orchestrates HIV-1 provirus transcriptional regulation. Previous studies have demonstrated that Tat function is highly dependent on specific interactions with a range of cellular proteins. However they can only partially account for the intricate molecular mechanisms underlying the dynamics of proviral gene expression. To obtain a comprehensive nuclear interaction map of Tat in T-cells, we have designed a proteomic strategy based on affinity chromatography coupled with mass spectrometry. RESULTS Our approach resulted in the identification of a total of 183 candidates as Tat nuclear partners, 90% of which have not been previously characterised. Subsequently we applied in silico analysis, to validate and characterise our dataset which revealed that the Tat nuclear interactome exhibits unique signature(s). First, motif composition analysis highlighted that our dataset is enriched for domains mediating protein, RNA and DNA interactions, and helicase and ATPase activities. Secondly, functional classification and network reconstruction clearly depicted Tat as a polyvalent protein adaptor and positioned Tat at the nexus of a densely interconnected interaction network involved in a range of biological processes which included gene expression regulation, RNA biogenesis, chromatin structure, chromosome organisation, DNA replication and nuclear architecture. CONCLUSION We have completed the in vitro Tat nuclear interactome and have highlighted its modular network properties and particularly those involved in the coordination of gene expression by Tat. Ultimately, the highly specialised set of molecular interactions identified will provide a framework to further advance our understanding of the mechanisms of HIV-1 proviral gene silencing and activation.
Collapse
Affiliation(s)
- Virginie W Gautier
- UCD-Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin (UCD), Belfield, Dublin 4, Ireland.
| | | | | | | | | | | |
Collapse
|
17
|
Cyclin T1-dependent genes in activated CD4 T and macrophage cell lines appear enriched in HIV-1 co-factors. PLoS One 2008; 3:e3146. [PMID: 18773076 PMCID: PMC2519787 DOI: 10.1371/journal.pone.0003146] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 08/15/2008] [Indexed: 11/19/2022] Open
Abstract
HIV-1 is dependent upon cellular co-factors to mediate its replication cycle in CD4+ T cells and macrophages, the two major cell types infected by the virus in vivo. One critical co-factor is Cyclin T1, a subunit of a general RNA polymerase II elongation factor known as P-TEFb. Cyclin T1 is targeted directly by the viral Tat protein to activate proviral transcription. Cyclin T1 is up-regulated when resting CD4+ T cells are activated and during macrophage differentiation or activation, conditions that are also necessary for high levels of HIV-1 replication. Because Cyclin T1 is a subunit of a transcription factor, the up-regulation of Cyclin T1 in these cells results in the induction of cellular genes, some of which might be HIV-1 co-factors. Using shRNA depletions of Cyclin T1 and transcriptional profiling, we identified 54 cellular mRNAs that appear to be Cyclin T1-dependent for their induction in activated CD4+ T Jurkat T cells and during differentiation and activation of MM6 cells, a human monocytic cell line. The promoters for these Cyclin T1-dependent genes (CTDGs) are over-represented in two transcription factor binding sites, SREBP1 and ARP1. Notably, 10 of these CTDGs have been reported to be involved in HIV-1 replication, a significant over-representation of such genes when compared to randomly generated lists of 54 genes (p value<0.00021). The results of siRNA depletion and dominant-negative protein experiments with two CTDGs identified here, CDK11 and Casein kinase 1 gamma 1, suggest that these genes are involved either directly or indirectly in HIV-1 replication. It is likely that the 54 CTDGs identified here include novel HIV-1 co-factors. The presence of CTDGs in the protein space that was available for HIV-1 to sample during its evolution and acquisition of Tat function may provide an explanation for why CTDGs are enriched in viral co-factors.
Collapse
|
18
|
Gatignol A. Transcription of HIV: Tat and cellular chromatin. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2007; 55:137-59. [PMID: 17586314 DOI: 10.1016/s1054-3589(07)55004-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Anne Gatignol
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research,, Department of Microbiology & Immunology and Experimental Medicine, McGill University, Montréal, Québec, Canada
| |
Collapse
|
19
|
Richter SN, Bélanger F, Zheng P, Rana TM. Dynamics of nascent mRNA folding and RNA-protein interactions: an alternative TAR RNA structure is involved in the control of HIV-1 mRNA transcription. Nucleic Acids Res 2006; 34:4278-92. [PMID: 16920743 PMCID: PMC1616951 DOI: 10.1093/nar/gkl499] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
HIV-1 Tat protein regulates transcription elongation by binding to the 59 nt TAR RNA stem–loop structure transcribed from the HIV-1 5′ long terminal repeat (5′-LTR). This established Tat–TAR interaction was used to investigate mRNA folding and RNA–protein interactions during early transcription elongation from the HIV-1 5′-LTR. Employing a new site-specific photo-cross-linking strategy to isolate transcription elongation complexes at early steps of elongation, we found that Tat interacts with HIV-1 transcripts before the formation of full-length TAR (TAR59). Analysis of RNA secondary structure by free energy profiling and ribonuclease digestion indicated that nascent transcripts folded into an alternative TAR RNA structure (TAR31), which requires only 31 nt to form and includes an analogous Tat-binding bulge structure. Functionally, TAR31, similar to TAR59, acts as a transcriptional terminator in vitro, and mRNA expression from TAR31-deficient HIV-1 5′-LTR mutant promoters is significantly decreased. Our results support a role for TAR31 in the control of HIV-1 mRNA transcription and we propose that this structure is important to stabilize the short early transcripts before the transcription complex commits for processive elongation. Overall, this study demonstrates that RNA folding during HIV-1 transcription is dynamic and that as the nascent RNA chain grows during transcription, it folds into a number of conformations that function to regulate gene expression. Finally, our results provide a new experimental strategy for studying mRNA conformation changes during transcription that can be applied to investigate the folding and function of nascent RNA structures transcribed from other promoters.
Collapse
Affiliation(s)
| | | | | | - Tariq M. Rana
- To whom correspondence should be addressed. Tel: +1 508 856 6216; Fax: +1 508 856 6696;
| |
Collapse
|
20
|
Yu W, Wang Y, Shaw CA, Qin XF, Rice AP. Induction of the HIV-1 Tat co-factor cyclin T1 during monocyte differentiation is required for the regulated expression of a large portion of cellular mRNAs. Retrovirology 2006; 3:32. [PMID: 16764723 PMCID: PMC1557533 DOI: 10.1186/1742-4690-3-32] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 06/09/2006] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND P-TEFb, a general RNA polymerase II elongation factor, is composed of CDK9 (cyclin-dependent kinase 9) as a catalytic unit and either cyclin T1, T2 or K as a regulatory subunit. The cyclin T1/P-TEFb complex is targeted by HIV to mediate Tat transactivation. Cyclin T1 protein expression is induced during early macrophage differentiation, suggesting a role in regulation of mRNA expression during the differentiation process. To study the functional significance of cyclin T1 induction during differentiation, we utilized the human Mono Mac 6 (MM6) monocytic cell line. RESULTS We found that cyclin T1 protein expression is induced by a post-transcriptional mechanism following PMA treatment of MM6 cells, similar to its induction in primary monocytes and macrophages. Also in agreement with findings in primary cells, cyclin T2a is present at relatively high levels in MM6 cells and is not induced by PMA. Although the knock-down of cyclin T1 in MM6 cells by shRNA inhibited HIV-1 Tat transactivation, MM6 cell growth was not affected by the depletion of cyclin T1. Using DNA microarray technology, we found that more than 20% of genes induced by PMA require cyclin T1 for their normal level of induction, and approximately 15% of genes repressed by PMA require cyclin T1 for their normal level of repression. Gene ontology analysis indicates that many of these cyclin T1-dependent genes are related to immune response and signal transduction. CONCLUSION These results suggest that cyclin T1 serves a critical role in the program of macrophage differentiation, and this raises questions about the feasibility of cyclin T1 serving as an antiviral therapeutic target.
