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Yandrapally S, Sarkar S, Banerjee S. HIV-1 Tat commandeers nuclear export of Rev-viral RNA complex by controlling hnRNPA2-mediated splicing. J Virol 2023; 97:e0104423. [PMID: 37905837 PMCID: PMC10688328 DOI: 10.1128/jvi.01044-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE HIV-infected host cells impose varied degrees of regulation on viral replication, from very high to abortive. Proliferation of HIV in astrocytes is limited when compared to immune cells, such as CD4+ T lymphocytes. Understanding such differential regulation is one of the key questions in the field as these cells permit HIV persistence and rebound viremia, challenging HIV treatment and clinical cure. This study focuses on understanding the molecular mechanism behind such cell-specific disparities. We show that one of the key mechanisms is the regulation of heterogenous nuclear ribonucleoprotein A2, a host factor involved in alternative splicing and RNA processing, by HIV-1 Tat in CD4+ T lymphocytes, not observed in astrocytes. This regulation causes an increase in the levels of unspliced/partially spliced viral RNA and nuclear export of Rev-RNA complexes which results in high viral propagation in CD4+ T lymphocytes. The study reveals a new mechanism imposed by HIV on host cells that determines the fate of infection.
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Affiliation(s)
- Sriram Yandrapally
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Satarupa Sarkar
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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2
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Chumillas S, Loharch S, Beltrán M, Szewczyk MP, Bernal S, Puertas MC, Martinez-Picado J, Alcamí J, Bedoya LM, Marchán V, Gallego J. Exploring the HIV-1 Rev Recognition Element (RRE)-Rev Inhibitory Capacity and Antiretroviral Action of Benfluron Analogs. Molecules 2023; 28:7031. [PMID: 37894510 PMCID: PMC10609163 DOI: 10.3390/molecules28207031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Human immunodeficiency virus-type 1 (HIV-1) remains one of the leading contributors to the global burden of disease, and novel antiretroviral agents with alternative mechanisms are needed to cure this infection. Here, we describe an exploratory attempt to optimize the antiretroviral properties of benfluron, a cytostatic agent previously reported to exhibit strong anti-HIV activity likely based on inhibitory actions on virus transcription and Rev-mediated viral RNA export. After obtaining six analogs designed to modify the benzo[c]fluorenone system of the parent molecule, we examined their antiretroviral and toxicity properties together with their capacity to recognize the Rev Recognition Element (RRE) of the virus RNA and inhibit the RRE-Rev interaction. The results indicated that both the benzo[c] and cyclopentanone components of benfluron are required for strong RRE-Rev target engagement and antiretroviral activity and revealed the relative impact of these moieties on RRE affinity, RRE-Rev inhibition, antiviral action and cellular toxicity. These data provide insights into the biological properties of the benzo[c]fluorenone scaffold and contribute to facilitating the design of new anti-HIV agents based on the inhibition of Rev function.
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Affiliation(s)
- Sergi Chumillas
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Saurabh Loharch
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain; (S.L.); (M.P.S.)
| | - Manuela Beltrán
- Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.B.); (L.M.B.)
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Mateusz P. Szewczyk
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain; (S.L.); (M.P.S.)
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain
| | - Silvia Bernal
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain
- Infectious Diseases and Immunity Department, University of Vic—Central University of Catalonia, 08500 Vic, Spain
| | - Maria C. Puertas
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain
- Germans Trias i Pujol Research Institute, 08916 Badalona, Spain
| | - Javier Martinez-Picado
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- IrsiCaixa AIDS Research Institute, 08916 Badalona, Spain
- Infectious Diseases and Immunity Department, University of Vic—Central University of Catalonia, 08500 Vic, Spain
- Germans Trias i Pujol Research Institute, 08916 Badalona, Spain
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain
| | - José Alcamí
- Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.B.); (L.M.B.)
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Luis M. Bedoya
- Instituto de Salud Carlos III, 28220 Majadahonda, Spain; (M.B.); (L.M.B.)
- CIBERINFEC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Vicente Marchán
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, IBUB, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - José Gallego
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain; (S.L.); (M.P.S.)
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Evans EL, Pocock GM, Einsdorf G, Behrens RT, Dobson ETA, Wiedenmann M, Birkhold C, Ahlquist P, Eliceiri KW, Sherer NM. HIV RGB: Automated Single-Cell Analysis of HIV-1 Rev-Dependent RNA Nuclear Export and Translation Using Image Processing in KNIME. Viruses 2022; 14:903. [PMID: 35632645 PMCID: PMC9145009 DOI: 10.3390/v14050903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Single-cell imaging has emerged as a powerful means to study viral replication dynamics and identify sites of virus−host interactions. Multivariate aspects of viral replication cycles yield challenges inherent to handling large, complex imaging datasets. Herein, we describe the design and implementation of an automated, imaging-based strategy, “Human Immunodeficiency Virus Red-Green-Blue” (HIV RGB), for deriving comprehensive single-cell measurements of HIV-1 unspliced (US) RNA nuclear export, translation, and bulk changes to viral RNA and protein (HIV-1 Rev and Gag) subcellular distribution over time. Differentially tagged fluorescent viral RNA and protein species are recorded using multicolor long-term (>24 h) time-lapse video microscopy, followed by image processing using a new open-source computational imaging workflow dubbed “Nuclear Ring Segmentation Analysis and Tracking” (NR-SAT) based on ImageJ plugins that have been integrated into the Konstanz Information Miner (KNIME) analytics platform. We describe a typical HIV RGB experimental setup, detail the image acquisition and NR-SAT workflow accompanied by a step-by-step tutorial, and demonstrate a use case wherein we test the effects of perturbing subcellular localization of the Rev protein, which is essential for viral US RNA nuclear export, on the kinetics of HIV-1 late-stage gene regulation. Collectively, HIV RGB represents a powerful platform for single-cell studies of HIV-1 post-transcriptional RNA regulation. Moreover, we discuss how similar NR-SAT-based design principles and open-source tools might be readily adapted to study a broad range of dynamic viral or cellular processes.
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Affiliation(s)
- Edward L. Evans
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Ginger M. Pocock
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Gabriel Einsdorf
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | - Ryan T. Behrens
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
| | - Ellen T. A. Dobson
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
| | - Marcel Wiedenmann
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- KNIME GmbH, 78467 Konstanz, Germany;
| | | | - Paul Ahlquist
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
- Morgridge Institute for Research, Madison, WI 53715, USA
- John and Jeanne Rowe Center for Research in Virology, Madison, WI 53715, USA
| | - Kevin W. Eliceiri
- Laboratory for Optical and Computational Instrumentation, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA; (G.E.); (E.T.A.D.); (M.W.)
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research (Department of Oncology), Institute for Molecular Virology, and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53706, USA; (E.L.E.III); (G.M.P.); (R.T.B.)
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4
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Ali H, Bhange D, Mehta K, Gohil Y, Prajapati HK, Byrareddy SN, Buch S, Ranga U. An emerging and variant viral promoter of HIV-1 subtype C exhibits low-level gene expression noise. Retrovirology 2021; 18:27. [PMID: 34538278 PMCID: PMC8451104 DOI: 10.1186/s12977-021-00572-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/27/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND We observe the emergence of several promoter-variant viral strains in India during recent years. The variant viral promoters contain additional copies of transcription factor binding sites present in the viral modulatory region or enhancer, including RBEIII, LEF-1, Ap-1 and/or NF-κB. These sites are crucial for governing viral gene expression and latency. Here, we infer that one variant viral promoter R2N3-LTR containing two copies of RBF-2 binding sites (an RBEIII site duplication) and three copies of NF-κB motifs may demonstrate low levels of gene expression noise as compared to the canonical RN3-LTR or a different variant R2N4-LTR (a duplication of an RBEIII site and an NF-κB motif). To demonstrate this, we constructed a panel of sub-genomic viral vectors of promoter-variant LTRs co-expressing two reporter proteins (mScarlet and Gaussia luciferase) under the dual-control of Tat and Rev. We established stable pools of CEM.NKR-CCR5 cells (CEM-CCR5RL reporter cells) and evaluated reporter gene expression under different conditions of cell activation. RESULTS The R2N3-LTR established stringent latency that was highly resistant to reversal by potent cell activators such as TNF-α or PMA, or even to a cocktail of activators, compared to the canonical RN3- or the variant R2N4-LTR. The R2N3-LTR exhibited low-level basal gene expression in the absence of cell activation that enhanced marginally but significantly when activated. In the presence of Tat and Rev, trans-complemented in the form of an infectious virus, the R2N3-LTR demonstrated gene expression at levels comparable to the wild-type viral promoter. The R2N3-LTR is responsive to Tat and Rev factors derived from viral strains representing diverse genetic subtypes. CONCLUSION With extremely low-level transcriptional noise, the R2N3-LTR can serve as an excellent model to examine the establishment, maintenance, and reversal of HIV-1 latency. The R2N3-LTR would also be an ideal viral promoter to develop high-throughput screening assays to identify potent latency-reversing agents since the LTR is not affected by the usual background noise of the cell.
