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Ranga U, Panchapakesan A, Saini C. HIV-1 subtypes and latent reservoirs. Curr Opin HIV AIDS 2024; 19:87-92. [PMID: 38169308 DOI: 10.1097/coh.0000000000000835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW We explore the current status of research on HIV-1 subtype-specific variations and their impact on HIV-1 latency. We also briefly address the controversy surrounding the decision-making process governing the ON/OFF states of HIV-1 transcription, specifically focusing on the regulatory elements, the long terminal repeat (LTR), and Tat. Understanding the decision-making process is crucial for developing effective intervention strategies, such as the 'shock-and-kill' approach, to reactivate latent HIV-1. RECENT FINDINGS Attention has been drawn to subtype-specific transcription factor binding site (TFBS) variations and the possible impact of these variations on viral latency. Further, diverse subtype-specific assays have been developed to quantify the latent viral reservoirs. One interesting observation is the relatively larger latent reservoirs in HIV-1B infection than those of other viral subtypes, which needs rigorous validation. The emergence of LTR-variant viral strains in HIV-1C demonstrating significantly higher levels of latency reversal has been reported. SUMMARY Despite persistent and substantial efforts, latent HIV-1 remains a formidable challenge to a functional cure. Determined and continued commitment is needed to understand the ON/OFF decision-making process of HIV-1 latency, develop rigorous assays for accurately quantifying the latent reservoirs, and identify potent latency-reversing agents and cocktails targeting multiple latency stages. The review emphasizes the importance of including diverse viral subtypes in future latency research.
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Affiliation(s)
- Udaykumar Ranga
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
| | - Arun Panchapakesan
- Molecular Biology Laboratory, Y R Gaitonde Centre for AIDS Research and Education (YRG CARE), Chennai, Tamil Nadu, India
| | - Chhavi Saini
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, Karnataka
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2
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Nkuwi E, Judicate GP, Tan TS, Barabona G, Toyoda M, Sunguya B, Kamori D, Ueno T. Relative resistance of patient-derived envelope sequences to SERINC5-mediated restriction of HIV-1 infectivity. J Virol 2023; 97:e0082323. [PMID: 37768085 PMCID: PMC10617508 DOI: 10.1128/jvi.00823-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/13/2023] [Indexed: 09/29/2023] Open
Abstract
IMPORTANCE Pathogenesis of HIV-1 is enhanced through several viral-encoded proteins that counteract a range of host restriction molecules. HIV-1 Nef counteracts the cell membrane protein SERINC5 by downregulating it from the cell surface, thereby enhancing virion infectivity. Some subtype B reference Envelope sequences have shown the ability to bypass SERINC5 infectivity restriction independent of Nef. However, it is not clear if and to what extent circulating HIV-1 strains can exhibit resistance to SERINC5 restriction. Using a panel of Envelope sequences isolated from 50 Tanzanians infected with non-B HIV-1 subtypes, we show that the lentiviral reporters pseudotyped with patient-derived Envelopes have reduced sensitivity to SERINC5 and that this sensitivity differed among viral subtypes. Moreover, we found that SERINC5 sensitivity within patient-derived Envelopes can be modulated by separate regions, highlighting the complexity of viral/host interactions.
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Affiliation(s)
- Emmanuel Nkuwi
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Department of Microbiology and Parasitology, The University of Dodoma, Dodoma, Tanzania
| | - George P. Judicate
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
| | - Toong Seng Tan
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
| | - Godfrey Barabona
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
| | - Mako Toyoda
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
| | - Bruno Sunguya
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Community Health, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Doreen Kamori
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection Kumamoto University, Kumamoto, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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3
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Herd CL, Mellet J, Mashingaidze T, Durandt C, Pepper MS. Consequences of HIV infection in the bone marrow niche. Front Immunol 2023; 14:1163012. [PMID: 37497228 PMCID: PMC10366613 DOI: 10.3389/fimmu.2023.1163012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Dysregulation of the bone marrow niche resulting from the direct and indirect effects of HIV infection contributes to haematological abnormalities observed in HIV patients. The bone marrow niche is a complex, multicellular environment which functions primarily in the maintenance of haematopoietic stem/progenitor cells (HSPCs). These adult stem cells are responsible for replacing blood and immune cells over the course of a lifetime. Cells of the bone marrow niche support HSPCs and help to orchestrate the quiescence, self-renewal and differentiation of HSPCs through chemical and molecular signals and cell-cell interactions. This narrative review discusses the HIV-associated dysregulation of the bone marrow niche, as well as the susceptibility of HSPCs to infection by HIV.
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Madlala P, Mkhize Z, Naicker S, Khathi SP, Maikoo S, Gopee K, Dong KL, Ndung’u T. Genetic variation of the HIV-1 subtype C transmitted/founder viruses long terminal repeat elements and the impact on transcription activation potential and clinical disease outcomes. PLoS Pathog 2023; 19:e1011194. [PMID: 37307292 PMCID: PMC10289673 DOI: 10.1371/journal.ppat.1011194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/23/2023] [Accepted: 05/04/2023] [Indexed: 06/14/2023] Open
Abstract
A genetic bottleneck is a hallmark of HIV-1 transmission such that only very few viral strains, termed transmitted/founder (T/F) variants establish infection in a newly infected host. Phenotypic characteristics of these variants may determine the subsequent course of disease. The HIV-1 5' long terminal repeat (LTR) promoter drives viral gene transcription and is genetically identical to the 3' LTR. We hypothesized that HIV-1 subtype C (HIV-1C) T/F virus LTR genetic variation is a determinant of transcriptional activation potential and clinical disease outcome. The 3'LTR was amplified from plasma samples of 41 study participants acutely infected with HIV-1C (Fiebig stages I and V/VI). Paired longitudinal samples were also available at one year post-infection for 31 of the 41 participants. 3' LTR amplicons were cloned into a pGL3-basic luciferase expression vector, and transfected alone or together with Transactivator of transcription (tat) into Jurkat cells in the absence or presence of cell activators (TNF-α, PMA, Prostratin and SAHA). Inter-patient T/F LTR sequence diversity was 5.7% (Renge: 2-12) with subsequent intrahost viral evolution observed in 48.4% of the participants analyzed at 12 months post-infection. T/F LTR variants exhibited differential basal transcriptional activity, with significantly higher Tat-mediated transcriptional activity compared to basal (p<0.001). Basal and Tat-mediated T/F LTR transcriptional activity showed significant positive correlation with contemporaneous viral loads and negative correlation with CD4 T cell counts (p<0.05) during acute infection respectively. Furthermore, Tat-mediated T/F LTR transcriptional activity significanly correlated positively with viral load set point and viral load; and negatively with CD4 T cell counts at one year post infection (all p<0.05). Lastly, PMA, Prostratin, TNF-α and SAHA cell stimulation resulted in enhanced yet heterologous transcriptional activation of different T/F LTR variants. Our data suggest that T/F LTR variants may influence viral transcriptional activity, disease outcomes and sensitivity to cell activation, with potential implications for therapeutic interventions.
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Affiliation(s)
- Paradise Madlala
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zakithi Mkhize
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shamara Naicker
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Samukelisiwe P. Khathi
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Shreyal Maikoo
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Kasmira Gopee
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Krista L. Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts, United States of America
- Africa Health Research Institute (AHRI), Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
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5
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Nahand JS, Bokharaei-Salim F, Karimzadeh M, Moghoofei M, Karampoor S, Mirzaei HR, Tbibzadeh A, Jafari A, Ghaderi A, Asemi Z, Mirzaei H, Hamblin MR. MicroRNAs and exosomes: key players in HIV pathogenesis. HIV Med 2020; 21:246-278. [PMID: 31756034 PMCID: PMC7069804 DOI: 10.1111/hiv.12822] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2019] [Indexed: 12/29/2022]
Abstract
OBJECTIVES HIV infection is well known to cause impairment of the human immune system, and until recently was a leading cause of death. It has been shown that T lymphocytes are the main targets of HIV. The virus inactivates T lymphocytes by interfering with a wide range of cellular and molecular targets, leading to suppression of the immune system. The objective of this review is to investigate to what extent microRNAs (miRNAs) are involved in HIV pathogenesis. METHODS The scientific literature (Pubmed and Google scholar) for the period 1988-2019 was searched. RESULTS Mounting evidence has revealed that miRNAs are involved in viral replication and immune response, whether by direct targeting of viral transcripts or through indirect modulation of virus-related host pathways. In addition, exosomes have been found to act as nanoscale carriers involved in HIV pathogenesis. These nanovehicles target their cargos (i.e. DNA, RNA, viral proteins and miRNAs) leading to alteration of the behaviour of recipient cells. CONCLUSIONS miRNAs and exosomes are important players in HIV pathogenesis. Additionally, there are potential diagnostic applications of miRNAs as biomarkers in HIV infection.
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Affiliation(s)
- Javid Sadri Nahand
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Karimzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Karampoor
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Tbibzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Jafari
- Department of Medical Nanotechnology, Faculty of Advanced Technology in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Amir Ghaderi
- Department of Addiction Studies, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, I.R. Iran
| | - Michael R. Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, 40 Blossom Street, Boston, MA, 02114, USA
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6
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HIV-1 Latency and Latency Reversal: Does Subtype Matter? Viruses 2019; 11:v11121104. [PMID: 31795223 PMCID: PMC6950696 DOI: 10.3390/v11121104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
Cells that are latently infected with HIV-1 preclude an HIV-1 cure, as antiretroviral therapy does not target this latent population. HIV-1 is highly genetically diverse, with over 10 subtypes and numerous recombinant forms circulating worldwide. In spite of this vast diversity, much of our understanding of latency and latency reversal is largely based on subtype B viruses. As such, most of the development of cure strategies targeting HIV-1 are solely based on subtype B. It is currently assumed that subtype does not influence the establishment or reactivation of latent viruses. However, this has not been conclusively proven one way or the other. A better understanding of the factors that influence HIV-1 latency in all viral subtypes will help develop therapeutic strategies that can be applied worldwide. Here, we review the latest literature on subtype-specific factors that affect viral replication, pathogenesis, and, most importantly, latency and its reversal.