Collapse
Affiliation(s)
- Wendong Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yan Wang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chad A Shaw
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Xiao-Feng Qin
- Center for Cancer Immunology Research, Department of Immunology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Andrew P Rice
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
21
|
Haaland RE, Herrmann CH, Rice AP. siRNA depletion of 7SK snRNA induces apoptosis but does not affect expression of the HIV-1 LTR or P-TEFb-dependent cellular genes. J Cell Physiol 2006; 205:463-70. [PMID: 16152622 DOI: 10.1002/jcp.20528] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
P-TEFb is a general transcriptional elongation factor composed of Cdk9 and either cyclin T1, T2, or K. A substantial portion of P-TEFb is associated with the 7SK small nuclear RNA (7SK) and the HEXIM1 or HEXIM2 proteins; this complex has reduced kinase activity in vitro relative to free P-TEFb. Here we report that 7SK and HEXIM1 levels are induced in activated lymphocytes concomitantly with increased P-TEFb activity and global transcription. We used siRNA-mediated depletion to probe the function of 7SK in HeLa cells. Depletion of 7SK caused a large reduction in the association of HEXIM1 with Cdk9 and cyclin T1, and greatly reduced the amount of the cyclin T1 present in the 7SK/HEXIM1/P-TEFb complex. Similar to previous studies, siRNA-mediated depletion of 7SK resulted in increased expression of several reporter plasmids tested, including a plasmid lacking promoter elements. However, in contrast to previous studies, which did not examine the effects of 7SK depletion on endogenous gene expression, depletion of 7SK did not appear to affect the expression of the corresponding endogenous genes. Moreover, 7SK depletion had no effect on expression from the integrated HIV-1 provirus or the c-myc and MCL-1 genes, three transcription units known to be highly dependent upon P-TEFb. Importantly, depletion of 7SK was found to cause apoptosis by 72 h post-transfection in HeLa cells. These results suggest that 7SK may provide an essential cellular function whose relation to P-TEFb function is unclear.
Collapse
Affiliation(s)
- Richard E Haaland
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | |
Collapse
|
22
|
Desfosses Y, Solis M, Sun Q, Grandvaux N, Van Lint C, Burny A, Gatignol A, Wainberg MA, Lin R, Hiscott J. Regulation of human immunodeficiency virus type 1 gene expression by clade-specific Tat proteins. J Virol 2005; 79:9180-91. [PMID: 15994812 PMCID: PMC1168763 DOI: 10.1128/jvi.79.14.9180-9191.2005] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major group of human immunodeficiency virus type 1 (HIV-1) strains that comprise the current global pandemic have diversified during their worldwide spread into at least 10 distinct subtypes, or clades. Subtype C predominates in sub-Saharan Africa and is responsible for the majority of worldwide HIV-1 infections, subtype B predominates in North America and Europe, and subtype E is prevalent in Southeast Asia. Significant amino acid variations have been observed among the clade-specific Tat proteins. For the present study, we examined clade-specific interactions between Tat, transactivation-responsive (TAR) element, and P-TEFb proteins and how these interactions may modulate the efficiency of HIV-1 transcription. Clade-specific Tat proteins significantly modified viral gene expression. Tat proteins derived from HIV-1 clades C and E were strong transactivators of long terminal repeat (LTR) activity; Tat E also had a longer half-life than the other Tat proteins and interacted more efficiently with the stem-loop TAR element. Chimeric Tat proteins harboring the Tat E activation domain were strong transactivators of LTR expression. While Tat B, C, and E were able to rescue a Tat-defective HIV-1 proviral clone, Tat E was significantly more efficient at rescue than Tat C, possibly due to the relative stability of the Tat protein. Swapping the activation domains of Tat B, C, and E identified the cyclin T1 association domain as a critical determinant of the transactivation efficiency and of Tat-defective HIV-1 provirus rescue.
Collapse
Affiliation(s)
- Yan Desfosses
- McGill AIDS Center, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, 3755 Cote Ste. Catherine, Montreal, Quebec, Canada H3T1E2
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Hetzer C, Dormeyer W, Schnölzer M, Ott M. Decoding Tat: the biology of HIV Tat posttranslational modifications. Microbes Infect 2005; 7:1364-9. [PMID: 16046164 DOI: 10.1016/j.micinf.2005.06.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 04/29/2005] [Indexed: 10/25/2022]
Abstract
The Tat protein is a viral transactivator that activates HIV transcription through complex interactions with RNA and host cell factors. Tat undergoes multiple posttranslational modifications that regulate the dynamics and complexity of these interactions. The biology of these modifications and their role in Tat function are reviewed.
Collapse
Affiliation(s)
- Claudia Hetzer
- Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | | | | | | |
Collapse
|
24
|
de Oliveira T, Salemi M, Gordon M, Vandamme AM, van Rensburg EJ, Engelbrecht S, Coovadia HM, Cassol S. Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design? Genetics 2005; 167:1047-58. [PMID: 15280222 PMCID: PMC1470929 DOI: 10.1534/genetics.103.018135] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A safe and effective HIV-1 vaccine is urgently needed to control the worldwide AIDS epidemic. Traditional methods of vaccine development have been frustratingly slow, and it is becoming increasingly apparent that radical new approaches may be required. Computational and mathematical approaches, combined with evolutionary reasoning, may provide new insights for the design of an efficacious AIDS vaccine. Here, we used codon-based substitution models and maximum-likelihood (ML) methods to identify positively selected sites that are likely to be involved in the immune control of HIV-1. Analysis of subtypes B and C revealed widespread adaptive evolution. Positively selected amino acids were detected in all nine HIV-1 proteins, including Env. Of particular interest was the high level of positive selection within the C-terminal regions of the immediate-early regulatory proteins, Tat and Rev. Many of the amino acid replacements were associated with the emergence of novel (or alternative) myristylation and casein kinase II (CKII) phosphorylation sites. The impact of these changes on the conformation and antigenicity of Tat and Rev remains to be established. In rhesus macaques, a single CTL-associated amino substitution in Tat has been linked to escape from acute SIV infection. Understanding the relationship between host-driven positive selection and antigenic variation may lead to the development of novel vaccine strategies that preempt the escape process.