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Affiliation(s)
- Haider Ali
- Molecular Biology and Genetics Unit, HIV AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064 India
| | - Disha Bhange
- Molecular Biology and Genetics Unit, HIV AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064 India
| | - Kavita Mehta
- Molecular Biology and Genetics Unit, HIV AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064 India
| | - Yuvrajsinh Gohil
- Molecular Biology and Genetics Unit, HIV AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064 India
| | -
Harshit Kumar Prajapati
- Molecular Biology and Genetics Unit, HIV AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064 India
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE USA
| | - Shilpa Buch
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE USA
| | - Udaykumar Ranga
- Molecular Biology and Genetics Unit, HIV AIDS Laboratory, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064 India
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5
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Pai S, Mudgal J, Kamath BV, Pai KSR. An insight on promising strategies hoping to cure HIV-1 infection by targeting Rev protein-short review. Pharmacol Rep 2021; 73:1265-1272. [PMID: 33840054 PMCID: PMC8460518 DOI: 10.1007/s43440-021-00257-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 01/23/2023]
Abstract
Human immunodeficiency virus-1 (HIV-1) infection remains to be one of the major threats throughout the world. Many researchers are working in this area to find a cure for HIV-1. The group of the FDA approved drugs which are currently used against HIV-1 in the clinical practice include nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), integrase inhibitors (InIs), and protease inhibitors (PIs). Fixed dose combinations (FDCs) of these drugs are available and are used as per the anti-retroviral therapy (ART) guidelines. Despite these, unfortunately, there is no cure for HIV1 infection to date. The present review is focused upon describing the importance of a post-transcriptional regulatory protein "Rev", responsible for latent HIV-1 infection as a possible, and promising therapeutic target against HIV-1.
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Affiliation(s)
- Sahana Pai
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Jayesh Mudgal
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - B Venkatesh Kamath
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - K Sreedhara Ranganath Pai
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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6
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Abstract
The transcription of the HIV-1 provirus results in only one type of transcript-full length genomic RNA. To make the mRNA transcripts for the accessory proteins Tat and Rev, the genomic RNA must completely splice. The mRNA transcripts for Vif, Vpr, and Env must undergo splicing but not completely. Genomic RNA (which also functions as mRNA for the Gag and Gag/Pro/Pol precursor polyproteins) must not splice at all. HIV-1 can tolerate a surprising range in the relative abundance of individual transcript types, and a surprising amount of aberrant and even odd splicing; however, it must not over-splice, which results in the loss of full-length genomic RNA and has a dramatic fitness cost. Cells typically do not tolerate unspliced/incompletely spliced transcripts, so HIV-1 must circumvent this cell policing mechanism to allow some splicing while suppressing most. Splicing is controlled by RNA secondary structure, cis-acting regulatory sequences which bind splicing factors, and the viral protein Rev. There is still much work to be done to clarify the combinatorial effects of these splicing regulators. These control mechanisms represent attractive targets to induce over-splicing as an antiviral strategy. Finally, splicing has been implicated in latency, but to date there is little supporting evidence for such a mechanism. In this review we apply what is known of cellular splicing to understand splicing in HIV-1, and present data from our newer and more sensitive deep sequencing assays quantifying the different HIV-1 transcript types.
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MESH Headings
- Alternative Splicing
- Exons
- Gene Expression Regulation, Viral
- HIV-1/genetics
- Nucleic Acid Conformation
- RNA Splicing
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Regulatory Sequences, Nucleic Acid
- Virus Latency/genetics
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Ann Emery
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA;
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA;
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
- Center for AIDS Research, University of North Carolina, Chapel Hill, NC 27599, USA
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7
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Liu H, Hu PW, Budhiraja S, Misra A, Couturier J, Lloyd RE, Lewis DE, Kimata JT, Rice AP. PACS1 is an HIV-1 cofactor that functions in Rev-mediated nuclear export of viral RNA. Virology 2020; 540:88-96. [PMID: 31759187 PMCID: PMC7335006 DOI: 10.1016/j.virol.2019.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 10/25/2022]
Abstract
HIV-1 is dependent upon cellular proteins to mediate the many processes required for viral replication. One such protein, PACS1, functions to localize Furin to the trans-Golgi network where Furin cleaves HIV-1 gp160 Envelope into gp41 and gp120. We show here that PACS1 also shuttles between the nucleus and cytoplasm, associates with the viral Rev protein and its cofactor CRM1, and contributes to nuclear export of viral transcripts. PACS1 appears specific to the Rev-CRM1 pathway and not other retroviral RNA export pathways. Over-expression of PACS1 increases nuclear export of unspliced viral RNA and significantly increases p24 expression in HIV-1-infected Jurkat CD4+ T cells. SiRNA depletion and over-expression experiments suggest that PACS1 may promote trafficking of HIV-1 GagPol RNA to a pathway distinct from that of translation on polyribosomes.
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Affiliation(s)
- Hongbing Liu
- Department of Molecular Virology and Microbiology, USA
| | - Pei-Wen Hu
- Department of Molecular Virology and Microbiology, USA
| | | | - Anisha Misra
- Department of Molecular Virology and Microbiology, USA
| | - Jacob Couturier
- Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | | | - Dorothy E Lewis
- Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | | | - Andrew P Rice
- Department of Molecular Virology and Microbiology, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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8
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Gray LR, Jackson RE, Jackson PEH, Bekiranov S, Rekosh D, Hammarskjöld ML. HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNA. Retrovirology 2019; 16:40. [PMID: 31842941 PMCID: PMC6916052 DOI: 10.1186/s12977-019-0505-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 12/07/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The HERV-K (HML-2) viruses are the youngest of the human endogenous retroviruses. They are present as several almost complete proviral copies and numerous fragments in the human genome. Many HERV-K proviruses express a regulatory protein Rec, which binds to an element present in HERV-K mRNAs called the RcRE. This interaction is necessary for the nucleo-cytoplasmic export and expression of HERV-K mRNAs that retain introns and plays a role analogous to that of Rev and the RRE in HIV replication. There are over 900 HERV-K RcREs distributed throughout the human genome. Thus, it was of interest to determine if Rev could functionally interact with selected RcRE elements that map either to HERV-K proviruses or human gene regions. This interaction would have the potential to alter the expression of both HERV-K mRNAs and cellular mRNAs during HIV-1 infection. RESULTS In this study we employed a combination of RNAseq, bioinformatics and cell-based functional assays. Potential RcREs were identified through a number of bioinformatic approaches. They were then tested for their ability to promote export and translation of a reporter mRNA with a retained intron in conjunction with Rev or Rec. Some of the selected elements functioned well with either Rev, Rec or both, whereas some showed little or no function. Rev function on individual RcREs varied and was also dependent on the Rev sequence. We also performed RNAseq on total and cytoplasmic RNA isolated from SupT1 cells expressing HIV Rev, with or without Tat, or HERV-K Rec. Proviral mRNA from three HERV-K loci (4p16.1b, 22q11.23 and most significantly 3q12.3) accumulated in the cytoplasm in the presence of Rev or Tat and Rev, but not Rec. Consistent with this, the 3' RcRE from 3q12.3 functioned well with HIV-Rev in our reporter assay. In contrast, this RcRE showed little or no function with Rec. CONCLUSIONS The HIV Rev protein can functionally interact with many RcREs present in the human genome, depending on the RcRE sequence, as well as the Rev sequence. This leads to export of some of the HERV-K proviral mRNAs and also has the potential to change the expression of non-viral genes.
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Affiliation(s)
- Laurie R Gray
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Rachel E Jackson
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Patrick E H Jackson
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, 22908, USA
| | - Stefan Bekiranov
- Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, 22908, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Marie-Louise Hammarskjöld
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA.
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9
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Chu CC, Liu B, Plangger R, Kreutz C, Al-Hashimi HM. m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB. PLoS One 2019; 14:e0224850. [PMID: 31825959 PMCID: PMC6905585 DOI: 10.1371/journal.pone.0224850] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/26/2019] [Indexed: 02/02/2023] Open
Abstract
N6-methyladenosine (m6A) is a ubiquitous RNA post-transcriptional modification found in coding as well as non-coding RNAs. m6A has also been found in viral RNAs where it is proposed to modulate host-pathogen interactions. Two m6A sites have been reported in the HIV-1 Rev response element (RRE) stem IIB, one of which was shown to enhance binding to the viral protein Rev and viral RNA export. However, because these m6A sites have not been observed in other studies mapping m6A in HIV-1 RNA, their significance remains to be firmly established. Here, using optical melting experiments, NMR spectroscopy, and in vitro binding assays, we show that m6A minimally impacts the stability, structure, and dynamics of RRE stem IIB as well as its binding affinity to the Rev arginine-rich-motif (ARM) in vitro. Our results indicate that if present in stem IIB, m6A is unlikely to substantially alter the conformational properties of the RNA. Our results add to a growing view that the impact of m6A on RNA depends on sequence context and Mg2+.
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Affiliation(s)
- Chia-Chieh Chu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States of America
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States of America
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, Innsbruck, Austria
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States of America
- Department of Chemistry, Duke University, Durham, NC, United States of America
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10
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Wang Y, Zhang H, Na L, Du C, Zhang Z, Zheng YH, Wang X. ANP32A and ANP32B are key factors in the Rev-dependent CRM1 pathway for nuclear export of HIV-1 unspliced mRNA. J Biol Chem 2019; 294:15346-15357. [PMID: 31444273 PMCID: PMC6802516 DOI: 10.1074/jbc.ra119.008450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/10/2019] [Indexed: 12/21/2022] Open
Abstract
The nuclear export receptor CRM1 is an important regulator involved in the shuttling of various cellular and viral RNAs between the nucleus and the cytoplasm. HIV-1 Rev interacts with CRM1 in the late phase of HIV-1 replication to promote nuclear export of unspliced and single spliced HIV-1 transcripts. However, other cellular factors involved in the CRM1-dependent viral RNA nuclear export remain largely unknown. Here, we demonstrate that ANP32A and ANP32B mediate the export of unspliced or partially spliced viral mRNA via interactions with Rev and CRM1. We found that a double, but not single, knockout of ANP32A and ANP32B significantly decreased the expression of gag protein. Reconstitution of either ANP32A or ANP32B restored the viral production equally. Disruption of both ANP32A and ANP32B expression led to a dramatic accumulation of unspliced viral mRNA in the nucleus. We further identified that ANP32A and ANP32B interact with both Rev and CRM1 to promote RNA transport. Our data strongly suggest that ANP32A and ANP32B play an important role in the Rev-CRM1 pathway, which is essential for HIV-1 replication, and our findings provide a candidate therapeutic target for host defense against retroviral infection.
