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Ballarin G, Biasiotto M, Reisbitzer A, Hegels M, Bolte M, Krauß S, Berdnikova DV. A novel aurone RNA CAG binder inhibits the huntingtin RNA-protein interaction. RSC Med Chem 2024; 15:3092-3096. [PMID: 39309355 PMCID: PMC11411626 DOI: 10.1039/d4md00403e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/14/2024] [Indexed: 09/25/2024] Open
Abstract
Huntington's disease (HD) is a devastating, incurable condition whose pathophysiological mechanism relies on mutant RNA CAG repeat expansions. Aberrant recruitment of RNA-binding proteins by mutant CAG hairpins contributes to the progress of neurodegeneration. In this work, we identified a novel binder based on an aurone scaffold that reduces the level of binding of HTT mRNA to the MID1 protein in vitro. The obtained results introduce aurones as a novel platform for the design of functional ligands for disease-related RNA sequences.
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Affiliation(s)
- Giovanna Ballarin
- University of Padova, School of Pharmaceutical Sciences via Marzolo 5 35131 Padova Italy
- Institut für Biologie, Universität Siegen Adolf-Reichwein-Str. 2 57076 Siegen Germany
- Organische Chemie II, Universität Siegen Adolf-Reichwein-Str. 2 57076 Siegen Germany
| | - Maddalena Biasiotto
- University of Padova, School of Pharmaceutical Sciences via Marzolo 5 35131 Padova Italy
- Institut für Biologie, Universität Siegen Adolf-Reichwein-Str. 2 57076 Siegen Germany
- Organische Chemie II, Universität Siegen Adolf-Reichwein-Str. 2 57076 Siegen Germany
| | - Annika Reisbitzer
- Institut für Biologie, Universität Siegen Adolf-Reichwein-Str. 2 57076 Siegen Germany
| | - Marlen Hegels
- Organische Chemie II, Universität Siegen Adolf-Reichwein-Str. 2 57076 Siegen Germany
| | - Michael Bolte
- Institut für Anorganische Chemie, J.-W.-Goethe-Universität Max-von-Laue-Str. 7 60438 Frankfurt-am-Main Germany
| | - Sybille Krauß
- Institut für Biologie, Universität Siegen Adolf-Reichwein-Str. 2 57076 Siegen Germany
| | - Daria V Berdnikova
- Organische Chemie II, Universität Siegen Adolf-Reichwein-Str. 2 57076 Siegen Germany
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2
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Sharma AL, Tyagi P, Khumallambam M, Tyagi M. Cocaine-induced DNA-PK relieves RNAP II pausing by promoting TRIM28 phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608673. [PMID: 39229050 PMCID: PMC11370412 DOI: 10.1101/2024.08.19.608673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Drug abuse continues to pose a significant challenge in HIV control efforts. In our investigation, we discovered that cocaine not only upregulates the expression of DNA-dependent protein kinase (DNA-PK) but also augments DNA-PK activation by enhancing its phosphorylation at S2056. Moreover, DNA-PK phosphorylation triggers the translocation of DNA-PK into the nucleus. The finding that cocaine promotes nuclear translocation of DNA-PK further validates our observation of enhanced DNA-PK recruitment at the HIV long terminal repeat (LTR) following cocaine exposure. By activating and facilitating the nuclear translocation of DNA-PK, cocaine effectively orchestrates multiple stages of HIV transcription, thereby promoting HIV replication. Additionally, our study indicates that cocaine-induced DNA-PK promotes hyper-phosphorylation of RNA polymerase II (RNAP II) carboxyl-terminal domain (CTD) at Ser5 and Ser2 sites, enhancing both initiation and elongation phases, respectively, of HIV transcription. Cocaine's enhancement of transcription initiation and elongation is further supported by its activation of cyclin-dependent kinase 7 (CDK7) and subsequent phosphorylation of CDK9, thereby promoting positive transcriptional elongation factor b (P-TEFb) activity. We demonstrate for the first time that cocaine, through DNA-PK activation, promotes the specific phosphorylation of TRIM28 at Serine 824 (p-TRIM28, S824). This modification converts TRIM28 from a transcriptional inhibitor to a transactivator for HIV transcription. Additionally, we observe that phosphorylation of TRIM28 (p-TRIM28, S824) promotes the transition from the pausing phase to the elongation phase of HIV transcription, thereby facilitating the production of full-length HIV genomic transcripts. This finding corroborates the observed enhanced RNAP II CTD phosphorylation at Ser2, a marker of transcriptional elongation, following cocaine exposure. Accordingly, upon cocaine treatment, we observed elevated recruitment of p-TRIM28-(S824) at the HIV LTR. Overall, our results have unraveled the intricate molecular mechanisms underlying cocaine-induced HIV transcription and gene expression. These findings hold promise for the development of highly targeted therapeutics aimed at mitigating the detrimental effects of cocaine in individuals living with HIV.
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Affiliation(s)
| | - Priya Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Meenata Khumallambam
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
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Hokello J, Tyagi K, Owor RO, Sharma AL, Bhushan A, Daniel R, Tyagi M. New Insights into HIV Life Cycle, Th1/Th2 Shift during HIV Infection and Preferential Virus Infection of Th2 Cells: Implications of Early HIV Treatment Initiation and Care. Life (Basel) 2024; 14:104. [PMID: 38255719 PMCID: PMC10817636 DOI: 10.3390/life14010104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/05/2024] [Accepted: 01/07/2024] [Indexed: 01/24/2024] Open
Abstract
The theory of immune regulation involves a homeostatic balance between T-helper 1 (Th1) and T-helper 2 (Th2) responses. The Th1 and Th2 theories were introduced in 1986 as a result of studies in mice, whereby T-helper cell subsets were found to direct different immune response pathways. Subsequently, this hypothesis was extended to human immunity, with Th1 cells mediating cellular immunity to fight intracellular pathogens, while Th2 cells mediated humoral immunity to fight extracellular pathogens. Several disease conditions were later found to tilt the balance between Th1 and Th2 immune response pathways, including HIV infection, but the exact mechanism for the shift from Th1 to Th2 cells was poorly understood. This review provides new insights into the molecular biology of HIV, wherein the HIV life cycle is discussed in detail. Insights into the possible mechanism for the Th1 to Th2 shift during HIV infection and the preferential infection of Th2 cells during the late symptomatic stage of HIV disease are also discussed.
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Affiliation(s)
- Joseph Hokello
- Department of Biology, Faculty of Science and Education, Busitema University, Tororo P.O. Box 236, Uganda;
| | - Kratika Tyagi
- Department of Biotechnology, Banasthali Vidyapith, Jaipur 304022, India;
| | - Richard Oriko Owor
- Department of Chemistry, Faculty of Science and Education, Busitema University, Tororo P.O. Box 236, Uganda;
| | - Adhikarimayum Lakhikumar Sharma
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (A.L.S.); (R.D.)
| | - Alok Bhushan
- Department of Pharmaceutical Sciences, Jefferson College of Pharmacy, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Rene Daniel
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (A.L.S.); (R.D.)
| | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (A.L.S.); (R.D.)
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4
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Qi L, Zhang J, Liu Q, Gao X. Ligand "switching on" fluorescence of HIV-1 RNA-templated copper nanoclusters for ligand-RNA interaction assays. Int J Biol Macromol 2024; 256:127779. [PMID: 37981280 DOI: 10.1016/j.ijbiomac.2023.127779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/15/2023] [Accepted: 10/27/2023] [Indexed: 11/21/2023]
Abstract
Ligand-RNA interaction assay provides the basis for developing new RNA-binding small molecules. In this study, fluorescent copper nanoclusters (CuNCs) were first prepared using two kinds of HIV-1 RNA targets, rev-responsive element (RRE) and transactivator response element (TAR) RNA, as new templates, and it was found that the fluorescence of the single RNA-templated CuNCs was negligible. Using neomycin as a model drug, the fluorescence could be augmented (approximately 6 times) for the neomycin/RNA-templated CuNCs. Thus, a novel method was developed for ligand-RNA interactions by observing the fluorescence changes in CuNCs prepared using RNA before and after the addition of ligands. The preparation parameters of neomycin/RNA-CuNCs were optimized. The as-prepared CuNCs were characterized using UV-vis spectroscopy, fluorescence spectroscopy, and high-resolution transmission electron microscope. Circular dichroism spectral analysis showed that RRE and TAR were inclined to form a double-stranded structure after interaction with neomycin, which was more conducive to the formation of CuNCs. The interactions of neomycin and three test drugs (amikacin, gentamicin, and tobramycin) with RNA were investigated using the proposed method, and the binding constants and number of binding sites were obtained through theoretical calculations. This study provides a novel approach for ligand-RNA interaction assays.
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Affiliation(s)
- Liang Qi
- School of Biomedical and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an 710021, China.
| | - Jiayun Zhang
- School of Biomedical and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Qiaoning Liu
- School of Biomedical and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Xiang Gao
- School of Biomedical and Pharmaceutical Sciences, Shaanxi University of Science & Technology, Xi'an 710021, China.
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5
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Maia LB, Maiti BK, Moura I, Moura JJG. Selenium-More than Just a Fortuitous Sulfur Substitute in Redox Biology. Molecules 2023; 29:120. [PMID: 38202704 PMCID: PMC10779653 DOI: 10.3390/molecules29010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Living organisms use selenium mainly in the form of selenocysteine in the active site of oxidoreductases. Here, selenium's unique chemistry is believed to modulate the reaction mechanism and enhance the catalytic efficiency of specific enzymes in ways not achievable with a sulfur-containing cysteine. However, despite the fact that selenium/sulfur have different physicochemical properties, several selenoproteins have fully functional cysteine-containing homologues and some organisms do not use selenocysteine at all. In this review, selected selenocysteine-containing proteins will be discussed to showcase both situations: (i) selenium as an obligatory element for the protein's physiological function, and (ii) selenium presenting no clear advantage over sulfur (functional proteins with either selenium or sulfur). Selenium's physiological roles in antioxidant defence (to maintain cellular redox status/hinder oxidative stress), hormone metabolism, DNA synthesis, and repair (maintain genetic stability) will be also highlighted, as well as selenium's role in human health. Formate dehydrogenases, hydrogenases, glutathione peroxidases, thioredoxin reductases, and iodothyronine deiodinases will be herein featured.
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Affiliation(s)
- Luisa B. Maia
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - Biplab K. Maiti
- Department of Chemistry, School of Sciences, Cluster University of Jammu, Canal Road, Jammu 180001, India
| | - Isabel Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
| | - José J. G. Moura
- LAQV, REQUIMTE, Department of Chemistry, NOVA School of Science and Technology | NOVA FCT, 2829-516 Caparica, Portugal; (I.M.); (J.J.G.M.)