Collapse
Affiliation(s)
- Tulio de Oliveira
- HIV Molecular Virology and Bioinformatics Laboratory, Africa Centre for Health and Population Studies, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4013, South Africa
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Zhou M, Deng L, Lacoste V, Park HU, Pumfery A, Kashanchi F, Brady JN, Kumar A. Coordination of transcription factor phosphorylation and histone methylation by the P-TEFb kinase during human immunodeficiency virus type 1 transcription. J Virol 2004; 78:13522-33. [PMID: 15564463 PMCID: PMC533906 DOI: 10.1128/jvi.78.24.13522-13533.2004] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) Tat protein recruits positive transcription elongation factor b (P-TEFb) to the transactivation response (TAR) RNA structure to facilitate formation of processive transcription elongation complexes (TECs). Here we examine the role of the Tat/TAR-specified cyclin-dependent kinase 9 (CDK9) kinase activity in regulation of HIV-1 transcription elongation and histone methylation. In HIV-1 TECs, P-TEFb phosphorylates the RNA polymerase II (RNAP II) carboxyl-terminal domain (CTD) and the transcription elongation factors SPT5 and Tat-SF1 in a Tat/TAR-dependent manner. Using in vivo chromatin immunoprecipitation analysis, we demonstrate the following distinct properties of the HIV-1 transcription complexes. First, the RNAP II CTD is phosphorylated at Ser 2 and Ser 5 near the promoter and at downstream coding regions. Second, the stable association of SPT5 with the TECs is dependent upon P-TEFb kinase activity. Third, P-TEFb kinase activity is critical for the induction of methylation of histone H3 at lysine 4 and lysine 36 on HIV-1 genes. Flavopiridol, a potent P-TEFb kinase inhibitor, inhibits CTD phosphorylation, stable SPT5 binding, and histone methylation, suggesting that its potent antiviral activity is due to its ability to inhibit several critical and unique steps in HIV-1 transcription elongation.
Collapse
Affiliation(s)
- Meisheng Zhou
- Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, DC 20037, USA
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Haaland RE, Herrmann CH, Rice AP. Increased association of 7SK snRNA with Tat cofactor P-TEFb following activation of peripheral blood lymphocytes. AIDS 2003; 17:2429-36. [PMID: 14600513 DOI: 10.1097/00002030-200311210-00004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
OBJECTIVE This study was undertaken to determine whether 7SK small nuclear RNA (snRNA), which has been proposed to function as an inhibitor of Tat cofactor P-TEFb, plays a role in transcriptional latency in T cells. DESIGN AND METHODS The association of 7SK snRNA with P-TEFb was investigated in resting and activated peripheral blood lymphocytes (PBLs). Primary PBLs were isolated by standard methods and activated with phytohemagglutinin (PHA). Levels of 7SK snRNA were determined by Northern blotting and levels of the P-TEFb subunits cyclin-dependent kinase 9 and cyclin T1 were analyzed by immunoblotting. RESULTS The association of 7SK snRNA with P-TEFb complexes was specific. Following activation of PBLs, the levels of 7SK snRNA increased in a manner similar to U1 and U6 snRNA, sn RNAs involved in positive aspects of cellular gene expression. Unexpectedly, the association of 7SK snRNA with P-TEFb increased dramatically following lymphocyte activation. CONCLUSION Increased association of 7SK snRNA with P-TEFb in activated lymphocytes correlates with increased global transcription. This suggests that 7SK snRNA is unlikely to promote transcriptional latency in lymphocytes through an association with P-TEFb; it also suggests that the proposal that the association of 7SK snRNA with P-TEFb acts to inhibit transcriptional elongation needs to be re-evaluated.
Collapse
Affiliation(s)
- Richard E Haaland
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | |
Collapse
|
27
|
Battisti PL, Daher A, Bannwarth S, Voortman J, Peden KWC, Hiscott J, Mouland AJ, Benarous R, Gatignol A. Additive activity between the trans-activation response RNA-binding protein, TRBP2, and cyclin T1 on HIV type 1 expression and viral production in murine cells. AIDS Res Hum Retroviruses 2003; 19:767-78. [PMID: 14585207 DOI: 10.1089/088922203769232566] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Tat-mediated trans-activation of the HIV-1 long terminal repeat (LTR) occurs through the phosphorylation of the carboxy-terminal domain of the RNA polymerase II. The kinase complex, pTEFb, composed of cyclin T1 (CycT1) and CDK9, mediates this process. The trans-activation response (TAR) RNA-binding protein 2 (TRBP2) increases HIV-1 LTR expression through TAR and protein kinase R (PKR) binding, but not through interactions with the Tat-CycT1-CDK9 complex. TRBP2 and the Tat-CycT1-CDK9 complex have overlapping binding sites on TAR RNA. TRBP2 and CycT1 increased Tat trans-activation in NIH 3T3 cells with additive effects. Upon transfection of HIV-1 pLAI, pNL4-3, pMAL, and pAD molecular clones, reverse transcriptase (RT) activity and p24 concentration were decreased 200- to 900-fold in NIH 3T3 cells compared with HeLa cells in both cells and supernatants. In murine cells, cotransfection of the HIV clones with CycT1 or TRBP2 increased modestly the expression of RT activity in cell extracts. The analysis of Gag expression in murine cells transfected with CycT1 compared with human cells showed a 20-fold decrease in expression and a strong processing defect. The expression of both CycT1 and TRBP2 had a more than additive activity on RT function in cell extracts and on viral particle production in supernatant of murine cells. These results suggest an activity of CycT1 and TRBP2 at different steps in HIV-1 expression and indicate the requirement for another posttranscriptional factor in murine cells for full HIV replication.
Collapse
Affiliation(s)
- Pier-Luigi Battisti
- Molecular Oncology Group, Lady Davis Institute for Medical Research, Montréal, Québec H3T 1E2, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Brès V, Tagami H, Péloponèse JM, Loret E, Jeang KT, Nakatani Y, Emiliani S, Benkirane M, Kiernan RE. Differential acetylation of Tat coordinates its interaction with the co-activators cyclin T1 and PCAF. EMBO J 2002; 21:6811-9. [PMID: 12486002 PMCID: PMC139090 DOI: 10.1093/emboj/cdf669] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV-1 transactivator protein, Tat, is an atypical transcriptional activator that functions through binding, not to DNA, but to a short leader RNA, TAR. Although details of its functional mechanism are still unknown, emerging findings suggest that Tat serves primarily to adapt co-activator complexes such as p300, PCAF and P-TEFb to the HIV-1 long terminal repeat. Hence, an understanding of how Tat interacts with these cofactors is crucial. It has recently been shown that acetylation at a single lysine, residue 50, regulated the association of Tat with PCAF. Here, we report that in the absence of Tat acetylation, PCAF binds to amino acids 20-40 within Tat. Interestingly, acetylation of Tat at Lys28 abrogates Tat-PCAF interaction. Acetylation at Lys50 creates a new site for binding to PCAF and dictates the formation of a ternary complex of Tat-PCAF-P-TEFb. Thus, differential lysine acetylation of Tat coordinates the interactions with its co-activators, cyclin T1 and PCAF. Our results may help in understanding the ordered recruitment of Tat co-activators to the HIV-1 promoter.