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Affiliation(s)
- Yujie Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Haili Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Lei Na
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Cheng Du
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Zhenyu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Yong-Hui Zheng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
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11
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Chu CC, Plangger R, Kreutz C, Al-Hashimi HM. Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site. Nucleic Acids Res 2019; 47:7105-7117. [PMID: 31199872 PMCID: PMC6649712 DOI: 10.1093/nar/gkz498] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/21/2019] [Accepted: 06/07/2019] [Indexed: 01/01/2023] Open
Abstract
The HIV-1 Rev response element (RRE) RNA element mediates the nuclear export of intron containing viral RNAs by forming an oligomeric complex with the viral protein Rev. Stem IIB and nearby stem II three-way junction nucleate oligomerization through cooperative binding of two Rev molecules. Conformational flexibility at this RRE region has been shown to be important for Rev binding. However, the nature of the flexibility has remained elusive. Here, using NMR relaxation dispersion, including a new strategy for directly observing transient conformational states in large RNAs, we find that stem IIB alone or when part of the larger RREII three-way junction robustly exists in dynamic equilibrium with non-native excited state (ES) conformations that have a combined population of ∼20%. The ESs disrupt the Rev-binding site by changing local secondary structure, and their stabilization via point substitution mutations decreases the binding affinity to the Rev arginine-rich motif (ARM) by 15- to 80-fold. The ensemble clarifies the conformational flexibility observed in stem IIB, reveals long-range conformational coupling between stem IIB and the three-way junction that may play roles in cooperative Rev binding, and also identifies non-native RRE conformational states as new targets for the development of anti-HIV therapeutics.
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Affiliation(s)
- Chia-Chieh Chu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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12
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Banerjee S, Maurya S, Roy R. Single-molecule fluorescence imaging: Generating insights into molecular interactions in virology. J Biosci 2018; 43:519-540. [PMID: 30002270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Single-molecule fluorescence methods remain a challenging yet information-rich set of techniques that allow one to probe the dynamics, stoichiometry and conformation of biomolecules one molecule at a time. Viruses are small (nanometers) in size, can achieve cellular infections with a small number of virions and their lifecycle is inherently heterogeneous with a large number of structural and functional intermediates. Single-molecule measurements that reveal the complete distribution of properties rather than the average can hence reveal new insights into virus infections and biology that are inaccessible otherwise. This article highlights some of the methods and recent applications of single-molecule fluorescence in the field of virology. Here, we have focused on new findings in virus-cell interaction, virus cell entry and transport, viral membrane fusion, genome release, replication, translation, assembly, genome packaging, egress and interaction with host immune proteins that underline the advantage of single-molecule approach to the question at hand. Finally, we discuss the challenges, outlook and potential areas for improvement and future use of single-molecule fluorescence that could further aid our understanding of viruses.
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Affiliation(s)
- Sunaina Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
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13
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Rustanti L, Jin H, Li D, Lor M, Sivakumaran H, Harrich D. Differential Effects of Strategies to Improve the Transduction Efficiency of Lentiviral Vector that Conveys an Anti-HIV Protein, Nullbasic, in Human T Cells. Virol Sin 2018. [PMID: 29541943 DOI: 10.1007/s12250-018-0004-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Nullbasic is a mutant form of HIV-1 Tat that has strong ability to protect cells from HIV-1 replication by inhibiting three different steps of viral replication: reverse transcription, Rev export of viral mRNA from the nucleus to the cytoplasm and transcription of viral mRNA by RNA polymerase II. We previously showed that Nullbasic inhibits transduction of human cells including T cells by HIV-1-based lentiviral vectors. Here we investigated whether the Nullbasic antagonists huTat2 (a Tat targeting intrabody), HIV-1 Tat or Rev proteins or cellular DDX1 protein could improve transduction by a HIV-1 lentiviral vector conveying Nullbasic-ZsGreen1 to human T cells. We show that overexpression of huTat2, Tat-FLAG and DDX1-HA in virus-like particle (VLP) producer cells significantly improved transduction efficiency of VLPs that convey Nullbasic in Jurkat cells. Specifically, co-expression of Tat-FLAG and DDX1-HA in the VLP producer cell improved transduction efficiency better than if used individually. Transduction efficiencies could be further improved by including a spinoculation step. However, the same optimised protocol and using the same VLPs failed to transduce primary human CD4+ T cells. The results imply that the effects of Nullbasic on VLPs on early HIV-1 replication are robust in human CD4+ T cells. Given this significant block to lentiviral vector transduction by Nullbasic in primary CD4+ T cells, our data indicate that gammaretroviral, but not lentiviral, vectors are suitable for delivering Nullbasic to primary human T cells.
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Affiliation(s)
- Lina Rustanti
- Faculty of Medicine, The University of Queensland, Herston, QLD, 4029, Australia
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia
- National Institute of Health Research and Development, the Ministry of Health of Republic of Indonesia, Central Jakarta, DKI Jakarta, 10560, Indonesia
| | - Hongping Jin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia
| | - Dongsheng Li
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia
| | - Mary Lor
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia
| | - Haran Sivakumaran
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia
| | - David Harrich
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, QLD, 4029, Australia.
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14
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Ajamian L, Abel K, Rao S, Vyboh K, García-de-Gracia F, Soto-Rifo R, Kulozik AE, Gehring NH, Mouland AJ. HIV-1 Recruits UPF1 but Excludes UPF2 to Promote Nucleocytoplasmic Export of the Genomic RNA. Biomolecules 2015; 5:2808-39. [PMID: 26492277 PMCID: PMC4693258 DOI: 10.3390/biom5042808] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022] Open
Abstract
Unspliced, genomic HIV-1 RNA (vRNA) is a component of several ribonucleoprotein complexes (RNP) during the viral replication cycle. In earlier work, we demonstrated that the host upframeshift protein 1 (UPF1), a key factor in nonsense-mediated mRNA decay (NMD), colocalized and associated to the viral structural protein Gag during viral egress. In this work, we demonstrate a new function for UPF1 in the regulation of vRNA nuclear export. OPEN ACCESS Biomolecules 2015, 5 2809 We establish that the nucleocytoplasmic shuttling of UPF1 is required for this function and demonstrate that UPF1 exists in two essential viral RNPs during the late phase of HIV-1 replication: the first, in a nuclear export RNP that contains Rev, CRM1, DDX3 and the nucleoporin p62, and the second, which excludes these nuclear export markers but contains Gag in the cytoplasm. Interestingly, we observed that both UPF2 and the long isoform of UPF3a, UPF3aL, but not the shorter isoforms UPF3aS and UPF3b, are excluded from the UPF1-Rev-CRM1-DDX3 complex as they are negative regulators of vRNA nuclear export. In silico protein-protein docking analyses suggest that Rev binds UPF1 in a region that overlaps the UPF2 binding site, thus explaining the exclusion of this negative regulatory factor by HIV-1 that is necessary for vRNA trafficking. This work uncovers a novel and unique regulatory circuit involving several UPF proteins that ultimately regulate vRNA nuclear export and trafficking.
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Affiliation(s)
- Lara Ajamian
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal QC H3A 2B4, Canada.
| | - Karen Abel
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Shringar Rao
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Kishanda Vyboh
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
| | - Francisco García-de-Gracia
- Laboratory of Molecular and Cellular Virology, Virology Program, Biomedical Sciences Institute, Faculty of Medicine, Universidad de Chile, Independencia 8389100, Santiago, Chile.
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Biomedical Sciences Institute, Faculty of Medicine, Universidad de Chile, Independencia 8389100, Santiago, Chile.
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg 69120, Germany.
- European Molecular Biology Laboratory, Partnership Unit, University of Heidelberg Molecular Medicine, Heidelberg 69117, Germany.
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, Cologne 50674, Germany.
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital, Montréal QC H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal QC H3A 2B4, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal QC H3T 1E2, Canada.
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15
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Boons E, Vanstreels E, Jacquemyn M, Nogueira TC, Neggers JE, Vercruysse T, van den Oord J, Tamir S, Shacham S, Landesman Y, Snoeck R, Pannecouque C, Andrei G, Daelemans D. Human Exportin-1 is a Target for Combined Therapy of HIV and AIDS Related Lymphoma. EBioMedicine 2015; 2:1102-13. [PMID: 26501108 PMCID: PMC4588406 DOI: 10.1016/j.ebiom.2015.07.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 11/12/2022] Open
Abstract
Infection with HIV ultimately leads to advanced immunodeficiency resulting in an increased incidence of cancer. For example primary effusion lymphoma (PEL) is an aggressive non-Hodgkin lymphoma with very poor prognosis that typically affects HIV infected individuals in advanced stages of immunodeficiency. Here we report on the dual anti-HIV and anti-PEL effect of targeting a single process common in both diseases. Inhibition of the exportin-1 (XPO1) mediated nuclear transport by clinical stage orally bioavailable small molecule inhibitors (SINE) prevented the nuclear export of the late intron-containing HIV RNA species and consequently potently suppressed viral replication. In contrast, in CRISPR-Cas9 genome edited cells expressing mutant C528S XPO1, viral replication was unaffected upon treatment, clearly demonstrating the anti-XPO1 mechanism of action. At the same time, SINE caused the nuclear accumulation of p53 tumor suppressor protein as well as inhibition of NF-κB activity in PEL cells resulting in cell cycle arrest and effective apoptosis induction. In vivo, oral administration arrested PEL tumor growth in engrafted mice. Our findings provide strong rationale for inhibiting XPO1 as an innovative strategy for the combined anti-retroviral and anti-neoplastic treatment of HIV and PEL and offer perspectives for the treatment of other AIDS-associated cancers and potentially other virus-related malignancies.