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7
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Spector C, Mele AR, Wigdahl B, Nonnemacher MR. Genetic variation and function of the HIV-1 Tat protein. Med Microbiol Immunol 2019; 208:131-169. [PMID: 30834965 DOI: 10.1007/s00430-019-00583-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/11/2019] [Indexed: 12/14/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) encodes a transactivator of transcription (Tat) protein, which has several functions that promote viral replication, pathogenesis, and disease. Amino acid variation within Tat has been observed to alter the functional properties of Tat and, depending on the HIV-1 subtype, may produce Tat phenotypes differing from viruses' representative of each subtype and commonly used in in vivo and in vitro experimentation. The molecular properties of Tat allow for distinctive functional activities to be determined such as the subcellular localization and other intracellular and extracellular functional aspects of this important viral protein influenced by variation within the Tat sequence. Once Tat has been transported into the nucleus and becomes engaged in transactivation of the long terminal repeat (LTR), various Tat variants may differ in their capacity to activate viral transcription. Post-translational modification patterns based on these amino acid variations may alter interactions between Tat and host factors, which may positively or negatively affect this process. In addition, the ability of HIV-1 to utilize or not utilize the transactivation response (TAR) element within the LTR, based on genetic variation and cellular phenotype, adds a layer of complexity to the processes that govern Tat-mediated proviral DNA-driven transcription and replication. In contrast, cytoplasmic or extracellular localization of Tat may cause pathogenic effects in the form of altered cell activation, apoptosis, or neurotoxicity. Tat variants have been shown to differentially induce these processes, which may have implications for long-term HIV-1-infected patient care in the antiretroviral therapy era. Future studies concerning genetic variation of Tat with respect to function should focus on variants derived from HIV-1-infected individuals to efficiently guide Tat-targeted therapies and elucidate mechanisms of pathogenesis within the global patient population.
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Affiliation(s)
- Cassandra Spector
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Anthony R Mele
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Michael R Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N 15th St, Philadelphia, PA, 19102, USA.
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, USA.
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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8
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van der Kuyl AC, Vink M, Zorgdrager F, Bakker M, Wymant C, Hall M, Gall A, Blanquart F, Berkhout B, Fraser C, Cornelissen M. The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012. Virus Res 2018; 250:51-64. [PMID: 29654800 DOI: 10.1016/j.virusres.2018.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/05/2018] [Accepted: 04/05/2018] [Indexed: 12/18/2022]
Abstract
For the production of viral genomic RNA, HIV-1 is dependent on an early viral protein, Tat, which is required for high-level transcription. The quantity of viral RNA detectable in blood of HIV-1 infected individuals varies dramatically, and a factor involved could be the efficiency of Tat protein variants to stimulate RNA transcription. HIV-1 virulence, measured by set-point viral load, has been observed to increase over time in the Netherlands and elsewhere. Investigation of tat gene evolution in clinical isolates could discover a role of Tat in this changing virulence. A dataset of 291 Dutch HIV-1 subtype B tat genes, derived from full-length HIV-1 genome sequences from samples obtained between 1985-2012, was used to analyse the evolution of Tat. Twenty-two patient-derived tat genes, and the control TatHXB2 were analysed for their capacity to stimulate expression of an LTR-luciferase reporter gene construct in diverse cell lines, as well as for their ability to complement a tat-defective HIV-1LAI clone. Analysis of 291 historical tat sequences from the Netherlands showed ample amino acid (aa) variation between isolates, although no specific mutations were selected for over time. Of note, however, the encoded protein varied its length over the years through the loss or gain of stop codons in the second exon. In transmission clusters, a selection against the shorter Tat86 ORF was apparent in favour of the more common Tat101 version, likely due to negative selection against Tat86 itself, although random drift, transmission bottlenecks, or linkage to other variants could also explain the observation. There was no correlation between Tat length and set-point viral load; however, the number of non-intermediate variants in our study was small. In addition, variation in the length of Tat did not significantly change its capacity to stimulate transcription. From 1985 till 2012, variation in the length of the HIV-1 subtype B tat gene is increasingly found in the Dutch epidemic. However, as Tat proteins did not differ significantly in their capacity to stimulate transcription elongation in vitro, the increased HIV-1 virulence seen in recent years could not be linked to an evolving viral Tat protein.
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Affiliation(s)
- Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
| | - Monique Vink
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Fokla Zorgdrager
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Chris Wymant
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - François Blanquart
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Christophe Fraser
- Medical Research Council Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W21PG, United Kingdom; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
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9
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Qu D, Li C, Sang F, Li Q, Jiang ZQ, Xu LR, Guo HJ, Zhang C, Wang JH. The variances of Sp1 and NF-κB elements correlate with the greater capacity of Chinese HIV-1 B'-LTR for driving gene expression. Sci Rep 2016; 6:34532. [PMID: 27698388 PMCID: PMC5048295 DOI: 10.1038/srep34532] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/15/2016] [Indexed: 12/28/2022] Open
Abstract
The 5' end of HIV-1 long terminal repeat (LTR) serves as a promoter that plays an essential role in driving viral gene transcription. Manipulation of HIV-1 LTR provides a potential therapeutic strategy for suppressing viral gene expression or excising integrated provirus. Subtype-specific genetic diversity in the LTR region has been observed. The minor variance of LTR, particularly in the transcription factor binding sites, can have a profound impact on its activity. However, the LTR profiles from major endemic Chinese subtypes are not well characterized. Here, by characterizing the sequences and functions of LTRs from endemic Chinese HIV-1 subtypes, we showed that nucleotide variances of Sp1 core promoter and NF-κB element are associated with varied LTR capacity for driving viral gene transcription. The greater responsiveness of Chinese HIV-1 B'-LTR for driving viral gene transcription upon stimulation is associated with an increased level of viral reactivation. Moreover, we demonstrated that the introduction of CRISPR/dead Cas9 targeting Sp1 or NF-κB element suppressed viral gene expression. Taken together, our study characterized LTRs from endemic HIV-1 subtypes in China and suggests a potential target for the suppression of viral gene expression and a novel strategy that facilitates the accomplishment of a functional cure.
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Affiliation(s)
- Di Qu
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Chuan Li
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Feng Sang
- Key laboratory of Prevention and Treatment with Traditional Chinese Medicine on Viral Infection Disease, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Qiang Li
- Key laboratory of Prevention and Treatment with Traditional Chinese Medicine on Viral Infection Disease, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Zhi-Qiang Jiang
- Key laboratory of Prevention and Treatment with Traditional Chinese Medicine on Viral Infection Disease, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Li-Ran Xu
- Key laboratory of Prevention and Treatment with Traditional Chinese Medicine on Viral Infection Disease, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Hui-Jun Guo
- Key laboratory of Prevention and Treatment with Traditional Chinese Medicine on Viral Infection Disease, the First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Chiyu Zhang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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10
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Functional Incompatibility between the Generic NF-κB Motif and a Subtype-Specific Sp1III Element Drives the Formation of the HIV-1 Subtype C Viral Promoter. J Virol 2016; 90:7046-7065. [PMID: 27194770 DOI: 10.1128/jvi.00308-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/12/2016] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED Of the various genetic subtypes of human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) and simian immunodeficiency virus (SIV), only in subtype C of HIV-1 is a genetically variant NF-κB binding site found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-κB and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be replaced by a corresponding TFBS variant. The variant NF-κB motif binds NF-κB with an affinity 2-fold higher than that of the generic NF-κB site. Importantly, in the context of an infectious virus, the subtype-specific Sp1III motif demonstrates a profound loss of function in association with the generic NF-κB motif. An additional substitution of the Sp1III motif fully restores viral replication, suggesting that the subtype C-specific Sp1III has evolved to function with the variant, but not generic, NF-κB motif. A change of only two base pairs in the central NF-κB motif completely suppresses viral transcription from the provirus and converts the promoter into heterochromatin refractory to tumor necrosis factor alpha (TNF-α) induction. The present work represents the first demonstration of functional incompatibility between an otherwise functional NF-κB motif and a unique Sp1 site in the context of an HIV-1 promoter. Our work provides important leads as to the evolution of the HIV-1 subtype C viral promoter with relevance for gene expression regulation and viral latency. IMPORTANCE Subtype-specific genetic variations provide a powerful tool to examine how these variations offer a replication advantage to specific viral subtypes, if any. Only in subtype C of HIV-1 are two genetically distinct transcription factor binding sites positioned at the most critical location of the viral promoter. Since a single promoter regulates viral gene expression, the promoter variations can play a critical role in determining the replication fitness of the viral strains. Our work for the first time provides a scientific explanation for the presence of a unique NF-κB binding motif in subtype C, a major HIV-1 genetic family responsible for half of the global HIV-1 infections. The results offer compelling evidence that the subtype C viral promoter not only is stronger but also is endowed with a qualitative gain-of-function advantage. The genetically variant NF-κB and the Sp1III motifs may be respond differently to specific cell signal pathways, and these mechanisms must be examined.
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11
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Nicoli F, Chachage M, Clowes P, Bauer A, Kowour D, Ensoli B, Cafaro A, Maboko L, Hoelscher M, Gavioli R, Saathoff E, Geldmacher C. Association between different anti-Tat antibody isotypes and HIV disease progression: data from an African cohort. BMC Infect Dis 2016; 16:344. [PMID: 27450538 PMCID: PMC4957276 DOI: 10.1186/s12879-016-1647-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 06/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The presence of IgG and IgM against Tat, an HIV protein important for viral replication and immune dysfunction, is associated with slow disease progression in clade B HIV-infected individuals. However, although Tat activities strictly depend on the viral clade, our knowledge about the importance of anti-Tat antibodies in non-clade B HIV infection is poor. The objective of this study was to investigate the association of different anti-Tat antibody isotypes with disease progression in non-clade B HIV-infected subjects and to study the relationship between anti-Tat humoral responses and immunological abnormalities. METHODS Anti-clade B and -clade C Tat IgG, IgM and IgA titers were assessed in serum samples from 96 cART-naïve subjects with chronic HIV infection from Mbeya, Tanzania, and associated with CD4(+) T cell count, plasma viremia and CD4(+) and CD8(+) T cell phenotypes. RESULTS Anti-Tat IgM were preferentially detected in chronic HIV-infected subjects with low T cell activation (p-value = 0.03) and correlated with higher CD4(+) T cell counts and lower viral loads irrespective of the duration of infection (p-value = 0.019 and p-value = 0.037 respectively). Conversely, anti-Tat IgA were preferentially detected in individuals with low CD4(+) T cell counts and high viral load (p-value = 0.02 and p-value < 0.001 respectively). The simultaneous presence of anti-Tat IgG and IgM protected from fast CD4(+) T cell decline (p-value < 0.01) and accumulation of CD38(+)HLADR(+)CD8(+) T cells (p- value = 0.029). CONCLUSIONS Anti-Tat IgG alone are not protective in non-clade B infected subjects, unless concomitant with IgM, suggesting a protective role of persistent anti-Tat IgM irrespective of the infecting clade.
