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Yapo V, Majumder K, Tedbury PR, Wen X, Ong YT, Johnson MC, Sarafianos SG. HIV-2 inhibits HIV-1 gene expression via two independent mechanisms during cellular co-infection. J Virol 2023; 97:e0187022. [PMID: 37991365 PMCID: PMC10734542 DOI: 10.1128/jvi.01870-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/28/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Twenty-five years after the first report that HIV-2 infection can reduce HIV-1-associated pathogenesis in dual-infected patients, the mechanisms are still not well understood. We explored these mechanisms in cell culture and showed first that these viruses can co-infect individual cells. Under specific conditions, HIV-2 inhibits HIV-1 through two distinct mechanisms, a broad-spectrum interferon response and an HIV-1-specific inhibition conferred by the HIV-2 TAR. The former could play a prominent role in dually infected individuals, whereas the latter targets HIV-1 promoter activity through competition for HIV-1 Tat binding when the same target cell is dually infected. That mechanism suppresses HIV-1 transcription by stalling RNA polymerase II complexes at the promoter through a minimal inhibitory region within the HIV-2 TAR. This work delineates the sequence of appearance and the modus operandi of each mechanism.
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Affiliation(s)
- Vincent Yapo
- CS Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Kinjal Majumder
- CS Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Philip R. Tedbury
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Xin Wen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Yee T. Ong
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Marc C. Johnson
- CS Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
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2
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Behrens RT, Rajashekar JK, Bruce JW, Evans EL, Hansen AM, Salazar-Quiroz N, Simons LM, Ahlquist P, Hultquist JF, Kumar P, Sherer NM. Exploiting a rodent cell block for intrinsic resistance to HIV-1 gene expression in human T cells. mBio 2023; 14:e0042023. [PMID: 37676006 PMCID: PMC10653828 DOI: 10.1128/mbio.00420-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Unlike humans, mice are unable to support HIV-1 infection. This is due, in part, to a constellation of defined minor, species-specific differences in conserved host proteins needed for viral gene expression. Here, we used precision CRISPR/Cas9 gene editing to engineer a "mousified" version of one such host protein, cyclin T1 (CCNT1), in human T cells. CCNT1 is essential for efficient HIV-1 transcription, making it an intriguing target for gene-based inactivation of virus replication. We show that isogenic cell lines engineered to encode CCNT1 bearing a single mouse-informed amino acid change (tyrosine in place of cysteine at position 261) exhibit potent, durable, and broad-spectrum resistance to HIV-1 and other pathogenic lentiviruses, and with no discernible impact on host cell biology. These results provide proof of concept for targeting CCNT1 in the context of one or more functional HIV-1 cure strategies.
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Affiliation(s)
- Ryan T. Behrens
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jyothi Krishnaswamy Rajashekar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James W. Bruce
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Edward L. Evans
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amelia M. Hansen
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Natalia Salazar-Quiroz
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lacy M. Simons
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Judd F. Hultquist
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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3
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Hafer TL, Felton A, Delgado Y, Srinivasan H, Emerman M. A CRISPR Screen of HIV Dependency Factors Reveals That CCNT1 Is Non-Essential in T Cells but Required for HIV-1 Reactivation from Latency. Viruses 2023; 15:1863. [PMID: 37766271 PMCID: PMC10535513 DOI: 10.3390/v15091863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV-1 dependency factors that play a key role in HIV-1 latency reactivation including ELL, UBE2M, TBL1XR1, HDAC3, AMBRA1, and ALYREF. The knockout of Cyclin T1 (CCNT1), a component of the P-TEFb complex that is important for transcription elongation, was the top hit in the screen and had the largest effect on HIV latency reversal with a wide variety of latency reversal agents. Moreover, CCNT1 knockout prevents latency reactivation in a primary CD4+ T cell model of HIV latency without affecting the activation of these cells. RNA sequencing data showed that CCNT1 regulates HIV-1 proviral genes to a larger extent than any other host gene and had no significant effects on RNA transcripts in primary T cells after activation. We conclude that CCNT1 function is non-essential in T cells but is absolutely required for HIV latency reversal.
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Affiliation(s)
- Terry L. Hafer
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA;
| | - Abby Felton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Yennifer Delgado
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Harini Srinivasan
- Bioinformatics Shared Resource, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
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4
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Li C, Mori LP, Lyu S, Bronson R, Getzler AJ, Pipkin ME, Valente ST. The chaperone protein p32 stabilizes HIV-1 Tat and strengthens the p-TEFb/RNAPII/TAR complex promoting HIV transcription elongation. Proc Natl Acad Sci U S A 2023; 120:e2217476120. [PMID: 36584296 PMCID: PMC9910500 DOI: 10.1073/pnas.2217476120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/29/2022] [Indexed: 12/31/2022] Open
Abstract
HIV gene expression is modulated by the combinatorial activity of the HIV transcriptional activator, Tat, host transcription factors, and chromatin remodeling complexes. To identify host factors regulating HIV transcription, we used specific single-guide RNAs and endonuclease-deficient Cas9 to perform chromatin affinity purification of the integrated HIV promoter followed by mass spectrometry. The scaffold protein, p32, also called ASF/SF2 splicing factor-associated protein, was identified among the top enriched factors present in actively transcribing HIV promoters but absent in silenced ones. Chromatin immunoprecipitation analysis confirmed the presence of p32 on active HIV promoters and its enhanced recruitment by Tat. HIV uses Tat to efficiently recruit positive transcription elongation factor b (p-TEFb) (CDK9/CCNT1) to TAR, an RNA secondary structure that forms from the first 59 bp of HIV transcripts, to enhance RNAPII transcriptional elongation. The RNA interference of p32 significantly reduced HIV transcription in primary CD4+T cells and in HIV chronically infected cells, independently of either HIV splicing or p32 anti-splicing activity. Conversely, overexpression of p32 specifically increased Tat-dependent HIV transcription. p32 was found to directly interact with Tat's basic domain enhancing Tat stability and half-life. Conversely, p32 associates with Tat via N- and C-terminal domains. Likely due its scaffold properties, p32 also promoted Tat association with TAR, p-TEFb, and RNAPII enhancing Tat-dependent HIV transcription. In sum, we identified p32 as a host factor that interacts with and stabilizes Tat protein, promotes Tat-dependent transcriptional regulation, and may be explored for HIV-targeted transcriptional inhibition.
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Affiliation(s)
- Chuan Li
- Department of Immunology and Microbiology, University of Florida Scripps Biomedical Research, Jupiter, FL33458
| | - Luisa P. Mori
- Department of Immunology and Microbiology, University of Florida Scripps Biomedical Research, Jupiter, FL33458
- The Skaggs Graduate School, The Scripps Research Institute, Jupiter, FL33458
| | - Shuang Lyu
- Department of Immunology and Microbiology, University of Florida Scripps Biomedical Research, Jupiter, FL33458
| | - Ronald Bronson
- Department of Immunology and Microbiology, University of Florida Scripps Biomedical Research, Jupiter, FL33458
| | - Adam J. Getzler
- Department of Immunology and Microbiology, University of Florida Scripps Biomedical Research, Jupiter, FL33458
- The Skaggs Graduate School, The Scripps Research Institute, Jupiter, FL33458
| | - Matthew E. Pipkin
- Department of Immunology and Microbiology, University of Florida Scripps Biomedical Research, Jupiter, FL33458
- The Skaggs Graduate School, The Scripps Research Institute, Jupiter, FL33458
| | - Susana T. Valente
- Department of Immunology and Microbiology, University of Florida Scripps Biomedical Research, Jupiter, FL33458
- The Skaggs Graduate School, The Scripps Research Institute, Jupiter, FL33458
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5
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Asamitsu K, Hirokawa T, Okamoto T. Identification of a novel CDK9 inhibitor targeting the intramolecular hidden cavity of CDK9 induced by Tat binding. PLoS One 2022; 17:e0277024. [PMCID: PMC9665388 DOI: 10.1371/journal.pone.0277024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-1 transcription is specifically augmented by a transcriptional activator complex composed of Tat, an HIV-1-encoded activator, and the host transcription elongation factor P-TEFb, which is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1. Several observations suggest that P-TEFb is an attractive anti-HIV-1 drug target. However, the long-term cytotoxicity of CDK9 inhibitors hinders their widespread use in HIV-1 therapy. Thus, novel and safe inhibitors are sorely needed. By performing molecular dynamics simulations of the 3D structure of Tat/P-TEFb, we previously identified a unique cavity structure of CDK9, the CDK9 hidden cavity, that is specifically induced by Tat binding. Here, we attempted to identify compounds that fit this cavity and inhibit CDK9 activity by in silico screening. We identified compounds that could inhibit CDK9 activity. One of such compound, 127, showed the strongest inhibitory activity against CDK9. Interestingly, it also inhibited CDK6 to a similar extent. We inspected the amino acid sequence and structural properties of the CDK9 hidden cavity to determine whether it is conserved in other CDKs, such as CDK6. The Ile61, comprising the center of the CDK9 hidden cavity, appears to be crucial for its kinase activity, thus indicating that the identification of the CDK9 hidden cavity may provide vital information for the development of novel CDK9 inhibitors.