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MESH Headings
- Acrylates/chemistry
- Acrylates/pharmacology
- Acrylates/therapeutic use
- Active Transport, Cell Nucleus/drug effects
- Animals
- Apoptosis/drug effects
- Base Sequence
- CRISPR-Cas Systems/genetics
- Cell Cycle Checkpoints/drug effects
- Cell Line
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- Female
- HIV/drug effects
- HIV/isolation & purification
- Humans
- Karyopherins/antagonists & inhibitors
- Karyopherins/metabolism
- Lymphoma, AIDS-Related/drug therapy
- Mice, Nude
- Molecular Sequence Data
- Molecular Targeted Therapy
- NF-kappa B/metabolism
- Protein Binding/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/metabolism
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/metabolism
- Reproducibility of Results
- Triazoles/chemistry
- Triazoles/pharmacology
- Triazoles/therapeutic use
- Tumor Suppressor Protein p53/metabolism
- Virus Replication/drug effects
- Xenograft Model Antitumor Assays
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- Exportin 1 Protein
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Affiliation(s)
- Eline Boons
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Els Vanstreels
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Maarten Jacquemyn
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Tatiane C. Nogueira
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Jasper E. Neggers
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Joost van den Oord
- KU Leuven, Department of Imaging and Pathology, Translational Cell & Tissue Research, B-3000 Leuven, Belgium
| | | | | | | | - Robert Snoeck
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Graciela Andrei
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
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16
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Zhou Z, Li Y, Yuan C, Zhang Y, Qu L. Oral Administration of TAT-PTD-Diapause Hormone Fusion Protein Interferes With Helicoverpa armigera (Lepidoptera: Noctuidae) Development. J Insect Sci 2015; 15:iev102. [PMID: 26320262 PMCID: PMC4672221 DOI: 10.1093/jisesa/iev102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 08/08/2015] [Indexed: 06/02/2023]
Abstract
Diapause hormone (DH), which can terminate diapause in Helicoverpa armigera Hübner (Lepidoptera: Noctuidae), has shown promise as a pest control method. However, the main challenge in using DH as an insecticide lies in achieving effective oral delivery, since the peptide may be degraded by digestive enzymes in the gut. To improve the efficacy of oral DH application, the Clostera anastomosis (L.) (Lepidoptera: Notodontidae) diapause hormone (caDH) was fused to the Protein Transduction Domain (PTD) of the human immunodeficiency virus-1 transactivator of transcription (TAT). Cellular transduction of TAT-caDH was verified with the use of a green fluorescent protein fusion, and its ability to terminate diapause was verified by injection into diapausing H. armigera pupae. Orally administered TAT-caDH resulted in larval growth inhibition. In TAT-caDH-treated insects, larval duration was delayed and the pupation rates were decreased at both development promoting conditions [27 °C, a photoperiod of 14:10(L:D) h] and diapause inducing conditions [20 °C, a photoperiod of 10:14(L:D) h]. No significant difference in diapause rate was observed between the TAT-caDH-treated and caDH-treated or control pupae maintained at diapause inducing conditions. Our results show that treatment with a recombinant TAT-caDH protein can affect larval development in H. armigera, and it suggest that TAT-DH treatment may be useful for controlling pests. This study is the first record of oral DH application in insect.
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Affiliation(s)
- Zhou Zhou
- College of Forestry, Henan University of Science and Technology, Luoyang 471003, People's Republic of China
| | - Yongli Li
- College of Forestry, Henan University of Science and Technology, Luoyang 471003, People's Republic of China
| | - Chunyan Yuan
- College of Forestry, Henan University of Science and Technology, Luoyang 471003, People's Republic of China
| | - Yongan Zhang
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Haidian District, Beijing 100091, People's Republic of China
| | - Liangjian Qu
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Haidian District, Beijing 100091, People's Republic of China
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17
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Budhiraja S, Liu H, Couturier J, Malovannaya A, Qin J, Lewis DE, Rice AP. Mining the human complexome database identifies RBM14 as an XPO1-associated protein involved in HIV-1 Rev function. J Virol 2015; 89:3557-67. [PMID: 25589658 PMCID: PMC4403413 DOI: 10.1128/jvi.03232-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/06/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED By recruiting the host protein XPO1 (CRM1), the HIV-1 Rev protein mediates the nuclear export of incompletely spliced viral transcripts. We mined data from the recently described human nuclear complexome to identify a host protein, RBM14, which associates with XPO1 and Rev and is involved in Rev function. Using a Rev-dependent p24 reporter plasmid, we found that RBM14 depletion decreased Rev activity and Rev-mediated enhancement of the cytoplasmic levels of unspliced viral transcripts. RBM14 depletion also reduced p24 expression during viral infection, indicating that RBM14 is limiting for Rev function. RBM14 has previously been shown to localize to nuclear paraspeckles, a structure implicated in retaining unspliced HIV-1 transcripts for either Rev-mediated nuclear export or degradation. We found that depletion of NEAT1 RNA, a long noncoding RNA required for paraspeckle integrity, abolished the ability of overexpressed RBM14 to enhance Rev function, indicating the dependence of RBM14 function on paraspeckle integrity. Our study extends the known host cell interactome of Rev and XPO1 and further substantiates a critical role for paraspeckles in the mechanism of action of Rev. Our study also validates the nuclear complexome as a database from which viral cofactors can be mined. IMPORTANCE This study mined a database of nuclear protein complexes to identify a cellular protein named RBM14 that is associated with XPO1 (CRM1), a nuclear protein that binds to the HIV-1 Rev protein and mediates nuclear export of incompletely spliced viral RNAs. Functional assays demonstrated that RBM14, a protein found in paraspeckle structures in the nucleus, is involved in HIV-1 Rev function. This study validates the nuclear complexome database as a reference that can be mined to identify viral cofactors.
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Affiliation(s)
- Sona Budhiraja
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hongbing Liu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Jacob Couturier
- Department of Internal Medicine, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Anna Malovannaya
- Department of Biochemistry, Baylor College of Medicine, Houston, Texas, USA
| | - Jun Qin
- Department of Biochemistry, Baylor College of Medicine, Houston, Texas, USA
| | - Dorothy E Lewis
- Department of Internal Medicine, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Andrew P Rice
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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18
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Abstract
Two new structures shed additional light on the nuclear transport of viral transcripts.
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Affiliation(s)
- James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
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19
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Jayaraman B, Crosby DC, Homer C, Ribeiro I, Mavor D, Frankel AD. RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. eLife 2014; 3:e04120. [PMID: 25486594 PMCID: PMC4360532 DOI: 10.7554/elife.04120] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/06/2014] [Indexed: 12/27/2022] Open
Abstract
The HIV-1 protein Rev controls a critical step in viral replication by mediating the nuclear export of unspliced and singly-spliced viral mRNAs. Multiple Rev subunits assemble on the Rev Response Element (RRE), a structured region present in these RNAs, and direct their export through the Crm1 pathway. Rev-RRE assembly occurs via several Rev oligomerization and RNA-binding steps, but how these steps are coordinated to form an export-competent complex is unclear. Here, we report the first crystal structure of a Rev dimer-RRE complex, revealing a dramatic rearrangement of the Rev-dimer upon RRE binding through re-packing of its hydrophobic protein-protein interface. Rev-RNA recognition relies on sequence-specific contacts at the well-characterized IIB site and local RNA architecture at the second site. The structure supports a model in which the RRE utilizes the inherent plasticity of Rev subunit interfaces to guide the formation of a functional complex.
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MESH Headings
- Active Transport, Cell Nucleus
- Binding Sites
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Cell Nucleus/virology
- Crystallography, X-Ray
- Cytosol/metabolism
- Cytosol/virology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation
- HEK293 Cells
- HIV-1/genetics
- HIV-1/metabolism
- HeLa Cells
- Host-Pathogen Interactions
- Humans
- Karyopherins/genetics
- Karyopherins/metabolism
- Models, Molecular
- Protein Binding
- RNA Splicing
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Response Elements
- Signal Transduction
- T-Lymphocytes/metabolism
- T-Lymphocytes/virology
- Virus Replication/genetics
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- Exportin 1 Protein
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Affiliation(s)
- Bhargavi Jayaraman
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - David C Crosby
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Christina Homer
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Isabel Ribeiro
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - David Mavor
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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20
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Abstract
The HIV Rev protein routes viral RNAs containing the Rev Response Element (RRE) through the Crm1 nuclear export pathway to the cytoplasm where viral proteins are expressed and genomic RNA is delivered to assembling virions. The RRE assembles a Rev oligomer that displays nuclear export sequences (NESs) for recognition by the Crm1-Ran(GTP) nuclear receptor complex. Here we provide the first view of an assembled HIV-host nuclear export complex using single-particle electron microscopy. Unexpectedly, Crm1 forms a dimer with an extensive interface that enhances association with Rev-RRE and poises NES binding sites to interact with a Rev oligomer. The interface between Crm1 monomers explains differences between Crm1 orthologs that alter nuclear export and determine cellular tropism for viral replication. The arrangement of the export complex identifies a novel binding surface to possibly target an HIV inhibitor and may point to a broader role for Crm1 dimerization in regulating host gene expression.