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Affiliation(s)
- Francesco Nicoli
- Center for International Health, Ludwig-Maximilians-Universität München, Leopoldstraße 7, 80802, Munich, Germany. .,Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy. .,Current address: CIMI INSERM U1135, 91 bd del'Hopital, 75013, Paris, France.
| | - Mkunde Chachage
- Center for International Health, Ludwig-Maximilians-Universität München, Leopoldstraße 7, 80802, Munich, Germany.,National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Petra Clowes
- National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania.,Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Asli Bauer
- National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania.,Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Dickens Kowour
- National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Barbara Ensoli
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Aurelio Cafaro
- National AIDS Center, Istituto Superiore di Sanità, Rome, Italy
| | - Leonard Maboko
- National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Riccardo Gavioli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Elmar Saathoff
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
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12
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Zhao X, Qian L, Zhou D, Qi D, Liu C, Kong X. Stability of HIV-1 subtype B and C Tat is associated with variation in the carboxyl-terminal region. Virol Sin 2016; 31:199-206. [PMID: 27007880 DOI: 10.1007/s12250-016-3681-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/01/2016] [Indexed: 12/14/2022] Open
Abstract
The multifunctional trans-activator Tat is an essential regulatory protein for HIV-1 replication and is characterized by high sequence diversity. Numerous experimental studies have examined Tat in HIV-1 subtype B, but research on subtype C Tat is lacking, despite the high prevalence of infections caused by subtype C worldwide. We hypothesized that amino acid differences contribute to functional differences among Tat proteins. In the present study, we found that subtype B NL4-3 Tat and subtype C isolate HIV1084i Tat exhibited differences in stability by overexpressing the fusion protein Tat-Flag. In addition, 1084i Tat can activate LTR and NF-κB more efficiently than NL4-3 Tat. In analyses of the activities of the truncated forms of Tat, we found that the carboxyl-terminal region of Tat regulates its stability and transactivity. According to our results, we speculated that the differences in stability between B-Tat and C-Tat result in differences in transactivation ability.
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Affiliation(s)
- Xuechao Zhao
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Lingyu Qian
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Deyu Zhou
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Di Qi
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Chang Liu
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Xiaohong Kong
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China.
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13
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Jiang G, Dandekar S. Targeting NF-κB signaling with protein kinase C agonists as an emerging strategy for combating HIV latency. AIDS Res Hum Retroviruses 2015; 31:4-12. [PMID: 25287643 DOI: 10.1089/aid.2014.0199] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Highly active antiretroviral therapy (HAART) is very effective in suppressing HIV-1 replication and restoring immune functions in HIV-infected individuals. However, it fails to eradicate the latent viral reservoirs and fully resolve chronic inflammation in HIV infection. The "shock-and-kill" strategy was recently proposed to induce latent HIV expression in the presence of HAART. Recent studies have shown that the protein kinase C (PKC) agonists are highly potent in inducing latent HIV expression from the viral reservoirs in vitro and ex vivo and in protecting primary CD4(+) T cells from HIV infection through down-modulation of their HIV coreceptor expression. The PKC agonists are excellent candidates for advancing to clinical HIV eradication strategies. This article will present a critical review of the structure and function of known PKC agonists, their mechanisms for the reactivation of latent HIV expression, and the potential of these compounds for advancing clinical HIV eradication strategies.
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Affiliation(s)
- Guochun Jiang
- Department of Medical Microbiology and Immunology, University of California, Davis, California
| | - Satya Dandekar
- Department of Medical Microbiology and Immunology, University of California, Davis, California
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14
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Reactivation of latent HIV-1 by new semi-synthetic ingenol esters. Virology 2014; 462-463:328-39. [PMID: 25014309 DOI: 10.1016/j.virol.2014.05.033] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 04/28/2014] [Accepted: 05/29/2014] [Indexed: 11/21/2022]
Abstract
The ability of HIV to establish long-lived latent infection is mainly due to transcriptional silencing of viral genome in resting memory T lymphocytes. Here, we show that new semi-synthetic ingenol esters reactivate latent HIV reservoirs. Amongst the tested compounds, 3-caproyl-ingenol (ING B) was more potent in reactivating latent HIV than known activators such as SAHA, ingenol 3,20-dibenzoate, TNF-α, PMA and HMBA. ING B activated PKC isoforms followed by NF-κB nuclear translocation. As virus reactivation is dependent on intact NF-κB binding sites in the LTR promoter region ING B, we have shown that. ING B was able to reactivate virus transcription in primary HIV-infected resting cells up to 12 fold and up to 25 fold in combination with SAHA. Additionally, ING B promoted up-regulation of P-TEFb subunits CDK9/Cyclin T1. The role of ING B on promoting both transcription initiation and elongation makes this compound a strong candidate for an anti-HIV latency drug combined with suppressive HAART.
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15
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van der Sluis RM, Derking R, Breidel S, Speijer D, Berkhout B, Jeeninga RE. Interplay between viral Tat protein and c-Jun transcription factor in controlling LTR promoter activity in different human immunodeficiency virus type I subtypes. J Gen Virol 2014; 95:968-979. [PMID: 24447950 DOI: 10.1099/vir.0.059642-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
HIV-1 transcription depends on cellular transcription factors that bind to sequences in the long-terminal repeat (LTR) promoter. Each HIV-1 subtype has a specific LTR promoter configuration, and minor sequence changes in transcription factor binding sites (TFBSs) or their arrangement can influence transcriptional activity, virus replication and latency properties. Previously, we investigated the proviral latency properties of different HIV-1 subtypes in the SupT1 T cell line. Here, subtype-specific latency and replication properties were studied in primary PHA-activated T lymphocytes. No major differences in latency and replication capacity were measured among the HIV-1 subtypes. Subtype B and AE LTRs were studied in more detail with regard to a putative AP-1 binding site using luciferase reporter constructs. c-Jun, a member of the AP-1 transcription factor family, can activate both subtype B and AE LTRs, but the latter showed a stronger response, reflecting a closer match with the consensus AP-1 binding site. c-Jun overexpression enhanced Tat-mediated transcription of the viral LTR, but in the absence of Tat inhibited basal promoter activity. Thus, c-Jun can exert a positive or negative effect via the AP-1 binding site in the HIV-1 LTR promoter, depending on the presence or absence of Tat.
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Affiliation(s)
- Renée M van der Sluis
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ronald Derking
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Seyguerney Breidel
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Rienk E Jeeninga
- Laboratory of Experimental Virology, Department of Medical Microbiology, Centre for Infection and Immunity Amsterdam (CINIMA), Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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16
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Bagashev A, Sawaya BE. Roles and functions of HIV-1 Tat protein in the CNS: an overview. Virol J 2013; 10:358. [PMID: 24359561 PMCID: PMC3879180 DOI: 10.1186/1743-422x-10-358] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/06/2013] [Indexed: 01/01/2023] Open
Abstract
Nearly 50% of HIV-infected individuals suffer from some form of HIV-associated neurocognitive disorders (HAND). HIV-1 Tat (a key HIV transactivator of transcription) protein is one of the first HIV proteins to be expressed after infection occurs and is absolutely required for the initiation of the HIV genome transcription. In addition to its canonical functions, various studies have shown the deleterious role of HIV-1 Tat in the development and progression of HAND. Within the CNS, only specific cell types can support productive viral replication (astrocytes and microglia), however Tat protein can be released form infected cells to affects HIV non-permissive cells such as neurons. Therefore, in this review, we will summarize the functions of HIV-1 Tat proteins in neural cells and its ability to promote HAND.
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Affiliation(s)
| | - Bassel E Sawaya
- Molecular Studies of Neurodegenerative Diseases Lab, The Fels Institute for Cancer Research & Molecular Biology, Philadelphia, PA 19140, USA.
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17
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Singh A, Palanichamy JK, Ramalingam P, Kassab MA, Bhagat M, Andrabi R, Luthra K, Sinha S, Chattopadhyay P. Long-term suppression of HIV-1C virus production in human peripheral blood mononuclear cells by LTR heterochromatization with a short double-stranded RNA. J Antimicrob Chemother 2013; 69:404-15. [PMID: 24022068 DOI: 10.1093/jac/dkt348] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES A region in the conserved 5' long terminal repeat (LTR) promoter of the integrated HIV-1C provirus was identified for effective targeting by a short double-stranded RNA (dsRNA) to cause heterochromatization leading to a long-lasting decrease in viral transcription, replication and subsequent productive infection in human host cells. METHODS Small interfering RNAs (siRNAs) were transfected into siHa cells containing integrated LTR-luciferase reporter constructs and screened for efficiency of inducing transcriptional gene silencing (TGS). TGS was assessed by a dual luciferase assay and real-time PCR. Chromatin modification at the targeted region was also studied. The efficacy of potent siRNA was then checked for effectiveness in TZM-bl cells and human peripheral blood mononuclear cells (PBMCs) infected with HIV-1C virus. Viral Gag-p24 antigen levels were determined by ELISA. RESULTS One HIV-1C LTR-specific siRNA significantly decreased luciferase activity and its mRNA expression with no such effect on HIV-1B LTR. This siRNA-mediated TGS was induced by histone methylation, which leads to heterochromatization of the targeted LTR region. The same siRNA also substantially suppressed viral replication in TZM-bl cells and human PBMCs infected with various HIV-1C clinical isolates for ≥3 weeks after a single transfection, even of a strain that had a mismatch in the target region. CONCLUSIONS We have identified a potent dsRNA that causes long-term suppression of HIV-1C virus production in vitro and ex vivo by heritable epigenetic modification at the targeted C-LTR region. This dsRNA has promising therapeutic potential in HIV-1C infection, the clade responsible for more than half of AIDS cases worldwide.