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Affiliation(s)
- Kaori Asamitsu
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
- * E-mail: (KA); (TH)
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaragi, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaragi, Japan
- * E-mail: (KA); (TH)
| | - Takashi Okamoto
- Department of Neurocognitive Science, Institute of Brain Science, Graduate School of Medical Sciences, Nagoya City University, Nagoya, Aichi, Japan
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Yang X, Zhao X, Zhu Y, Xun J, Wen Q, Pan H, Yang J, Wang J, Liang Z, Shen X, Liang Y, Lin Q, Liang H, Li M, Chen J, Jiang S, Xu J, Lu H, Zhu H. FBXO34 promotes latent HIV-1 activation by post-transcriptional modulation. Emerg Microbes Infect 2022; 11:2785-2799. [PMID: 36285453 PMCID: PMC9665091 DOI: 10.1080/22221751.2022.2140605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS) cannot be completely cured, mainly due to the existence of a latent HIV-1 reservoir. However, our current understanding of the molecular mechanisms underlying the establishment and maintenance of HIV-1 latent reservoir is not comprehensive. Here, using a genome-wide CRISPR-Cas9 activation library screening, we identified E3 ubiquitin ligase F-box protein 34 (FBXO34) and the substrate of FBXO34, heterogeneous nuclear ribonucleoprotein U (hnRNP U) was identified by affinity purification mass spectrometry, as new host factors related to HIV-1 latent maintenance. Overexpression of FBXO34 or knockout of hnRNP U can activate latent HIV-1 in multiple latent cell lines. FBXO34 mainly promotes hnRNP U ubiquitination, which leads to hnRNP U degradation and abolishment of the interaction between hnRNP U and HIV-1 mRNA. In a latently infected cell line, hnRNP U interacts with the ReV region of HIV-1 mRNA through amino acids 1-339 to hinder HIV-1 translation, thereby, promoting HIV-1 latency. Importantly, we confirmed the role of the FBXO34/hnRNP U axis in the primary CD4+ T lymphocyte model, and detected differences in hnRNP U expression levels in samples from patients treated with antiretroviral therapy (ART) and healthy people, which further suggests that the FBXO34/hnRNP U axis is a new pathway involved in HIV-1 latency. These results provide mechanistic insights into the critical role of ubiquitination and hnRNP U in HIV-1 latency. This novel FBXO34/hnRNP U axis in HIV transcription may be directly targeted to control HIV reservoirs in patients in the future.
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Affiliation(s)
- Xinyi Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaying Zhao
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yuqi Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jingna Xun
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Qin Wen
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hanyu Pan
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinlong Yang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jing Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhimin Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaoting Shen
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yue Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qinru Lin
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huitong Liang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Min Li
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Chen
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shibo Jiang
- Department of Infectious Disease, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jianqing Xu
- Department of Infectious Disease, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Hongzhou Lu
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Huanzhang Zhu
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology, Ministry of Education, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
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Abstract
The majority of virally suppressed individuals will experience rapid viral rebound upon antiretroviral therapy (ART) interruption, providing a strong rationale for the development of cure strategies. Moreover, despite ART virological control, HIV infection is still associated with chronic immune activation, inflammation, comorbidities, and accelerated aging. These effects are believed to be due, in part, to low-grade persistent transcription and trickling production of viral proteins from the pool of latent proviruses constituting the viral reservoir. In recent years there has been an increasing interest in developing what has been termed a functional cure for HIV. This approach entails the long-term, durable control of viral expression in the absence of therapy, preventing disease progression and transmission, despite the presence of detectable integrated proviruses. One such strategy, the block-and-lock approach for a functional cure, proposes the epigenetic silencing of proviral expression, locking the virus in a profound latent state, from which reactivation is very unlikely. The proof-of-concept for this approach was demonstrated with the use of a specific small molecule targeting HIV transcription. Here we review the principles behind the block-and-lock approach and some of the additional strategies proposed to silence HIV expression.
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Affiliation(s)
- Luisa Mori
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Susana T Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA.
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8
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Yang X, Zhao X, Zhu Y, Shen Y, Wang Y, Lu P, Jiang Z, Pan H, Yang J, Xun J, Zhao L, Wang J, Liang Z, Shen X, Liang Y, Lin Q, Liang H, Jin L, Zhang D, Liu J, Wang B, Jiang S, Xu J, Wu H, Lu H, Zhu H. FKBP3 Induces Human Immunodeficiency Virus Type 1 Latency by Recruiting Histone Deacetylase 1/2 to the Viral Long Terminal Repeat. mBio 2021; 12:e0079521. [PMID: 34281390 DOI: 10.1128/mBio.00795-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) cannot be completely eliminated because of existence of the latent HIV-1 reservoir. However, the facts of HIV-1 latency, including its establishment and maintenance, are incomplete. FKBP3, encoded by the FKBP3 gene, belongs to the immunophilin family of proteins and is involved in immunoregulation and such cellular processes as protein folding. In a previous study, we found that FKBP3 may be related to HIV-1 latency using CRISPR screening. In this study, we knocked out the FKBP3 gene in multiple latently infected cell lines to promote latent HIV-1 activation. We found that FKBP3 could indirectly bind to the HIV-1 long terminal repeat through interaction with YY1, thereby recruiting histone deacetylase 1/2 to it. This promotes histone deacetylation and induces HIV-1 latency. Finally, in a primary latent cell model, we confirmed the effect of FKBP3 knockout on the latent activation of HIV-1. Our results suggest a new mechanism for the epigenetic regulation of HIV-1 latency and a new potential target for activating latent HIV-1.
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9
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Tang P, Das JR, Li J, Yu J, Ray PE. An HIV-Tat inducible mouse model system of childhood HIV-associated nephropathy. Dis Model Mech 2020; 13:dmm045641. [PMID: 32917744 PMCID: PMC7648609 DOI: 10.1242/dmm.045641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023] Open
Abstract
Modern antiretroviral therapies (ART) have decreased the prevalence of HIV-associated nephropathy (HIVAN). Nonetheless, we continue to see children and adolescents with HIVAN all over the world. Furthermore, once HIVAN is established in children, it is difficult to revert its long-term progression, and we need better animal models of childhood HIVAN to test new treatments. To define whether the HIV-1 trans-activator (Tat) gene precipitates HIVAN in young mice, and to develop an inducible mouse model of childhood HIVAN, an HIV-Tat gene cloned from a child with HIVAN was used to generate recombinant adenoviral vectors (rAd-Tat). rAd-Tat and LacZ control vectors (2×109) were expressed in the kidney of newborn wild-type and HIV-transgenic (Tg26) FVB/N mice without significant proteinuria (n=5; 8 per group). Mice were sacrificed 7 and 35 days later to assess their renal outcome, the expression of HIV-genes and growth factors, and markers of cell growth and differentiation by RT-qPCR, immunohistochemistry and/or western blots. HIV-Tat induced the expression of HIV-1 genes and heparin-binding growth factors in the kidney of HIV-Tg26 mice, and precipitated HIVAN in the first month of life. No significant renal changes were detected in wild-type mice infected with rAd-Tat vectors, suggesting that HIV-Tat alone does not induce renal disease. This new mouse model of childhood HIVAN highlights the critical role that HIV-Tat plays in the pathogenesis of HIVAN, and could be used to study the pathogenesis and treatment of HIVAN in children and adolescents.
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Affiliation(s)
- Pingtao Tang
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
- Department of Pediatrics, The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Jharna R Das
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
- Department of Pediatrics, The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Jinliang Li
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
- Department of Pediatrics, The George Washington University School of Medicine, Washington, DC 20052, USA
| | - Jing Yu
- Child Health Research Center, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Patricio E Ray
- Child Health Research Center, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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10
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Sampey GC, Iordanskiy S, Pleet ML, DeMarino C, Romerio F, Mahieux R, Kashanchi F. Identification of Modulators of HIV-1 Proviral Transcription from a Library of FDA-Approved Pharmaceuticals. Viruses 2020; 12:E1067. [PMID: 32977702 DOI: 10.3390/v12101067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 09/01/2020] [Accepted: 09/10/2020] [Indexed: 12/21/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) is the most prevalent human retrovirus. Recent data show that 34 million people are living with HIV-1 worldwide. HIV-1 infections can lead to AIDS which still causes nearly 20,000 deaths annually in the USA alone. As this retrovirus leads to high morbidity and mortality conditions, more effective therapeutic regimens must be developed to treat these viral infections. A key target for intervention for which there are no current FDA-approved modulators is at the point of proviral transcription. One successful method for identifying novel therapeutics for treating infectious diseases is the repurposing of pharmaceuticals that are approved by the FDA for alternate indications. Major benefits of using FDA-approved drugs include the fact that the compounds have well established toxicity profiles, approved manufacturing processes, and immediate commercial availability to the patients. Here, we demonstrate that pharmaceuticals previously approved for other indications can be utilized to either activate or inhibit HIV-1 proviral transcription. Specifically, we found febuxostat, eltrombopag, and resveratrol to be activators of HIV-1 transcription, while mycophenolate was our lead inhibitor of HIV-1 transcription. Additionally, we observed that the infected cells of lymphoid and myeloid lineage responded differently to our lead transcriptional modulators. Finally, we demonstrated that the use of a multi-dose regimen allowed for enhanced activation with our transcriptional activators.
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11
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Viola HM, Shah AA, Kretzmann JA, Evans CW, Norret M, Iyer KS, Hool LC. A dendronized polymer variant that facilitates safe delivery of a calcium channel antagonist to the heart. Nanomedicine 2020; 29:102264. [PMID: 32659322 DOI: 10.1016/j.nano.2020.102264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/29/2020] [Accepted: 07/02/2020] [Indexed: 11/27/2022]
Abstract
Therapeutic approaches for myocardial ischemia-reperfusion injury (MI) have been ineffective due to limited bioavailability and poor specificity. We have previously shown that a peptide that targets the α-interaction domain of the cardiac L-type calcium channel (AID-peptide) attenuates MI when tethered to transactivator of transcription sequence (TAT) or spherical nanoparticles. However some reservations remain regarding use of these delivery platforms due to the relationship with human immunodeficiency virus, off-target effects and toxicity. Here we investigate the use of linear dendronized polymers (denpols) to deliver AID-peptide as a potential MI therapy using in vitro, ex vivo and in vivo models. Optimized denpol-complexed AID-peptide facilitated in vitro cardiac uptake of AID-peptide, and reduced MI. Maximal in vivo cardiac uptake was achieved within the 2 h therapeutic time window for acute myocardial infarction. Importantly, optimized denpol-complexed AID-peptide was not toxic. This platform may represent an alternative therapeutic approach for the prevention of MI.