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MESH Headings
- Active Transport, Cell Nucleus
- Binding Sites
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Cell Nucleus/virology
- Crystallography, X-Ray
- Cytosol/metabolism
- Cytosol/virology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation
- HEK293 Cells
- HIV-1/genetics
- HIV-1/metabolism
- HeLa Cells
- Host-Pathogen Interactions
- Humans
- Karyopherins/chemistry
- Karyopherins/genetics
- Karyopherins/metabolism
- Models, Molecular
- Protein Binding
- Protein Multimerization
- RNA Splicing
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Response Elements
- Signal Transduction
- T-Lymphocytes/metabolism
- T-Lymphocytes/virology
- Virus Replication/genetics
- ran GTP-Binding Protein/chemistry
- ran GTP-Binding Protein/genetics
- ran GTP-Binding Protein/metabolism
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- Exportin 1 Protein
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Affiliation(s)
- David S Booth
- Graduate Group in Biophysics, University of California, San Francisco, San Francisco, United States
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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21
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Aligeti M, Behrens RT, Pocock GM, Schindelin J, Dietz C, Eliceiri KW, Swanson CM, Malim MH, Ahlquist P, Sherer NM. Cooperativity among Rev-associated nuclear export signals regulates HIV-1 gene expression and is a determinant of virus species tropism. J Virol 2014; 88:14207-21. [PMID: 25275125 PMCID: PMC4249125 DOI: 10.1128/jvi.01897-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/23/2014] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED Murine cells exhibit a profound block to HIV-1 virion production that was recently mapped to a species-specific structural attribute of the murine version of the chromosomal region maintenance 1 (mCRM1) nuclear export receptor and rescued by the expression of human CRM1 (hCRM1). In human cells, the HIV-1 Rev protein recruits hCRM1 to intron-containing viral mRNAs encoding the Rev response element (RRE), thereby facilitating viral late gene expression. Here we exploited murine 3T3 fibroblasts as a gain-of-function system to study hCRM1's species-specific role in regulating Rev's effector functions. We show that Rev is rapidly exported from the nucleus by mCRM1 despite only weak contributions to HIV-1's posttranscriptional stages. Indeed, Rev preferentially accumulates in the cytoplasm of murine 3T3 cells with or without hCRM1 expression, in contrast to human HeLa cells, where Rev exhibits striking en masse transitions between the nuclear and cytoplasmic compartments. Efforts to bias Rev's trafficking either into or out of the nucleus revealed that Rev encoding a second CRM1 binding domain (Rev-2xNES) or Rev-dependent viral gag-pol mRNAs bearing tandem RREs (GP-2xRRE), rescue virus particle production in murine cells even in the absence of hCRM1. Combined, these results suggest a model wherein Rev-associated nuclear export signals cooperate to regulate the number or quality of CRM1's interactions with viral Rev/RRE ribonucleoprotein complexes in the nucleus. This mechanism regulates CRM1-dependent viral gene expression and is a determinant of HIV-1's capacity to produce virions in nonhuman cell types. IMPORTANCE Cells derived from mice and other nonhuman species exhibit profound blocks to HIV-1 replication. Here we elucidate a block to HIV-1 gene expression attributable to the murine version of the CRM1 (mCRM1) nuclear export receptor. In human cells, hCRM1 regulates the nuclear export of viral intron-containing mRNAs through the activity of the viral Rev adapter protein that forms a multimeric complex on these mRNAs prior to recruiting hCRM1. We demonstrate that Rev-dependent gene expression is poor in murine cells despite the finding that, surprisingly, the bulk of Rev interacts efficiently with mCRM1 and is rapidly exported from the nucleus. Instead, we map the mCRM1 defect to the apparent inability of this factor to engage Rev multimers in the context of large viral Rev/RNA ribonucleoprotein complexes. These findings shed new light on HIV-1 gene regulation and could inform the development of novel antiviral strategies that target viral gene expression.
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Affiliation(s)
- Mounavya Aligeti
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan T Behrens
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ginger M Pocock
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Johannes Schindelin
- Morgridge Institute for Research, Madison, Wisconsin, USA Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christian Dietz
- Department of Computer and Information Science, University of Constance, Constance, Germany
| | - Kevin W Eliceiri
- Morgridge Institute for Research, Madison, Wisconsin, USA Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chad M Swanson
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Michael H Malim
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA Morgridge Institute for Research, Madison, Wisconsin, USA Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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22
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Abstract
Astrocytes protect neurons, but also evoke proinflammatory responses to injury and viral infections, including HIV. There is a prevailing notion that HIV-1 Rev protein function in astrocytes is perturbed, leading to restricted viral replication. In earlier studies, our finding of restricted viral entry into astrocytes led us to investigate whether there are any intracellular restrictions, including crippled Rev function, in astrocytes. Despite barely detectable levels of DDX3 (Rev-supporting RNA helicase) and TRBP (anti-PKR) in primary astrocytes compared to astrocytic cells, Rev function was unperturbed in wild-type, but not DDX3-ablated astrocytes. As in permissive cells, after HIV-1 entry bypass in astrocytes, viral-encoded Tat and Rev proteins had robust regulatory activities, leading to efficient viral replication. Productive HIV-1 infection in astrocytes persisted for several weeks. Our findings on HIV-1 entry bypass in astrocytes demonstrated that the intracellular environment is conducive to viral replication and that Tat and Rev functions are unperturbed.
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Affiliation(s)
- Ashok Chauhan
- Department of Pathology, Microbiology and Immunology, and Department of Pharmacology, Physiology and Neuroscience, University of South Carolina School of Medicine, Columbia, South Carolina, United States of America
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23
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Cunyat F, Beerens N, García E, Clotet B, Kjems J, Cabrera C. Functional analyses reveal extensive RRE plasticity in primary HIV-1 sequences selected under selective pressure. PLoS One 2014; 9:e106299. [PMID: 25170621 PMCID: PMC4149556 DOI: 10.1371/journal.pone.0106299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/05/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND HIV-1 Rev response element (RRE) is a functional region of viral RNA lying immediately downstream to the junction of gp120 and gp41 in the env coding sequence. The RRE is essential for HIV replication and binds with the Rev protein to facilitate the export of viral mRNA from nucleus to cytoplasm. It has been suggested that changes in the predicted secondary structure of primary RRE sequences impact the function of the RREs; however, functional assays have not yet been performed. The aim of this study was to characterize the genetic, structural and functional variation in the RRE primary sequences selected in vivo by Enfuvirtide pressure. RESULTS Multiple RRE variants were obtained from viruses isolated from patients who failed an Enfuvirtide-containing regimen. Different alterations were observed in the predicted RRE secondary structures, with the abrogation of the primary Rev binding site in one of the variants. In spite of this, most of the RRE variants were able to bind Rev and promote the cytoplasmic export of the viral mRNAs with equivalent efficiency in a cell-based assay. Only RRE45 and RRE40-45 showed an impaired ability to bind Rev in a gel-shift binding assay. Unexpectedly, this impairment was not reflected in functional capacity when RNA export was evaluated using a reporter assay, or during virus replication in lymphoid cells, suggesting that in vivo the RRE would be highly malleable. CONCLUSIONS The Rev-RRE functionality is unaffected in RRE variants selected in patients failing an ENF-containing regimen. Our data show that the current understanding of the Rev-RRE complex structure does not suffice and fails to rationally predict the function of naturally occurring RRE mutants. Therefore, this data should be taken into account in the development of antiviral agents that target the RRE-Rev complex.
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Affiliation(s)
- Francesc Cunyat
- IrsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, Badalona, Barcelona, Catalonia, Spain
| | - Nancy Beerens
- Department of Molecular Biology, Aarhus University, Aarhus, Denmark
| | - Elisabet García
- IrsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, Badalona, Barcelona, Catalonia, Spain
| | - Bonaventura Clotet
- IrsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, Badalona, Barcelona, Catalonia, Spain
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Molecular Biology and Genetics Department, Aarhus University, Aarhus, Denmark
| | - Cecilia Cabrera
- IrsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, Badalona, Barcelona, Catalonia, Spain
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24
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Abstract
HIV replication requires nuclear export of unspliced and singly spliced viral transcripts. Although a unique RNA structure has been proposed for the Rev-response element (RRE) responsible for viral mRNA export, how it recruits multiple HIV Rev proteins to form an export complex has been unclear. We show here that initial binding of Rev to the RRE triggers RNA tertiary structural changes, enabling further Rev binding and the rapid formation of a viral export complex. Analysis of the Rev-RRE assembly pathway using SHAPE-Seq and small-angle X-ray scattering (SAXS) reveals two major steps of Rev-RRE complex formation, beginning with rapid Rev binding to a pre-organized region presenting multiple Rev binding sites. This step induces long-range remodeling of the RNA to expose a cryptic Rev binding site, enabling rapid assembly of additional Rev proteins into the RNA export complex. This kinetic pathway may help maintain the balance between viral replication and maturation.DOI: http://dx.doi.org/10.7554/eLife.03656.001.
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Affiliation(s)
- Yun Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Akshay Tambe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Kaihong Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States Department of Chemistry, University of California, Berkeley, Berkeley, United States Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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25
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Zhabokritsky A, Mansouri S, Hudak KA. Pokeweed antiviral protein alters splicing of HIV-1 RNAs, resulting in reduced virus production. RNA 2014; 20:1238-1247. [PMID: 24951553 PMCID: PMC4105749 DOI: 10.1261/rna.043141.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
Processing of HIV-1 transcripts results in three populations in the cytoplasm of infected cells: full-length RNA, singly spliced, and multiply spliced RNAs. Rev, regulator of virion expression, is an essential regulatory protein of HIV-1 required for transporting unspliced and singly spliced viral transcripts from the nucleus to the cytoplasm. Export allows these RNAs to be translated and the full-length RNA to be packaged into virus particles. In our study, we investigate the activity of pokeweed antiviral protein (PAP), a glycosidase isolated from the pokeweed plant Phytolacca americana, on the processing of viral RNAs. We show that coexpression of PAP with a proviral clone alters the splicing ratio of HIV-1 RNAs. Specifically, PAP causes the accumulation of multiply spliced 2-kb RNAs at the expense of full-length 9-kb and singly spliced 4-kb RNAs. The change in splicing ratio is due to a decrease in activity of Rev. We show that PAP depurinates the rev open reading frame and that this damage to the viral RNA inhibits its translation. By decreasing Rev expression, PAP indirectly reduces the availability of full-length 9-kb RNA for packaging and translation of the encoded structural proteins required for synthesis of viral particles. The decline we observe in virus protein expression is not due to cellular toxicity as PAP did not diminish translation rate. Our results describing the reduced activity of a regulatory protein of HIV-1, with resulting change in virus mRNA ratios, provides new insight into the antiviral mechanism of PAP.