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Affiliation(s)
- Anand Singh
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
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18
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tat Exon 1 exhibits functional diversity during HIV-1 subtype C primary infection. J Virol 2013; 87:5732-45. [PMID: 23487450 DOI: 10.1128/jvi.03297-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) Tat is a mediator of viral transcription and is involved in the control of virus replication. However, associations between HIV-1 Tat diversity and functional effects during primary HIV-1 infection are still unclear. We estimated selection pressures in tat exon 1 using the mixed-effects model of evolution with 672 viral sequences generated from 20 patients infected with HIV-1 subtype C (HIV-1C) over 500 days postseroconversion. tat exon 1 residues 3, 4, 21, 24, 29, 39, and 68 were under positive selection, and we established that specific amino acid signature patterns were apparent in primary HIV-1C infection compared with chronic infection. We assessed the impact of these mutations on long terminal repeat (LTR) activity and found that Tat activity was negatively affected by the Ala(21) substitution identified in 13/20 (65%) of patients, which reduced LTR activity by 88% (± 1%) (P < 0.001). The greatest increase in Tat activity was seen with the Gln(35)/Lys(39) double mutant that resulted in an additional 49% (± 14%) production of LTR-driven luciferase (P = 0.012). There was a moderate positive correlation between Tat-mediated LTR activity and HIV-1 RNA in plasma (P = 0.026; r = 0.400) after 180 days postseroconversion that was reduced by 500 days postseroconversion (P = 0.043; r = 0.266). Although Tat activation of the LTR is not a strong predictor of these clinical variables, there are significant linear relationships between Tat transactivation and patients' plasma viral loads and CD4 counts, highlighting the complex interplay between Tat mutations in early HIV-1C infection.
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19
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Bachu M, Yalla S, Asokan M, Verma A, Neogi U, Sharma S, Murali RV, Mukthey AB, Bhatt R, Chatterjee S, Rajan RE, Cheedarla N, Yadavalli VS, Mahadevan A, Shankar SK, Rajagopalan N, Shet A, Saravanan S, Balakrishnan P, Solomon S, Vajpayee M, Satish KS, Kundu TK, Jeang KT, Ranga U. Multiple NF-κB sites in HIV-1 subtype C long terminal repeat confer superior magnitude of transcription and thereby the enhanced viral predominance. J Biol Chem 2012; 287:44714-35. [PMID: 23132857 DOI: 10.1074/jbc.m112.397158] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We demonstrate that at least three different promoter variant strains of HIV-1 subtype C have been gradually expanding and replacing the standard subtype C viruses in India, and possibly in South Africa and other global regions, over the past decade. The new viral strains contain an additional NF-κB, NF-κB-like, or RBEIII site in the viral promoter. Although the acquisition of an additional RBEIII site is a property shared by all the HIV-1 subtypes, acquiring an additional NF-κB site remains an exclusive property of subtype C. The acquired κB site is genetically distinct, binds the p50-p65 heterodimer, and strengthens the viral promoter at the levels of transcription initiation and elongation. The 4-κB viruses dominate the 3-κB "isogenic" viral strains in pairwise competition assays in T-cell lines, primary cells, and the ecotropic human immunodeficiency virus mouse model. The dominance of the 4-κB viral strains is also evident in the natural context when the subjects are coinfected with κB-variant viral strains. The mean plasma viral loads, but not CD4 counts, are significantly different in 4-κB infection suggesting that these newly emerging strains are probably more infectious. It is possible that higher plasma viral loads underlie selective transmission of the 4-κB viral strains. Several publications previously reported duplication or deletion of diverse transcription factor-binding sites in the viral promoter. Unlike previous reports, our study provides experimental evidence that the new viral strains gained a potential selective advantage as a consequence of the acquired transcription factor-binding sites and importantly that these strains have been expanding at the population level.
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Affiliation(s)
- Mahesh Bachu
- HIV-AIDS Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India
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20
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Narayanan A, Sampey G, Van Duyne R, Guendel I, Kehn-Hall K, Roman J, Currer R, Galons H, Oumata N, Joseph B, Meijer L, Caputi M, Nekhai S, Kashanchi F. Use of ATP analogs to inhibit HIV-1 transcription. Virology 2012; 432:219-31. [PMID: 22771113 DOI: 10.1016/j.virol.2012.06.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 02/21/2012] [Accepted: 06/02/2012] [Indexed: 12/18/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) is the etiological agent of AIDS. Chronic persistent infection is an important reason for the presence of "latent cell populations" even after Anti-Retroviral Therapy (ART). We have analyzed the effect of ATP analogs in inhibiting cdk9/T1 complex in infected cells. A third generation drug named CR8#13 is an effective inhibitor of Tat activated transcription. Following drug treatment, we observed a decreased loading of cdk9 onto the HIV-1 DNA. We found multiple novel cdk9/T1 complexes present in infected and uninfected cells with one complex being unique to infected cells. This complex is sensitive to CR8#13 in kinase assays. Treatment of PBMC with CR8#13 does not kill infected cells as compared to Flavopiridol. Interestingly, there is a difference in sensitivity of various clades to these analogs. Collectively, these results point to targeting novel complexes for inhibition of cellular proteins that are unique to infected cells.
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Affiliation(s)
- Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, USA
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21
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HIV develops indirect cross-resistance to combinatorial RNAi targeting two distinct and spatially distant sites. Mol Ther 2012; 20:840-8. [PMID: 22294151 DOI: 10.1038/mt.2012.3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Resistance to existing HIV therapies is an increasing problem, and alternative treatments are urgently needed. RNA interference (RNAi), an innate mechanism for sequence-specific gene silencing, can be harnessed therapeutically to treat viral infections, yet viral resistance can still emerge. Here, we demonstrate that HIV can develop indirect resistance to individual and combinatorial RNAi-targeting protein-coding regions up to 5,500 nucleotides (nt) downstream of the viral promoter. We identify several variants harboring mutations in the HIV promoter, and not within the RNAi targets, that produce more fully elongated transcripts. Furthermore, these variants are resistant to the RNAi, potentially by stoichiometrically overwhelming this cellular mechanism. Alarmingly, virus resistant to one short hairpin RNA (shRNA) also exhibits cross-resistance to a different shRNA, which targets a distinct and spatially distant region to which the virus has not been previously exposed. To our knowledge, this is the first example of HIV "cross-resistance" to viral inhibitors targeting different loci. Finally, combining anti-HIV RNAi with a small molecule enhancer of RNAi can inhibit the replication of an indirectly resistant mutant. These results suggest that indirect resistance to RNAi is a general mechanism that should be considered when investigating viral resistance and designing combinatorial RNAi therapies.
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Zhang HS, Ruan Z, Sang WW. HDAC1/NFκB pathway is involved in curcumin inhibiting of Tat-mediated long terminal repeat transactivation. J Cell Physiol 2011; 226:3385-91. [PMID: 21344388 DOI: 10.1002/jcp.22691] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Chromatin remodeling, especially in relation to the transactivator Tat, is an essential event for human immunodeficiency virus-1 (HIV-1) transcription. Curcumin has been shown to suppress pathways linked to HIV-1 replication. We investigated whether curcumin had the potential to inhibit Tat-induced long terminal repeat region (LTR) transactivation. As we shown, curcumin inhibited Tat-induced LTR transcativation, while knockdown of histone deacetylase 1 (HDAC1) by siRNA potentiated Tat-induced HIV-1 transcativation. Curcumin reversed Tat-induced down-regulation of HDAC1 expression in multinuclear activation of galactosidase indicator (MAGI) cells. Treatment with curcumin reversed Tat-induced dissociation of HDAC1 from LTR; and curcumin caused a decline in the binding of p65/NFκB to LTR promoters stimulated by Tat. Curcumin attenuated Tat-induced p65 phosphorylation and IKK phosphorylation. Curcumin reversed Tat-mediated reduction in AMPK activation and downstream acetyl-CoA carboxylase (ACC) activation. Collectively, our data provide new insights into understanding of the molecular mechanisms of curcumin inhibited Tat-regulated transcription, suggesting that targeting AMPK/HDAC1/NFκB pathway could serve as new anti-HIV-1 agents.
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Affiliation(s)
- Hong-Sheng Zhang
- College of Life Science & Bioengineering, Beijing University of Technology, Beijing, China.
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23
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Latency profiles of full length HIV-1 molecular clone variants with a subtype specific promoter. Retrovirology 2011; 8:73. [PMID: 21923919 PMCID: PMC3182984 DOI: 10.1186/1742-4690-8-73] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 09/16/2011] [Indexed: 12/31/2022] Open
Abstract
Background HIV-1 transcription initiation depends on cellular transcription factors that bind to promoter sequences in the Long Terminal Repeat (LTR). Each HIV-1 subtype has a specific LTR promoter configuration and even minor sequence changes in the transcription factor binding sites (TFBS) or their arrangement can impact transcriptional activity. Most latency studies have focused on HIV-1 subtype B strains, and the degree to which LTR promoter variation contributes to differences in proviral latency is therefore largely unknown. Latency differences may influence establishment and size of viral reservoirs as well as the possibility to clear the virus by therapeutic intervention. Results We investigated the proviral transcriptional latency properties of different HIV-1 subtypes as their LTRs have unique assemblies of transcription factor binding sites. We constructed recombinant viral genomes with the subtype-specific promoters inserted in the common backbone of the subtype B LAI isolate. The recombinant viruses are isogenic, except for the core promoter region that encodes all major TFBS, including NFκB and Sp1 sites. We developed and optimized an assay to investigate HIV-1 proviral latency in T cell lines. Our data show that the majority of HIV-1 infected T cells only start viral gene expression after TNFα activation. Conclusions There were no gross differences among the subtypes, both in the initial latency level and the activation response, except for subtype AE that combines an increased level of basal transcription with a reduced TNFα response. This subtype AE property is related to the presence of a GABP instead of NFκB binding site in the LTR.
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24
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Liu Y, Nonnemacher MR, Stauff DL, Li L, Banerjee A, Irish B, Kilareski E, Rajagopalan N, Suchitra JB, Khan ZK, Ranga U, Wigdahl B. Structural and functional studies of CCAAT/enhancer binding sites within the human immunodeficiency virus type 1 subtype C LTR. Biomed Pharmacother 2010; 64:672-80. [PMID: 20970301 DOI: 10.1016/j.biopha.2010.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 09/05/2010] [Indexed: 11/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C, which is most predominant in sub-Saharan Africa as well as in Asia and India, is the most prevalent subtype worldwide. A large number of transcription factor families have been shown to be involved in regulating HIV-1 gene expression in T lymphocytes and cells of the monocyte-macrophage lineage. Among these, proteins of the CCAAT/enhancer binding protein (C/EBP) family are of particular importance in regulating HIV-1 gene expression within cells of the monocytic lineage during the course of hematologic development and cellular activation. Few studies have examined the role of C/EBPs in long terminal repeat (LTR)-directed viral gene expression of HIV-1 subtypes other than subtype B. Within subtype B viruses, two functional C/EBP sites located upstream of the TATA box are required for efficient viral replication in cells of the monocyte-macrophage lineage. We report the identification of three putative subtype C C/EBP sites, upstream site 1 and 2 (C-US1 and C-US2) and downstream site 1 (C-DS1). C-US1 and C-DS1 were shown to form specific DNA-protein complexes with members of the C/EBP family (C/EBPα, β, and δ). Functionally, within the U-937 monocytic cell line, subtype B and C LTRs were shown to be equally responsive to C/EBPβ-2, although the basal activity of subtype C LTRs appeared to be higher. Furthermore, the synergistic interaction between C/EBPβ-2 and Tat with the subtype C LTR was also observed in U-937 cells as previously demonstrated with the subtype B LTR.