Collapse
Affiliation(s)
- Vanessa Brès
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| | - Hideaki Tagami
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| | - Jean-Marie Péloponèse
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| | - Erwan Loret
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| | - Kuan-Teh Jeang
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| | - Yoshihiro Nakatani
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| | - Stephane Emiliani
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| | - Monsef Benkirane
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| | - Rosemary E. Kiernan
- Laboratoire de Virologie Moléculaire et Transfert de Gène, Institut de Génétique Humaine, CNRS UPR1142, Montpellier, Laboratoire d’Ingenierie des Systemes Macromoleculaires, Institut de Biologie Structurale et Microbiologie, CNRS UPR 9027, Marseille, Institut Cochin, Departement des Maladies Infectieuses, Paris, France, Laboratory of Molecular Virology, NIAID, NIH, Bethesda, MD and Dana Farber Cancer Research Center, Boston, MA, USA Corresponding author e-mail:
| |
Collapse
|
29
|
Abstract
Human immunodeficiency virus type I (HIV) is the etiologic agent of acquired immunodeficiency syndrome or AIDS. Vectors based upon HIV have been in use for over a decade. Beginning in 1996, with the demonstration of improved pseudotyping using vesicular stomatitis virus (VSV) G protein along with transduction of resting mammalian cells, a series of improvements have been made in these vectors, making them both safer and more efficacious. Taking a cue from vector development of murine leukemia virus (MLV), split coding and self-inactivating HIV vectors now appear quite suitable for phase I clinical trials. In parallel, a number of pre-clinical efficacy studies in animals have demonstrated the utility of these vectors for various diseases processes, especially neurodegenerative and hematopoietic illnesses. These vectors are also appropriate for the study of other viruses (specifically of viral entry) and investigation of the HIV replicative cycle, along with straightforward transgene delivery to target cells of interest. Vectors based upon other lentiviruses have shown similar abilities and promise. Although concerns remain, particularly with regards to detection and propagation of replication-competent lentivirus, it is almost certain that these vectors will be introduced into the clinic within the next 3-5 years.
Collapse
Affiliation(s)
- Ricardo Quinonez
- Department of Molecular Virology and Microbiology, Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030, USA
| | | |
Collapse
|
30
|
Sano M, Abdellatif M, Oh H, Xie M, Bagella L, Giordano A, Michael LH, DeMayo FJ, Schneider MD. Activation and function of cyclin T-Cdk9 (positive transcription elongation factor-b) in cardiac muscle-cell hypertrophy. Nat Med 2002; 8:1310-7. [PMID: 12368904 DOI: 10.1038/nm778] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2002] [Accepted: 09/16/2002] [Indexed: 12/12/2022]
Abstract
Hypertrophic growth is a risk factor for mortality in heart diseases. Mechanisms are lacking for this global increase in RNA and protein per cell, which underlies hypertrophy. Hypertrophic signals cause phosphorylation of the RNA polymerase II C-terminal domain, required for transcript elongation. RNA polymerase II kinases include cyclin-dependent kinases-7 (Cdk7) and Cdk9, components of two basal transcription factors. We report activation of Cdk7 and -9 in hypertrophy triggered by signaling proteins (Galphaq, calcineurin) or chronic mechanical stress. Only Cdk9 was activated by acute load or, in culture, by endothelin. A preferential role for Cdk9 was shown in RNA polymerase II phosphorylation and growth induced by endothelin, using pharmacological and dominant-negative inhibitors. All four hypertrophic signals dissociated 7SK small nuclear RNA, an endogenous inhibitor, from cyclin T-Cdk9. Cdk9 was limiting for cardiac growth, shown by suppressing its inhibitor (7SK) in culture and preventing downregulation of its activator (cyclin T1) in mouse myocardium.Note: In the AOP version of this article, the numbering of the author affiliations was incorrect. This has now been fixed, and the affiliations appear correctly online and in print.
Collapse
Affiliation(s)
- Motoaki Sano
- Center for Cardiovascular Development, Baylor College of Medicine, Texas, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Liou LY, Herrmann CH, Rice AP. Transient induction of cyclin T1 during human macrophage differentiation regulates human immunodeficiency virus type 1 Tat transactivation function. J Virol 2002; 76:10579-87. [PMID: 12368300 PMCID: PMC136632 DOI: 10.1128/jvi.76.21.10579-10587.2002] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) Tat protein is essential for viral replication and stimulates transcription of the integrated provirus by recruiting the kinase complex TAK/P-TEFb, composed of cyclin T1 (CycT1) and Cdk9, to the viral TAR RNA element. TAK/P-TEFb phosphorylates the RNA polymerase II complex and stimulates transcriptional elongation. In this report, we investigated the regulation of TAK/P-TEFb in primary human macrophages, a major target cell of HIV infection. While Cdk9 levels remained constant, CycT1 protein expression in freshly isolated monocytes was very low, increased early during macrophage differentiation, and, unexpectedly, decreased to very low levels after about 1 week in culture. The kinase activity of TAK/P-TEFb paralleled the changes in CycT1 protein expression. RNA analysis indicated that the transient induction of CycT1 protein expression involves a posttranscriptional mechanism. In transient transfection assays, the ability of Tat to transactivate the HIV long terminal repeat (LTR) in the late differentiated macrophages was greatly diminished relative to its ability to transactivate the HIV LTR in early differentiated cells, strongly suggesting that CycT1 is limiting for Tat function in late differentiated macrophages. Interestingly, lipopolysaccharide, a component of the cell wall of gram-negative bacteria, reinduced CycT1 expression late in macrophage differentiation. These results raise the possibility that regulation of CycT1 expression may be involved in establishing latent infection in macrophages and that opportunistic infection may reactivate the virus by inducing CycT1 expression.
Collapse
Affiliation(s)
- Li-Ying Liou
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | | | | |
Collapse
|
32
|
Lin PS, Marshall NF, Dahmus ME. CTD phosphatase: role in RNA polymerase II cycling and the regulation of transcript elongation. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2002; 72:333-65. [PMID: 12206456 DOI: 10.1016/s0079-6603(02)72074-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The repetitive C-terminal domain (CTD) of the largest RNA polymerase II subunit plays a critical role in the regulation of gene expression. The activity of the CTD is dependent on its state of phosphorylation. A variety of CTD kinases act on RNA polymerase II at specific steps in the transcription cycle and preferentially phosphorylate distinct positions within the CTD consensus repeat. A single CTD phosphatase has been identified and characterized that in concert with CTD kinases establishes the level of CTD phosphorylation. The involvement of CTD phosphatase in controlling the progression of RNAP II around the transcription cycle, the mobilization of stored RNAP IIO, and the regulation of transcript elongation and RNA processing is discussed.