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Van Gulck E, Pardons M, Nijs E, Verheyen N, Dockx K, Van Den Eynde C, Battivelli E, Vega J, Florence E, Autran B, Archin NM, Margolis DM, Katlama C, Hamimi C, Van Den Wyngaert I, Eyassu F, Vandekerckhove L, Boden D. A truncated HIV Tat demonstrates potent and specific latency reversal activity. Antimicrob Agents Chemother 2023; 67:e0041723. [PMID: 37874295 PMCID: PMC10649039 DOI: 10.1128/aac.00417-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/09/2023] [Indexed: 10/25/2023] Open
Abstract
A major barrier to HIV-1 cure is caused by the pool of latently infected CD4 T-cells that persist under combination antiretroviral therapy (cART). This latent reservoir is capable of producing replication-competent infectious viruses once prolonged suppressive cART is withdrawn. Inducing the reactivation of HIV-1 gene expression in T-cells harboring a latent provirus in people living with HIV-1 under cART may result in depletion of this latent reservoir due to cytopathic effects or immune clearance. Studies have investigated molecules that reactivate HIV-1 gene expression, but to date, no latency reversal agent has been identified to eliminate latently infected cells harboring replication-competent HIV in cART-treated individuals. Stochastic fluctuations in HIV-1 tat gene expression have been described and hypothesized to allow the progression into proviral latency. We hypothesized that exposing latently infected CD4+ T-cells to Tat would result in effective latency reversal. Our results indicate the capacity of a truncated Tat protein and mRNA to reactivate HIV-1 in latently infected T-cells ex vivo to a similar degree as the protein kinase C agonist: phorbol 12-myristate 13-acetate, without T-cell activation or any significant transcriptome perturbation.
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Affiliation(s)
- Ellen Van Gulck
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Marion Pardons
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Erik Nijs
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Nick Verheyen
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Koen Dockx
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Christel Van Den Eynde
- Janssen Infectious Diseases, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Emilie Battivelli
- Janssen Infectious Diseases, A Division of Janssen Pharmaceutica NV, Brisbane, California, USA
| | - Jerel Vega
- Arcturus Therapeutics, Science Center Drive, San Diego, California, USA
| | | | - Brigitte Autran
- Faculty of Medicine Sorbonne-University, CIMI-Paris, UPMC/Inserm, Paris, France
| | - Nancie M. Archin
- University of North Carolina School of Medicine and UNC, HIV Cure Center, Chapel Hill, North Carolina, USA
| | - David M. Margolis
- University of North Carolina School of Medicine and UNC, HIV Cure Center, Chapel Hill, North Carolina, USA
| | - Christine Katlama
- Department Infectious Diseases, Hospital Pitié Salpetière, Sorbonne-University and IPLESP, Paris, France
| | - Chiraz Hamimi
- Faculty of Medicine Sorbonne-University, CIMI-Paris, UPMC/Inserm, Paris, France
| | - Ilse Van Den Wyngaert
- Discovery Sciences, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Filmon Eyassu
- Discovery Sciences, Janssen Research and Development, A Division of Janssen Pharmaceutica NV, Beerse, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Daniel Boden
- Janssen Infectious Diseases, A Division of Janssen Pharmaceutica NV, Brisbane, California, USA
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7
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Gotora PT, van der Sluis R, Williams ME. HIV-1 Tat amino acid residues that influence Tat-TAR binding affinity: a scoping review. BMC Infect Dis 2023; 23:164. [PMID: 36932337 PMCID: PMC10020771 DOI: 10.1186/s12879-023-08123-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/27/2023] [Indexed: 03/19/2023] Open
Abstract
HIV-1 remains a global health concern and to date, nearly 38 million people are living with HIV. The complexity of HIV-1 pathogenesis and its subsequent prevalence is influenced by several factors including the HIV-1 subtype. HIV-1 subtype variation extends to sequence variation in the amino acids of the HIV-1 viral proteins. Of particular interest is the transactivation of transcription (Tat) protein due to its key function in viral transcription. The Tat protein predominantly functions by binding to the transactivation response (TAR) RNA element to activate HIV-1 transcriptional elongation. Subtype-specific Tat protein sequence variation influences Tat-TAR binding affinity. Despite several studies investigating Tat-TAR binding, it is not clear which regions of the Tat protein and/or individual Tat amino acid residues may contribute to TAR binding affinity. We, therefore, conducted a scoping review on studies investigating Tat-TAR binding. We aimed to synthesize the published data to determine (1) the regions of the Tat protein that may be involved in TAR binding, (2) key Tat amino acids involved in TAR binding and (3) if Tat subtype-specific variation influences TAR binding. A total of thirteen studies met our inclusion criteria and the key findings were that (1) both N-terminal and C-terminal amino acids outside the basic domain (47-59) may be important in increasing Tat-TAR binding affinity, (2) substitution of the amino acids Lysine and Arginine (47-59) resulted in a reduction in binding affinity to TAR, and (3) none of the included studies have investigated Tat subtype-specific substitutions and therefore no commentary could be made regarding which subtype may have a higher Tat-TAR binding affinity. Future studies investigating Tat-TAR binding should therefore use full-length Tat proteins and compare subtype-specific variations. Studies of such a nature may help explain why we see differential pathogenesis and prevalence when comparing HIV-1 subtypes.
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8
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Mi L, Yu Q, Mudiyanselage APK, Wu R, Sun Z, Zheng R, Ren K, You M. Genetically Encoded RNA-Based Bioluminescence Resonance Energy Transfer (BRET) Sensors. ACS Sens 2023; 8:308-316. [PMID: 36608281 PMCID: PMC10630924 DOI: 10.1021/acssensors.2c02213] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
RNA-based nanostructures and molecular devices have become popular for developing biosensors and genetic regulators. These programmable RNA nanodevices can be genetically encoded and modularly engineered to detect various cellular targets and then induce output signals, most often a fluorescence readout. Although powerful, the high reliance of fluorescence on the external excitation light raises concerns about its high background, photobleaching, and phototoxicity. Bioluminescence signals can be an ideal complementary readout for these genetically encoded RNA nanodevices. However, RNA-based real-time bioluminescent reporters have been rarely developed. In this study, we reported the first type of genetically encoded RNA-based bioluminescence resonance energy transfer (BRET) sensors that can be used for real-time target detection in living cells. By coupling a luciferase bioluminescence donor with a fluorogenic RNA-based acceptor, our BRET system can be modularly designed to image and detect various cellular analytes. We expect that this novel RNA-based bioluminescent system can be potentially used broadly in bioanalysis and nanomedicine for engineering biosensors, characterizing cellular RNA-protein interactions, and high-throughput screening or in vivo imaging.
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Affiliation(s)
- Lan Mi
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
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9
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Iyer K, Mitra A, Mitra D. Identification of 5' upstream sequence involved in HSPBP1 gene transcription and its downregulation during HIV-1 infection. Virus Res 2023; 324:199034. [PMID: 36581045 DOI: 10.1016/j.virusres.2022.199034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 12/14/2022] [Accepted: 12/25/2022] [Indexed: 12/27/2022]
Abstract
The Human Immunodeficiency Virus-1 (HIV-1) is known to modulate the host environment for successful replication and propagation like other viruses. The virus utilises its proteins to interact with or modulate host factors and host signalling pathways that may otherwise restrict the virus. A previous study from our lab has shown that the host heat shock protein 70 (HSP70) binding protein (HSPBP1) is a co-chaperone that inhibits viral replication. We have also shown that the virus downregulates HSPBP1 during infection. However, the mechanism of downregulation remains to be elucidated. In the present study, we hypothesized that the HSPBP1 promoter may be repressed during infection leading to its downmodulation at the RNA and protein levels. The 5' upstream region of the HSPBP1 gene was first mapped and it was identified that a fragment comprising of a ∼600 bp upstream region of the transcription start site show the highest promoter-like activity. Further, the Sp1 transcription factor was shown to be essential for normal promoter activation. Our results further demonstrate that HIV-1 downregulates the activity of the identified promoter. It was seen that the viral transactivator protein, Tat, was responsible for the downmodulation of the HSPBP1 promoter. HIV-1 Tat is known to bind and regulate several cellular promoters during infection, thereby making the environment conducive for establishment of the virus. Our results further show that Tat is recruited to the HSPBP1 promoter and in the presence of Tat, recruitment of Sp1 on HSPBP1 promoter was decreased, which explains the suppression of HSPBP1 during HIV-1 infection. Therefore, this study further adds to the list of cellular promoters that are modulated by Tat during HIV-1 infection either directly or indirectly.
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Affiliation(s)
- Kruthika Iyer
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Alapani Mitra
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Debashis Mitra
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India.
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Sharma AL, Wang H, Zhang Z, Millien G, Tyagi M, Hongpaisan J. HIV Promotes Neurocognitive Impairment by Damaging the Hippocampal Microvessels. Mol Neurobiol 2022; 59:4966-4986. [PMID: 35665894 PMCID: PMC10071835 DOI: 10.1007/s12035-022-02890-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/18/2022] [Indexed: 10/18/2022]
Abstract
Current evidence suggests that mild cerebrovascular changes could induce neurodegeneration and contribute to HIV-associated neurocognitive disease (HAND) in HIV patients. We investigated both the quantitative and qualitative impact of HIV infection on brain microvessels, especially on hippocampal microvessels, which are crucial for optimal O2 supply, and thus for maintaining memory and cognitive abilities. The results obtained using cultured human brain microvascular endothelial cells (HBMEC) were reproduced using a suitable mouse model and autopsied human HIV hippocampus. In HBMEC, we found significantly higher oxidative stress-dependent apoptotic cell loss following 5 h of treatment of GST-Tat (1 µg/ml) compared to GST (1 µg/ml) control. We noticed complete recovery of HBMEC cells after 24 h of GST-Tat treatment, due to temporal degradation or inactivation of GST-Tat. Interestingly, we found a sustained increase in mitochondrial oxidative DNA damage marker 8-OHdG, as well as an increase in hypoxia-inducible factor hypoxia-inducible factor-1α (HIF-1α). In our mouse studies, upon short-term injection of GST-Tat, we found the loss of small microvessels (mostly capillaries) and vascular endothelial growth factor (VEGF), but not large microvessels (arterioles and venules) in the hippocampus. In addition to capillary loss, in the post-mortem HIV-infected human hippocampus, we observed large microvessels with increased wall cells and perivascular tissue degeneration. Together, our data show a crucial role of Tat in inducing HIF-1α-dependent inhibition of mitochondrial transcriptional factor A (TFAM) and dilated perivascular space. Thus, our results further define the underlying molecular mechanism promoting mild cerebrovascular disease, neuropathy, and HAND pathogenesis in HIV patients.