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Affiliation(s)
- Helena M Viola
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, WA, Australia
| | - Ashay A Shah
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, WA, Australia
| | - Jessica A Kretzmann
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Marck Norret
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - K Swaminathan Iyer
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Livia C Hool
- School of Human Sciences (Physiology), The University of Western Australia, Crawley, WA, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.
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12
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Abstract
The positive transcription elongation factor b (P-TEFb) was first identified as a general factor that stimulates transcription elongation by RNA polymerase II (RNAPII), but soon afterwards it turned out to be an essential cellular co-factor of human immunodeficiency virus (HIV) transcription mediated by viral Tat proteins. Studies on the mechanisms of Tat-dependent HIV transcription have led to radical advances in our knowledge regarding the mechanism of eukaryotic transcription, including the discoveries that P-TEFb-mediated elongation control of cellular transcription is a main regulatory step of gene expression in eukaryotes, and deregulation of P-TEFb activity plays critical roles in many human diseases and conditions in addition to HIV/AIDS. P-TEFb is now recognized as an attractive and promising therapeutic target for inflammation/autoimmune diseases, cardiac hypertrophy, cancer, infectious diseases, etc. In this review article, I will summarize our knowledge about basic P-TEFb functions, the regulatory mechanism of P-TEFb-dependent transcription, P-TEFb’s involvement in biological processes and diseases, and current approaches to manipulating P-TEFb functions for the treatment of these diseases.
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13
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Hulver MJ, Trautman JP, Goodwin AP, Roszczenko SK, Fogarty KH, Miller HB. Human Tat-specific factor 1 binds the HIV-1 genome and selectively transports HIV-1 RNAs. Mol Biol Rep 2020; 47:1759-1772. [PMID: 32016635 DOI: 10.1007/s11033-020-05267-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 01/20/2020] [Indexed: 01/09/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) propagation requires many human cofactors. Multiple groups have demonstrated that Tat-specific factor 1 (Tat-SF1) is an HIV-1 dependency factor. Depletion of this protein lowers HIV-1 infectivity, however, it does not affect the overall levels of viral RNA. Rather, Tat-SF1 regulates the relative levels of each RNA size class. This would be consistent with roles in splicing, transport, and/or stability of viral RNAs. We hypothesized that if Tat-SF1 plays any of these roles, then we should detect binding of the protein to the RNA genome. Furthermore, knocking down Tat-SF1 should result in altered RNA stability and/or localization in human cells. Fragments of the HIV-1 genome were used as RNA probes in electrophoretic mobility shift assays and fluorescence correlation spectroscopy experiments. Our results show that Tat-SF1 can form a complex with TAR RNA in vitro, independent of Tat. This factor interacts with at least one additional location in the 5' end of the HIV-1 genome. Tat seems to enhance the formation of this complex. To analyze HIV-1 RNA localization, HeLa cells with Tat-SF1 knocked down were also transfected with a proviral clone. RNA from nuclear and cytoplasmic fractions was purified, followed by RT-qPCR analysis. Tat-SF1 likely binds the HIV-1 RNA genome at TAR and potentially other locations and selectively transports HIV-1 RNAs, facilitating the unspliced RNA's nuclear export while retaining singly spliced RNAs in the nucleus. This is a novel role for this HIV-1 dependency factor.
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Affiliation(s)
- Molly J Hulver
- Biochemistry and Molecular Biology Program, University of Rochester Medical Center, Rochester, NY, 14627, USA
| | - Julia P Trautman
- Department of Biology, High Point University, High Point, NC, 27268, USA
| | | | | | - Keir H Fogarty
- Department of Chemistry, High Point University, High Point, NC, 27268, USA
| | - Heather B Miller
- Department of Chemistry, High Point University, High Point, NC, 27268, USA.
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14
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de Sousa-Pereira P, Abrantes J, Bauernfried S, Pierini V, Esteves PJ, Keppler OT, Pizzato M, Hornung V, Fackler OT, Baldauf HM. The antiviral activity of rodent and lagomorph SERINC3 and SERINC5 is counteracted by known viral antagonists. J Gen Virol 2018; 100:278-288. [PMID: 30566072 DOI: 10.1099/jgv.0.001201] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A first step towards the development of a human immunodeficiency virus (HIV) animal model has been the identification and surmounting of species-specific barriers encountered by HIV along its replication cycle in cells from small animals. Serine incorporator proteins 3 (SERINC3) and 5 (SERINC5) were recently identified as restriction factors that reduce HIV-1 infectivity. Here, we compared the antiviral activity of SERINC3 and SERINC5 among mice, rats and rabbits, and their susceptibility to viral counteraction to their human counterparts. In the absence of viral antagonists, rodent and lagomorph SERINC3 and SERINC5 displayed anti-HIV activity in a similar range to human controls. Vesicular stomatitis virus G protein (VSV-G) pseudotyped virions were considerably less sensitive to restriction by all SERINC3/5 orthologs. Interestingly, HIV-1 Nef, murine leukemia virus (MLV) GlycoGag and equine infectious anemia virus (EIAV) S2 counteracted the antiviral activity of all SERINC3/5 orthologs with similar efficiency. Our results demonstrate that the antiviral activity of SERINC3/5 proteins is conserved in rodents and rabbits, and can be overcome by all three previously reported viral antagonists.
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Affiliation(s)
- Patrícia de Sousa-Pereira
- 3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal.,5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,2Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Joana Abrantes
- 1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal
| | - Stefan Bauernfried
- 6Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Virginia Pierini
- 7Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Pedro José Esteves
- 1CIBIO/InBIO- Research Network in Biodiversity and Evolutionary Biology, Campus de Vairão, University of Porto, Vairão, Portugal.,2Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal.,8CITS - Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal
| | - Oliver T Keppler
- 3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany.,5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany
| | - Massimo Pizzato
- 9University of Trento, Centre for Integrative Biology, Trento, Italy
| | - Veit Hornung
- 6Gene Center and Department of Biochemistry, LMU München, Munich, Germany
| | - Oliver T Fackler
- 7Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hanna-Mari Baldauf
- 5Institute of Virology, Technische Universität München/Helmholtz Zentrum, Munich, Germany.,3Institute of Medical Virology, University Hospital Frankfurt, Frankfurt, Germany.,4Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
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15
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Roebuck KA, Saifuddin M. Regulation of HIV-1 transcription. Gene Expr 2018; 8:67-84. [PMID: 10551796 PMCID: PMC6157391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Human immunodeficiency virus type-1 (HIV-1) is a highly pathogenic lentivirus that requires transcription of its provirus genome for completion of the viral life cycle and the production of progeny virions. Since the first genetic analysis of HIV-1 in 1985, much has been learned about the transcriptional regulation of the HIV-1 genome in infected cells. It has been demonstrated that HIV-1 transcription depends on a varied and complex interaction of host cell transcription factors with the viral long terminal repeat (LTR) promoter. The regulatory elements within the LTR interact with constitutive and inducible transcription factors to direct the assembly of a stable transcription complex that stimulates multiple rounds of transcription by RNA polymerase II (RNAPII). However, the majority of these transcripts terminate prematurely in the absence of the virally encoded trans-activator protein Tat, which stimulates HIV-1 transcription elongation by interacting with a stem-loop RNA element (TAR) formed at the extreme 5' end of all viral transcripts. The Tat-TAR interaction recruits a cellular kinase into the initiation-elongation complex that alters the elongation properties of RNAPII during its transit through TAR. This review summarizes our current knowledge and understanding of the regulation of HIV-1 transcription in infected cells and highlights the important contributions human lentivirus gene regulation has made to our general understanding of the transcription process.
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Affiliation(s)
- K A Roebuck
- Department of Immunology/Microbiology, Rush Presbyterian St. Luke's Medical Center, Chicago, IL 60612, USA.
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16
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Asamitsu K, Fujinaga K, Okamoto T. HIV Tat/P-TEFb Interaction: A Potential Target for Novel Anti-HIV Therapies. Molecules 2018; 23:E933. [PMID: 29673219 PMCID: PMC6017356 DOI: 10.3390/molecules23040933] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 11/16/2022] Open
Abstract
Transcription is a crucial step in the life cycle of the human immunodeficiency virus type 1 (HIV 1) and is primarily involved in the maintenance of viral latency. Both viral and cellular transcription factors, including transcriptional activators, suppressor proteins and epigenetic factors, are involved in HIV transcription from the proviral DNA integrated within the host cell genome. Among them, the virus-encoded transcriptional activator Tat is the master regulator of HIV transcription. Interestingly, unlike other known transcriptional activators, Tat primarily activates transcriptional elongation and initiation by interacting with the cellular positive transcriptional elongation factor b (P-TEFb). In this review, we describe the molecular mechanism underlying how Tat activates viral transcription through interaction with P-TEFb. We propose a novel therapeutic strategy against HIV replication through blocking Tat action.
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Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan.
| | - Koh Fujinaga
- Department of Medicine, Microbiology and Immunology, University of California, San Francisco, CA 94143-0703, USA.
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan.