Collapse
|
33
|
Simone C, Bagella L, Bellan C, Giordano A. Physical interaction between pRb and cdk9/cyclinT2 complex. Oncogene 2002; 21:4158-65. [PMID: 12037672 DOI: 10.1038/sj.onc.1205511] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2001] [Revised: 03/13/2002] [Accepted: 03/21/2002] [Indexed: 11/09/2022]
Abstract
Cyclin-dependent kinase 9 (cdk9) is a multifunctional kinase with roles in different cellular pathways such as transcriptional elongation, differentiation and apoptosis. Cdk9/cyclin T differs functionally from other cdk/cyclin complexes that regulate cell cycle progression, but maintains structural affinity with those complexes. In addition, previous reports have demonstrated that the cdk9 complex is able to phosphorylate p56/pRb in vitro. In this report we show in vitro and in vivo interaction between cdk9/cyclinT2 and the protein product of the retinoblastoma gene (pRb) in human cell lines. The interaction involves the region composed of residues 129-195 of cdk9, cyclinT2 (1-642 aa) and the C-terminal domain of pRb (835-928 aa). We located the minimal region of cdk9 phosphorylation on the C-terminus of pRb, by identifying the residues between 793 and 834. This region contains at least three proline-directed serines (sp), S795, S807 and S811, which have been reported to be phosphorylated in vivo and which could be targeted by the cdk9 complex. These data suggest that, in logarithmically growing cells, cdk9/cyclin T2 and pRb are located in a nuclear multiprotein complex probably involved in transduction of cellular signals to the basal transcription machinery and that one of these signals could be the cdk9 phosphorylation of pRb.
Collapse
Affiliation(s)
- Cristiano Simone
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, PA 19107, USA
| | | | | | | |
Collapse
|
34
|
Simone C, Stiegler P, Bagella L, Pucci B, Bellan C, De Falco G, De Luca A, Guanti G, Puri PL, Giordano A. Activation of MyoD-dependent transcription by cdk9/cyclin T2. Oncogene 2002; 21:4137-48. [PMID: 12037670 DOI: 10.1038/sj.onc.1205493] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2001] [Revised: 03/01/2002] [Accepted: 03/18/2002] [Indexed: 11/09/2022]
Abstract
Myogenic transcription is repressed in myoblasts by serum-activated cyclin-dependent kinases, such as cdk2 and cdk4. Serum withdrawal promotes muscle-specific gene expression at least in part by down-regulating the activity of these cdks. Unlike the other cdks, cdk9 is not serum- or cell cycle-regulated and is instead involved in the regulation of transcriptional elongation by phosphorylating the carboxyl-terminal domain (CTD) of RNA polymerase II. While ectopic expression of cdk2 together with its regulatory subunits (cyclins E and A) inhibits myogenic transcription, overproduction of cdk9 and its associated cyclin (cyclin T2a) strengthens MyoD-dependent transcription and stimulates myogenic differentiation in both MyoD-converted fibroblasts and C2C12 muscle cells. Conversely, inhibition of cdk9 activity by a dominant negative form (cdk9-dn) represses the myogenic program. Cdk9, cyclinT2 and MyoD can be detected in a multimeric complex in C2C12 cells, with the minimal cdk9-binding region of MyoD mapping within 101-161 aa of the bHLH region. Finally, cdk9 can phosphorylate MyoD in vitro, suggesting the possibility that cdk9/cycT2a regulation of muscle differentiation includes the direct enzymatic activity of the kinase on MyoD.
Collapse
Affiliation(s)
- Cristiano Simone
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, Pennsylvania, PA 19122, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Dorr A, Kiermer V, Pedal A, Rackwitz HR, Henklein P, Schubert U, Zhou MM, Verdin E, Ott M. Transcriptional synergy between Tat and PCAF is dependent on the binding of acetylated Tat to the PCAF bromodomain. EMBO J 2002; 21:2715-23. [PMID: 12032084 PMCID: PMC125383 DOI: 10.1093/emboj/21.11.2715] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The human immunodeficiency virus (HIV) Tat protein plays an essential role in promoting efficient transcriptional elongation of viral transcripts. We report that the transcriptional co-activator PCAF and Tat interact and synergize to activate the HIV promoter. The binding of Tat and PCAF in vitro and in vivo is dependent on the acetylated state of Lys50 of Tat and on the PCAF bromodomain. Structural analysis of the acetylated Tat peptide bound to the PCAF bromodomain defined amino acids Y47 and R53 in Tat and V763, Y802, and Y809 in PCAF as critical interaction points between the two proteins. Mutation of each of these residues in either Tat or PCAF inhibited in a cumulative manner the Tat-PCAF interaction in vitro and in vivo, and abrogated the synergistic activation of the HIV promoter by both proteins. These observations demonstrate that acetylation of Tat establishes a novel protein-protein interaction domain at the surface of Tat that is necessary for the transcriptional activation of the HIV promoter.
Collapse
Affiliation(s)
| | - Veronique Kiermer
- Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg,
Humboldt University, Institute of Biochemistry, D-10115 Berlin, Germany, Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94141, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD 20892 and Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York,NY 10029-6574, USA Corresponding author e-mail: A.Dorr and V.Kiermer contributed equally to this work
| | | | | | - Peter Henklein
- Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg,
Humboldt University, Institute of Biochemistry, D-10115 Berlin, Germany, Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94141, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD 20892 and Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York,NY 10029-6574, USA Corresponding author e-mail: A.Dorr and V.Kiermer contributed equally to this work
| | - Ulrich Schubert
- Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg,
Humboldt University, Institute of Biochemistry, D-10115 Berlin, Germany, Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94141, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD 20892 and Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York,NY 10029-6574, USA Corresponding author e-mail: A.Dorr and V.Kiermer contributed equally to this work
| | - Ming-Ming Zhou
- Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg,
Humboldt University, Institute of Biochemistry, D-10115 Berlin, Germany, Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94141, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD 20892 and Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York,NY 10029-6574, USA Corresponding author e-mail: A.Dorr and V.Kiermer contributed equally to this work
| | - Eric Verdin
- Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg,
Humboldt University, Institute of Biochemistry, D-10115 Berlin, Germany, Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94141, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD 20892 and Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York,NY 10029-6574, USA Corresponding author e-mail: A.Dorr and V.Kiermer contributed equally to this work
| | - Melanie Ott
- Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg,
Humboldt University, Institute of Biochemistry, D-10115 Berlin, Germany, Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94141, Laboratory of Viral Diseases, National Institutes of Health, Bethesda, MD 20892 and Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York,NY 10029-6574, USA Corresponding author e-mail: A.Dorr and V.Kiermer contributed equally to this work
| |
Collapse
|
36
|
Fang JY, Lu YY. Effects of histone acetylation and DNA methylation on p21( WAF1) regulation. World J Gastroenterol 2002; 8:400-5. [PMID: 12046058 PMCID: PMC4656409 DOI: 10.3748/wjg.v8.i3.400] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2001] [Revised: 12/22/2001] [Accepted: 02/07/2002] [Indexed: 02/06/2023] Open
Abstract
Cell cycle progression is regulated by interactions between cyclins and cyclin-dependent kinases (CDKs). p21(WAF1) is one of the CIP/KIP family which inhibits CDKs activity. Increased expression of p21(WAF1) may play an important role in the growth arrest induced in transformed cells. Although the stability of the p21( WAF1) mRNA could be altered by different signals, cell differentiation and numerous influencing factors. However, recent studies suggest that two known mechanisms of epigenesis, i.e.gene inactivation by methylation in promoter region and changes to an inactive chromatin by histone deacetylation, seem to be the best candidate mechanisms for inactivation of p21( WAF1). To date, almost no coding region p21(WAF1) mutations have been found in tumor cells, despite extensive screening of hundreds of various tumors. Hypermethylation of the p21(WAF1) promoter region may represent an alternative mechanism by which the p21(WAF1/CIP1) gene can be inactivated. The reduction of cellular DNMT protein levels also induces a corresponding rapid increase in the cell cycle regulator p21(WAF1) protein demonstrating a regulatory link between DNMT and p21(WAF1) which is independent of methylation of DNA. Both histone hyperacetylation and hypoacetylation appear to be important in the carcinoma process, and induction of the p21(WAF1) gene by histone hyperacetylation may be a mechanism by which dietary fiber prevents carcinogenesis. Here, we review the influence of histone acetylation and DNA methylation on p21(WAF1) transcription, and affection of pathways or factors associated such as p 53, E2A, Sp1 as well as several histone deacetylation inhibitors.