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Affiliation(s)
- Adhikarimayum Lakhikumar Sharma
- Department of Medicine, Center for Translational Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Jefferson Alumni Hall, PA, 19107, Philadelphia, USA
| | - Huaixing Wang
- Department of Medicine, Center for Translational Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Jefferson Alumni Hall, PA, 19107, Philadelphia, USA
| | - Zongxiu Zhang
- Department of Medicine, Center for Translational Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Jefferson Alumni Hall, PA, 19107, Philadelphia, USA
| | - Guetchyn Millien
- Department of Medicine, Center for Translational Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Jefferson Alumni Hall, PA, 19107, Philadelphia, USA
| | - Mudit Tyagi
- Department of Medicine, Center for Translational Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Jefferson Alumni Hall, PA, 19107, Philadelphia, USA.
| | - Jarin Hongpaisan
- Department of Medicine, Center for Translational Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Jefferson Alumni Hall, PA, 19107, Philadelphia, USA.
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11
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Hokello J, Sharma AL, Tyagi P, Bhushan A, Tyagi M. Human Immunodeficiency Virus Type-1 (HIV-1) Transcriptional Regulation, Latency and Therapy in the Central Nervous System. Vaccines (Basel) 2021; 9:vaccines9111272. [PMID: 34835203 PMCID: PMC8618135 DOI: 10.3390/vaccines9111272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
The central nervous system (CNS) is highly compartmentalized and serves as a specific site of human immunodeficiency virus (HIV) infection. Therefore, an understanding of the cellular populations that are infected by HIV or that harbor latent HIV proviruses is imperative in the attempts to address cure strategies, taking into account that HIV infection and latency in the CNS may differ considerably from those in the periphery. HIV replication in the CNS is reported to persist despite prolonged combination antiretroviral therapy due to the inability of the current antiretroviral drugs to penetrate and cross the blood–brain barrier. Consequently, as a result of sustained HIV replication in the CNS even in the face of combination antiretroviral therapy, there is a high incidence of HIV-associated neurocognitive disorders (HAND). This article, therefore, provides a comprehensive review of HIV transcriptional regulation, latency, and therapy in the CNS.
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Affiliation(s)
- Joseph Hokello
- Department of Biology, Faculty of Science and Education, Busitema University, Tororo P.O. Box 236, Uganda;
| | | | - Priya Tyagi
- Cherry Hill East High School, 1750 Kresson Rd, Cherry Hill, NJ 08003, USA;
| | - Alok Bhushan
- Department of Pharmaceutical Sciences, Jefferson College of Pharmacy, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA;
- Correspondence:
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12
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Berdnikova DV. Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy. Chem Commun (Camb) 2021; 57:10819-10826. [PMID: 34585681 DOI: 10.1039/d1cc04241f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an emerging drug target that opens new perspectives in the treatment of viral and bacterial infections, cancer and a range of so far incurable genetic diseases. Among the various strategies towards the design and development of selective and efficient ligands for targeting and detection of therapeutically relevant RNA, photoswitchable RNA binders represent a very promising approach due to the possibility to control the ligand-RNA and protein-RNA interactions by light with high spatiotemporal resolution. However, the field of photoswitchable RNA binders still remains underexplored due to challenging design of lead structures that should combine high RNA binding selectivity with efficient photochemical performance. The aim of this highlight article is to describe the development of photoswitchable noncovalent RNA binders and to outline the current situation and perspectives of this emerging interdisciplinary field.
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Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
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13
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Mellors JW, Guo S, Naqvi A, Brandt LD, Su L, Sun Z, Joseph KW, Demirov D, Halvas EK, Butcher D, Scott B, Hamilton A, Heil M, Karim B, Wu X, Hughes SH. Insertional activation of STAT3 and LCK by HIV-1 proviruses in T cell lymphomas. SCIENCE ADVANCES 2021; 7:eabi8795. [PMID: 34644108 PMCID: PMC8514100 DOI: 10.1126/sciadv.abi8795] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Retroviruses cause cancers in animals by integrating in or near oncogenes. Although HIV-1 infection increases the risk of cancer, most of the risk is associated with immunodeficiency and coinfection by oncogenic virus (Epstein-Barr virus, Kaposi sarcoma herpesvirus, and human papillomavirus). HIV-1 proviruses integrated in some oncogenes cause clonal expansion of infected T cells in vivo; however, the infected cells are not transformed, and it is generally believed that HIV-1 does not cause cancer directly. We show that HIV-1 proviruses integrated in the first introns of signal transducer and activator of transcription 3 (STAT3) and lymphocyte-specific protein tyrosine kinase (LCK) can play an important role in the development of T cell lymphomas. The development of these cancers appears to be a multistep process involving additional nonviral mutations, which could help explain why T cell lymphomas are rare in persons with HIV-1 infection.
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Affiliation(s)
- John W. Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shuang Guo
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Asma Naqvi
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah D. Brandt
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ling Su
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Zhonghe Sun
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kevin W. Joseph
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dimiter Demirov
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donna Butcher
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Beth Scott
- Roche Molecular Diagnostics, Pleasanton, CA, USA
| | | | | | - Baktiar Karim
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, CCR, National Cancer Institute, Frederick, MD, USA
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14
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Mbonye U, Leskov K, Shukla M, Valadkhan S, Karn J. Biogenesis of P-TEFb in CD4+ T cells to reverse HIV latency is mediated by protein kinase C (PKC)-independent signaling pathways. PLoS Pathog 2021; 17:e1009581. [PMID: 34529720 PMCID: PMC8478230 DOI: 10.1371/journal.ppat.1009581] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/28/2021] [Accepted: 09/04/2021] [Indexed: 01/09/2023] Open
Abstract
The switch between HIV latency and productive transcription is regulated by an auto-feedback mechanism initiated by the viral trans-activator Tat, which functions to recruit the host transcription elongation factor P-TEFb to proviral HIV. A heterodimeric complex of CDK9 and one of three cyclin T subunits, P-TEFb is expressed at vanishingly low levels in resting memory CD4+ T cells and cellular mechanisms controlling its availability are central to regulation of the emergence of HIV from latency. Using a well-characterized primary T-cell model of HIV latency alongside healthy donor memory CD4+ T cells, we characterized specific T-cell receptor (TCR) signaling pathways that regulate the generation of transcriptionally active P-TEFb, defined as the coordinate expression of cyclin T1 and phospho-Ser175 CDK9. Protein kinase C (PKC) agonists, such as ingenol and prostratin, stimulated active P-TEFb expression and reactivated latent HIV with minimal cytotoxicity, even in the absence of intracellular calcium mobilization with an ionophore. Unexpectedly, inhibition-based experiments demonstrated that PKC agonists and TCR-mobilized diacylglycerol signal through MAP kinases ERK1/2 rather than through PKC to effect the reactivation of both P-TEFb and latent HIV. Single-cell and bulk RNA-seq analyses revealed that of the four known isoforms of the Ras guanine nucleotide exchange factor RasGRP, RasGRP1 is by far the predominantly expressed diacylglycerol-dependent isoform in CD4+ T cells. RasGRP1 should therefore mediate the activation of ERK1/2 via Ras-Raf signaling upon TCR co-stimulation or PKC agonist challenge. Combined inhibition of the PI3K-mTORC2-AKT-mTORC1 pathway and the ERK1/2 activator MEK prior to TCR co-stimulation abrogated active P-TEFb expression and substantially suppressed latent HIV reactivation. Therefore, contrary to prevailing models, the coordinate reactivation of P-TEFb and latent HIV in primary T cells following either TCR co-stimulation or PKC agonist challenge is independent of PKC but rather involves two complementary signaling arms of the TCR cascade, namely, RasGRP1-Ras-Raf-MEK-ERK1/2 and PI3K-mTORC2-AKT-mTORC1.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail: (UM); (JK)
| | - Konstantin Leskov
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Meenakshi Shukla
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, 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: (UM); (JK)
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15
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CDK9 keeps RNA polymerase II on track. Cell Mol Life Sci 2021; 78:5543-5567. [PMID: 34146121 PMCID: PMC8257543 DOI: 10.1007/s00018-021-03878-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9), the kinase component of positive transcription elongation factor b (P-TEFb), is essential for transcription of most protein-coding genes by RNA polymerase II (RNAPII). By releasing promoter-proximally paused RNAPII into gene bodies, CDK9 controls the entry of RNAPII into productive elongation and is, therefore, critical for efficient synthesis of full-length messenger (m)RNAs. In recent years, new players involved in P-TEFb-dependent processes have been identified and an important function of CDK9 in coordinating elongation with transcription initiation and termination has been unveiled. As the regulatory functions of CDK9 in gene expression continue to expand, a number of human pathologies, including cancers, have been associated with aberrant CDK9 activity, underscoring the need to properly regulate CDK9. Here, I provide an overview of CDK9 function and regulation, with an emphasis on CDK9 dysregulation in human diseases.
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16
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Guo T, Qiu Z, Shen M, Rong L. Dynamics of a new HIV model with the activation status of infected cells. J Math Biol 2021; 82:51. [PMID: 33860365 PMCID: PMC8049625 DOI: 10.1007/s00285-021-01604-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/28/2021] [Accepted: 04/03/2021] [Indexed: 11/06/2022]
Abstract
The activation status can dictate the fate of an HIV-infected CD4+ T cell. Infected cells with a low level of activation remain latent and do not produce virus, while cells with a higher level of activation are more productive and thus likely to transfer more virions to uninfected cells during cell-to-cell transmission. How the activation status of infected cells affects HIV dynamics under antiretroviral therapy remains unclear. We develop a new mathematical model that structures the population of infected cells continuously according to their activation status. The effectiveness of antiretroviral drugs in blocking cell-to-cell viral transmission decreases as the level of activation of infected cells increases because the more virions are transferred from infected to uninfected cells during cell-to-cell transmission, the less effectively the treatment is able to inhibit the transmission. The basic reproduction number \documentclass[12pt]{minimal}
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\begin{document}$$R_{0}$$\end{document}R0 of the model is shown to determine the existence and stability of the equilibria. Using the principal spectral theory and comparison principle, we show that the infection-free equilibrium is locally and globally asymptotically stable when \documentclass[12pt]{minimal}
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\begin{document}$$R_{0}$$\end{document}R0 is less than one. By constructing Lyapunov functional, we prove that the infected equilibrium is globally asymptotically stable when \documentclass[12pt]{minimal}
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\begin{document}$$R_{0}$$\end{document}R0 is greater than one. Numerical investigation shows that even when treatment can completely block cell-free virus infection, virus can still persist due to cell-to-cell transmission. The random switch between infected cells with different activation levels can also contribute to the replenishment of the latent reservoir, which is considered as a major barrier to viral eradication. This study provides a new modeling framework to study the observations, such as the low viral load persistence, extremely slow decay of latently infected cells and transient viral load measurements above the detection limit, in HIV-infected patients during suppressive antiretroviral therapy.