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17
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Evans EL, Becker JT, Fricke SL, Patel K, Sherer NM. HIV-1 Vif's Capacity To Manipulate the Cell Cycle Is Species Specific. J Virol 2018; 92:e02102-17. [PMID: 29321323 PMCID: PMC5972884 DOI: 10.1128/jvi.02102-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023] Open
Abstract
Cells derived from mice and other rodents exhibit profound blocks to HIV-1 virion production, reflecting species-specific incompatibilities between viral Tat and Rev proteins and essential host factors cyclin T1 (CCNT1) and exportin-1 (XPO1, also known as CRM1), respectively. To determine if mouse cell blocks other than CCNT1 and XPO1 affect HIV's postintegration stages, we studied HIV-1NL4-3 gene expression in mouse NIH 3T3 cells modified to constitutively express HIV-1-compatible versions of CCNT1 and XPO1 (3T3.CX cells). 3T3.CX cells supported both Rev-independent and Rev-dependent viral gene expression and produced relatively robust levels of virus particles, confirming that CCNT1 and XPO1 represent the predominant blocks to these stages. Unexpectedly, however, 3T3.CX cells were remarkably resistant to virus-induced cytopathic effects observed in human cell lines, which we mapped to the viral protein Vif and its apparent species-specific capacity to induce G2/M cell cycle arrest. Vif was able to mediate rapid degradation of human APOBEC3G and the PPP2R5D regulatory B56 subunit of the PP2A phosphatase holoenzyme in mouse cells, thus demonstrating that VifNL4-3's modulation of the cell cycle can be functionally uncoupled from some of its other defined roles in CUL5-dependent protein degradation. Vif was also unable to induce G2/M cell cycle arrest in other nonhuman cell types, including cells derived from nonhuman primates, leading us to propose that one or more human-specific cofactors underpin Vif's ability to modulate the cell cycle.IMPORTANCE Cells derived from mice and other rodents exhibit profound blocks to HIV-1 replication, thus hindering the development of a low-cost small-animal model for studying HIV/AIDS. Here, we engineered otherwise-nonpermissive mouse cells to express HIV-1-compatible versions of two species-specific host dependency factors, cyclin T1 (CCNT1) and exportin-1 (XPO1) (3T3.CX cells). We show that 3T3.CX cells rescue HIV-1 particle production but, unexpectedly, are completely resistant to virus-induced cytopathic effects. We mapped these effects to the viral accessory protein Vif, which induces a prolonged G2/M cell cycle arrest followed by apoptosis in human cells. Combined, our results indicate that one or more additional human-specific cofactors govern HIV-1's capacity to modulate the cell cycle, with potential relevance to viral pathogenesis in people and existing animal models.
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Affiliation(s)
- Edward L Evans
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jordan T Becker
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Stephanie L Fricke
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kishan Patel
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research, Institute for Molecular Virology, & Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
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18
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Abstract
PURPOSE OF REVIEW Recent discoveries of highly potent broadly HIV-1 neutralizing antibodies provide new opportunities to successfully prevent, treat, and potentially cure HIV-1 infection. To test their activity in vivo, humanized mice have been shown to be a powerful model and were used to investigate antibody-mediated prevention and therapy approaches. In this review, we will summarize recent findings in humanized mice that have informed on the potential use of broadly neutralizing antibodies targeting HIV-1 in humans. RECENT FINDINGS Humanized mouse models have been used to demonstrate the antiviral efficacy of HIV-1 neutralizing antibodies in vivo. It has been shown that a combination of antibodies can suppress viremia below the limit of detection and targets the HIV-1 reservoir. Moreover, passively administered antibodies and vector-mediated antibody production protect humanized mice from HIV-1 infection. Finally, immunization studies in knock-in/transgenic mice carrying human antibody gene segments have informed on potential vaccination strategies to induce broad and potent HIV-1 neutralizing antibodies. SUMMARY Humanized mouse models are of great value for HIV-1 research. They represent a highly versatile in vivo system to investigate novel approaches for HIV-1 prevention and therapy and expedite the critical translation from basic findings to clinical application.
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19
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Shida H, Okada H, Suzuki H, Zhang X, Chen J, Tsunetsugu-Yokota Y, Tanaka Y, Yakushiji F, Hayashi Y. HIV-1 susceptibility of transgenic rat-derived primary macrophage/T cells and a T cell line that express human receptors, CyclinT1 and CRM1 genes. Genes Cells 2017; 22:424-435. [PMID: 28326644 DOI: 10.1111/gtc.12486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/19/2017] [Indexed: 12/27/2022]
Abstract
We developed transgenic (Tg) rats that express human CD4, CCR5, CXCR4, CyclinT1, and CRM1 genes. Tg rat macrophages were efficiently infected with HIV-1 and supported production of infectious progeny virus. By contrast, both rat primary CD4+ T cells and established T cell lines expressing human CD4, CCR5, CyclinT1, and CRM1 genes were infected inefficiently, but this was ameliorated by inhibition of cyclophilin A. The infectivity of rat T cell-derived virus was lower than that of human T cell-derived virus.
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Affiliation(s)
- Hisatoshi Shida
- Institute for Genetic Medicine, Hokkaido University, Kita-ku, Sapporo, 060-0815, Japan
| | - Hiroyuki Okada
- Institute for Genetic Medicine, Hokkaido University, Kita-ku, Sapporo, 060-0815, Japan
| | - Hajime Suzuki
- Institute for Genetic Medicine, Hokkaido University, Kita-ku, Sapporo, 060-0815, Japan
| | - Xianfeng Zhang
- Institute for Genetic Medicine, Hokkaido University, Kita-ku, Sapporo, 060-0815, Japan
| | - Jing Chen
- Institute for Genetic Medicine, Hokkaido University, Kita-ku, Sapporo, 060-0815, Japan
| | - Yasuko Tsunetsugu-Yokota
- Department of Medical Technology, Tokyo University of Technology, 5-23-22 Nishikamata, Ohta-ku, Tokyo, 144-8535, Japan
| | - Yuetsu Tanaka
- Department of Immunology, Graduate School of Medicine, University of the Ryukyus, Uehara 207, Nishihara-cho, Okinawa, 903-0125, Japan
| | - Fumika Yakushiji
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Science, 1432-1, Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry, Tokyo University of Pharmacy and Life Science, 1432-1, Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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20
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Asamitsu K, Hirokawa T, Okamoto T. MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding. PLoS One 2017; 12:e0171727. [PMID: 28178316 PMCID: PMC5298246 DOI: 10.1371/journal.pone.0171727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/24/2017] [Indexed: 02/02/2023] Open
Abstract
In this study, we applied molecular dynamics (MD) simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs), lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.
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Grants
- Ministry of Education, Culture, Sports, Science, and Technology "The Platform Project for Supporting Drug Discovery and Life Science Research (Platform for Drug Discovery, Informatics, and Structural Life Science)"
- Ministry of Education, Culture, Sports, Science, and Technology
- Asahi Grass Foundation
- Japan Agency for Medical Research and Development
- Junwakai Foundation
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Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail: (TH); (TO)
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan
- * E-mail: (TH); (TO)
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21
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Peddi SR, Sivan SK, Manga V. Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors. J Biomol Struct Dyn 2017; 36:486-503. [PMID: 28081678 DOI: 10.1080/07391102.2017.1281762] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The interaction of HIV-1 transactivator protein Tat with its cognate transactivation response (TAR) RNA has emerged as a promising target for developing antiviral compounds and treating HIV infection, since it is a crucial step for efficient transcription and replication. In the present study, molecular dynamics (MD) simulations and MM/GBSA calculations have been performed on a series of neamine derivatives in order to estimate appropriate MD simulation time for acceptable correlation between ΔGbind and experimental pIC50 values. Initially, all inhibitors were docked into the active site of HIV-1 TAR RNA. Later to explore various conformations and examine the docking results, MD simulations were carried out. Finally, binding free energies were calculated using MM/GBSA method and were correlated with experimental pIC50 values at different time scales (0-1 to 0-10 ns). From this study, it is clear that in case of neamine derivatives as simulation time increased the correlation between binding free energy and experimental pIC50 values increased correspondingly. Therefore, the binding energies which can be interpreted at longer simulation times can be used to predict the bioactivity of new neamine derivatives. Moreover, in this work, we have identified some plausible critical nucleotide interactions with neamine derivatives that are responsible for potent inhibitory activity. Furthermore, we also provide some insights into a new class of oxadiazole-based back bone cyclic peptides designed by incorporating the structural features of neamine derivatives. On the whole, this approach can provide a valuable guidance for designing new potent inhibitors and modify the existing compounds targeting HIV-1 TAR RNA.