Collapse
Affiliation(s)
- Jing-Yuan Fang
- Renji Hospital, Shanghai Institute of Digestive Disease, Shanghai Second Medical School, Shanghai 200001, China.
| | | |
Collapse
|
37
|
Estable MC, Naghavi MH, Kato H, Xiao H, Qin J, Vahlne A, Roeder RG. MCEF, the newest member of the AF4 family of transcription factors involved in leukemia, is a positive transcription elongation factor-b-associated protein. J Biomed Sci 2002; 9:234-45. [PMID: 12065898 DOI: 10.1007/bf02256070] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Positive transcription elongation factor-b (P-TEFb) contains CDK9 and cyclin T(1). P-TEFb was affinity purified from a stably transfected cell line that expresses epitope-tagged CDK9, and proteins that appeared to be specifically bound were sequenced. In addition to CDK9, previously identified isoforms of cyclin T (including T(1), T(2A) and T(2B)), HSP90 and CDC37, this analysis identified a novel protein named MCEF. Cloning of its cognate cDNA revealed that MCEF is the newest member of the AF4 family of transcription factors involved in acute lymphoblastic leukemia. MCEF RNA was expressed in all human tissues examined, and antisera directed against recombinant MCEF specifically immunoprecipitated P-TEFb. Ectopic expression of MCEF did not activate HIV-1 replication, and tethering of MCEF to a promoter did not activate transcription.
Collapse
Affiliation(s)
- Mario Clemente Estable
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, N.Y., USA
| | | | | | | | | | | | | |
Collapse
|
38
|
Roof P, Ricci M, Genin P, Montano MA, Essex M, Wainberg MA, Gatignol A, Hiscott J. Differential regulation of HIV-1 clade-specific B, C, and E long terminal repeats by NF-kappaB and the Tat transactivator. Virology 2002; 296:77-83. [PMID: 12036319 DOI: 10.1006/viro.2001.1397] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The major group of human immunodeficiency viruses (HIV-1) that comprise the current global pandemic have diversified during their worldwide spread and may be divided into at least 10 distinct subtypes or clades, A through J. Subtype B predominates in North America and Europe, subtype E predominates in Southeast Asia, and subtype C predominates in sub-Saharan Africa. Functional distinctions in long terminal repeat (LTR) architecture among HIV subtypes have been identified, thus raising the possibility that regulatory divergence among the subtypes of HIV-1 has occurred. In addition to the transcriptional specificity of the HIV-1 LTR, productive HIV-1 replication is also dependent upon the viral Tat protein. Therefore, we sought to investigate whether interactions between host signaling pathways and the NF-kappaB regions of different HIV-1 subtypes, together with subtype-specific interactions between Tat, TAR, and cellular proteins, modulate the efficiency of HIV-1 clade-specific gene transcription. We demonstrate that the NF-kappaB sites of subtypes B and E both bind NF-kappaB-related complexes. However, the duplicated kappaB sites of the C subtype do not compete for NF-kappaB binding. Also, clade E Tat protein possesses the highest transactivation capacity, regardless of the LTR context. Furthermore, preliminary evidence suggests that the acetylation of subtype-specific Tat proteins may correlate with their transactivation efficiency.
Collapse
Affiliation(s)
- Philippe Roof
- McGill AIDS Center, McGill University, Montréal, Québec, Canada
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Zhou M, Nekhai S, Bharucha DC, Kumar A, Ge H, Price DH, Egly JM, Brady JN. TFIIH inhibits CDK9 phosphorylation during human immunodeficiency virus type 1 transcription. J Biol Chem 2001; 276:44633-40. [PMID: 11572868 DOI: 10.1074/jbc.m107466200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tat stimulates human immunodeficiency virus, type 1 (HIV-1), transcription elongation by recruitment of the human transcription elongation factor P-TEFb, consisting of CDK9 and cyclin T1, to the TAR RNA structure. It has been demonstrated further that CDK9 phosphorylation is required for high affinity binding of Tat/P-TEFb to the TAR RNA structure and that the state of P-TEFb phosphorylation may regulate Tat transactivation. We now demonstrate that CDK9 phosphorylation is uniquely regulated in the HIV-1 preinitiation and elongation complexes. The presence of TFIIH in the HIV-1 preinitiation complex inhibits CDK9 phosphorylation. As TFIIH is released from the elongation complex between +14 and +36, CDK9 phosphorylation is observed. In contrast to the activity in the "soluble" complex, phosphorylation of CDK9 is increased by the presence of Tat in the transcription complexes. Consistent with these observations, we have demonstrated that purified TFIIH directly inhibits CDK9 autophosphorylation. By using recombinant TFIIH subcomplexes, our results suggest that the XPB subunit of TFIIH is responsible for this inhibition of CDK9 phosphorylation. Interestingly, our results further suggest that the phosphorylated form of CDK9 is the active kinase for RNA polymerase II carboxyl-terminal domain phosphorylation.
Collapse
Affiliation(s)
- M Zhou
- Virus Tumor Biology Section, Basic Research Laboratory, Division of Basic Sciences, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Browning CM, Smith MJ, Clark NM, Lane BR, Parada C, Montano M, KewalRamani VN, Littman DR, Essex M, Roeder RG, Markovitz DM. Human GLI-2 is a tat activation response element-independent Tat cofactor. J Virol 2001; 75:2314-23. [PMID: 11160734 PMCID: PMC114814 DOI: 10.1128/jvi.75.5.2314-2323.2001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2000] [Accepted: 12/07/2000] [Indexed: 11/20/2022] Open
Abstract
Zinc finger-containing GLI proteins are involved in the development of Caenorhabditis elegans, Xenopus, Drosophila, zebrafish, mice, and humans. In this study, we show that an isoform of human GLI-2 strongly synergizes with the Tat transactivating proteins of human immunodeficiency virus types 1 and 2 (HIV-1 and -2) and markedly stimulates viral replication. GLI-2 also synergizes with the previously described Tat cofactor cyclin T1 to stimulate Tat function. Surprisingly, GLI-2/Tat synergy is not dependent on either a typical GLI DNA binding site or an intact Tat activation response element but does require an intact TATA box. Thus, GLI-2/Tat synergy results from a mechanism of action which is novel both for a GLI protein and for a Tat cofactor. These findings link the GLI family of transcriptional and developmental regulatory proteins to Tat function and HIV replication.