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Affiliation(s)
- Ting Guo
- School of Science, Nanjing University of Science and Technology, Nanjing, 210094, China.,Department of Mathematics, University of Florida, Gainesville, FL, 32611, USA
| | - Zhipeng Qiu
- Center for Basic Teaching and Experiment, Nanjing University of Science and Technology Jiangyin Campus, Jiangyin, 214443, China
| | - Mingwang Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Libin Rong
- Department of Mathematics, University of Florida, Gainesville, FL, 32611, USA.
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17
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Łukasik P, Załuski M, Gutowska I. Cyclin-Dependent Kinases (CDK) and Their Role in Diseases Development-Review. Int J Mol Sci 2021; 22:ijms22062935. [PMID: 33805800 PMCID: PMC7998717 DOI: 10.3390/ijms22062935] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) are involved in many crucial processes, such as cell cycle and transcription, as well as communication, metabolism, and apoptosis. The kinases are organized in a pathway to ensure that, during cell division, each cell accurately replicates its DNA, and ensure its segregation equally between the two daughter cells. Deregulation of any of the stages of the cell cycle or transcription leads to apoptosis but, if uncorrected, can result in a series of diseases, such as cancer, neurodegenerative diseases (Alzheimer’s or Parkinson’s disease), and stroke. This review presents the current state of knowledge about the characteristics of cyclin-dependent kinases as potential pharmacological targets.
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Affiliation(s)
- Paweł Łukasik
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Michał Załuski
- Department of Pharmaceutical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
| | - Izabela Gutowska
- Department of Medical Chemistry, Pomeranian Medical University in Szczecin, Powstancow Wlkp. 72 Av., 70-111 Szczecin, Poland;
- Correspondence:
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18
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Hokello J, Lakhikumar Sharma A, Tyagi M. AP-1 and NF-κB synergize to transcriptionally activate latent HIV upon T-cell receptor activation. FEBS Lett 2021; 595:577-594. [PMID: 33421101 DOI: 10.1002/1873-3468.14033] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/27/2022]
Abstract
Latent HIV-1 proviruses are capable of reactivating productive lytic infection, but the precise molecular mechanisms underlying emergence from latency are poorly understood. In this study, we determined the contribution of the transcription factors NF-κB, NFAT, and AP-1 in the reactivation of latent HIV following T-cell receptor (TCR) activation using Jurkat T-cell clones harboring single latent HIV proviruses. Our findings demonstrate that during reactivation from latency, NF-κB enhances HIV transcription while NFAT inhibits it by competing with NF-κB for overlapping binding sites on the HIV long terminal repeat (LTR). We have also demonstrated for the first time the molecular contribution of AP-1 in the reactivation of HIV from latency, whereby AP-1 synergizes with NF-κB to regulate HIV transcriptional elongation following TCR activation.
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Affiliation(s)
- Joseph Hokello
- Department of Basic Science, Faculty of Science and Technology, Kampala International University Western Campus, Bushenyi, Uganda
| | | | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, Philadelphia, PA, USA
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19
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Moranguinho I, Valente ST. Block-And-Lock: New Horizons for a Cure for HIV-1. Viruses 2020; 12:v12121443. [PMID: 33334019 PMCID: PMC7765451 DOI: 10.3390/v12121443] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
HIV-1/AIDS remains a global public health problem. The world health organization (WHO) reported at the end of 2019 that 38 million people were living with HIV-1 worldwide, of which only 67% were accessing antiretroviral therapy (ART). Despite great success in the clinical management of HIV-1 infection, ART does not eliminate the virus from the host genome. Instead, HIV-1 remains latent as a viral reservoir in any tissue containing resting memory CD4+ T cells. The elimination of these residual proviruses that can reseed full-blown infection upon treatment interruption remains the major barrier towards curing HIV-1. Novel approaches have recently been developed to excise or disrupt the virus from the host cells (e.g., gene editing with the CRISPR-Cas system) to permanently shut off transcription of the virus (block-and-lock and RNA interference strategies), or to reactivate the virus from cell reservoirs so that it can be eliminated by the immune system or cytopathic effects (shock-and-kill strategy). Here, we will review each of these approaches, with the major focus placed on the block-and-lock strategy.
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20
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Brillet K, Martinez-Zapien D, Bec G, Ennifar E, Dock-Bregeon AC, Lebars I. Different views of the dynamic landscape covered by the 5'-hairpin of the 7SK small nuclear RNA. RNA (NEW YORK, N.Y.) 2020; 26:1184-1197. [PMID: 32430362 PMCID: PMC7430674 DOI: 10.1261/rna.074955.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
The 7SK small nuclear RNA (7SKsnRNA) plays a key role in the regulation of RNA polymerase II by sequestrating and inhibiting the positive transcription elongation factor b (P-TEFb) in the 7SK ribonucleoprotein complex (7SKsnRNP), a process mediated by interaction with the protein HEXIM. P-TEFb is also an essential cellular factor recruited by the viral protein Tat to ensure the replication of the viral RNA in the infection cycle of the human immunodeficiency virus (HIV-1). Tat promotes the release of P-TEFb from the 7SKsnRNP and subsequent activation of transcription, by displacing HEXIM from the 5'-hairpin of the 7SKsnRNA. This hairpin (HP1), comprising the signature sequence of the 7SKsnRNA, has been the subject of three independent structural studies aimed at identifying the structural features that could drive the recognition by the two proteins, both depending on arginine-rich motifs (ARM). Interestingly, four distinct structures were determined. In an attempt to provide a comprehensive view of the structure-function relationship of this versatile RNA, we present here a structural analysis of the models, highlighting how HP1 is able to adopt distinct conformations with significant impact on the compactness of the molecule. Since these models are solved under different conditions by nuclear magnetic resonance (NMR) and crystallography, the impact of the buffer composition on the conformational variation was investigated by complementary biophysical approaches. Finally, using isothermal titration calorimetry, we determined the thermodynamic signatures of the Tat-ARM and HEXIM-ARM peptide interactions with the RNA, showing that they are associated with distinct binding mechanisms.
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Affiliation(s)
- Karl Brillet
- Université de Strasbourg, Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, F-67084 Strasbourg, France
| | - Denise Martinez-Zapien
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Guillaume Bec
- Université de Strasbourg, Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, F-67084 Strasbourg, France
| | - Eric Ennifar
- Université de Strasbourg, Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, F-67084 Strasbourg, France
| | - Anne-Catherine Dock-Bregeon
- Laboratory of Integrative Biology of Marine Models (LBI2M), Sorbonne University-CNRS UMR 8227, Station Biologique de Roscoff, 29680 Roscoff Cedex, France
| | - Isabelle Lebars
- Université de Strasbourg, Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, F-67084 Strasbourg, France
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21
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Szojka Z, Mótyán JA, Miczi M, Mahdi M, Tőzsér J. Y44A Mutation in the Acidic Domain of HIV-2 Tat Impairs Viral Reverse Transcription and LTR-Transactivation. Int J Mol Sci 2020; 21:ijms21165907. [PMID: 32824587 PMCID: PMC7460587 DOI: 10.3390/ijms21165907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/10/2020] [Accepted: 08/15/2020] [Indexed: 11/28/2022] Open
Abstract
HIV transactivator protein (Tat) plays a pivotal role in viral replication through modulation of cellular transcription factors and transactivation of viral genomic transcription. The effect of HIV-1 Tat on reverse transcription has long been described in the literature, however, that of HIV-2 is understudied. Sequence homology between Tat proteins of HIV-1 and 2 is estimated to be less than 30%, and the main difference lies within their N-terminal region. Here, we describe Y44A-inactivating mutation of HIV-2 Tat, studying its effect on capsid production, reverse transcription, and the efficiency of proviral transcription. Investigation of the mutation was performed using sequence- and structure-based in silico analysis and in vitro experiments. Our results indicate that the Y44A mutant HIV-2 Tat inhibited the activity and expression of RT (reverse transcriptase), in addition to diminishing Tat-dependent LTR (long terminal repeat) transactivation. These findings highlight the functional importance of the acidic domain of HIV-2 Tat in the regulation of reverse transcription and transactivation of the integrated provirions.
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Affiliation(s)
- Zsófia Szojka
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.S.); (J.A.M.); (M.M.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - János András Mótyán
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.S.); (J.A.M.); (M.M.)
| | - Márió Miczi
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.S.); (J.A.M.); (M.M.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Mohamed Mahdi
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.S.); (J.A.M.); (M.M.)
- Correspondence: (M.M.); (J.T.)
| | - József Tőzsér
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (Z.S.); (J.A.M.); (M.M.)
- Correspondence: (M.M.); (J.T.)
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22
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Hokello J, Sharma AL, Tyagi M. Efficient Non-Epigenetic Activation of HIV Latency through the T-Cell Receptor Signalosome. Viruses 2020; 12:v12080868. [PMID: 32784426 PMCID: PMC7472175 DOI: 10.3390/v12080868] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) can either undergo a lytic pathway to cause productive systemic infections or enter a latent state in which the integrated provirus remains transcriptionally silent for decades. The ability to latently infect T-cells enables HIV-1 to establish persistent infections in resting memory CD4+ T-lymphocytes which become reactivated following the disruption or cessation of intensive drug therapy. The maintenance of viral latency occurs through epigenetic and non-epigenetic mechanisms. Epigenetic mechanisms of HIV latency regulation involve the deacetylation and methylation of histone proteins within nucleosome 1 (nuc-1) at the viral long terminal repeats (LTR) such that the inhibition of histone deacetyltransferase and histone lysine methyltransferase activities, respectively, reactivates HIV from latency. Non-epigenetic mechanisms involve the nuclear restriction of critical cellular transcription factors such as nuclear factor-kappa beta (NF-κB) or nuclear factor of activated T-cells (NFAT) which activate transcription from the viral LTR, limiting the nuclear levels of the viral transcription transactivator protein Tat and its cellular co-factor positive transcription elongation factor b (P-TEFb), which together regulate HIV transcriptional elongation. In this article, we review how T-cell receptor (TCR) activation efficiently induces NF-κB, NFAT, and activator protein 1 (AP-1) transcription factors through multiple signal pathways and how these factors efficiently regulate HIV LTR transcription through the non-epigenetic mechanism. We further discuss how elongation factor P-TEFb, induced through an extracellular signal-regulated kinase (ERK)-dependent mechanism, regulates HIV transcriptional elongation before new Tat is synthesized and the role of AP-1 in the modulation of HIV transcriptional elongation through functional synergy with NF-κB. Furthermore, we discuss how TCR signaling induces critical post-translational modifications of the cyclin-dependent kinase 9 (CDK9) subunit of P-TEFb which enhances interactions between P-TEFb and the viral Tat protein and the resultant enhancement of HIV transcriptional elongation.