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Affiliation(s)
- Yujie Liu
- Department of Microbiology and Immunology, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, Pennsylvania 19129, USA
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de Arellano ER, Alcamí J, López M, Soriano V, Holguín A. Drastic decrease of transcription activity due to hypermutated long terminal repeat (LTR) region in different HIV-1 subtypes and recombinants. Antiviral Res 2010; 88:152-9. [PMID: 20713090 DOI: 10.1016/j.antiviral.2010.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 07/27/2010] [Accepted: 08/09/2010] [Indexed: 11/25/2022]
Abstract
Transcriptional activation of HIV-1 gene expression is partially controlled by the interaction between viral and cellular transcription factors acting at HIV-1 long terminal repeat (LTR) sequences. HIV-1 subtyping at LTR region and nucleotide LTR variability from clinical samples in 48 subjects carrying different HIV-1 subtypes (9A, 5C, 3D, 3F, 21G, 2H, 3J and 2 undefined) at the protease (PR) gene, were performed. LTR sequences from each HIV-1 clade were cloned in luciferase-expression vectors to determine basal and Tat-induced transcriptional activities in the presence and absence of PMA stimulation. A high number (37.8%) of recombinants at LTR/PR regions were identified. All HIV-1 promoters presented low basal transcriptional activity that was nevertheless induced by Tat and PMA. LTR activity was similar across the majority of HIV-1 variants in response to Tat and cell activation. Only subtype C and CRF01_AE LTRs presented higher basal and induced-PMA transcription activities than HXB2 clade B promoter. No basal or Tat/PMA induced activity was found in those promoters presenting G to A hypermutation compared to the wild type promoter activities. G to A hypermutation at some important transcription binding-factor sites within LTR compromised the activity of the viral promoter, decreasing the in vitro viral transcription of the luciferase gene.
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Affiliation(s)
- Eva Ramírez de Arellano
- Department of Infectious Diseases, Hospital Carlos III, Madrid, Spain; National Center for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
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Burnett JC, Lim KI, Calafi A, Rossi JJ, Schaffer DV, Arkin AP. Combinatorial latency reactivation for HIV-1 subtypes and variants. J Virol 2010; 84:5958-74. [PMID: 20357084 PMCID: PMC2876650 DOI: 10.1128/jvi.00161-10] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Accepted: 03/24/2010] [Indexed: 12/11/2022] Open
Abstract
The eradication of HIV-1 will likely require novel clinical approaches to purge the reservoir of latently infected cells from a patient. We hypothesize that this therapy should target a wide range of latent integration sites, act effectively against viral variants that have acquired mutations in their promoter regions, and function across multiple HIV-1 subtypes. By using primary CD4(+) and Jurkat cell-based in vitro HIV-1 latency models, we observe that single-agent latency reactivation therapy is ineffective against most HIV-1 subtypes. However, we demonstrate that the combination of two clinically promising drugs-namely, prostratin and suberoylanilide hydroxamic acid (SAHA)-overcomes the limitations of single-agent approaches and can act synergistically for many HIV-1 subtypes, including A, B, C, D, and F. Finally, by identifying the proviral integration position of latent Jurkat cell clones, we demonstrate that this drug combination does not significantly enhance the expression of endogenous genes nearest to the proviral integration site, indicating that its effects may be selective.
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Affiliation(s)
- John C. Burnett
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Kwang-il Lim
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Arash Calafi
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - John J. Rossi
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - David V. Schaffer
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Adam P. Arkin
- Department of Chemical Engineering and Helen Wills Neuroscience Institute, University of California, Berkeley, California 94720, Department of Bioengineering, University of California, Berkeley, California 94720, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California 91010
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Campbell GR, Loret EP, Spector SA. HIV-1 clade B Tat, but not clade C Tat, increases X4 HIV-1 entry into resting but not activated CD4+ T cells. J Biol Chem 2010; 285:1681-91. [PMID: 19917610 PMCID: PMC2804326 DOI: 10.1074/jbc.m109.049957] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 11/13/2009] [Indexed: 11/06/2022] Open
Abstract
CXCR4-using human immunodeficiency virus, type 1 (HIV-1) variants emerge late in the course of infection in >40% of individuals infected with clade B HIV-1 but are described less commonly with clade C isolates. Tat is secreted by HIV-1-infected cells where it acts on both uninfected bystander cells and infected cells. In this study, we show that clade B Tat, but not clade C Tat, increases CXCR4 surface expression on resting CD4+ T cells through a CCR2b-dependent mechanism that does not involve de novo protein synthesis. The expression of plectin, a cytolinker protein that plays an important role as a scaffolding platform for proteins involved in cellular signaling including CXCR4 signaling and trafficking, was found to be significantly increased following B Tat but not C Tat treatment. Knockdown of plectin using RNA interference showed that plectin is essential for the B Tat-induced translocation of CXCR4 to the surface of resting CD4+ T cells. The increased surface CXCR4 expression following B Tat treatment led to increased function of CXCR4 including increased chemoattraction toward CXCR4-using-gp120. Moreover, increased CXCR4 surface expression rendered resting CD4+ T cells more permissive to X4 but not R5 HIV-1 infection. However, neither B Tat nor C Tat was able to up-regulate surface expression of CXCR4 on activated CD4+ T cells, and both proteins inhibited the infection of activated CD4+ T cells with X4 but not R5 HIV-1. Thus, B Tat, but not C Tat, has the capacity to render resting, but not activated, CD4+ T cells more susceptible to X4 HIV-1 infection.
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Affiliation(s)
- Grant R. Campbell
- From the Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California 92093-0672
| | - Erwann P. Loret
- INSERM U911, Faculté de Pharmacie, Université de la Méditerranée, 13385 Marseille Cedex 5, France
| | - Stephen A. Spector
- From the Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California 92093-0672
- Rady Children's Hospital, San Diego, California 92123, and
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Van Duyne R, Kehn-Hall K, Carpio L, Kashanchi F. Cell-type-specific proteome and interactome: using HIV-1 Tat as a test case. Expert Rev Proteomics 2010; 6:515-26. [PMID: 19811073 DOI: 10.1586/epr.09.73] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
HIV-1 is a small retrovirus that wreaks havoc on the human immune system. It is a puzzle to the scientific community how a virus that encodes only nine proteins can take complete control of its host and redirect the cell to complete replication or maintain latency when necessary. One way to explain the control elicited by HIV-1 is through numerous protein partners that exist between viral and host proteins, allowing HIV-1 to be intimately involved in virtually every aspect of cellular biology. In addition, we postulate that the complexity exerted by HIV-1 can not merely be explained by the large number of protein-protein interactions documented in the literature but, rather, cell-type-specific interactions and post-translational modifications of viral proteins must be taken into account. We use HIV-1 Tat and its influence on viral transcription as an example of cell-type-specific complexity. The influence of post-translational modifications (acetylation and methylation), as well as subcellular localization on Tat binding partners, is also discussed.
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Affiliation(s)
- Rachel Van Duyne
- The George Washington University, Department of Microbiology, Immunology and Tropical Medicine, 2300 I Street, NW, Washington, DC 20037, USA
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Kandathil AJ, Kannangai R, Abraham OC, Pulimood SA, Sridharan G. Amino acid sequence divergence of Tat protein (exon1)of subtype B and C HIV-1 strains: Does it have implications for vaccine development? Bioinformation 2009; 4:237-41. [PMID: 20975916 PMCID: PMC2951709 DOI: 10.6026/97320630004237] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2009] [Accepted: 11/15/2009] [Indexed: 11/23/2022] Open
Abstract
Functional genes of HIV-1 like the tat express proteins essential for viral survival and propagation. There are variations reported in levels of Tat
transactivation among the different subtypes of HIV-1. This study looked at the amino acid differences in the different regions of Tat protein
(exon 1) of subtype B and C strains of HIV-1 and tried to observe a molecular basis for protein function. HIV-1 sequences of subtype B (n=30)
and C (n=60) strains were downloaded from HIV-1 Los Alamos data base. Among the 60 subtype C strain sequences, 30 each were from India
and Africa. A HIV-1 Tat protein (exon 1) sequence, the consensus B and C sequence was obtained from the ’sequence search interface‘ in the
Los Alamos HIV-1 sequence data. The sequences were visualized using Weblogo and the RNA binding regions of the three consensus sequences
were also determined using BindN software program. Compared to subtype B, there was a high level of divergence in the auxiliary domain of tat
exon 1 (amino acid positions 58- 69). The net charge of the subtype C (Indian) Tat protein (exon 1) auxiliary domain was -1.9 at pH 7 and it had
an isoelectric point of 4.1. The net charge of the subtype C (African) auxiliary domain was -2.9 at pH 7 and it had an isoelectric point of 3.7
while the net charge of same region in subtype B was -0.9 at pH 7 with an isoelectric point of 4.9. The ratio of the hydrophilic residues to the total
number of residues was 60% in the in both the Indian and African subtype C in the auxiliary domain while this was 50% in subtype B. The
consensus subtype B sequence was found to have 36 RNA binding sites while subtype C (India) had 33 and subtype C (Africa) had 32 RNA
binding sites. The HIV-1 Tat-TAR interaction is a potential target for inhibitors and being considered for its potential use in HIV-1 vaccines.
Development of such inhibitor/vaccines would have to take into consideration the variation in amino acid sequence analyzed in this study as this
could determine epitope presentation on MHC class I antigen for afferent immune response.