Collapse
Affiliation(s)
- C M Browning
- Department of Microbiology and Immunology, Ann Arbor, Michigan 48109-0640,USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Berkhout B. Multiple biological roles associated with the repeat (R) region of the HIV-1 RNA genome. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2001; 48:29-73. [PMID: 10987088 DOI: 10.1016/s1054-3589(00)48003-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- B Berkhout
- Department of Human Retrovirology, University of Amsterdam, The Netherlands
| |
Collapse
|
42
|
Gatignol A, Jeang KT. Tat as a transcriptional activator and a potential therapeutic target for HIV-1. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2001; 48:209-27. [PMID: 10987092 DOI: 10.1016/s1054-3589(00)48007-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- A Gatignol
- U529 INSERM, Institut Cochin de Génétique Moléculaire, Paris, France
| | | |
Collapse
|
43
|
Licciardo P, Napolitano G, Majello B, Lania L. Inhibition of Tat transactivation by the RNA polymerase II CTD-phosphatase FCP1. AIDS 2001; 15:301-7. [PMID: 11273209 DOI: 10.1097/00002030-200102160-00002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To asses the role of the RNAPII carboxy-terminal domain (CTD) phosphatase FCP1 on HIV-1 Tat-mediated transactivation. DESIGN Construction of expression vectors encoding FCP1 phosphatase and analysis of their functions on Tat activity. METHODS Basal and Tat-mediated transactivation of HIV-1 long terminal repeat (LTR)-driven transcription was compared, by transient transfections, in the presence of FCP1 phosphatase. Protein interactions were analysed by in vitro binding assays. RESULTS FCP1 specifically and effectively represses Tat transactivation but not HIV-1 LTR-basal transcription. Protein interaction assays demonstrated that FCP1 specifically and directly binds Tat in vitro. CONCLUSION The specific and efficient inhibitory function of FCP1 highlights the important role of this CTD-phosphatase in Tat-mediated transactivation, and it suggests that FCP1 might represent a specific target for modulation of Tat activity in infected cells.
Collapse
Affiliation(s)
- P Licciardo
- Department of Genetics, Molecular and General Biology, University of Naples Federico II and the International Institute of Genetics and Biophysics, Italy
| | | | | | | |
Collapse
|
44
|
Richard MJ, Guiraud P, Didier C, Seve M, Flores SC, Favier A. Human Immunodeficiency Virus Type 1 Tat Protein Impairs Selenoglutathione Peroxidase Expression and Activity by a Mechanism Independent of Cellular Selenium Uptake: Consequences on Cellular Resistance to UV-A Radiation. Arch Biochem Biophys 2001; 386:213-20. [PMID: 11368344 DOI: 10.1006/abbi.2000.2197] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The expression of the HIV-1 Tat protein in HeLa cells resulted in a 2.5-fold decrease in the activity of the antioxidant enzyme glutathione peroxidase (GPX). This decrease seemed not to be due to a disturbance in selenium (Se) uptake. Indeed, the intracellular level of Se was similar in parental and tat-transfected cells. A Se enrichment of the medium did not lead to an identical GPX activity in both cell lines, suggesting a disturbance in Se utilization. Total intracellular 75Se selenoproteins were analyzed. Several quantitative differences were observed between parental and tat-transfected cells. Mainly, cytoplasmic glutathione peroxidase and a 15-kDa selenoprotein were decreased in HeLa-tat cells, while phospholipid hydroperoxide glutathione peroxidase and low-molecular-mass selenocompounds were increased. Thioredoxin reductase activity and total levels of 75Se-labeled proteins were not different between the two cell types. The effect of Tat on GPX mRNA levels was also analyzed. Northern blots revealed a threefold decrease in the GPX/glyceraldehyde phosphate dehydrogenase mRNA ratio in HeLa-tat versus wild type cells. By deregulating the intracellular oxidant/antioxidant balance, the Tat protein amplified UV sensitivity. The LD50 for ultraviolet radiation A was 90 J/cm2 for HeLa cells and only 65 J/cm2 for HeLa-tat cells. The oxidative stress occurring in the Tat-expressing cells and demonstrated by the diminished ratio of reduced glutathione/oxidized glutathione was not correlated with the intracellular metal content. Cellular iron and copper levels were significantly decreased in HeLa-tat cells. All these disturbances, as well as the previously described decrease in Mn superoxide dismutase activity, are part of the viral strategy to modify the redox potential of cells and may have important consequences for patients.
Collapse
Affiliation(s)
- M J Richard
- LBSO/LCR7 No. 8, Université Joseph Fourier, Grenoble, France.
| | | | | | | | | | | |
Collapse
|
45
|
Deng L, de la Fuente C, Fu P, Wang L, Donnelly R, Wade JD, Lambert P, Li H, Lee CG, Kashanchi F. Acetylation of HIV-1 Tat by CBP/P300 increases transcription of integrated HIV-1 genome and enhances binding to core histones. Virology 2000; 277:278-95. [PMID: 11080476 DOI: 10.1006/viro.2000.0593] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The HIV-1 Tat protein is required for viral replication and is a potent stimulator of viral transcription. Although Tat has been extensively studied in various reductive paradigms, to date there is little information as to how this activator mediates transcription from natural nucleosomally packaged long terminal repeats. Here we show that CREB-binding protein (CBP)/p300 interacts with the HIV-1 Tat protein and serves as a coactivator of Tat-dependent HIV-1 gene expression on an integrated HIV-1 provirus. The site of acetylation of Tat was mapped to the double-lysine motif in a highly conserved region, (49)RKKRRQ(54), of the basic RNA-binding motif of Tat. Using HLM1 cells (HIV-1(+)/Tat(-)), which contain a single copy of full-length HIV-1 provirus with a triple termination codon at the first AUG of the Tat gene, we find that only wild type, and not K50A, K51A, or K50A/K51A alone or in combination of ectopic CBP/p300, is able to produce full-length infectious virions, as measured by p24 gag ELISAs. Tat binds CBP/p300 in the minimal histone acetyltransferase domain (1253-1710) and the binding is stable up to 0.85 M salt wash conditions. Interestingly, wild-type peptide 41-54, and not other Tat peptides, changes the conformation of the CBP/p300 such that it can acquire and bind better to basal factors such as TBP and TFIIB, indicating that Tat may influence the transcription machinery by helping CBP/p300 to recruit new partners into the transcription machinery. Finally, using biotinylated wild-type or acetylated peptides, we find that acetylation decreases Tat's ability to bind the TAR RNA element, as well as to bind basal factors such as TBP, CBP, Core-Pol II, or cyclin T. However, the acetylated Tat peptide is able to bind to core histones on a nucleosome assembled HIV-1 proviral DNA.