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Affiliation(s)
- Alice Zhabokritsky
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sheila Mansouri
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Katalin A Hudak
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
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26
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Taniguchi I, Mabuchi N, Ohno M. HIV-1 Rev protein specifies the viral RNA export pathway by suppressing TAP/NXF1 recruitment. Nucleic Acids Res 2014; 42:6645-58. [PMID: 24753416 PMCID: PMC4041468 DOI: 10.1093/nar/gku304] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 01/11/2023] Open
Abstract
Nuclear RNA export pathways in eukaryotes are often linked to the fate of a given RNA. Therefore, the choice of export pathway should be well-controlled to avoid an unfavorable effect on gene expression. Although some RNAs could be exported by more than one pathway, little is known about how the choice is regulated. This issue is highlighted when the human immunodeficiency virus type 1 (HIV-1) Rev protein induces the export of singly spliced and unspliced HIV-1 transcripts. How these RNAs are exported is not well understood because such transcripts should have the possibility of utilizing CRM1-dependent export via Rev or cellular TAP/NXF1-dependent export via the transcription/export (TREX) complex, or both. Here we found that Rev suppressed TAP/NXF1-dependent export of model RNA substrates that recapitulated viral transcripts. In this effect, Rev interacted with the cap-binding complex and inhibited the recruitment of the TREX complex. Thus, Rev controls the identity of the factor occupying the cap-proximal region that determines the RNA export pathway. This ribonucleoprotein remodeling activity of Rev may favor viral gene expression.
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Affiliation(s)
- Ichiro Taniguchi
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Naoto Mabuchi
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Mutsuhito Ohno
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
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27
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Fleta-Soriano E, Martinez JP, Hinkelmann B, Gerth K, Washausen P, Diez J, Frank R, Sasse F, Meyerhans A. The myxobacterial metabolite ratjadone A inhibits HIV infection by blocking the Rev/CRM1-mediated nuclear export pathway. Microb Cell Fact 2014; 13:17. [PMID: 24475978 PMCID: PMC3910686 DOI: 10.1186/1475-2859-13-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nuclear export of unspliced and partially spliced HIV-1 mRNA is mediated by the recognition of a leucine-rich nuclear export signal (NES) in the HIV Rev protein by the host protein CRM1/Exportin1. This makes the CRM1-Rev complex an attractive target for the development of new antiviral drugs. Here we tested the anti-HIV efficacy of ratjadone A, a CRM1 inhibitor derived from myxobacteria. RESULTS Ratjadone A inhibits HIV infection in vitro in a dose-dependent manner with EC₅₀ values at the nanomolar range. The inhibitory effect of ratjadone A occurs around 12 hours post-infection and is specific for the Rev/CRM1-mediated nuclear export pathway. By using a drug affinity responsive target stability (DARTS) assay we could demonstrate that ratjadone A interferes with the formation of the CRM1-Rev-NES complex by binding to CRM1 but not to Rev. CONCLUSION Ratjadone A exhibits strong anti-HIV activity but low selectivity due to toxic effects. Although this limits its potential use as a therapeutic drug, further studies with derivatives of ratjadones might help to overcome these difficulties in the future.
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Affiliation(s)
- Eric Fleta-Soriano
- Infection Biology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88 08003, Barcelona, Spain
| | - Javier P Martinez
- Infection Biology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88 08003, Barcelona, Spain
| | - Bettina Hinkelmann
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Klaus Gerth
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Peter Washausen
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Juana Diez
- Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ronald Frank
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Florenz Sasse
- Department of Chemical Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Meyerhans
- Infection Biology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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28
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Nawroth I, Mueller F, Basyuk E, Beerens N, Rahbek UL, Darzacq X, Bertrand E, Kjems J, Schmidt U. Stable assembly of HIV-1 export complexes occurs cotranscriptionally. RNA 2014; 20:1-8. [PMID: 24255166 PMCID: PMC3866638 DOI: 10.1261/rna.038182.113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 09/13/2013] [Indexed: 06/02/2023]
Abstract
The HIV-1 Rev protein mediates export of unspliced and singly spliced viral transcripts by binding to the Rev response element (RRE) and recruiting the cellular export factor CRM1. Here, we investigated the recruitment of Rev to the transcription sites of HIV-1 reporters that splice either post- or cotranscriptionally. In both cases, we observed that Rev localized to the transcription sites of the reporters and recruited CRM1. Rev and CRM1 remained at the reporter transcription sites when cells were treated with the splicing inhibitor Spliceostatin A (SSA), showing that the proteins associate with RNA prior to or during early spliceosome assembly. Fluorescence recovery after photobleaching (FRAP) revealed that Rev and CRM1 have similar kinetics as the HIV-1 RNA, indicating that Rev, CRM1, and RRE-containing RNAs are released from the site of transcription in one single export complex. These results suggest that cotranscriptional formation of a stable export complex serves as a means to ensure efficient export of unspliced viral RNAs.
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Affiliation(s)
- Isabel Nawroth
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
- Institut de Génétique Moléculaire de Montpellier?CNRS UMR 5535, 34293 Montpellier cedex 5, France
| | - Florian Mueller
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, 75230 Paris cedex 05, France
- Institut Pasteur, Imaging and Modeling Unit, CNRS URA 2582, 75015 Paris, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier?CNRS UMR 5535, 34293 Montpellier cedex 5, France
| | - Nancy Beerens
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Ulrik L. Rahbek
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Xavier Darzacq
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, 75230 Paris cedex 05, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier?CNRS UMR 5535, 34293 Montpellier cedex 5, France
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
| | - Ute Schmidt
- Institut de Génétique Moléculaire de Montpellier?CNRS UMR 5535, 34293 Montpellier cedex 5, France
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29
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Yin J, Zhu D, Zhang Z, Wang W, Fan J, Men D, Deng J, Wei H, Zhang XE, Cui Z. Imaging of mRNA-protein interactions in live cells using novel mCherry trimolecular fluorescence complementation systems. PLoS One 2013; 8:e80851. [PMID: 24260494 PMCID: PMC3829953 DOI: 10.1371/journal.pone.0080851] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
Live cell imaging of mRNA-protein interactions makes it possible to study posttranscriptional processes of cellular and viral gene expression under physiological conditions. In this study, red color mCherry-based trimolecular fluorescence complementation (TriFC) systems were constructed as new tools for visualizing mRNA-protein interaction in living cells using split mCherry fragments and HIV REV-RRE and TAT-TAR peptide-RNA interaction pairs. The new mCherry TriFC systems were successfully used to image RNA-protein interactions such as that between influenza viral protein NS1 and the 5' UTR of influenza viral mRNAs NS, M, and NP. Upon combination of an mCherry TriFC system with a Venus TriFC system, multiple mRNA-protein interactions could be detected simultaneously in the same cells. Then, the new mCherry TriFC system was used for imaging of interactions between influenza A virus mRNAs and some of adapter proteins in cellular TAP nuclear export pathway in live cells. Adapter proteins Aly and UAP56 were found to associate with three kinds of viral mRNAs. Another adapter protein, splicing factor 9G8, only interacted with intron-containing spliced M2 mRNA. Co-immunoprecipitation assays with influenza A virus-infected cells confirmed these interactions. This study provides long-wavelength-spectrum TriFC systems as new tools for visualizing RNA-protein interactions in live cells and help to understand the nuclear export mechanism of influenza A viral mRNAs.
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Affiliation(s)
- Juan Yin
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Duanhao Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Zhiping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jinyu Fan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jiaoyu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Hongping Wei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xian-En Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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30
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Fang X, Wang J, O’Carroll IP, Mitchell M, Zuo X, Wang Y, Yu P, Liu Y, Rausch JW, Dyba MA, Kjems J, Schwieters CD, Seifert S, Winans RE, Watts NR, Stahl SJ, Wingfield PT, Byrd RA, Le Grice SF, Rein A, Wang YX. An unusual topological structure of the HIV-1 Rev response element. Cell 2013; 155:594-605. [PMID: 24243017 PMCID: PMC3918456 DOI: 10.1016/j.cell.2013.10.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/22/2013] [Accepted: 10/07/2013] [Indexed: 01/15/2023]
Abstract
Nuclear export of unspliced and singly spliced viral mRNA is a critical step in the HIV life cycle. The structural basis by which the virus selects its own mRNA among more abundant host cellular RNAs for export has been a mystery for more than 25 years. Here, we describe an unusual topological structure that the virus uses to recognize its own mRNA. The viral Rev response element (RRE) adopts an "A"-like structure in which the two legs constitute two tracks of binding sites for the viral Rev protein and position the two primary known Rev-binding sites ~55 Å apart, matching the distance between the two RNA-binding motifs in the Rev dimer. Both the legs of the "A" and the separation between them are required for optimal RRE function. This structure accounts for the specificity of Rev for the RRE and thus the specific recognition of the viral RNA.