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Affiliation(s)
- Joseph Hokello
- Department of Basic Science, Faculty of Science and Technology, Kampala International University-Western Campus, P.O Box 71, Bushenyi, Uganda;
| | | | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA;
- Correspondence:
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23
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Mori L, Valente ST. Key Players in HIV-1 Transcriptional Regulation: Targets for a Functional Cure. Viruses 2020; 12:E529. [PMID: 32403278 PMCID: PMC7291152 DOI: 10.3390/v12050529] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022] Open
Abstract
HIV-1 establishes a life-long infection when proviral DNA integrates into the host genome. The provirus can then either actively transcribe RNA or enter a latent state, without viral production. The switch between these two states is governed in great part by the viral protein, Tat, which promotes RNA transcript elongation. Latency is also influenced by the availability of host transcription factors, integration site, and the surrounding chromatin environment. The latent reservoir is established in the first few days of infection and serves as the source of viral rebound upon treatment interruption. Despite effective suppression of HIV-1 replication by antiretroviral therapy (ART), to below the detection limit, ART is ineffective at reducing the latent reservoir size. Elimination of this reservoir has become a major goal of the HIV-1 cure field. However, aside from the ideal total HIV-1 eradication from the host genome, an HIV-1 remission or functional cure is probably more realistic. The "block-and-lock" approach aims at the transcriptional silencing of the viral reservoir, to render suppressed HIV-1 promoters extremely difficult to reactivate from latency. There are unfortunately no clinically available HIV-1 specific transcriptional inhibitors. Understanding the mechanisms that regulate latency is expected to provide novel targets to be explored in cure approaches.
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Affiliation(s)
| | - Susana T. Valente
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA;
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P-TEFb as A Promising Therapeutic Target. Molecules 2020; 25:molecules25040838. [PMID: 32075058 PMCID: PMC7070488 DOI: 10.3390/molecules25040838] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
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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25
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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] [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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Berdnikova DV. Visible-range hemi-indigo photoswitch: ON-OFF fluorescent binder for HIV-1 RNA. Chem Commun (Camb) 2019; 55:8402-8405. [PMID: 31257385 DOI: 10.1039/c9cc04270a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A proof-of-principle for the application of hemi-indigo derivatives as RNA binders with photocontrollable fluorescence is presented. The photoswitch binds to the human immunodeficiency virus type 1 (HIV-1) RNA with a significant light-up effect. The fluorescence of the RNA-bound ligand can be reversibly switched ON and OFF by light without destroying the ligand-RNA associates.
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Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
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Inhibitors of Signaling Pathways That Block Reversal of HIV-1 Latency. Antimicrob Agents Chemother 2019; 63:AAC.01744-18. [PMID: 30455231 DOI: 10.1128/aac.01744-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/14/2018] [Indexed: 01/01/2023] Open
Abstract
Signaling pathways play a key role in HIV-1 latency. In this study, we used the 24ST1NLESG cell line of HIV-1 latency to screen a library of structurally diverse, medicinally active, cell permeable kinase inhibitors, which target a wide range of signaling pathways, to identify inhibitors of HIV-1 latency reversal. The screen was carried out in the absence or presence of three mechanistically distinct latency-reversing agents (LRAs), namely, prostratin, panobinostat, and JQ-1. We identified inhibitors that only blocked the activity of a specific LRA, as well as inhibitors that blocked the activity of all LRAs. For example, we identified 12 inhibitors targeted toward protein kinase C or downstream kinases that blocked the activity of prostratin. We also identified 12 kinase inhibitors that blocked the reversal of HIV-1 latency irrespective of the LRA used in the screen. Of these, danusertib, an Aurora kinase inhibitor, and PF-3758309, a PAK4 inhibitor, were the most potent. The 50% inhibitory concentrations in the 24ST1NLESG cells ranged from 40 to 147 nM for danusertib (selectivity indices, >150) and from 0.1 to 1 nM for PF-3758309 (selectivity indices, >3,300). Both danusertib and PF-3758309 inhibited latency reversal in CD4+ T cells isolated from HIV-1-infected donors. Collectively, our study describes a chemical approach that can be applied to elucidate the role of signaling pathways involved in LRA activity or the maintenance of HIV-1 latency and also identifies inhibitors of latent HIV-1 reactivation that could be used with antiretroviral therapy to reduce residual viremia.
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Therapeutic Modulation of Virus-Induced Oxidative Stress via the Nrf2-Dependent Antioxidative Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:6208067. [PMID: 30515256 PMCID: PMC6234444 DOI: 10.1155/2018/6208067] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 09/24/2018] [Indexed: 12/17/2022]
Abstract
Virus-induced oxidative stress plays a critical role in the viral life cycle as well as the pathogenesis of viral diseases. In response to reactive oxygen species (ROS) generation by a virus, a host cell activates an antioxidative defense system for its own protection. Particularly, a nuclear factor erythroid 2p45-related factor 2 (Nrf2) pathway works in a front-line for cytoprotection and detoxification. Recently, a series of studies suggested that a group of clinically relevant viruses have the capacity for positive and negative regulations of the Nrf2 pathway. This virus-induced modulation of the host antioxidative response turned out to be a crucial determinant for the progression of several viral diseases. In this review, virus-specific examples of positive and negative modulations of the Nrf2 pathway will be summarized first. Then a number of successful genetic and pharmacological manipulations of the Nrf2 pathway for suppression of the viral replication and the pathogenesis-associated oxidative damage will be discussed later. Understanding of the interplay between virus-induced oxidative stress and antioxidative host response will aid in the discovery of potential antiviral supplements for better management of viral diseases.
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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] [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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Mbondji-wonje C, Dong M, Wang X, Zhao J, Ragupathy V, Sanchez AM, Denny TN, Hewlett I. Distinctive variation in the U3R region of the 5' Long Terminal Repeat from diverse HIV-1 strains. PLoS One 2018; 13:e0195661. [PMID: 29664930 PMCID: PMC5903597 DOI: 10.1371/journal.pone.0195661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Functional mapping of the 5’LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by extensive variability, here we aimed to describe mutations in the U3R from various HIV-1 clades and CRFs in order to highlight strain specific differences that may impact the biological properties of diverse HIV-1 strains. To achieve our purpose, the U3R sequence of plasma derived virus belonging to different clades (A1, B, C, D, F2) and recombinants (CRF02_AG, CRF01_AE and CRF22_01A1) was obtained using Illumina technology. Overall, the R region was very well conserved among and across different strains, while in the U3 region the average inter-strains nucleotide dissimilarity was up to 25%. The TAR hairpin displayed a strain-distinctive cluster of mutations affecting the bulge and the loop, but mostly the stem. Like in previous studies we found a TATAA motif in U3 promoter region from the majority of HIV-1 strains and a TAAAA motif in CRF01_AE; but also in LTRs from CRF22_01A1 isolates. Although LTRs from CRF22_01A1 specimens were assigned CRF01_AE, they contained two NF-kB sites instead of the single TFBS described in CRF01_AE. Also, as previously describe in clade C isolates, we found no C/EBP binding site directly upstream of the enhancer region in CRF22_01A1 specimens. In our study, one-third of CRF02_AG LTRs displayed three NF-kB sites which have been mainly described in clade C isolates. Overall, the number, location and binding patterns of potential regulatory elements found along the U3R might be specific to some HIV-1 strains such as clade F2, CRF02_AG, CRF01_AE and CRF22_01A1. These features may be worth consideration as they may be involved in distinctive regulation of HIV-1 transcription and replication by different and diverse infecting strains.
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Affiliation(s)
- Christelle Mbondji-wonje
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- Department of Molecular Biology, Faculty of Medicine, Pharmacy and Biomedical sciences, University of Douala, Douala, Cameroon
- * E-mail: (CM); (IH)
| | - Ming Dong
- U.S. Military HIV Research Program, Silver Spring, Maryland United States of America
| | - Xue Wang
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Jiangqin Zhao
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Viswanath Ragupathy
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Ana M. Sanchez
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Thomas N. Denny
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States
| | - Indira Hewlett
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail: (CM); (IH)
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31
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Fitting S, McLaurin KA, Booze RM, Mactutus CF. Dose-dependent neurocognitive deficits following postnatal day 10 HIV-1 viral protein exposure: Relationship to hippocampal anatomy parameters. Int J Dev Neurosci 2018; 65:66-82. [PMID: 29111178 PMCID: PMC5889695 DOI: 10.1016/j.ijdevneu.2017.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 11/25/2022] Open
Abstract
Despite the availability of antiretroviral prophylactic treatment, pediatric human immunodeficiency virus type 1 (HIV-1) continues to be a significant risk factor in the post-cART era. The time of infection (i.e., during pregnancy, delivery or breastfeeding) may play a role in the development of neurocognitive deficits in pediatric HIV-1. HIV-1 viral protein exposure on postnatal day (P)1, preceding the postnatal brain growth spurt in rats, had deleterious effects on neurocognitive development and anatomical parameters of the hippocampus (Fitting et al., 2008a,b). In the present study, rats were stereotaxically injected with HIV-1 viral proteins, including Tat1-86 and gp120, on P10 to further examine the role of timing on neurocognitive development and anatomical parameters of the hippocampus (Fitting et al., 2010). The dose-dependent virotoxin effects observed across development following P10 Tat1-86 exposure were specific to spatial learning and absent from prepulse inhibition and locomotor activity. A relationship between alterations in spatial learning and/or memory and hippocampal anatomical parameters was noted. Specifically, the estimated number of neurons and astrocytes in the hilus of the dentate gyrus explained 70% of the variance of search behavior in Morris water maze acquisition training for adolescents and 65% of the variance for adults; a brain-behavior relationship consistent with observations following P1 viral protein exposure. Collectively, late viral protein exposure (P10) results in selective alterations in neurocognitive development without modifying measures of somatic growth, preattentive processing, or locomotor activity, as characterized by early viral protein exposure (P1). Thus, timing may be a critical factor in disease progression, with children infected with HIV earlier in life being more vulnerable to CNS disease.