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Campbell GR, Loret EP. What does the structure-function relationship of the HIV-1 Tat protein teach us about developing an AIDS vaccine? Retrovirology 2009; 6:50. [PMID: 19467159 PMCID: PMC2693501 DOI: 10.1186/1742-4690-6-50] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 05/25/2009] [Indexed: 11/03/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) trans-activator of transcription protein Tat is an important factor in viral pathogenesis. In addition to its function as the key trans-activator of viral transcription, Tat is also secreted by the infected cell and taken up by neighboring cells where it has an effect both on infected and uninfected cells. In this review we will focus on the relationship between the structure of the Tat protein and its function as a secreted factor. To this end we will summarize some of the exogenous functions of Tat that have been implicated in HIV-1 pathogenesis and the impact of structural variations and viral subtype variants of Tat on those functions. Finally, since in some patients the presence of Tat-specific antibodies or CTL frequencies are associated with slow or non-progression to AIDS, we will also discuss the role of Tat as a potential vaccine candidate, the advances made in this field, and the importance of using a Tat protein capable of eliciting a protective or therapeutic immune response to viral challenge.
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Affiliation(s)
- Grant R Campbell
- Department of Pediatrics, Division of Infectious Diseases, University of California San Diego, La Jolla, California 92093-0672, USA.
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31
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Clade-specific differences in neurotoxicity of human immunodeficiency virus-1 B and C Tat of human neurons: significance of dicysteine C30C31 motif. Ann Neurol 2008; 63:366-76. [DOI: 10.1002/ana.21292] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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Zhou Y, Ma J, Bushan Roy B, Wu JYY, Pan Q, Rong L, Liang C. The packaging of human immunodeficiency virus type 1 RNA is restricted by overexpression of an RNA helicase DHX30. Virology 2007; 372:97-106. [PMID: 18022663 DOI: 10.1016/j.virol.2007.10.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 08/21/2007] [Accepted: 10/23/2007] [Indexed: 10/22/2022]
Abstract
RNA helicases are a large family of proteins that are able to unwind RNA duplex and remodel the structure of RNA-protein (RNP) complexes using energy derived from hydrolysis of nucleotide triphosphates (NTPs). Every step of cellular RNA metabolism involves the activity of RNA helicases. Not surprisingly, more and more RNA helicases are reported to participate in the replication of viruses including the human immunodeficiency virus type 1 (HIV-1). Here, we provide evidence that overexpression of an RNA helicase named DHX30 enhances HIV-1 gene expression, but leads to the generation of viruses that package significantly low levels of viral RNA and exhibit severely decreased infectivity. These data reveal the complex roles of DHX30 in HIV-1 replication and implicate an inhibitory activity of DHX30 in HIV-1 RNA packaging.
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Affiliation(s)
- Yongdong Zhou
- McGill AIDS Centre, Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
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Siddappa NB, Kashi VP, Venkatramanan M, Balasiddaiah A, Jayasuryan N, Mahadevan A, Desai A, Satish KS, Shankar SK, Ravi V, Ranga U. Gene expression analysis from human immunodeficiency virus type 1 subtype C promoter and construction of bicistronic reporter vectors. AIDS Res Hum Retroviruses 2007; 23:1268-78. [PMID: 17961115 DOI: 10.1089/aid.2006.0305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We report the cloning and sequence analysis of the long terminal repeat (LTR) of several primary HIV-1 subtype C strains of India. Phylogenetically, all the LTRs and the paired env sequences clustered with subtype C reference strains. The LTRs demonstrated extensive polymorphism in the transcription factor binding sites (TFBS) within the enhancer and the modulator regions. We generated reporter vectors under the control of a select subset of the subtype C LTRs. The reporter vectors are distinguished by the simultaneous expression of two independent reporter genes, secreted alkaline phosphatase (SEAP) and enhanced green fluorescence protein (EGFP), in response to Tat. Expression of EGFP was facilitated by engineering an internal ribosome entry site (IRES) into the expression cassette. Although subtype C strains cause a large majority of the global infections, and important differences in the transcription factor binding sites have been identified in the subtype C promoter, few reporter vectors containing subtype C-LTR have been described. We analyzed gene expression from the C-LTR reporter vectors in different cell lines under diverse experimental conditions and compared it to the B-LTR reporter vector. The reporter vectors were responsive to Tat derived from diverse viral subtypes. Furthermore, a positive correlation was observed between the expression of the reporter genes and the viral structural protein p24 when the cells were infected with viral molecular clones. The LTR reporters we developed could be of significant use in the study of viral transactivation, in the evaluation of biological properties of viral subtypes, and in the screening for antiviral inhibitors.
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Affiliation(s)
- Nagadenahalli Byrareddy Siddappa
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Venkatesh Prasanna Kashi
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Mohanram Venkatramanan
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Center for Infectious Medicine, Karolinska Institutet, Department of Medicine Karolinska Huddinge, Stockholm, Sweden
| | - Anangi Balasiddaiah
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Anita Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | | | - Susarla K. Shankar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Vasanthapuram Ravi
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Udaykumar Ranga
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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Boven LA, Noorbakhsh F, Bouma G, van der Zee R, Vargas DL, Pardo C, McArthur JC, Nottet HSLM, Power C. Brain-derived human immunodeficiency virus-1 Tat exerts differential effects on LTR transactivation and neuroimmune activation. J Neurovirol 2007; 13:173-84. [PMID: 17505986 DOI: 10.1080/13550280701258399] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular diversity within brain-derived HIV-1 sequences is highly variable depending on the individual gene examined and the neurological status of the patient. Herein, we examined different brain-derived human immunodeficiency virus (HIV)-1 tat sequences in terms of their effects on LTR transactivation and host gene induction in neural cells. Astrocytic and monocytoid cells co-transfected with prototypic tat clones derived from non-demented (ND) (n = 3) and demented (HAD) (n = 3) AIDS patients and different HIV-LTR constructs revealed that LTR transactivation mediated by tat clones derived from HAD patients was decreased (p < 0.05). A Tat-derived peptide containing the amino acid 24-38 domain from a ND clone caused down-regulation of the LTR transactivation (p < 0.05) in contrast to peptides from other Tat regions derived from HAD and ND tat clones. Both brain-derived HAD and ND tat constructs were able to induce the host immune genes, MCP-1 and IL-1beta. Microarray analysis revealed several host genes were selectively upregulated by a HAD-derived tat clone including an enzyme mediating heparan sulphate synthesis, HS3ST3B1 (p < 0.05), which was also found to be increased in the brains of patients with HAD. Expression of the pro-apoptotic gene, PDCD7, was reduced in cells transfected with the HAD-derived tat clone and moreover, this gene was also suppressed in monocytoid cells infected with a neurotropic HIV-1 strain. Thus, mutations within the HIV-1 tat gene may exert pathogenic effects contributing to the development of HAD, which are independent of its effects on LTR transactivation.
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Affiliation(s)
- Leonie A Boven
- Department of Immunology, Erasmus Medical Center, Rotterdam, The Netherlands
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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: 43] [Impact Index Per Article: 2.5] [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
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Hiscott J, Nguyen TLA, Arguello M, Nakhaei P, Paz S. Manipulation of the nuclear factor-kappaB pathway and the innate immune response by viruses. Oncogene 2006; 25:6844-67. [PMID: 17072332 PMCID: PMC7100320 DOI: 10.1038/sj.onc.1209941] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Viral and microbial constituents contain specific motifs or pathogen-associated molecular patterns (PAMPs) that are recognized by cell surface- and endosome-associated Toll-like receptors (TLRs). In addition, intracellular viral double-stranded RNA is detected by two recently characterized DExD/H box RNA helicases, RIG-I and Mda-5. Both TLR-dependent and -independent pathways engage the IkappaB kinase (IKK) complex and related kinases TBK-1 and IKKvarepsilon. Activation of the nuclear factor kappaB (NF-kappaB) and interferon regulatory factor (IRF) transcription factor pathways are essential immediate early steps of immune activation; as a result, both pathways represent prime candidates for viral interference. Many viruses have developed strategies to manipulate NF-kappaB signaling through the use of multifunctional viral proteins that target the host innate immune response pathways. This review discusses three rapidly evolving areas of research on viral pathogenesis: the recognition and signaling in response to virus infection through TLR-dependent and -independent mechanisms, the involvement of NF-kappaB in the host innate immune response and the multitude of strategies used by different viruses to short circuit the NF-kappaB pathway.
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Affiliation(s)
- J Hiscott
- Terry Fox Molecular Oncology Group, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada.
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Siddappa NB, Venkatramanan M, Venkatesh P, Janki MV, Jayasuryan N, Desai A, Ravi V, Ranga U. Transactivation and signaling functions of Tat are not correlated: biological and immunological characterization of HIV-1 subtype-C Tat protein. Retrovirology 2006; 3:53. [PMID: 16916472 PMCID: PMC1564039 DOI: 10.1186/1742-4690-3-53] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Accepted: 08/18/2006] [Indexed: 12/04/2022] Open
Abstract
Background Of the diverse subtypes of Human Immunodeficiency Virus Type-1 (HIV-1), subtype-C strains cause a large majority of infections worldwide. The reasons for the global dominance of HIV-1 subtype-C infections are not completely understood. Tat, being critical for viral infectivity and pathogenesis, may differentially modulate pathogenic properties of the viral subtypes. Biochemical studies on Tat are hampered by the limitations of the current purification protocols. Tat purified using standard protocols often is competent for transactivation activity but defective for a variety of other biological functions. Keeping this limitation in view, we developed an efficient protein purification strategy for Tat. Results Tat proteins obtained using the novel strategy described here were free of contaminants and retained biological functions as evaluated in a range of assays including the induction of cytokines, upregulation of chemokine coreceptor, transactivation of the viral promoter and rescue of a Tat-defective virus. Given the highly unstable nature of Tat, we evaluated the effect of the storage conditions on the biological function of Tat following purification. Tat stored in a lyophilized form retained complete biological activity regardless of the storage temperature. To understand if variations in the primary structure of Tat could influence the secondary structure of the protein and consequently its biological functions, we determined the CD spectra of subtype-C and -B Tat proteins. We demonstrate that subtype-C Tat may have a relatively higher ordered structure and be less flexible than subtype-B Tat. We show that subtype-C Tat as a protein, but not as a DNA expression vector, was consistently inferior to subtype-B Tat in a variety of biological assays. Furthermore, using ELISA, we evaluated the anti-Tat antibody titers in a large number of primary clinical samples (n = 200) collected from all four southern Indian states. Our analysis of the Indian populations demonstrated that Tat is non-immunodominant and that a large variation exists in the antigen-specific antibody titers. Conclusion Our report not only describes a simple protein purification strategy for Tat but also demonstrates important structural and functional differences between subtype-B and -C Tat proteins. Furthermore, this is the first report of protein purification and characterization of subtype-C Tat.