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MESH Headings
- Active Transport, Cell Nucleus
- Base Sequence
- Binding Sites
- Cell Nucleus/metabolism
- HEK293 Cells
- HIV-1/chemistry
- HIV-1/genetics
- Humans
- Molecular Sequence Data
- Nuclear Pore/metabolism
- Nucleic Acid Conformation
- RNA Folding
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Scattering, Small Angle
- X-Ray Diffraction
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Xianyang Fang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jinbu Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ina P. O’Carroll
- Retroviral Assembly Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Michelle Mitchell
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Xiaobing Zuo
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Wang
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ping Yu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- Structural Biophysics Laboratory, SAIC-Frederick, Frederick, MD 21702, USA
| | - Yu Liu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jason W. Rausch
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Marzena A. Dyba
- Structural Biophysics Laboratory, SAIC-Frederick, Frederick, MD 21702, USA
| | - Jørgen Kjems
- Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus C, Denmark
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Informational Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Soenke Seifert
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Randall E. Winans
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Norman R. Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen J. Stahl
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - R. Andrew Byrd
- Macromolecular NMR Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Stuart F.J. Le Grice
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Alan Rein
- Retroviral Assembly Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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31
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Zhou X, Luo J, Mills L, Wu S, Pan T, Geng G, Zhang J, Luo H, Liu C, Zhang H. DDX5 facilitates HIV-1 replication as a cellular co-factor of Rev. PLoS One 2013; 8:e65040. [PMID: 23741449 PMCID: PMC3669200 DOI: 10.1371/journal.pone.0065040] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/21/2013] [Indexed: 12/21/2022] Open
Abstract
HIV-1 Rev plays an important role in the late phase of HIV-1 replication, which facilitates export of unspliced viral mRNAs from the nucleus to cytoplasm in infected cells. Recent studies have shown that DDX1 and DDX3 are co-factors of Rev for the export of HIV-1 transcripts. In this report, we have demonstrated that DDX5 (p68), which is a multifunctional DEAD-box RNA helicase, functions as a new cellular co-factor of HIV-1 Rev. We found that DDX5 affects Rev function through the Rev-RRE axis and subsequently enhances HIV-1 replication. Confocal microscopy and co-immunoprecipitation analysis indicated that DDX5 binds to Rev and this interaction is largely dependent on RNA. If the DEAD-box motif of DDX5 is mutated, DDX5 loses almost all of its ability to bind to Rev, indicating that the DEAD-box motif of DDX5 is required for the interaction between DDX5 and Rev. Our data indicate that interference of DDX5-Rev interaction could reduce HIV-1 replication and potentially provide a new molecular target for anti-HIV-1 therapeutics.
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Affiliation(s)
- Xiuxia Zhou
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, First Affiliated Hospital, Soochow University, Suzhou, China
| | - Juan Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Lisa Mills
- Center for Human Virology, Division of Infectious Diseases, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Shuangxin Wu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ting Pan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Guannan Geng
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jim Zhang
- Center for Human Virology, Division of Infectious Diseases, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Haihua Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- * E-mail: (HZ); (CL)
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Human Virology, Division of Infectious Diseases, Department of Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail: (HZ); (CL)
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32
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Lin MH, Sivakumaran H, Apolloni A, Wei T, Jans DA, Harrich D. Nullbasic, a potent anti-HIV tat mutant, induces CRM1-dependent disruption of HIV rev trafficking. PLoS One 2012; 7:e51466. [PMID: 23251541 PMCID: PMC3519632 DOI: 10.1371/journal.pone.0051466] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 11/02/2012] [Indexed: 12/30/2022] Open
Abstract
Nullbasic, a mutant of the HIV-1 Tat protein, has anti-HIV-1 activity through mechanisms that include inhibition of Rev function and redistribution of the HIV-1 Rev protein from the nucleolus to the nucleoplasm and cytoplasm. Here we investigate the mechanism of this effect for the first time, establishing that redistribution of Rev by Nullbasic is not due to direct interaction between the two proteins. Rather, Nullbasic affects subcellular localization of cellular proteins that regulate Rev trafficking. In particular, Nullbasic induced redistribution of exportin 1 (CRM1), nucleophosmin (B23) and nucleolin (C23) from the nucleolus to the nucleus when Rev was coexpressed, but never in its absence. Inhibition of the Rev:CRM1 interaction by leptomycin B or a non-interacting RevM10 mutant completely blocked redistribution of Rev by Nullbasic. Finally, Nullbasic did not inhibit importin β- or transportin 1-mediated nuclear import, suggesting that cytoplasmic accumulation of Rev was due to increased export by CRM1. Overall, our data support the conclusion that CRM1-dependent subcellular redistribution of Rev from the nucleolus by Nullbasic is not through general perturbation of either nuclear import or export. Rather, Nullbasic appears to interact with and disrupt specific components of a Rev trafficking complex required for its nucleocytoplasmic shuttling and, in particular, its nucleolar accumulation.
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Affiliation(s)
- Min-Hsuan Lin
- Queensland Institute of Medical Research, Molecular Virology Laboratory, Herston, Brisbane, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Haran Sivakumaran
- Queensland Institute of Medical Research, Molecular Virology Laboratory, Herston, Brisbane, Australia
| | - Ann Apolloni
- Queensland Institute of Medical Research, Molecular Virology Laboratory, Herston, Brisbane, Australia
| | - Ting Wei
- Queensland Institute of Medical Research, Molecular Virology Laboratory, Herston, Brisbane, Australia
| | - David A. Jans
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - David Harrich
- Queensland Institute of Medical Research, Molecular Virology Laboratory, Herston, Brisbane, Australia
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33
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Hoffmann D, Schwarck D, Banning C, Brenner M, Mariyanna L, Krepstakies M, Schindler M, Millar DP, Hauber J. Formation of trans-activation competent HIV-1 Rev:RRE complexes requires the recruitment of multiple protein activation domains. PLoS One 2012; 7:e38305. [PMID: 22675540 PMCID: PMC3366918 DOI: 10.1371/journal.pone.0038305] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/07/2012] [Indexed: 12/13/2022] Open
Abstract
The HIV-1 Rev trans-activator is a nucleocytoplasmic shuttle protein that is essential for virus replication. Rev directly binds to unspliced and incompletely spliced viral RNA via the cis-acting Rev Response Element (RRE) sequence. Subsequently, Rev oligomerizes cooperatively and interacts with the cellular nuclear export receptor CRM1. In addition to mediating nuclear RNA export, Rev also affects the stability, translation and packaging of Rev-bound viral transcripts. Although it is established that Rev function requires the multimeric assembly of Rev molecules on the RRE, relatively little is known about how many Rev monomers are sufficient to form a trans-activation competent Rev:RRE complex, or which specific activity of Rev is affected by its oligomerization. We here analyzed by functional studies how homooligomer formation of Rev affects the trans-activation capacity of this essential HIV-1 regulatory protein. In a gain-of-function approach, we fused various heterologous dimerization domains to an otherwise oligomerization-defective Rev mutant and were able to demonstrate that oligomerization of Rev is not required per se for the nuclear export of this viral trans-activator. In contrast, however, the formation of Rev oligomers on the RRE is a precondition to trans-activation by directly affecting the nuclear export of Rev-regulated mRNA. Moreover, experimental evidence is provided showing that at least two protein activation domains are required for the formation of trans-activation competent Rev:RRE complexes. The presented data further refine the model of Rev trans-activation by directly demonstrating that Rev oligomerization on the RRE, thereby recruiting at least two protein activation domains, is required for nuclear export of unspliced and incompletely spliced viral RNA.
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Affiliation(s)
- Dirk Hoffmann
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Doreen Schwarck
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Carina Banning
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Matthias Brenner
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Lakshmikanth Mariyanna
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Marcel Krepstakies
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Michael Schindler
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - David P. Millar
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Joachim Hauber
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail:
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34
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Delgado E, Carrera C, Nebreda P, Fernández-García A, Pinilla M, García V, Pérez-Álvarez L, Thomson MM. Identification of new splice sites used for generation of rev transcripts in human immunodeficiency virus type 1 subtype C primary isolates. PLoS One 2012; 7:e30574. [PMID: 22363449 PMCID: PMC3281843 DOI: 10.1371/journal.pone.0030574] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 12/21/2011] [Indexed: 12/16/2022] Open
Abstract
The HIV-1 primary transcript undergoes a complex splicing process by which more than 40 different spliced RNAs are generated. One of the factors contributing to HIV-1 splicing complexity is the multiplicity of 3′ splice sites (3'ss) used for generation of rev RNAs, with two 3'ss, A4a and A4b, being most commonly used, a third site, A4c, used less frequently, and two additional sites, A4d and A4e, reported in only two and one isolates, respectively. HIV-1 splicing has been analyzed mostly in subtype B isolates, and data on other group M clades are lacking. Here we examine splice site usage in three primary isolates of subtype C, the most prevalent clade in the HIV-1 pandemic, by using an in vitro infection assay of peripheral blood mononuclear cells. Viral spliced RNAs were identified by RT-PCR amplification using a fluorescently-labeled primer and software analyses and by cloning and sequencing the amplified products. The results revealed that splice site usage for generation of rev transcripts in subtype C differs from that reported for subtype B, with most rev RNAs using two previously unreported 3'ss, one located 7 nucleotides upstream of 3'ss A4a, designated A4f, preferentially used by two isolates, and another located 14 nucleotides upstream of 3'ss A4c, designated A4g, preferentially used by the third isolate. A new 5′ splice site, designated D2a, was also identified in one virus. Usage of the newly identified splice sites is consistent with sequence features commonly found in subtype C viruses. These results show that splice site usage may differ between HIV-1 subtypes.
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Affiliation(s)
- Elena Delgado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Cristina Carrera
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Paloma Nebreda
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Milagros Pinilla
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Valentina García
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Lucía Pérez-Álvarez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Michael M. Thomson
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail:
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35
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Abstract
HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2). We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.