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Affiliation(s)
- Sylvia Fitting
- University of South Carolina, Behavioral Neuroscience Program, Department of Psychology, Columbia, SC 29208, USA; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kristen A McLaurin
- University of South Carolina, Behavioral Neuroscience Program, Department of Psychology, Columbia, SC 29208, USA
| | - Rosemarie M Booze
- University of South Carolina, Behavioral Neuroscience Program, Department of Psychology, Columbia, SC 29208, USA
| | - Charles F Mactutus
- University of South Carolina, Behavioral Neuroscience Program, Department of Psychology, Columbia, SC 29208, USA.
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32
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Yang Y, Wang S. RNA Characterization by Solid-State NMR Spectroscopy. Chemistry 2018; 24:8698-8707. [DOI: 10.1002/chem.201705583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Yufei Yang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
| | - Shenlin Wang
- College of Chemistry and Molecular Engineering and Beijing NMR Center; Peking University; No.5 Yiheyuan Road, Haidian District Beijing 100871 P. R. China
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33
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Kim JM, Choi HS, Seong BL. The folding competence of HIV-1 Tat mediated by interaction with TAR RNA. RNA Biol 2017; 14:926-937. [PMID: 28418268 DOI: 10.1080/15476286.2017.1311455] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The trans-activator Tat protein of HIV-1 belongs to the large family of intrinsically disordered proteins (IDPs), and is known to recruit various host proteins for the transactivation of viral RNA synthesis. Tat protein interacts with the transactivator response RNA (TAR RNA), exhibiting RNA chaperone activities for structural rearrangement of interacting RNAs. Here, considering that Tat-TAR RNA interaction is mutually cooperative, we examined the potential role of TAR RNA as Chaperna - RNA that provides chaperone function to proteins - for the folding of HIV-1 Tat. Using EGFP fusion as an indirect indicator for folding status, we monitored Tat-EGFP folding in HeLa cells via time-lapse fluorescence microscopy. The live cell imaging showed that the rate and the extent of folding of Tat-EGFP were stimulated by TAR RNA. The purified Tat-EGFP was denatured and the fluorescence was monitored in vitro under renaturation condition. The fluorescence was significantly increased by TAR RNA, and the mutations in TAR RNA that affected the interaction with Tat protein failed to promote Tat refolding. The results suggest that TAR RNA stabilizes Tat as unfolded, but prevents it from misfolding, and maintaining its folding competence for interaction with multiple host factors toward its transactivation. The Chaperna function of virally encoded RNA in establishing proteome link at the viral-host interface provides new insights to as yet largely unexplored RNA mediated protein folding in normal and dysregulated cellular metabolism.
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Affiliation(s)
- Jung Min Kim
- a Department of Biotechnology , College of Life Science and Biotechnology, Yonsei University , Seoul , South Korea.,b Vaccine Translational Research Center , Yonsei University , Seoul , South Korea
| | - Hee Sun Choi
- c Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Baik Lin Seong
- a Department of Biotechnology , College of Life Science and Biotechnology, Yonsei University , Seoul , South Korea.,b Vaccine Translational Research Center , Yonsei University , Seoul , South Korea
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34
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Qi L, Zhang J, He T, Huo Y, Zhang ZQ. Probing interaction of a fluorescent ligand with HIV TAR RNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:93-98. [PMID: 27611591 DOI: 10.1016/j.saa.2016.08.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/15/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.
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MESH Headings
- Aminacrine/analogs & derivatives
- Aminacrine/chemistry
- Aminacrine/metabolism
- Aminacrine/pharmacology
- Binding, Competitive
- Circular Dichroism
- Drug Evaluation, Preclinical/methods
- Fluorescent Dyes/chemistry
- Fluorescent Dyes/metabolism
- Framycetin/chemistry
- Framycetin/metabolism
- HIV Long Terminal Repeat
- Models, Molecular
- Molecular Docking Simulation
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Spectrometry, Fluorescence
- Spectrometry, Mass, Electrospray Ionization
- tat Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors
- tat Gene Products, Human Immunodeficiency Virus/chemistry
- tat Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Liang Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), Ministry of Education, Xi'an 710062, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Tian He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huo
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), Ministry of Education, Xi'an 710062, China.
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35
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Chen HS, De Leo A, Wang Z, Kerekovic A, Hills R, Lieberman PM. BET-Inhibitors Disrupt Rad21-Dependent Conformational Control of KSHV Latency. PLoS Pathog 2017; 13:e1006100. [PMID: 28107481 PMCID: PMC5287475 DOI: 10.1371/journal.ppat.1006100] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 02/01/2017] [Accepted: 11/29/2016] [Indexed: 12/11/2022] Open
Abstract
Kaposi’s Sarcoma-associated Herpesvirus (KSHV) establishes stable latent infection in B-lymphocytes and pleural effusion lymphomas (PELs). During latency, the viral genome persists as an epigenetically constrained episome with restricted gene expression programs. To identify epigenetic regulators of KSHV latency, we screened a focused small molecule library containing known inhibitors of epigenetic factors. We identified JQ1, a Bromodomain and Extended Terminal (BET) protein inhibitor, as a potent activator of KSHV lytic reactivation from B-cells carrying episomal KSHV. We validated that JQ1 and other BET inhibitors efficiently stimulated reactivation of KSHV from latently infected PEL cells. We found that BET proteins BRD2 and BRD4 localize to several regions of the viral genome, including the LANA binding sites within the terminal repeats (TR), as well as at CTCF-cohesin sites in the latent and lytic control regions. JQ1 did not disrupt the interaction of BRD4 or BRD2 with LANA, but did reduce the binding of LANA with KSHV TR. We have previously demonstrated a cohesin-dependent DNA-loop interaction between the latent and lytic control regions that restrict expression of ORF50/RTA and ORF45 immediate early gene transcripts. JQ1 reduced binding of cohesin subunit Rad21 with the CTCF binding sites in the latency and lytic control regions. JQ1 also reduced DNA-loop interaction between latent and lytic control regions. These findings implicate BET proteins BRD2 and BRD4 in the maintenance of KSHV chromatin architecture during latency and reveal BET inhibitors as potent activators of KSHV reactivation from latency. KSHV is an oncogenic human herpesvirus implicated as the causative agent of KS and cofactor in pleural effusion lymphomas (PELs). The latent virus persists in PELs as an epigenetically regulated episome. We found that small molecule inhibitors of BET family have potent activity in triggering the lytic switch during latent infection in PELs. The BET family inhibitor JQ1 disrupted the latent virus from maintaining a closed DNA loop conformation. These findings have implications for treatment of KSHV-associated malignancies with epigenetic modulators of the BET inhibitor family.
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MESH Headings
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Azepines/pharmacology
- B-Lymphocytes/virology
- Binding Sites/drug effects
- Cell Cycle Proteins
- Cell Line, Tumor
- DNA-Binding Proteins
- Gene Expression Regulation, Viral
- HEK293 Cells
- Herpesvirus 8, Human/drug effects
- Herpesvirus 8, Human/genetics
- Herpesvirus 8, Human/physiology
- Humans
- Immediate-Early Proteins/biosynthesis
- Immediate-Early Proteins/genetics
- Nuclear Proteins/antagonists & inhibitors
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Phosphoproteins/metabolism
- Pleural Effusion, Malignant/virology
- Protein Binding/drug effects
- Protein Serine-Threonine Kinases/antagonists & inhibitors
- Protein Serine-Threonine Kinases/metabolism
- RNA Interference
- RNA, Small Interfering
- Sarcoma, Kaposi/virology
- Trans-Activators/biosynthesis
- Trans-Activators/genetics
- Transcription Factors/antagonists & inhibitors
- Transcription Factors/metabolism
- Triazoles/pharmacology
- Virus Activation/drug effects
- Virus Latency/drug effects
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Affiliation(s)
- Horng-Shen Chen
- The Wistar Institute, Philadelphia, PA, United States of America
| | | | - Zhuo Wang
- The Wistar Institute, Philadelphia, PA, United States of America
| | - Andrew Kerekovic
- The Wistar Institute, Philadelphia, PA, United States of America
| | - Robert Hills
- The Wistar Institute, Philadelphia, PA, United States of America
| | - Paul M. Lieberman
- The Wistar Institute, Philadelphia, PA, United States of America
- * E-mail:
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36
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Assays for precise quantification of total (including short) and elongated HIV-1 transcripts. J Virol Methods 2016; 242:1-8. [PMID: 28034670 DOI: 10.1016/j.jviromet.2016.12.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/21/2016] [Accepted: 12/23/2016] [Indexed: 11/24/2022]
Abstract
Despite intensive study, it is unclear which mechanisms are responsible for latent HIV infection in vivo. One potential mechanism is inhibition of HIV transcriptional elongation, which results in short abortive transcripts containing the trans-activation response (TAR) region. Because the relative levels of total (including short) and processive transcripts provide measures of HIV transcriptional initiation and elongation, there is a compelling need for techniques that accurately measure both. Nonetheless, prior assays for total transcripts have been semi-quantitative and have seen limited application to patient samples. This manuscript reports the validation of quantitative reverse transcription (RT) droplet digital PCR assays for measurement of total (TAR) and processive (R-U5/gag) HIV transcripts. Traditional RT priming strategies can efficiently detect the TAR region on long HIV transcripts but detect <4% of true short transcripts. The TAR assay presented here utilizes an initial polyadenylation step, which provides an accessible RT priming site and detects short and long transcripts with approximately equal efficiency (70%). By applying these assays to blood samples from 8 ART-treated HIV+ individuals, total HIV transcripts were detected at levels >10-fold higher than elongated transcripts, implying a substantial block to transcriptional elongation in vivo. This approach may be applied to other difficult-to-prime RNA targets.