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Affiliation(s)
- Nagadenahalli Byrareddy Siddappa
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Mohanram Venkatramanan
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Prasanna Venkatesh
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | | | | | - Anita Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Vasanthapuram Ravi
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Udaykumar Ranga
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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Berro R, Kehn K, de la Fuente C, Pumfery A, Adair R, Wade J, Colberg-Poley AM, Hiscott J, Kashanchi F. Acetylated Tat regulates human immunodeficiency virus type 1 splicing through its interaction with the splicing regulator p32. J Virol 2006; 80:3189-204. [PMID: 16537587 PMCID: PMC1440361 DOI: 10.1128/jvi.80.7.3189-3204.2006] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) potent transactivator Tat protein mediates pleiotropic effects on various cell functions. Posttranslational modification of Tat affects its activity during viral transcription. Tat binds to TAR and subsequently becomes acetylated on lysine residues by histone acetyltransferases. Novel protein-protein interaction domains on acetylated Tat are then established, which are necessary for both sustained transcriptional activation of the HIV-1 promoter and viral transcription elongation. In this study, we investigated the identity of proteins that preferentially bound acetylated Tat. Using a proteomic approach, we identified a number of proteins that preferentially bound AcTat, among which p32, a cofactor of splicing factor ASF/SF-2, was identified. We found that p32 was recruited to the HIV-1 genome, suggesting a mechanism by which acetylation of Tat may inhibit HIV-1 splicing needed for the production of full-length transcripts. Using Tat from different clades, harboring a different number of acetylation sites, as well as Tat mutated at lysine residues, we demonstrated that Tat acetylation affected splicing in vivo. Finally, using confocal microscopy, we found that p32 and Tat colocalize in vivo in HIV-1-infected cells.
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Affiliation(s)
- Reem Berro
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
| | - Kylene Kehn
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
| | - Cynthia de la Fuente
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
| | - Anne Pumfery
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
| | - Richard Adair
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
| | - John Wade
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
| | - Anamaris M. Colberg-Poley
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
| | - John Hiscott
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
| | - Fatah Kashanchi
- Genetics Program, The George Washington University, Washington, D.C. 20037, Department of Biochemistry and Molecular Biology, The George Washington University School of Medicine, Washington, D.C. 20037, Center for Cancer and Immunology Research, Children's Research Institute, Children's National Medical Center, Washington, D.C. 20010, Howard Florey Institute, University of Melbourne, Victoria 3010, Australia, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada, The Institute for Genomic Research, Rockville, Maryland 20850
- Corresponding author. Mailing address: The George Washington University, 2300 I St., NW, Ross Hall, Room 551, Washington, DC 20037. Phone: (202) 994-1781. Fax: (202) 994-1780. E-mail:
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De Arellano ER, Soriano V, Holguín A. Genetic analysis of regulatory, promoter, and TAR regions of LTR sequences belonging to HIV type 1 Non-B subtypes. AIDS Res Hum Retroviruses 2005; 21:949-54. [PMID: 16386112 DOI: 10.1089/aid.2005.21.949] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Transcriptional activation of HIV-1 gene expression is controlled by the interaction of sequence-specific transcription factors with the long terminal repeat (LTR). Information about differences between LTR regions in distinct HIV-1 subtypes is scarce. LTR sequences, including regulatory, enhancer, promoter, and TAR regions, were genetically characterized and compared in 59 HIV-1-infected individuals known to be infected with non-B subtypes. Phylogenetic analyses ascribed the LTR regions to the following subtypes: 10A, 2B, 6C, 1D, 2E, 2F, 16G, 3J, 2H, and 2U. Up to 34% of the samples were LTR/PR recombinants. The LTR region revealed a high degree of genetic variability among distinct HIV-1 subtypes and showed several subtype-specific markers, which hypothetically could influence the interactions with cellular transcription factors, leading to different transcriptional levels among distinct HIV-1 clades. To our knowledge, this is the first characterization of LTR sequences belonging to subtypes J and H.
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40
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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: 1.9] [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.
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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
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41
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Ramírez de Arellano E, Soriano V, Holguín A. [Regulation of transcription in different HIV-1 subtypes]. Enferm Infecc Microbiol Clin 2005; 23:156-62. [PMID: 15757588 DOI: 10.1157/13072166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transcriptional activation of HIV-1 gene expression is controlled in part by the interaction of viral and cellular transcription factors with the HIV-1 long terminal repeat (LTR) sequences. LTR variability among different HIV-1 subtypes could affect LTR binding of either cellular or viral elements, influencing the transcription level. This effect, in turn, may have consequences on the biology of the different HIV-1 clades and on disease progression. In some circumstances, a relationship between replication capacity in vitro and changes in binding sequences for transcription factors located at the LTR has been proven.
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Affiliation(s)
- Eva Ramírez de Arellano
- Laboratorio de Biología Molecular, Servicio de Enfermedades Infecciosas, Hospital Carlos III, Madrid, Spain
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42
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Centlivre M, Sommer P, Michel M, Ho Tsong Fang R, Gofflo S, Valladeau J, Schmitt N, Thierry F, Hurtrel B, Wain-Hobson S, Sala M. HIV-1 clade promoters strongly influence spatial and temporal dynamics of viral replication in vivo. J Clin Invest 2005; 115:348-58. [PMID: 15690084 PMCID: PMC546425 DOI: 10.1172/jci22873] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Accepted: 12/12/2004] [Indexed: 01/25/2023] Open
Abstract
Although the primary determinant of cell tropism is the interaction of viral envelope or capsid proteins with cellular receptors, other viral elements can strongly modulate viral replication. While the HIV-1 promoter is polymorphic for a variety of transcription factor binding sites, the impact of these polymorphisms on viral replication in vivo is not known. To address this issue, we engineered isogenic SIVmac239 chimeras harboring the core promoter/enhancer from HIV-1 clades B, C, and E. Here it is shown that the clade C and E core promoters/enhancers bear a noncanonical activator protein-1 (AP-1) binding site, absent from the corresponding clade B region. Relative ex vivo replication of chimeras was strongly dependent on the tissue culture system used. Notably, in thymic histocultures, replication of the clade C chimera was favored by IL-7 enrichment, which suggests that the clade C polymorphism in the AP-1 and NF-kappaB binding sites is involved. Simultaneous infection of rhesus macaques with the 3 chimeras revealed a strong predominance of the clade C chimera during primary infection. Thereafter, the B chimera dominated in all tissues. These data show that the clade C promoter is particularly adapted to sustain viral replication in primary viremia and that clade-specific promoter polymorphisms constitute a major determinant for viral replication.
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Affiliation(s)
- Mireille Centlivre
- Unité de Rétrovirologie Moléculaire, Unité de Biologie Cellulaire du Noyau, Institut Pasteur, Paris, France
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43
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Sun Q, Matta H, Chaudhary PM. Kaposi's sarcoma associated herpes virus-encoded viral FLICE inhibitory protein activates transcription from HIV-1 Long Terminal Repeat via the classical NF-kappaB pathway and functionally cooperates with Tat. Retrovirology 2005; 2:9. [PMID: 15713234 PMCID: PMC554086 DOI: 10.1186/1742-4690-2-9] [Citation(s) in RCA: 20] [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: 09/24/2004] [Accepted: 02/15/2005] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The nuclear transcription factor NF-kappaB binds to the HIV-1 long terminal repeat (LTR) and is a key regulator of HIV-1 gene expression in cells latently infected with this virus. In this report, we have analyzed the ability of Kaposi's sarcoma associate herpes virus (KSHV, also known as Human Herpes virus 8)-encoded viral FLIP (Fas-associated death domain-like IL-1 beta-converting enzyme inhibitory protein) K13 to activate the HIV-1 LTR. RESULTS We present evidence that vFLIP K13 activates HIV-1 LTR via the activation of the classical NF-kappaB pathway involving c-Rel, p65 and p50 subunits. K13-induced HIV-1 LTR transcriptional activation requires the cooperative interaction of all three components of the IKK complex and can be effectively blocked by inhibitors of the classical NF-kappaB pathway. K13 mutants that lacked the ability to activate the NF-kappaB pathway also failed to activate the HIV-1 LTR. K13 could effectively activate a HIV-1 LTR reporter construct lacking the Tat binding site but failed to activate a construct lacking the NF-kappaB binding sites. However, coexpression of HIV-1 Tat with K13 led to synergistic activation of HIV-1 LTR. Finally, K13 differentially activated HIV-1 LTRs derived from different strains of HIV-1, which correlated with their responsiveness to NF-kappaB pathway. CONCLUSIONS Our results suggest that concomitant infection with KSHV/HHV8 may stimulate HIV-1 LTR via vFLIP K13-induced classical NF-kappaB pathway which cooperates with HIV-1 Tat protein.
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Affiliation(s)
- Qinmiao Sun
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas TX 75390-8593, USA
| | - Hittu Matta
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas TX 75390-8593, USA
- Department of Medicine, Division of Hematology-Oncology and the Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
| | - Preet M Chaudhary
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas TX 75390-8593, USA
- Department of Medicine, Division of Hematology-Oncology and the Hillman Cancer Center, University of Pittsburgh, PA 15213, USA
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44
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Centlivre M, Sommer P, Michel M, Fang RHT, Gofflo S, Valladeau J, Schmitt N, Thierry F, Hurtrel B, Wain-Hobson S, Sala M. HIV-1 clade promoters strongly influence spatial and temporal dynamics of viral replication in vivo. J Clin Invest 2005. [DOI: 10.1172/jci200522873] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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Boulanger MC, Liang C, Russell RS, Lin R, Bedford MT, Wainberg MA, Richard S. Methylation of Tat by PRMT6 regulates human immunodeficiency virus type 1 gene expression. J Virol 2005; 79:124-31. [PMID: 15596808 PMCID: PMC538702 DOI: 10.1128/jvi.79.1.124-131.2005] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus (HIV) transactivator protein, Tat, stimulates transcription from the viral long terminal repeats via an arginine-rich transactivating domain. Since arginines are often known to be methylated, we investigated whether HIV type 1 (HIV-1) Tat was a substrate for known protein arginine methyltransferases (PRMTs). Here we identify Tat as a substrate for the arginine methyltransferase, PRMT6. Tat is specifically associated with and methylated by PRMT6 within cells. Overexpression of wild-type PRMT6, but not a methylase-inactive PRMT6 mutant, decreased Tat transactivation of an HIV-1 long terminal repeat luciferase reporter plasmid in a dose-dependent manner. Knocking down PRMT6 consistently increased HIV-1 production in HEK293T cells and also led to increased viral infectiousness as shown in multinuclear activation of a galactosidase indicator assays. Our study demonstrates that arginine methylation of Tat negatively regulates its transactivation activity and that PRMT6 acts as a restriction factor for HIV replication.