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Affiliation(s)
- Saikiran Reddy Peddi
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad 500 007 , Telangana , India
| | - Sree Kanth Sivan
- b Department of Chemistry , Nizam College, Osmania University , Hyderabad 500 001 , Telangana , India
| | - Vijjulatha Manga
- a Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry , University College of Science, Osmania University , Hyderabad 500 007 , Telangana , India
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22
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Tanaka T, Okuyama-Dobashi K, Murakami S, Chen W, Okamoto T, Ueda K, Hosoya T, Matsuura Y, Ryo A, Tanaka Y, Hagiwara M, Moriishi K. Inhibitory effect of CDK9 inhibitor FIT-039 on hepatitis B virus propagation. Antiviral Res 2016; 133:156-64. [PMID: 27515132 DOI: 10.1016/j.antiviral.2016.08.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/04/2016] [Accepted: 08/07/2016] [Indexed: 02/07/2023]
Abstract
Current therapies for hepatitis B virus (HBV) cannot completely eliminate the HBV genome because of the stable population of covalently closed circular DNA (cccDNA) and so on. FIT-039, which is a cyclin-dependent kinase (CDK) 9 inhibitor, is known to suppress the replication of several DNA viruses including HSV, HPV and human adenovirus. In this study, we investigated the antiviral effect of FIT-039 on HBV infection. HepG2 cells expressing human sodium taurocholate cotransporting polypeptide (HepG2/NTCP cells) were infected with HBV in the presence of FIT-039. FIT-039 dose-dependently reduced intracellular viral RNA, nucleocapsid-associated viral DNA, and supernatant viral antigens without cytotoxicity in the infected cells (IC50 = 0.33 μM, CC50 > 50 μM). The antiviral activity of FIT-039 was prominent at an early phase of viral infection, although the compound did not inhibit preS1-binding to HepG2/NTCP cells. FIT-039 reduced cccDNA in HBV-replicating or HBV-infected cells. Furthermore, the antiviral activity of entecavir was significantly enhanced by the combination with FIT-039 in the chimeric mice having human hepatocytes infected with HBV. None of the mice had significant drug-related body weight or serum human-albumin concentration changes. These data suggest that CDK9 inhibitor FIT-039 is a promising antiviral candidate for HBV infection.
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Affiliation(s)
- Tomohisa Tanaka
- Department of Microbiology, Graduate School of Medical Science, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Kaori Okuyama-Dobashi
- Department of Microbiology, Graduate School of Medical Science, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Shuko Murakami
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Wenjia Chen
- Department of Microbiology, Graduate School of Medical Science, University of Yamanashi, Yamanashi 409-3898, Japan
| | - Toru Okamoto
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Keiji Ueda
- Division of Virology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Takamitsu Hosoya
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Akihide Ryo
- Department of Molecular Biodefense Research, Yokohama City University Graduate School of Medicine, Kanagawa 236-0004, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Kohji Moriishi
- Department of Microbiology, Graduate School of Medical Science, University of Yamanashi, Yamanashi 409-3898, Japan.
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Asamitsu K, Omagari K, Okuda T, Hibi Y, Okamoto T. Quantification of the HIV transcriptional activator complex in live cells by image-based protein-protein interaction analysis. Genes Cells 2016; 21:706-16. [PMID: 27193293 DOI: 10.1111/gtc.12375] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/17/2016] [Indexed: 01/16/2023]
Abstract
The virus-encoded Tat protein is essential for HIV transcription in infected cells. The interaction of Tat with the cellular transcription elongation factor P-TEFb (positive transcriptional elongation factor b) containing cyclin T1 (CycT1) and cyclin-dependent kinase 9 (CDK9) is critical for its activity. In this study, we use the Fluoppi (fluorescent-based technology detecting protein-protein interaction) system, which enables the quantification of interactions between biomolecules, such as proteins, in live cells. Quantitative measurement of the molecular interactions among Tat, CycT1 and CDK9 has showed that any third molecule enhances the binding between the other two molecules. These findings suggest that each component of the Tat:P-TEFb complex stabilizes the overall complex, thereby supporting the efficient transcriptional elongation during viral RNA synthesis. These interactions may serve as appropriate targets for novel anti-HIV therapy.
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Affiliation(s)
- Kaori Asamitsu
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Katsumi Omagari
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Tomoya Okuda
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Yurina Hibi
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
| | - Takashi Okamoto
- Department of Molecular and Cellular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, 467-8601, Japan
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24
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The KT Jeang Retrovirology prize 2015: Paul Bieniasz. Retrovirology 2015; 12:84. [PMID: 26438335 PMCID: PMC4595249 DOI: 10.1186/s12977-015-0208-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 11/13/2022] Open
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25
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Asamitsu K, Hirokawa T, Hibi Y, Okamoto T. Molecular dynamics simulation and experimental verification of the interaction between cyclin T1 and HIV-1 Tat proteins. PLoS One 2015; 10:e0119451. [PMID: 25781978 DOI: 10.1371/journal.pone.0119451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/13/2015] [Indexed: 11/19/2022] Open
Abstract
The viral encoded Tat protein is essential for the transcriptional activation of HIV proviral DNA. Interaction of Tat with a cellular transcription elongation factor P-TEFb containing CycT1 is critically required for its action. In this study, we performed MD simulation using the 3D data for wild-type and 4CycT1mutants3D data. We found that the dynamic structural change of CycT1 H2’ helix is indispensable for its activity for the Tat action. Moreover, we detected flexible structural changes of the Tat-recognition cavity in the WT CycT1 comprising of ten AAs that are in contact with Tat. These structural fluctuations in WT were lost in the CycT1 mutants. We also found the critical importance of the hydrogen bond network involving H1, H1’ and H2 helices of CycT1. Since similar AA substitutions of the Tat-CycT1 chimera retained the Tat-supporting activity, these interactions are considered primarily involved in interaction with Tat. These findings described in this paper should provide vital information for the development of effective anti-Tat compound.
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26
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Abstract
Antiretroviral therapy (ART) potently suppresses HIV-1 replication, but the virus persists in quiescent infected CD4(+)T cells as a latent integrated provirus, and patients must indefinitely remain on therapy. If ART is terminated, these integrated proviruses can reactivate, driving new rounds of infection. A functional cure for HIV requires eliminating low-level ongoing viral replication that persists in certain tissue sanctuaries and preventing viral reactivation. The HIV Tat protein plays an essential role in HIV transcription by recruiting the kinase activity of the P-TEFb complex to the viral mRNA's stem-bulge-loop structure, TAR, activating transcriptional elongation. Because the Tat-mediated transactivation cascade is critical for robust HIV replication, the Tat/TAR/P-TEFb complex is one of the most attractive targets for drug development. Importantly, compounds that interfere with transcription could impair viral reactivation, low-level ongoing replication, and replenishment of the latent reservoir, thereby reducing the size of the latent reservoir pool. Here, we discuss the potential importance of transcriptional inhibitors in the treatment of latent HIV-1 disease and review recent findings on targeting Tat, TAR, and P-TEFb individually or as part of a complex. Finally, we discuss the impact of extracellular Tat in HIV-associated neurocognitive disorders and cancers.
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27
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Aligeti M, Behrens RT, Pocock GM, Schindelin J, Dietz C, Eliceiri KW, Swanson CM, Malim MH, Ahlquist P, Sherer NM. Cooperativity among Rev-associated nuclear export signals regulates HIV-1 gene expression and is a determinant of virus species tropism. J Virol 2014; 88:14207-21. [PMID: 25275125 PMCID: PMC4249125 DOI: 10.1128/jvi.01897-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/23/2014] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED Murine cells exhibit a profound block to HIV-1 virion production that was recently mapped to a species-specific structural attribute of the murine version of the chromosomal region maintenance 1 (mCRM1) nuclear export receptor and rescued by the expression of human CRM1 (hCRM1). In human cells, the HIV-1 Rev protein recruits hCRM1 to intron-containing viral mRNAs encoding the Rev response element (RRE), thereby facilitating viral late gene expression. Here we exploited murine 3T3 fibroblasts as a gain-of-function system to study hCRM1's species-specific role in regulating Rev's effector functions. We show that Rev is rapidly exported from the nucleus by mCRM1 despite only weak contributions to HIV-1's posttranscriptional stages. Indeed, Rev preferentially accumulates in the cytoplasm of murine 3T3 cells with or without hCRM1 expression, in contrast to human HeLa cells, where Rev exhibits striking en masse transitions between the nuclear and cytoplasmic compartments. Efforts to bias Rev's trafficking either into or out of the nucleus revealed that Rev encoding a second CRM1 binding domain (Rev-2xNES) or Rev-dependent viral gag-pol mRNAs bearing tandem RREs (GP-2xRRE), rescue virus particle production in murine cells even in the absence of hCRM1. Combined, these results suggest a model wherein Rev-associated nuclear export signals cooperate to regulate the number or quality of CRM1's interactions with viral Rev/RRE ribonucleoprotein complexes in the nucleus. This mechanism regulates CRM1-dependent viral gene expression and is a determinant of HIV-1's capacity to produce virions in nonhuman cell types. IMPORTANCE Cells derived from mice and other nonhuman species exhibit profound blocks to HIV-1 replication. Here we elucidate a block to HIV-1 gene expression attributable to the murine version of the CRM1 (mCRM1) nuclear export receptor. In human cells, hCRM1 regulates the nuclear export of viral intron-containing mRNAs through the activity of the viral Rev adapter protein that forms a multimeric complex on these mRNAs prior to recruiting hCRM1. We demonstrate that Rev-dependent gene expression is poor in murine cells despite the finding that, surprisingly, the bulk of Rev interacts efficiently with mCRM1 and is rapidly exported from the nucleus. Instead, we map the mCRM1 defect to the apparent inability of this factor to engage Rev multimers in the context of large viral Rev/RNA ribonucleoprotein complexes. These findings shed new light on HIV-1 gene regulation and could inform the development of novel antiviral strategies that target viral gene expression.