Collapse
Affiliation(s)
- L Deng
- Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, MSB E-635, Newark, New Jersey 07103, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Marshall NF, Dahmus ME. C-terminal domain phosphatase sensitivity of RNA polymerase II in early elongation complexes on the HIV-1 and adenovirus 2 major late templates. J Biol Chem 2000; 275:32430-7. [PMID: 10938286 DOI: 10.1074/jbc.m005898200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fate of RNA polymerase II in early elongation complexes is under the control of factors that regulate and respond to the phosphorylation state of the C-terminal domain (CTD). Phosphorylation of the CTD protects early elongation complexes from negative transcription elongation factors such as NELF, DSIF, and factor 2. To understand the relationship between transcript elongation and the sensitivity of RNA polymerase IIO to dephosphorylation, elongation complexes at defined positions on the Ad2-ML and human immunodeficiency virus type 1 (HIV-1) templates were purified, and their sensitivity to CTD phosphatase was determined. Purified elongation complexes treated with 1% Sarkosyl and paused at U(14)/G(16) on an HIV-1 template and at G(11) on the Ad2-ML template are equally sensitive to dephosphorylation by CTD phosphatase. Multiple elongation complexes paused at more promoter distal sites are more resistant to dephosphorylation than are U(14)/G(16) and G(11) complexes. The HIV-1 long terminal repeat and adenovirus 2 major late promoter do not appear to differentially influence the CTD phosphatase sensitivity of stringently washed complexes. Subsequent elongation by 1% Sarkosyl-washed U(14)/G(16) complexes is unaffected by prior CTD phosphatase treatment. This result is consistent with the hypothesis that CTD phosphatase requires the presence of specific elongation factors to propagate a negative effect on transcript elongation. The action of CTD phosphatase on elongation complexes is inhibited by HIV-1 Tat protein. This observation is consistent with the idea that Tat suppression of CTD phosphatase plays a role in transactivation.
Collapse
Affiliation(s)
- N F Marshall
- Section of Molecular and Cellular Biology, Division of Biological Sciences, University of California, Davis, California 95616, USA
| | | |
Collapse
|
47
|
Abstract
Equine infectious anemia virus (EIAV) is an ungulate lentivirus that is related to human immunodeficiency virus (HIV). Much of the understanding of lentiviral gene regulation comes from studies using HIV. HIV studies have provided insights into molecular regulation of EIAV expression; however, much of the regulation of EIAV expression stands in stark contrast to that of HIV. This review provides an overview of the current state of knowledge of EIAV regulation by comparing and contrasting EIAV gene regulation to HIV. The role of EIAV gene regulation is discussed in relation to EIAV pathogenesis.
Collapse
Affiliation(s)
- W Maury
- Department of Microbiology, University of South Dakota School of Medicine, Vermillion 57069, USA.
| |
Collapse
|
48
|
Abstract
The HIV-1 Tat protein is an RNA-binding transcriptional transactivator. Recent findings suggest that Tat associates with a cellular kinase that phosphorylates the carboxyl-terminal domain of the largest subunit of RNA polymerase II. Here we review, in brief, the role of Tat-associated kinase in Tat-activated transcription. We discuss evidence that suggests involvement of TFIIH and/or P-TEFb.
Collapse
Affiliation(s)
- K T Jeang
- Molecular Virology Section, Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD 20892-0460, USA.
| |
Collapse
|
49
|
Napolitano G, Majello B, Licciardo P, Giordano A, Lania L. Transcriptional activity of positive transcription elongation factor b kinase in vivo requires the C-terminal domain of RNA polymerase II. Gene 2000; 254:139-45. [PMID: 10974544 DOI: 10.1016/s0378-1119(00)00278-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phosphorylation of the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAPII) is an important step in transcription and the positive transcription elongation factor b (P-TEFb) has been proposed to facilitate elongation at many genes. The P-TEFb contains a catalytic subunit (Cdk9) that, in association with a cyclin subunit (cyclinT1), has the ability to phosphorylate the CTD substrate in vitro. Here, we demonstrate that cyclinT1/Cdk9-mediated transcription requires CTD-containing RNAPII, suggesting that the CTD is the major target of the cyclinT1/Cdk9 complex in vivo. Unlike Cdk7 and Cdk8, two other cyclin-dependent kinases that are capable of phosphorylating the CTD in vitro, we found that only the Cdk9 activates gene expression in a catalysis-dependent manner. Finally, unlike cyclinT1 and T2, we found that the targeted recruitment to promoter DNA of cyclinK (a recently described alternative partner of Cdk9) does not stimulate transcription in vivo. Collectively, our data strongly indicate that the P-TEFb kinase subunits cyclinT/Cdk9 are specifically involved in transcription and the CTD domain of RNAPII is the major functional target of this complex in vivo.
Collapse
Affiliation(s)
- G Napolitano
- Department of Genetics, Molecular and General Biology, University of Naples 'Federico II' and International Institute of Genetics and Biophysics, CNR, Via Mezzocannone 8, 80134, Naples, Italy
| | | | | | | | | |
Collapse
|
50
|
Fong YW, Zhou Q. Relief of two built-In autoinhibitory mechanisms in P-TEFb is required for assembly of a multicomponent transcription elongation complex at the human immunodeficiency virus type 1 promoter. Mol Cell Biol 2000; 20:5897-907. [PMID: 10913173 PMCID: PMC86067 DOI: 10.1128/mcb.20.16.5897-5907.2000] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tat stimulation of human immunodeficiency virus type 1 (HIV-1) transcription requires Tat-dependent recruitment of human positive transcription elongation factor b (P-TEFb) to the HIV-1 promoter and the formation on the trans-acting response element (TAR) RNA of a P-TEFb-Tat-TAR ternary complex. We show here that the P-TEFb heterodimer of Cdk9-cyclin T1 is intrinsically incapable of forming a stable complex with Tat and TAR due to two built-in autoinhibitory mechanisms in P-TEFb. Both mechanisms exert little effect on the P-TEFb-Tat interaction but prevent the P-TEFb-Tat complex from binding to TAR RNA. The first autoinhibition arises from the unphosphorylated state of Cdk9, which establishes a P-TEFb conformation unfavorable for TAR recognition. Autophosphorylation of Cdk9 overcomes this inhibition by inducing conformational changes in P-TEFb, thereby exposing a region in cyclin T1 for possible TAR binding. An intramolecular interaction between the N- and C-terminal regions of cyclin T1 sterically blocks the P-TEFb-TAR interaction and constitutes the second autoinhibitory mechanism. This inhibition is relieved by the binding of the C-terminal region of cyclin T1 to the transcription elongation factor Tat-SF1 and perhaps other cellular factors. Upon release from the intramolecular interaction, the C-terminal region also interacts with RNA polymerase II and is required for HIV-1 transcription, suggesting its role in bridging the P-TEFb-Tat-TAR complex and the basal elongation apparatus. These data reveal novel control mechanisms for the assembly of a multicomponent transcription elongation complex at the HIV-1 promoter.
Collapse
Affiliation(s)
- Y W Fong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3206, USA
| | | |
Collapse
|