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Affiliation(s)
- Marie-Chloé Boulanger
- Terry Fox Molecular Oncology Group, Lady Davis Institute, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
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46
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Grisson RD, Chenine AL, Yeh LY, He J, Wood C, Bhat GJ, Xu W, Kankasa C, Ruprecht RM. Infectious molecular clone of a recently transmitted pediatric human immunodeficiency virus clade C isolate from Africa: evidence of intraclade recombination. J Virol 2004; 78:14066-9. [PMID: 15564517 PMCID: PMC533957 DOI: 10.1128/jvi.78.24.14066-14069.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although human immunodeficiency virus type 1 (HIV-1) clade C continues to dominate the pandemic, only two infectious clade C proviral DNA clones have been described (N. Mochizuki, N. Otsuka, K. Matsuo, T. Shiino, A. Kojima, T. Kurata, K. Sakai, N. Yamamoto, S. Isomura, T. N. Dhole, Y. Takebe, M. Matsuda, and M. Tatsumi, AIDS Res. Hum. Retrovir. 15:1321-1324, 1999; T. Ndung'u, B. Renjifo, and M. Essex, J. Virol. 75:4964-4972, 2001). We have generated an infectious molecular clone of a pediatric clade C strain, HIV1084i, which was isolated from a Zambian infant infected either intrapartum or through breastfeeding. HIV1084i is an R5, non-syncytium-inducing isolate that bears all known clade C signatures; gag, pol, and env consistently mapped within clade C. Interestingly, gag resembled Asian isolates, whereas pol and env resembled African isolates, indicating that HIV1084i probably arose from an intraclade recombination. As a recently transmitted clade C strain, HIV1084i will be a useful vaccine development tool.
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Affiliation(s)
- Ricky D Grisson
- Department of Cancer, Immunology and AIDS, Dana-Farber Cancer Institute, 44 Binney St., Boston, MA 02115-6084, USA
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47
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Opi S, Péloponèse JM, Esquieu D, Watkins J, Campbell G, De Mareuil J, Jeang KT, Yirrell DL, Kaleebu P, Loret EP. Full-length HIV-1 Tat protein necessary for a vaccine. Vaccine 2004; 22:3105-11. [PMID: 15297062 DOI: 10.1016/j.vaccine.2004.01.057] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2003] [Revised: 01/27/2004] [Accepted: 01/30/2004] [Indexed: 11/18/2022]
Abstract
AIDS vaccines now use a truncated version of 86 residues of the Tat protein related to the HIV-1 HXB2 strain predominant in Europe and North America. We compared antibodies raised in rabbits using a B subtype short Tat HXB2(86) and a full-length Tat HXB2(100). Serum against HXB2(86) recognizes only B and D subtypes while serum against HXB2(100) recognizes B, D, and C subtype variants. Conformational epitopes appear to be involved in the capacity of anti-Tat HXB2 sera to recognized non-homologous Tat variants. A linear B-epitope identified in sequence 71-81 in HXB2(86) disappears in HXB2(100), which has a new linear B-epitope identified at the C-terminus. Anti-HXB2(100) serum has a higher titer in neutralizing antibody against homologous and non-homologous variants compared to anti-HXB2(86) serum. We suggest that a Tat vaccine should contain a Tat variant with regular size, up to 99-101 residues now found in the field.
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Affiliation(s)
- Sandrine Opi
- CNRS FRE 2737, Faculté de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
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48
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Lemieux AM, Paré ME, Audet B, Legault E, Lefort S, Boucher N, Landry S, van Opijnen T, Berkhout B, Naghavi MH, Tremblay MJ, Barbeau B. T-cell activation leads to poor activation of the HIV-1 clade E long terminal repeat and weak association of nuclear factor-kappaB and NFAT with its enhancer region. J Biol Chem 2004; 279:52949-60. [PMID: 15466412 DOI: 10.1074/jbc.m409896200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enhancer region in the human immunodeficiency virus type 1 (HIV-1) 5'-long terminal repeat (LTR) is very important for viral transcription. This promoter sequence binds both nuclear factor-kappaB and NFAT, two important modulators of HIV-1 gene expression. Previous studies have indicated that the enhancer regions of the different HIV-1 clade LTRs differ in their number of NF-kappaB-binding sites. In this study, we have compared the activation potential of the different HIV-1 clade and HIV-2 LTRs and assessed their interaction with NFAT and NF-kappaB. In T-cell lines and primary CD4(+) T-cells, the results showed that the HIV-1 clade E LTR (with a single NF-kappaB-binding site) was the weakest LTR regardless of the tested activators, whereas the HIV-2 LTR was the most responsive LTR. The clade E enhancer region was also demonstrated to be the weakest enhancer region in transfection experiments with luciferase reporter-based vectors. Electrophoretic mobility shift assays with extracts from activated CD4(+) T-cells indicated that, although NF-kappaB and NFAT bound all enhancers, HIV-1 clade E and HIV-2 LTR enhancers were poor binding targets for these two factors. Weak NFAT binding to clade E enhancers was also confirmed using NFAT1-expressing 293T cells in competition experiments. We have also shown the absence of interaction of NF-kappaB or NFAT with the third NF-kappaB repeat present in clade C. However, the clade C enhancer bound NFAT more efficiently than all other enhancer regions tested. Our results hence demonstrate for the first time that differences in the binding of NF-kappaB and NFAT to the enhancer regions could be responsible for some of the observed variation in HIV-1 clade LTR activation, whereas HIV-2 LTR activation seems mostly independent of these interactions.
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Affiliation(s)
- Anne-Marie Lemieux
- Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec, Pavillon CHUL, 2705 Blvd. Laurier, Sainte-Foy, Quebec G1V 4G2, Canada
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Siddappa NB, Dash PK, Mahadevan A, Jayasuryan N, Hu F, Dice B, Keefe R, Satish KS, Satish B, Sreekanthan K, Chatterjee R, Venu K, Satishchandra P, Ravi V, Shankar SK, Shankarappa R, Ranga U. Identification of subtype C human immunodeficiency virus type 1 by subtype-specific PCR and its use in the characterization of viruses circulating in the southern parts of India. J Clin Microbiol 2004; 42:2742-51. [PMID: 15184461 PMCID: PMC427845 DOI: 10.1128/jcm.42.6.2742-2751.2004] [Citation(s) in RCA: 58] [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
Human immunodeficiency virus type 1 (HIV-1) subtype C viruses are associated with nearly half of worldwide HIV-1 infections and are most predominant in India and the southern and eastern parts of Africa. Earlier reports from India identified the preponderance of subtype C and a small proportion of subtype A viruses. Subsequent reports identifying multiple subtypes suggest new introductions and/or their detection due to extended screening. The southern parts of India constitute emerging areas of the epidemic, but it is not known whether HIV-1 infection in these areas is associated with subtype C viruses or is due to the potential new introduction of non-subtype C viruses. Here, we describe the development of a specific and sensitive PCR-based strategy to identify subtype C-viruses (C-PCR). The strategy is based on amplifying a region encompassing a long terminal repeat and gag in the first round, followed by two sets of nested primers; one amplifies multiple subtypes, while the other is specific to subtype C. The common HIV and subtype C-specific fragments are distinguishable by length differences in agarose gels and by the difference in the numbers of NF-kappaB sites encoded in the subtype C-specific fragment. We implemented this method to screen 256 HIV-1-infected individuals from 35 towns and cities in four states in the south and a city in the east. With the exception of single samples of subtypes A and B and a B/C recombinant, we found all to be infected with subtype C viruses, and the subtype assignments were confirmed in a subset by using heteroduplex mobility assays and phylogenetic analysis of sequences. We propose the use of C-PCR to facilitate rapid molecular epidemiologic characterization to aid vaccine and therapeutic strategies.
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Affiliation(s)
- Nagadenahalli B Siddappa
- Molecular Virology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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50
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Pollakis G, Abebe A, Kliphuis A, Chalaby MIM, Bakker M, Mengistu Y, Brouwer M, Goudsmit J, Schuitemaker H, Paxton WA. Phenotypic and genotypic comparisons of CCR5- and CXCR4-tropic human immunodeficiency virus type 1 biological clones isolated from subtype C-infected individuals. J Virol 2004; 78:2841-52. [PMID: 14990703 PMCID: PMC353763 DOI: 10.1128/jvi.78.6.2841-2852.2004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Individuals infected with human immunodeficiency virus type 1 (HIV-1) subtype C infrequently harbour X4 viruses. We studied R5 and X4 biological clones generated from HIV-1 subtype C-infected individuals. All subtype C R5 viruses demonstrated slower profiles of replication on CD4(+) lymphocytes in comparison to subtype B viruses, whereas subtype C X4 viruses replicated with comparable efficiency to subtype B X4 viruses. No differences were identified in CC or CXC chemokine inhibitions (RANTES and SDF-1alpha, respectively) between subtype C and subtype B viruses. Immature dendritic cells were shown in coculture experiments to similarly enhance the infection of subtype C and subtype B R5 as well as X4 viruses. By amino acid sequence analysis, we showed that the R5 and X4 subtype C gp120 envelope gene alterations were similar to those for a switching subtype B virus, specifically with respect to the V3 charge and envelope N-linked glycosylation patterns. By phylogenetic analysis, we showed that one patient was infected with HIV-1 C' and the other was infected with HIV-1 C" and that one of the patients harbored a virus that was a recombinant in the gp120 env gene between an R5 and an X4 virus, with the resultant virus being R5. No differences were identified between the long terminal repeat regions of the subtype C R5 and X4 biological clones. These results indicate that even though R5 subtype C viruses are restrictive for virus replication, the R5-to-X4 phenotype switch can occur and does so in a manner similar to that of subtype B viruses.
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Affiliation(s)
- Georgios Pollakis
- Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, The Netherlands.
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