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Affiliation(s)
- Mounavya Aligeti
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan T Behrens
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ginger M Pocock
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Johannes Schindelin
- Morgridge Institute for Research, Madison, Wisconsin, USA Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christian Dietz
- Department of Computer and Information Science, University of Constance, Constance, Germany
| | - Kevin W Eliceiri
- Morgridge Institute for Research, Madison, Wisconsin, USA Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chad M Swanson
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Michael H Malim
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA Morgridge Institute for Research, Madison, Wisconsin, USA Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Das B, Dobrowolski C, Shahir AM, Feng Z, Yu X, Sha J, Bissada NF, Weinberg A, Karn J, Ye F. Short chain fatty acids potently induce latent HIV-1 in T-cells by activating P-TEFb and multiple histone modifications. Virology 2014; 474:65-81. [PMID: 25463605 DOI: 10.1016/j.virol.2014.10.033] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 10/25/2014] [Accepted: 10/27/2014] [Indexed: 12/14/2022]
Abstract
HIV patients with severe periodontitis have high levels of residual virus in their saliva and plasma despite effective therapy (HAART). Multiple short chain fatty acids (SCFAs) from periodontal pathogens reactivate HIV-1 in both Jurkat and primary T-cell models of latency. SCFAs not only activate positive transcription elongation factor b (P-TEFb), which is an essential cellular cofactor for Tat, but can also reverse chromatin blocks by inducing histone modifications. SCFAs simultaneously increase histone acetylation by inhibiting class-1/2 histone deacetylases (HDACs) and decrease repressive histone tri-methylation at the proviral LTR by downregulating expression of the class-3 HDAC sirtuin-1 (SIRT1), and the histone methyltransferases enhancer of Zeste homolog 2 (EZH2) and suppressor of variegation 3-9 homolog 1 (SUV39H1). Our findings provide a mechanistic link between periodontal disease and enhanced HIV-1 replication, and suggest that treatment of periodontal disease, or blocking the activities of SCFAs, will have a therapeutic benefit for HIV patients.
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Affiliation(s)
- Biswajit Das
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States
| | - Curtis Dobrowolski
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States
| | - Abdel-Malek Shahir
- Department of Periodontics, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, United States
| | - Zhimin Feng
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States
| | - Xiaolan Yu
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States
| | - Jinfeng Sha
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States
| | - Nabil F Bissada
- Department of Periodontics, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, United States
| | - Aaron Weinberg
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States.
| | - Fengchun Ye
- Department of Biological Sciences, School of Dental Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, United States.
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Napolitano G, Lania L, Majello B. Role of noncoding RNAs in the regulation of P-TEFb availability and enzymatic activity. Biomed Res Int 2014; 2014:643805. [PMID: 24701579 DOI: 10.1155/2014/643805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 01/13/2014] [Indexed: 11/23/2022]
Abstract
P-TEFb is a transcriptional factor that specifically regulates the elongation step of RNA polymerase II-dependent transcription and its activity strictly required for Human Immunodeficiency Virus (HIV) infection and during cardiac differentiation. P-TEFb role has emerged as a crucial regulator of transcription elongation and its activity found finely tuned in vivo at transcriptional level as well as posttranscriptionally by dynamic association with different multisubunit molecular particles. Both physiological and pathological cellular signals rapidly converge on P-TEFb regulation by modifying expression and activity of the complex to allow cells to properly respond to different stimuli. In this review we will give a panoramic view on P-TEFb regulation by noncoding RNAs in both physiological and pathological conditions.
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30
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Mbonye U, Karn J. Transcriptional control of HIV latency: cellular signaling pathways, epigenetics, happenstance and the hope for a cure. Virology 2014; 454-455:328-39. [PMID: 24565118 DOI: 10.1016/j.virol.2014.02.008] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 01/23/2014] [Accepted: 02/07/2014] [Indexed: 02/06/2023]
Abstract
Replication-competent latent HIV-1 proviruses that persist in the genomes of a very small subset of resting memory T cells in infected individuals under life-long antiretroviral therapy present a major barrier towards viral eradication. Multiple molecular mechanisms are required to repress the viral trans-activating factor Tat and disrupt the regulatory Tat feedback circuit leading to the establishment of the latent viral reservoir. In particular, latency is due to a combination of transcriptional silencing of proviruses via host epigenetic mechanisms and restrictions on the expression of P-TEFb, an essential co-factor for Tat. Induction of latent proviruses in the presence of antiretroviral therapy is expected to enable clearance of latently infected cells by viral cytopathic effects and host antiviral immune responses. An in-depth comprehensive understanding of the molecular control of HIV-1 transcription should inform the development of optimal combinatorial reactivation strategies that are intended to purge the latent viral reservoir.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States.
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31
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Kuzembayeva M, Dilley K, Sardo L, Hu WS. Life of psi: how full-length HIV-1 RNAs become packaged genomes in the viral particles. Virology 2014; 454-455:362-70. [PMID: 24530126 DOI: 10.1016/j.virol.2014.01.019] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 01/03/2014] [Accepted: 01/24/2014] [Indexed: 12/27/2022]
Abstract
As a member of the retrovirus family, HIV-1 packages its RNA genome into particles and replicates through a DNA intermediate that integrates into the host cellular genome. The multiple genes encoded by HIV-1 are expressed from the same promoter and their expression is regulated by splicing and ribosomal frameshift. The full-length HIV-1 RNA plays a central role in viral replication as it serves as the genome in the progeny virus and is used as the template for Gag and GagPol translation. In this review, we summarize findings that contribute to our current understanding of how full-length RNA is expressed and transported, cis- and trans-acting elements important for RNA packaging, the locations and timing of RNA:RNA and RNA:Gag interactions, and the processes required for this RNA to be packaged into viral particles.
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Affiliation(s)
- Malika Kuzembayeva
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Kari Dilley
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Luca Sardo
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA.
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32
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Nekhai S, Petukhov M, Breuer D. Regulation of CDK9 activity by phosphorylation and dephosphorylation. Biomed Res Int 2014; 2014:964964. [PMID: 24524087 DOI: 10.1155/2014/964964] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 12/11/2013] [Indexed: 11/18/2022]
Abstract
HIV-1 transcription is regulated by CDK9/cyclin T1, which, unlike a typical cell cycle-dependent kinase, is regulated by associating with 7SK small nuclear ribonuclear protein complex (snRNP). While the protein components of this complex are well studied, the mechanism of the complex formation is still not fully understood. The association of CDK9/cyclin T1 with 7SK snRNP is, in part, regulated by a reversible CDK9 phosphorylation. Here, we present a comprehensive review of the kinases and phosphatases involved in CDK9 phosphorylation and discuss their role in regulation of HIV-1 replication and potential for being targeted for drug development. We propose a novel pathway of HIV-1 transcription regulation via CDK9 Ser-90 phosphorylation by CDK2 and CDK9 Ser-175 dephosphorylation by protein phosphatase-1.
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Abstract
RNA viruses represent the predominant cause of many clinically relevant viral diseases in humans. Among several evolutionary advantages acquired by RNA viruses, the ability to usurp host cellular machinery and evade antiviral immune responses is imperative. During the past decade, RNA interference mechanisms, especially microRNA (miRNA)-mediated regulation of cellular protein expression, have revolutionized our understanding of host-viral interactions. Although it is well established that several DNA viruses express miRNAs that play crucial roles in their pathogenesis, expression of miRNAs by RNA viruses remains controversial. However, modulation of the miRNA machinery by RNA viruses may confer multiple benefits for enhanced viral replication and survival in host cells. In this review, we discuss the current literature on RNA viruses that may encode miRNAs and the varied advantages of engineering RNA viruses to express miRNAs as potential vectors for gene therapy. In addition, we review how different families of RNA viruses can alter miRNA machinery for productive replication, evasion of antiviral immune responses, and prolonged survival. We underscore the need to further explore the complex interactions of RNA viruses with host miRNAs to augment our understanding of host-virus interplay.
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Affiliation(s)
- Gokul Swaminathan
- Microbiology and Immunology Graduate Program, Drexel University College of Medicine, Philadelphia, Pennsylvania
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34
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Jiang L, Huang Y, Deng M, Liu T, Lai W, Ye X. Polo-like kinase 1 inhibits the activity of positive transcription elongation factor of RNA Pol II b (P-TEFb). PLoS One 2013; 8:e72289. [PMID: 23977272 PMCID: PMC3745420 DOI: 10.1371/journal.pone.0072289] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 07/15/2013] [Indexed: 11/19/2022] Open
Abstract
Polo-like kinase 1 (Plk1) is a highly conserved Ser/Thr kinase in eukaryotes and plays a critical role in various aspects of the cell cycle. Plk1 exerts its multiple functions by phosphorylating its substrates. In this study, we found that Plk1 can interact with cyclin T1/Cdk9 complex-the main form of the positive transcription elongation complex b (P-TEFb), and its C-terminal polo-box domain is responsible for the binding. Further analysis indicated that Plk1 could phosphorylate cyclin T1 at Ser564 and inhibit the kinase activity of cyclin T1/Cdk9 complex on phosphorylation of the C-terminal domain (CTD) of RNA polymerase II. By taking the approach of luciferase assay, we demonstrated that over-expression of both wild type Plk1 and constitutively active form of Plk1 inhibits the P-TEFb dependent HIV-1 LTR transcription, while knockdown of Plk1 increases the HIV-1 LTR transcription. Consistently, the data from the HIV-1 pseudovirus reporter assay indicated that Plk1 blocks the gene expression of HIV-1 pseudovirus. Taken together, our results revealed that Plk1 negatively regulates the RNA polymerase II-dependent transcription through inhibiting the activity of cyclin T1/Cdk9 complex.
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Affiliation(s)
- Liangzhen Jiang
- Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Yan Huang
- Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Min Deng
- Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Ting Liu
- Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Wenbin Lai
- Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- Graduate University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Xin Ye
- Center for Molecular Immunology, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
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35
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Abstract
Control of HIV-1 gene expression depends on two viral regulatory proteins, Tat and Rev. Tat stimulates transcription elongation by directing the cellular transcriptional elongation factor P-TEFb to nascent RNA polymerases. Rev is required for the transport from the nucleus to the cytoplasm of the unspliced and incompletely spliced mRNAs that encode the structural proteins of the virus. Molecular studies of both proteins have revealed how they interact with the cellular machinery to control transcription from the viral LTR and regulate the levels of spliced and unspliced mRNAs. The regulatory feedback mechanisms driven by HIV-1 Tat and Rev ensure that HIV-1 transcription proceeds through distinct phases. In cells that are not fully activated, limiting levels of Tat and Rev act as potent blocks to premature virus production.