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Bourbigot S, Dock-Bregeon AC, Eberling P, Coutant J, Kieffer B, Lebars I. Solution structure of the 5'-terminal hairpin of the 7SK small nuclear RNA. RNA (NEW YORK, N.Y.) 2016; 22:1844-1858. [PMID: 27852926 PMCID: PMC5113205 DOI: 10.1261/rna.056523.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 09/10/2016] [Indexed: 05/10/2023]
Abstract
The small nuclear 7SK RNA regulates RNA polymerase II (RNA Pol II) transcription, by sequestering and inhibiting the positive transcription elongation factor b (P-TEFb). P-TEFb is stored in the 7SK ribonucleoprotein (RNP) that contains the three nuclear proteins Hexim1, LaRP7, and MePCE. P-TEFb interacts with the protein Hexim1 and the 7SK RNA. Once P-TEFb is released from the 7SK RNP, it activates transcription by phosphorylating the C-terminal domain of RNA Pol II. P-TEFb also plays a crucial role in the replication of the human immunodeficiency virus HIV-1, through its recruitment by the viral transactivator Tat. Previous work demonstrated that the protein Tat promotes the release of P-TEFb from the 7SK RNP through direct binding to the 7SK RNA. Hexim1 and Tat proteins both comprise conserved and similar arginine-rich motifs that were identified to bind the 7SK RNA at a repeated GAUC site located at the top of the 5'-terminal hairpin (HPI). Here, we report the solution structure of this region as determined by nuclear magnetic resonance, to identify HPI structural features recognized by Hexim1 and Tat. The HPI solution structure displays an elongated shape featuring four helical segments interrupted by one internal loop and three bulges with distinct folds. In particular, the repeated GAUC motif adopts a pre-organized geometry. Our results suggest that the binding of Hexim1 and Tat to the 7SK RNA could originate from a conformational selection of this motif, highlighting how RNA local structure could lead to an adaptive recognition of their partners.
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Affiliation(s)
- Sarah Bourbigot
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Anne-Catherine Dock-Bregeon
- Department of Functional Genomics, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 75005 Paris, France
| | - Pascal Eberling
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Jérôme Coutant
- Bruker BioSpin SAS, BP 10002, 67166 Wissembourg Cedex, France
| | - Bruno Kieffer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
| | - Isabelle Lebars
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch Cedex, France
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Bivalkar-Mehla S, Mehla R, Chauhan A. Chimeric peptide-mediated siRNA transduction to inhibit HIV-1 infection. J Drug Target 2016; 25:307-319. [PMID: 27800697 DOI: 10.1080/1061186x.2016.1245311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Persistent human immunodeficiency virus 1 (HIV-1) infection provokes immune activation and depletes CD4+ lymphocytes, leading to acquired immunodeficiency syndrome. Uninterrupted administration of combination antiretroviral therapy (cART) in HIV-infected patients suppresses viral replication to below the detectable level and partially restores the immune system. However, cART-unresponsive residual HIV-1 infection and elusive transcriptionally silent but reactivatable viral reservoirs maintain a permanent viral DNA blue print. The virus rebounds within a few weeks after interruption of suppressive therapy. Adjunct gene therapy to control viral replication by ribonucleic acid interference (RNAi) is a post-transcriptional gene silencing strategy that could suppress residual HIV-1 burden and overcome viral resistance. Small interfering ribonucleic acids (siRNAs) are efficient transcriptional inhibitors, but need delivery systems to reach inside target cells. We investigated the potential of chimeric peptide (FP-PTD) to deliver specific siRNAs to HIV-1-susceptible and permissive cells. Chimeric FP-PTD peptide was designed with an RNA binding domain (PTD) to bind siRNA and a cell fusion peptide domain (FP) to enter cells. FP-PTD-siRNA complex entered and inhibited HIV-1 replication in susceptible cells, and could be a candidate for in vivo testing.
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Affiliation(s)
- Shalmali Bivalkar-Mehla
- a Department of Pathology, Microbiology and Immunology , University of South Carolina School of Medicine , Columbia , SC , USA
| | - Rajeev Mehla
- a Department of Pathology, Microbiology and Immunology , University of South Carolina School of Medicine , Columbia , SC , USA
| | - Ashok Chauhan
- a Department of Pathology, Microbiology and Immunology , University of South Carolina School of Medicine , Columbia , SC , USA
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Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M. Structure of a low-population binding intermediate in protein-RNA recognition. Proc Natl Acad Sci U S A 2016; 113:7171-6. [PMID: 27286828 PMCID: PMC4932932 DOI: 10.1073/pnas.1521349113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michael F Bardaro
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
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40
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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] [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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41
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Zhao X, Qian L, Zhou D, Qi D, Liu C, Kong X. Stability of HIV-1 subtype B and C Tat is associated with variation in the carboxyl-terminal region. Virol Sin 2016; 31:199-206. [PMID: 27007880 DOI: 10.1007/s12250-016-3681-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/01/2016] [Indexed: 12/14/2022] Open
Abstract
The multifunctional trans-activator Tat is an essential regulatory protein for HIV-1 replication and is characterized by high sequence diversity. Numerous experimental studies have examined Tat in HIV-1 subtype B, but research on subtype C Tat is lacking, despite the high prevalence of infections caused by subtype C worldwide. We hypothesized that amino acid differences contribute to functional differences among Tat proteins. In the present study, we found that subtype B NL4-3 Tat and subtype C isolate HIV1084i Tat exhibited differences in stability by overexpressing the fusion protein Tat-Flag. In addition, 1084i Tat can activate LTR and NF-κB more efficiently than NL4-3 Tat. In analyses of the activities of the truncated forms of Tat, we found that the carboxyl-terminal region of Tat regulates its stability and transactivity. According to our results, we speculated that the differences in stability between B-Tat and C-Tat result in differences in transactivation ability.
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Affiliation(s)
- Xuechao Zhao
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Lingyu Qian
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Deyu Zhou
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Di Qi
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Chang Liu
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Xiaohong Kong
- Laboratory of Medical Molecular Virology, School of Medicine, Nankai University, Tianjin, 300071, China.
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42
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Berman JW, Carvallo L, Buckner CM, Luers A, Prevedel L, Bennett MV, Eugenin EA. HIV-tat alters Connexin43 expression and trafficking in human astrocytes: role in NeuroAIDS. J Neuroinflammation 2016; 13:54. [PMID: 26934876 PMCID: PMC4774036 DOI: 10.1186/s12974-016-0510-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/14/2016] [Indexed: 11/16/2022] Open
Abstract
Background HIV-associated neurocognitive disorders (HAND) are a major complication in at least half of the infected population despite effective antiretroviral treatment and immune reconstitution. HIV-associated CNS damage is not correlated with active viral replication but instead is associated with mechanisms that regulate inflammation and neuronal compromise. Our data indicate that one of these mechanisms is mediated by gap junction channels and/or hemichannels. Normally, gap junction channels shutdown under inflammatory conditions, including viral diseases. However, HIV infection upregulates Connexin43 (Cx43) expression and maintains gap junctional communication by unknown mechanism(s). Methods Human primary astrocytes were exposed to several HIV proteins as well as to HIV, and expression and function of Connexin43- and Connexin30-containing channels were determined by western blot, immunofluorescence, microinjection of a fluorescent tracer and chromatin immunoprecipitation (ChIP). Results Here, we demonstrate that HIV infection increases Cx43 expression in vivo. HIV-tat, the transactivator of the virus, and no other HIV proteins tested, increases Cx43 expression and maintains functional gap junctional communication in human astrocytes. Cx43 upregulation is mediated by binding of the HIV-tat protein to the Cx43 promoter, but not to the Cx30 promoter, resulting in increased Cx43 messenger RNA (mRNA) and protein as well as gap junctional communication. Conclusions We propose that HIV-tat contributes to the spread of intracellular toxic signals generated in a few HIV-infected cells into surrounding uninfected cells by upregulating gap junctional communication. In the current antiretroviral era, where HIV replication is often completely suppressed, viral factors such as HIV-tat are still produced and released from infected cells. Thus, blocking the effects of HIV-tat could result in new strategies to reduce the damaging consequences of HIV infection of the CNS.
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Affiliation(s)
- Joan W Berman
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Loreto Carvallo
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Clarisa M Buckner
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Current address: Laboratory of Immunoregulation, NIAID, Bethesda, MD, USA.
| | - Aimée Luers
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Lisa Prevedel
- Public Health Research Institute (PHRI), 225 Warren Street, Newark, NJ, 07103, USA.,Department of Microbiology and Molecular Genetics, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
| | - Michael V Bennett
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Eliseo A Eugenin
- Public Health Research Institute (PHRI), 225 Warren Street, Newark, NJ, 07103, USA. .,Department of Microbiology and Molecular Genetics, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA.
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43
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Tyagi M, Weber J, Bukrinsky M, Simon GL. The effects of cocaine on HIV transcription. J Neurovirol 2015; 22:261-74. [PMID: 26572787 DOI: 10.1007/s13365-015-0398-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 10/01/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
Abstract
Illicit drug users are a high-risk population for infection with the human immunodeficiency virus (HIV). A strong correlation exists between prohibited drug use and an increased rate of HIV transmission. Cocaine stands out as one of the most frequently abused illicit drugs, and its use is correlated with HIV infection and disease progression. The central nervous system (CNS) is a common target for both drugs of abuse and HIV, and cocaine intake further accelerates neuronal injury in HIV patients. Although the high incidence of HIV infection in illicit drug abusers is primarily due to high-risk activities such as needle sharing and unprotected sex, several studies have demonstrated that cocaine enhances the rate of HIV gene expression and replication by activating various signal transduction pathways and downstream transcription factors. In order to generate mature HIV genomic transcript, HIV gene expression has to pass through both the initiation and elongation phases of transcription, which requires discrete transcription factors. In this review, we will provide a detailed analysis of the molecular mechanisms that regulate HIV transcription and discuss how cocaine modulates those mechanisms to upregulate HIV transcription and eventually HIV replication.
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Affiliation(s)
- Mudit Tyagi
- Division of Infectious Diseases, Department of Medicine, The George Washington University, 2300 Eye Street, N.W., Washington, DC, 20037, USA. .,Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, 20037, USA.
| | - Jaime Weber
- Division of Infectious Diseases, Department of Medicine, The George Washington University, 2300 Eye Street, N.W., Washington, DC, 20037, USA
| | - Michael Bukrinsky
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, 20037, USA
| | - Gary L Simon
- Division of Infectious Diseases, Department of Medicine, The George Washington University, 2300 Eye Street, N.W., Washington, DC, 20037, USA
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44
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Pontrello JK. Bringing research into a first semester organic chemistry laboratory with the multistep synthesis of carbohydrate-based HIV inhibitor mimics. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 43:417-427. [PMID: 26449849 DOI: 10.1002/bmb.20915] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/29/2015] [Accepted: 08/12/2015] [Indexed: 06/05/2023]
Abstract
Benefits of incorporating research experiences into laboratory courses have been well documented, yet examples of research projects designed for the first semester introductory organic chemistry lab course are extremely rare. To address this deficiency, a Carbohydrate-Based human immunodeficiency virus (HIV) Inhibitor project consisting of a synthetic scheme of four reactions was developed for and implemented in the first semester organic lab. Students carried out the synthetic reactions during the last 6 of 10 total labs in the course, generating carbohydrate-based dimeric target molecules modeled after published dimers with application in HIV therapy. The project was designed to provide a research experience through use of literature procedures for reactions performed, exploration of variation in linker length in the target structure, and synthesis of compounds not previously reported in the scientific literature. Project assessment revealed strong student support, indicating enhanced engagement and interest in the course as a direct result of the use of scientific literature and the applications of the synthesized carbohydrate-based molecules. Regardless of discussed challenges in designing a research project for the first semester lab course, the finding from data analysis that a project implemented in the first semester lab had significantly greater student impact than a second semester project should provide motivation for development of additional research projects for a first semester organic course.