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Affiliation(s)
- Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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36
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Mbonye UR, Gokulrangan G, Datt M, Dobrowolski C, Cooper M, Chance MR, Karn J. Phosphorylation of CDK9 at Ser175 enhances HIV transcription and is a marker of activated P-TEFb in CD4(+) T lymphocytes. PLoS Pathog 2013; 9:e1003338. [PMID: 23658523 PMCID: PMC3642088 DOI: 10.1371/journal.ppat.1003338] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 03/20/2013] [Indexed: 11/26/2022] Open
Abstract
The HIV transactivator protein, Tat, enhances HIV transcription by recruiting P-TEFb from the inactive 7SK snRNP complex and directing it to proviral elongation complexes. To test the hypothesis that T-cell receptor (TCR) signaling induces critical post-translational modifications leading to enhanced interactions between P-TEFb and Tat, we employed affinity purification–tandem mass spectrometry to analyze P-TEFb. TCR or phorbal ester (PMA) signaling strongly induced phosphorylation of the CDK9 kinase at Ser175. Molecular modeling studies based on the Tat/P-TEFb X-ray structure suggested that pSer175 strengthens the intermolecular interactions between CDK9 and Tat. Mutations in Ser175 confirm that this residue could mediate critical interactions with Tat and with the bromodomain protein BRD4. The S175A mutation reduced CDK9 interactions with Tat by an average of 1.7-fold, but also completely blocked CDK9 association with BRD4. The phosphomimetic S175D mutation modestly enhanced Tat association with CDK9 while causing a 2-fold disruption in BRD4 association with CDK9. Since BRD4 is unable to compete for binding to CDK9 carrying S175A, expression of CDK9 carrying the S175A mutation in latently infected cells resulted in a robust Tat-dependent reactivation of the provirus. Similarly, the stable knockdown of BRD4 led to a strong enhancement of proviral expression. Immunoprecipitation experiments show that CDK9 phosphorylated at Ser175 is excluded from the 7SK RNP complex. Immunofluorescence and flow cytometry studies carried out using a phospho-Ser175-specific antibody demonstrated that Ser175 phosphorylation occurs during TCR activation of primary resting memory CD4+ T cells together with upregulation of the Cyclin T1 regulatory subunit of P-TEFb, and Thr186 phosphorylation of CDK9. We conclude that the phosphorylation of CDK9 at Ser175 plays a critical role in altering the competitive binding of Tat and BRD4 to P-TEFb and provides an informative molecular marker for the identification of the transcriptionally active form of P-TEFb. The release of the transcription elongation factor P-TEFb from the 7SK RNP complex and its binding to the HIV Tat transactivator protein enables the efficient transcription of HIV proviruses. In resting memory T-cells, which carry the bulk of the latent HIV viral pool, limiting the cellular levels of P-TEFb ensures that the provirus remains silenced unless the host cell is activated. Here we demonstrate that T-cell receptor (TCR) activation induces phosphorylation of Ser175, a residue which is located at the interface between CycT1, CDK9 and Tat. Phosphorylation of Ser175 occurs on free or 7SK-dissociated P-TEFb and genetic experiments indicate that this modification enhances P-TEFb interaction with Tat resulting in Tat-dependent reactivation of HIV proviral transcription. Modification of Ser175 appears critical for controlling the competitive binding of Tat and the bromodomain protein BRD4 to P-TEFb. Activation of P-TEFb in resting T-cells thus involves both the initial assembly of the 7SK snRNP complex and the subsequent mobilization of P-TEFb by cellular signaling and Tat. Therefore, pSer175 provides an informative molecular marker for the identification of the transcriptionally active form of P-TEFb that can be used to monitor the extent of T-cell activation during therapeutic interventions aimed at virus eradication.
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Affiliation(s)
- Uri R. Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Giridharan Gokulrangan
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Manish Datt
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Curtis Dobrowolski
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Maxwell Cooper
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Mark R. Chance
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail:
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Guo HY, Ma YG, Gai YM, Liang ZB, Ma J, Su Y, Zhang QC, Chen QM, Tan J. Bovine HEXIM1 inhibits bovine immunodeficiency virus replication through regulating BTat-mediated transactivation. Vet Res 2013; 44:21. [PMID: 23537346 PMCID: PMC3630055 DOI: 10.1186/1297-9716-44-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 03/05/2013] [Indexed: 11/11/2022] Open
Abstract
The bovine immunodeficiency virus (BIV) transactivator (BTat) recruits the bovine cyclin T1 (B-cyclin T1) to the LTR to facilitate the transcription of BIV. Here, we demonstrate that bovine hexamethylene bisacetamide (HMBA)-induced protein 1 (BHEXIM1) inhibits BTat-mediated BIV LTR transcription. The results of in vivo and in vitro assays show direct binding of BHEXIM1 to the B-cyclin T1. These results suggest that the repression arises from BHEXIM1-BTat competition for B-cyclin T1, which allows BHEXIM1 to displace BTat from B-cyclin T1. Furthermore, we found that the C-terminal region and the centrally located region of BHEXIM1 are required for BHEXIM1 to associate with B-cyclin T1. Knockdown of BHEXIM1 enhances BIV replication. Taken together, our study provides the first clear evidence that BHEXIM1 is involved in BIV replication through regulating BTat-mediated transactivation.
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Affiliation(s)
- Hong-yan Guo
- Key Laboratory of Molecular Microbiology and Biotechnology (Ministry of Education) and Key Laboratory Microbial Functional Genomics (Tianjin), College of Life Sciences, Nankai University, Tianjin, 300071, China.
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Tomo N, Goto T, Morikawa Y. Trans-packaging of human immunodeficiency virus type 1 genome into Gag virus-like particles in Saccharomyces cerevisiae. Microb Cell Fact 2013; 12:28. [PMID: 23530915 PMCID: PMC3623794 DOI: 10.1186/1475-2859-12-28] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/15/2013] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Yeast is recognized as a generally safe microorganism and is utilized for the production of pharmaceutical products, including vaccines. We previously showed that expression of human immunodeficiency virus type 1 (HIV-1) Gag protein in Saccharomyces cerevisiae spheroplasts released Gag virus-like particles (VLPs) extracellularly, suggesting that the production system could be used in vaccine development. In this study, we further establish HIV-1 genome packaging into Gag VLPs in a yeast cell system. RESULTS The nearly full-length HIV-1 genome containing the entire 5' long terminal repeat, U3-R-U5, did not transcribe gag mRNA in yeast. Co-expression of HIV-1 Tat, a transcription activator, did not support the transcription. When the HIV-1 promoter U3 was replaced with the promoter for the yeast glyceraldehyde-3-phosphate dehydrogenase gene, gag mRNA transcription was restored, but no Gag protein expression was observed. Co-expression of HIV-1 Rev, a factor that facilitates nuclear export of gag mRNA, did not support the protein synthesis. Progressive deletions of R-U5 and its downstream stem-loop-rich region (SL) to the gag start ATG codon restored Gag protein expression, suggesting that a highly structured noncoding RNA generated from the R-U5-SL region had an inhibitory effect on gag mRNA translation. When a plasmid containing the HIV-1 genome with the R-U5-SL region was coexpressed with an expression plasmid for Gag protein, the HIV-1 genomic RNA was transcribed and incorporated into Gag VLPs formed by Gag protein assembly, indicative of the trans-packaging of HIV-1 genomic RNA into Gag VLPs in a yeast cell system. The concentration of HIV-1 genomic RNA in Gag VLPs released from yeast was approximately 500-fold higher than that in yeast cytoplasm. The deletion of R-U5 to the gag gene resulted in the failure of HIV-1 RNA packaging into Gag VLPs, indicating that the packaging signal of HIV-1 genomic RNA present in the R-U5 to gag region functions similarly in yeast cells. CONCLUSIONS Our data indicate that selective trans-packaging of HIV-1 genomic RNA into Gag VLPs occurs in a yeast cell system, analogous to a mammalian cell system, suggesting that yeast may provide an alternative packaging system for lentiviral RNA.
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Affiliation(s)
- Naoki Tomo
- Kitasato Institute for Life Sciences and Graduate School for Infection Control, Kitasato University, Shirokane 5-9-1, Minato-ku, Tokyo, 108-8641, Japan
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Martin F. Fifteen years of the yeast three-hybrid system: RNA-protein interactions under investigation. Methods 2012; 58:367-75. [PMID: 22841566 DOI: 10.1016/j.ymeth.2012.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 05/04/2012] [Accepted: 07/13/2012] [Indexed: 01/14/2023] Open
Abstract
In 1996, the Wickens and the Kuhl labs developed the yeast three-hybrid system independently. By expressing two chimeric proteins and one chimeric RNA molecule in Saccharomyces cerevisiae, this method allows in vivo monitoring of RNA-protein interactions by measuring the expression levels of HIS3 and LacZ reporter genes. Specific RNA targets have been used to characterize unknown RNA binding proteins. Previously described RNA binding proteins have also been used as bait to select new RNA targets. Finally, this method has been widely used to investigate or confirm previously suspected RNA-protein interactions. However, this method falls short in some aspects, such as RNA display and selection of false positive molecules. This review will summarize the results obtained with this method from the past 15years, as well as on recent efforts to improve its specificity.
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Affiliation(s)
- Franck Martin
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg CEDEX, France.