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Affiliation(s)
- Jason K Pontrello
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, 02454
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45
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Qi L, Huo Y, Wang H, Zhang J, Dang FQ, Zhang ZQ. Fluorescent DNA-Protected Silver Nanoclusters for Ligand-HIV RNA Interaction Assay. Anal Chem 2015; 87:11078-83. [PMID: 26447651 DOI: 10.1021/acs.analchem.5b03166] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Studying ligand-biomacromolecule interactions provides opportunities for creating new compounds that can efficiently regulate specific biological processes. Ribonucleic acid (RNA) molecules have become attractive drug targets since the discovery of their roles in modulating gene expression, while only a limited number of studies have investigated interactions between ligands and functional RNA molecules, especially those based on nanotechnology. DNA-protected silver nanoclusters (AgNCs) were used to investigate ligand-RNA interactions for the first time in this study. The anthracycline anticancer drug mitoxantrone (MTX) was found to quench the fluorescence of AgNCs. After adding human immunodeficiency virus trans-activation responsive region (TAR) RNA or Rev-response element (RRE) RNA to AgNCs-MTX mixtures, the fluorescence of the AgNCs recovered due to interactions between MTX with RNAs. The binding constants and number of binding sites of MTX to TAR and RRE RNA were determined through theoretical calculations. MTX-RNA interactions were further confirmed in fluorescence polarization and mass spectrometry experiments. The mechanism of MTX-based fluorescence quenching of the AgNCs was also explored. This study provides a new strategy for ligand-RNA binding interaction assay.
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Affiliation(s)
- Liang Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Yuan Huo
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Huan Wang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Fu-Quan Dang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, and ‡Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry and Ministry of Education, Shaanxi Normal University , Xi'an 710062, China
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Bose D, Gagnon J, Chebloune Y. Comparative Analysis of Tat-Dependent and Tat-Deficient Natural Lentiviruses. Vet Sci 2015; 2:293-348. [PMID: 29061947 PMCID: PMC5644649 DOI: 10.3390/vetsci2040293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 01/10/2023] Open
Abstract
The emergence of human immunodeficiency virus (HIV) causing acquired immunodeficiency syndrome (AIDS) in infected humans has resulted in a global pandemic that has killed millions. HIV-1 and HIV-2 belong to the lentivirus genus of the Retroviridae family. This genus also includes viruses that infect other vertebrate animals, among them caprine arthritis-encephalitis virus (CAEV) and Maedi-Visna virus (MVV), the prototypes of a heterogeneous group of viruses known as small ruminant lentiviruses (SRLVs), affecting both goat and sheep worldwide. Despite their long host-SRLV natural history, SRLVs were never found to be responsible for immunodeficiency in contrast to primate lentiviruses. SRLVs only replicate productively in monocytes/macrophages in infected animals but not in CD4+ T cells. The focus of this review is to examine and compare the biological and pathological properties of SRLVs as prototypic Tat-independent lentiviruses with HIV-1 as prototypic Tat-dependent lentiviruses. Results from this analysis will help to improve the understanding of why and how these two prototypic lentiviruses evolved in opposite directions in term of virulence and pathogenicity. Results may also help develop new strategies based on the attenuation of SRLVs to control the highly pathogenic HIV-1 in humans.
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Affiliation(s)
- Deepanwita Bose
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Jean Gagnon
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Yahia Chebloune
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
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47
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Gordon N, Rosenblum R, Nussbaum-Shochat A, Eliahoo E, Amster-Choder O. A Search for Ribonucleic Antiterminator Sites in Bacterial Genomes: Not Only Antitermination? J Mol Microbiol Biotechnol 2015; 25:143-53. [PMID: 26159075 DOI: 10.1159/000375263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BglG/LicT-like proteins are transcriptional antiterminators that prevent termination of transcription at intrinsic terminators by binding to ribonucleic antiterminator (RAT) sites and stabilizing an RNA conformation which is mutually exclusive with the terminator structure. The known RAT sites, which are located in intergenic regions of sugar utilization operons, show low sequence conservation but significant structural analogy. To assess the prevalence of RATs in bacterial genomes, we employed bioinformatic tools that describe RNA motifs based on both sequence and structural constraints. Using descriptors with different stringency, we searched the genomes of Escherichiacoli K12, uropathogenic E. coli and Bacillus subtilis for putative RATs. Our search identified all known RATs and additional putative RAT elements. Surprisingly, most putative RATs do not overlap an intrinsic terminator and many reside within open reading frames (ORFs). The ability of one of the putative RATs, which is located within an antiterminator-encoding ORF and does not overlap a terminator, to bind to its cognate antiterminator protein in vitro and in vivo was confirmed experimentally. Our results suggest that the capacity of RAT elements has been exploited during evolution to mediate activities other than antitermination, for example control of transcription elongation or of RNA stability.
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Affiliation(s)
- Noa Gordon
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem, Israel
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48
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Le Grice SFJ. Targeting the HIV RNA genome: high-hanging fruit only needs a longer ladder. Curr Top Microbiol Immunol 2015; 389:147-69. [PMID: 25735922 PMCID: PMC7120518 DOI: 10.1007/82_2015_434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Small molecules targeting the enzymes responsible for human immunodeficiency virus (HIV) maturation, DNA synthesis and its subsequent chromosomal integration as ribonucleotide-free double-stranded DNA remain the mainstay of combination antiretroviral therapy. For infected individuals harboring drug-susceptible virus, this approach has afforded complete or near-complete viral suppression. However, in the absence of a curative strategy, the predictable emergence of drug-resistant variants requires continued development of improved antiviral strategies, inherent to which is the necessity of identifying novel targets. Regulatory elements that mediate transcription, translation, nucleocytoplasmic transport, dimerization, packaging and reverse transcription of the (+) strand RNA genome should now be considered viable targets for small molecule, peptide- and oligonucleotide-based therapeutics. Where target specificity and cellular penetration and toxicity have been the primary obstacle to successful “macromolecule therapeutics”, this chapter summarizes (a) novel approaches targeting RNA motifs whose three-dimensional structure is critical for biological function and consequently may be less prone to resistance-conferring mutations and (b) improved methods for delivery.
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Affiliation(s)
- Stuart F J Le Grice
- RT Biochemistry Section, Basic Research Laboratory, National Cancer Institute, Frederick, MD, 21702, USA,
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49
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Martinez-Zapien D, Saliou JM, Han X, Atmanene C, Proux F, Cianférani S, Dock-Bregeon AC. Intermolecular recognition of the non-coding RNA 7SK and HEXIM protein in perspective. Biochimie 2015; 117:63-71. [PMID: 25863285 DOI: 10.1016/j.biochi.2015.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/25/2015] [Indexed: 11/18/2022]
Abstract
A 7SKsnRNP complex, comprising the non-coding RNA 7SK and proteins MePCE and LARP7, participates in the regulation of the transcription elongation by RNA-polymerase II in higher eukaryotes. Binding of a HEXIM protein triggers the inhibition of the kinase complex P-TEFb, a key actor of the switch from paused transcription to elongation. The present paper reviews what is known about the specific recognition of the 7SK RNA by the HEXIM protein. HEXIM uses an arginine-rich motif (ARM) peptide to bind one specific site in the 5'-hairpin of the 7SK RNA. Since HEXIM forms a dimer, what happens with the second ARM impacts the assembly symmetry. In order to help sort through possible models, a combination of native mass spectrometry and electrophoretic mobility shift assays was used. It provides evidence that only one ARM of the HEXIM dimer is directly binding to the RNA hairpin and that another sequence downstream of the ARM participates in a second binding event allowing the other monomer of HEXIM to bind the RNA.
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Affiliation(s)
- Denise Martinez-Zapien
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), Institute of Genetics and of Molecular and Cellular Biology (IGBMC) 67404 Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France; Biotechnologie et Signalisation Cellulaire UMR 7242, Ecole Supérieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, BP 10413, F-67412 Illkirch, France.
| | - Jean-Michel Saliou
- BioOrganic Mass Spectrometry Laboratory (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France; Center for Infection and Immunity of Lille (CIIL), Institut Pasteur de Lille, CNRS UMR 8204, INSERM U1019, Université Lille Nord de France, 1 rue du Pr. Calmette, 59000 Lille, France.
| | - Xiao Han
- Department of Functional Genomics, Institut de Biologie de l''Ecole Normale Supérieure (IBENS), 75005 Paris, France; CNRS UMR 8197, 75005 Paris, France; INSERM U1024, 75005 Paris, France; Key Laboratory of Brain Functional Genomics, East China Normal University (ECNU), Shanghai, PR China.
| | - Cedric Atmanene
- BioOrganic Mass Spectrometry Laboratory (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France.
| | - Florence Proux
- Department of Functional Genomics, Institut de Biologie de l''Ecole Normale Supérieure (IBENS), 75005 Paris, France; CNRS UMR 8197, 75005 Paris, France; INSERM U1024, 75005 Paris, France.
| | - Sarah Cianférani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel, 67087 Strasbourg, France; CNRS, UMR7178, 67087 Strasbourg, France.
| | - Anne-Catherine Dock-Bregeon
- Department of Functional Genomics, Institut de Biologie de l''Ecole Normale Supérieure (IBENS), 75005 Paris, France; CNRS UMR 8197, 75005 Paris, France; INSERM U1024, 75005 Paris, France.
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Molecular dynamics simulation and experimental verification of the interaction between cyclin T1 and HIV-1 Tat proteins. PLoS One 2015; 10:e0119451. [PMID: 25781978 PMCID: PMC4363469 DOI: 10.1371/journal.pone.0119451] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [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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