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Abstract
Many studies have documented how extensively HIV-1 and related viruses interact with host cells. Virus-host interactions are of two conceptual types. First, viruses have evolved to make use of numerous host-cell functions to facilitate their own replication. Second, hosts have evolved a number of activities to inhibit virus replication. Understanding the scope and details of HIV-host interactions has been an extraordinary rich scientific endeavor, and in addition to their biomedical importance, studies in this area have established HIV as a model system in virology. Here, I present an overview of how HIV-1 interacts with some key host cell factors during its replication cycle.
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Ramakrishnan R, Chiang K, Liu H, Budhiraja S, Donahue H, Rice AP. Making a Short Story Long: Regulation of P-TEFb and HIV-1 Transcriptional Elongation in CD4+ T Lymphocytes and Macrophages. Biology (Basel) 2012; 1:94-115. [PMID: 24832049 PMCID: PMC4011037 DOI: 10.3390/biology1010094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 06/07/2012] [Accepted: 06/11/2012] [Indexed: 12/22/2022]
Abstract
Productive transcription of the integrated HIV-1 provirus is restricted by cellular factors that inhibit RNA polymerase II elongation. The viral Tat protein overcomes this by recruiting a general elongation factor, P-TEFb, to the TAR RNA element that forms at the 5' end of nascent viral transcripts. P-TEFb exists in multiple complexes in cells, and its core consists of a kinase, Cdk9, and a regulatory subunit, either Cyclin T1 or Cyclin T2. Tat binds directly to Cyclin T1 and thereby targets the Cyclin T1/P-TEFb complex that phosphorylates the CTD of RNA polymerase II and the negative factors that inhibit elongation, resulting in efficient transcriptional elongation. P-TEFb is tightly regulated in cells infected by HIV-1-CD4+ T lymphocytes and monocytes/macrophages. A number of mechanisms have been identified that inhibit P-TEFb in resting CD4+ T lymphocytes and monocytes, including miRNAs that repress Cyclin T1 protein expression and dephosphorylation of residue Thr186 in the Cdk9 T-loop. These repressive mechanisms are overcome upon T cell activation and macrophage differentiation when the permissivity for HIV-1 replication is greatly increased. This review will summarize what is currently known about mechanisms that regulate P-TEFb and how this regulation impacts HIV-1 replication and latency.
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Affiliation(s)
- Rajesh Ramakrishnan
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Karen Chiang
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hongbing Liu
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Sona Budhiraja
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Hart Donahue
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Andrew P Rice
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.
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Abstract
Retroviruses have evolved mechanisms for transporting their intron-containing RNAs (including genomic and messenger RNAs, which encode virion components) from the nucleus to the cytoplasm of the infected cell. Human retroviruses, such as human immunodeficiency virus (HIV) and human T cell leukemia virus type 1 (HTLV-1), encode the regulatory proteins Rev and Rex, which form a bridge between the viral RNA and the export receptor CRM1. Recent studies show that these transport systems are not only involved in RNA export, but also in the encapsidation of genomic RNA; furthermore, they influence subsequent events in the cytoplasm, including the translation of the cognate mRNA, transport of Gag proteins to the plasma membrane, and the formation of virus particles. Moreover, the mode of interaction between the viral and cellular RNA transport machinery underlies the species-specific propagation of HIV-1 and HTLV-1, forming the basis for constructing animal models of infection. This review article discusses recent progress regarding these issues.
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Affiliation(s)
- Hisatoshi Shida
- Division of Molecular Virology, Institute of Immunological Science, Hokkaido University Sapporo, Japan
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Abstract
Three-dimensional molecular structures can provide detailed information on biological mechanisms and, for cases in which the molecular function affects human health, can significantly aid in the development of therapeutic interventions. For almost 25 years, key components of the lentivirus HIV-1, including the envelope glycoproteins, the capsid and the replication enzymes reverse transcriptase, integrase and protease, have been scrutinized to near atomic-scale resolution. Moreover, structural analyses of the interactions between viral and host cell components have yielded key insights into the mechanisms of viral entry, chromosomal integration, transcription and egress from cells. Here, we review recent advances in HIV-1 structural biology, focusing on the molecular mechanisms of viral replication and on the development of new therapeutics.
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Abstract
Intensive antiretroviral therapy successfully suppresses viral replication but is unable to eradicate the virus. HIV persists in a small number of resting memory T cells where HIV has been transcriptionally silenced. This review will focus on recent insights into the HIV transcriptional control mechanisms that provide the biochemical basis for understanding latency. There are no specific repressors of HIV transcription encoded by the virus, instead latency arises when the regulatory feedback mechanism driven by HIV Tat expression is disrupted. Small changes in transcriptional initiation, induced by epigenetic silencing, lead to profound restrictions in Tat levels and force the entry of proviruses into latency. In resting memory T cells, which carry the bulk of the latent viral pool, additional restrictions, especially the limiting cellular levels of the essential Tat cofactor P-TEFb and the transcription initiation factors NF-κB and NFAT ensure that the provirus remains silenced unless the host cell is activated. The detailed understanding of HIV transcription is providing a framework for devising new therapeutic strategies designed to purge the latent viral pool. Importantly, the recognition that there are multiple restrictions imposed on latent proviruses suggest that proviral reactivation will not be achieved when only a single reactivation step is targeted and that any optimal activation strategy will require both removal of epigenetic blocks and the activation of P-TEFb.
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Affiliation(s)
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sherer NM, Swanson CM, Hué S, Roberts RG, Bergeron JRC, Malim MH. Evolution of a species-specific determinant within human CRM1 that regulates the post-transcriptional phases of HIV-1 replication. PLoS Pathog 2011; 7:e1002395. [PMID: 22114565 PMCID: PMC3219727 DOI: 10.1371/journal.ppat.1002395] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 10/09/2011] [Indexed: 11/18/2022] Open
Abstract
The human immunodeficiency virus type-1 (HIV-1) Rev protein regulates the nuclear export of intron-containing viral RNAs by recruiting the CRM1 nuclear export receptor. Here, we employed a combination of functional and phylogenetic analyses to identify and characterize a species-specific determinant within human CRM1 (hCRM1) that largely overcomes established defects in murine cells to the post-transcriptional stages of the HIV-1 life cycle. hCRM1 expression in murine cells promotes the cytoplasmic accumulation of intron-containing viral RNAs, resulting in a substantial stimulation of the net production of infectious HIV-1 particles. These stimulatory effects require a novel surface-exposed element within HEAT repeats 9A and 10A, discrete from the binding cleft previously shown to engage Rev's leucine-rich nuclear export signal. Moreover, we show that this element is a unique feature of higher primate CRM1 proteins, and discuss how this sequence has evolved from a non-functional, ancestral sequence.
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Affiliation(s)
- Nathan M. Sherer
- Department of Infectious Diseases, King's College London School of Medicine, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, King's College London School of Medicine, London, United Kingdom
| | - Stéphane Hué
- MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Roland G. Roberts
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, United Kingdom
| | - Julien R. C. Bergeron
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael H. Malim
- Department of Infectious Diseases, King's College London School of Medicine, London, United Kingdom
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Xue B, Mizianty MJ, Kurgan L, Uversky VN. Protein intrinsic disorder as a flexible armor and a weapon of HIV-1. Cell Mol Life Sci 2011; 69:1211-59. [PMID: 22033837 DOI: 10.1007/s00018-011-0859-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 01/19/2023]
Abstract
Many proteins and protein regions are disordered in their native, biologically active states. These proteins/regions are abundant in different organisms and carry out important biological functions that complement the functional repertoire of ordered proteins. Viruses, with their highly compact genomes, small proteomes, and high adaptability for fast change in their biological and physical environment utilize many of the advantages of intrinsic disorder. In fact, viral proteins are generally rich in intrinsic disorder, and intrinsically disordered regions are commonly used by viruses to invade the host organisms, to hijack various host systems, and to help viruses in accommodation to their hostile habitats and to manage their economic usage of genetic material. In this review, we focus on the structural peculiarities of HIV-1 proteins, on the abundance of intrinsic disorder in viral proteins, and on the role of intrinsic disorder in their functions.
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Affiliation(s)
- Bin Xue
- Department of Molecular Medicine, University of South Florida, College of Medicine, Tampa, FL 33612, USA
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48
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Abstract
The current anti-HIV treatments fail to completely eradicate the virus in HIV-infected individuals, mainly as a result of a small pool of latently infected cells. This issue, together with the emergence of multidrug-resistant viruses, clearly highlights the need to find additional strategies. An overview of the Tat-mediated transcription inhibitors 6-desfluoroquinolones (6-DFQs), identified by our group, is given in this review along with a critical appraisal of their advantages and drawbacks. Attempts are also made to place them within the context of new potential anti-HIV therapeutics. Due to their innovative mechanism of action, the 6-DFQs could be interesting candidates for use in association with the currently used cocktail of drugs. Their potential as antivirals deserves further investigation.
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Asamitsu K, Hibi Y, Imai K, Victoriano AFB, Kurimoto E, Kato K, Okamoto T. Functional Characterization of Human Cyclin T1 N-Terminal Region for Human Immunodeficiency Virus-1 Tat Transcriptional Activation. J Mol Biol 2011; 410:887-95. [DOI: 10.1016/j.jmb.2011.04.061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 11/23/2022]
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McQueen P, Donald LJ, Vo TN, Nguyen DH, Griffiths H, Shojania S, Standing KG, O'Neil JD. Tat peptide-calmodulin binding studies and bioinformatics of HIV-1 protein-calmodulin interactions. Proteins 2011; 79:2233-46. [DOI: 10.1002/prot.23048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 03/18/2011] [Accepted: 03/22/2011] [Indexed: 01/08/2023]
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