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MESH Headings
- Amino Acid Motifs/genetics
- Amino Acid Sequence
- Binding Sites/genetics
- CREB-Binding Protein/metabolism
- Calcium-Calmodulin-Dependent Protein Kinases/metabolism
- Calmodulin/metabolism
- Casein Kinase II/metabolism
- Databases, Protein
- Human Immunodeficiency Virus Proteins/chemistry
- Human Immunodeficiency Virus Proteins/genetics
- Human Immunodeficiency Virus Proteins/metabolism
- Humans
- Hydrophobic and Hydrophilic Interactions
- Mitogen-Activated Protein Kinase 1/metabolism
- Models, Molecular
- Protein Binding
- Protein Interaction Mapping/methods
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Proteins/genetics
- Proteins/metabolism
- env Gene Products, Human Immunodeficiency Virus/chemistry
- env Gene Products, Human Immunodeficiency Virus/genetics
- env Gene Products, Human Immunodeficiency Virus/metabolism
- gag Gene Products, Human Immunodeficiency Virus/chemistry
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
- nef Gene Products, Human Immunodeficiency Virus/chemistry
- nef Gene Products, Human Immunodeficiency Virus/genetics
- nef Gene Products, Human Immunodeficiency Virus/metabolism
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- tat Gene Products, Human Immunodeficiency Virus/chemistry
- tat Gene Products, Human Immunodeficiency Virus/genetics
- tat Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Mahdi Sarmady
- Center for Integrated Bioinformatics, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - William Dampier
- Center for Integrated Bioinformatics, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Aydin Tozeren
- Center for Integrated Bioinformatics, Drexel University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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36
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Coyle JH, Bor YC, Rekosh D, Hammarskjold ML. The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway. RNA 2011; 17:1344-56. [PMID: 21613532 PMCID: PMC3138570 DOI: 10.1261/rna.2616111] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 04/18/2011] [Indexed: 05/22/2023]
Abstract
Post-transcriptional regulation of mRNA includes restriction mechanisms to prevent export and expression of mRNAs that are incompletely spliced. Here we present evidence that the mammalian protein Tpr is involved in this restriction. To study the role of Tpr in export of mRNA with retained introns, we used reporters in which the mRNA was exported either via the Nxf1/Nxt1 pathway using a CTE or via the Crm1 pathway using Rev/RRE. Our data show that even modest knockdown of Tpr using RNAi leads to a significant increase in export and translation from the mRNA containing the CTE. In contrast, Tpr perturbation has no effect on export of mRNA containing the RRE, either in the absence or presence of Rev. Also, no effects were observed on export of a completely spliced mRNA. Taken together, our results indicate that Tpr plays an important role in quality control of mRNA trafficked on the Nxf1 pathway.
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Affiliation(s)
- John H. Coyle
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Yeou-Cherng Bor
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA
- Corresponding author.E-mail .
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37
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Urcuqui-Inchima S, Patiño C, Zapata X, García MP, Arteaga J, Chamot C, Kumar A, Hernandez-Verdun D. Production of HIV particles is regulated by altering sub-cellular localization and dynamics of Rev induced by double-strand RNA binding protein. PLoS One 2011; 6:e16686. [PMID: 21364984 PMCID: PMC3043055 DOI: 10.1371/journal.pone.0016686] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Accepted: 01/11/2011] [Indexed: 02/06/2023] Open
Abstract
Human immunodeficiency virus (HIV)-1 encoded Rev is essential for export from the nucleus to the cytoplasm, of unspliced and singly spliced transcripts coding for structural and nonstructural viral proteins. This process is spatially and temporally coordinated resulting from the interactions between cellular and viral proteins. Here we examined the effects of the sub-cellular localization and dynamics of Rev on the efficiency of nucleocytoplasmic transport of HIV-1 Gag transcripts and virus particle production. Using confocal microscopy and fluorescence recovery after bleaching (FRAP), we report that NF90ctv, a cellular protein involved in Rev function, alters both the sub-cellular localization and dynamics of Rev in vivo, which drastically affects the accumulation of the viral protein p24. The CRM1–dependent nuclear export of Gag mRNA linked to the Rev Response Element (RRE) is dependent on specific domains of the NF90ctv protein. Taken together, our results demonstrate that the appropriate intracellular localization and dynamics of Rev could regulate Gag assembly and HIV-1 replication.
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Affiliation(s)
- Silvio Urcuqui-Inchima
- Grupo de Inmunoviología, Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia.
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38
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Güttler T, Madl T, Neumann P, Deichsel D, Corsini L, Monecke T, Ficner R, Sattler M, Görlich D. NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1. Nat Struct Mol Biol 2010; 17:1367-76. [PMID: 20972448 DOI: 10.1038/nsmb.1931] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Accepted: 09/07/2010] [Indexed: 12/24/2022]
Abstract
Classic nuclear export signals (NESs) confer CRM1-dependent nuclear export. Here we present crystal structures of the RanGTP-CRM1 complex alone and bound to the prototypic PKI or HIV-1 Rev NESs. These NESs differ markedly in the spacing of their key hydrophobic (Φ) residues, yet CRM1 recognizes them with the same rigid set of five Φ pockets. The different Φ spacings are compensated for by different conformations of the bound NESs: in the case of PKI, an α-helical conformation, and in the case of Rev, an extended conformation with a critical proline docking into a Φ pocket. NMR analyses of CRM1-bound and CRM1-free PKI NES suggest that CRM1 selects NES conformers that pre-exist in solution. Our data lead to a new structure-based NES consensus, and explain why NESs differ in their affinities for CRM1 and why supraphysiological NESs bind the exportin so tightly.
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Affiliation(s)
- Thomas Güttler
- Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
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39
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Daugherty MD, Liu B, Frankel AD. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat Struct Mol Biol 2010; 17:1337-42. [PMID: 20953181 PMCID: PMC2988976 DOI: 10.1038/nsmb.1902] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 08/06/2010] [Indexed: 12/28/2022]
Abstract
HIV replication requires nuclear export of unspliced viral RNAs to translate structural proteins and package genomic RNA. Export is mediated by cooperative binding of the Rev protein to the Rev response element (RRE) RNA, to form a highly specific oligomeric ribonucleoprotein (RNP) that binds to the Crm1 host export factor. To understand how protein oligomerization generates cooperativity and specificity for RRE binding, we solved the crystal structure of a Rev dimer at 2.5-Å resolution. The dimer arrangement organizes arginine-rich helices at the ends of a V-shaped assembly to bind adjacent RNA sites and structurally couple dimerization and RNA recognition. A second protein-protein interface arranges higher-order Rev oligomers to act as an adaptor to the host export machinery, with viral RNA bound to one face and Crm1 to another, the oligomers thereby using small, interconnected modules to physically arrange the RNP for efficient export.
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MESH Headings
- Amino Acid Sequence
- Binding Sites
- Conserved Sequence
- Crystallography, X-Ray
- Dimerization
- HIV-1/physiology
- Karyopherins/metabolism
- Models, Molecular
- Molecular Sequence Data
- Protein Structure, Tertiary
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Cytoplasmic and Nuclear/metabolism
- Response Elements
- Sequence Alignment
- Virus Replication
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- rev Gene Products, Human Immunodeficiency Virus/physiology
- Exportin 1 Protein
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Affiliation(s)
- Matthew D. Daugherty
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco San Francisco, CA 94158
| | - Bella Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco San Francisco, CA 94158
| | - Alan D. Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco San Francisco, CA 94158
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40
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41
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Levin A, Hayouka Z, Helfer M, Brack-Werner R, Friedler A, Loyter A. Stimulation of the HIV-1 integrase enzymatic activity and cDNA integration by a peptide derived from the integrase protein. Biopolymers 2010; 93:740-51. [PMID: 20517955 DOI: 10.1002/bip.21469] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Here we describe the features of a peptide that was selected from the human immunodeficiency virus Type 1 (HIV-1) Integrase (IN) peptide library which interacts with both, the viral Rev and IN proteins. Because of its ability to stimulate the IN enzymatic activity this peptide was designated INS (IN stimulatory). Modification of its amino acid sequence revealed that replacement of its C-terminal lysine by glutamic acid (INS K188E) converts it from a stimulatory peptide to an inhibitory one. Both peptides promoted the dissociation of a previously described complex formed between Rev and IN whose formation results in IN inactivation. INS and INS K188E penetrated HIV-1-infected cells and caused stimulation and inhibition of viral genome integration, respectively. Using cultured cells infected with a DeltaRev HIV revealed that INS can directly activate the viral IN. These results suggest that the stimulatory effect of INS in wild-type virus-infected cells is due to a dual effect: it dissociates the inactive Rev-IN complex and directly activates the free IN.
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Affiliation(s)
- Aviad Levin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Takeda A, Sarma NJ, Abdul-Nabi AM, Yaseen NR. Inhibition of CRM1-mediated nuclear export of transcription factors by leukemogenic NUP98 fusion proteins. J Biol Chem 2010; 285:16248-57. [PMID: 20233715 PMCID: PMC2871492 DOI: 10.1074/jbc.m109.048785] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 02/15/2010] [Indexed: 12/29/2022] Open
Abstract
NUP98 is a nucleoporin that plays complex roles in the nucleocytoplasmic trafficking of macromolecules. Rearrangements of the NUP98 gene in human leukemia result in the expression of numerous fusion oncoproteins whose effect on nucleocytoplasmic trafficking is poorly understood. The present study was undertaken to determine the effects of leukemogenic NUP98 fusion proteins on CRM1-mediated nuclear export. NUP98-HOXA9, a prototypic NUP98 fusion, inhibited the nuclear export of two known CRM1 substrates: mutated cytoplasmic nucleophosmin and HIV-1 Rev. In vitro binding assays revealed that NUP98-HOXA9 binds CRM1 through the FG repeat motif in a Ran-GTP-dependent manner similar to but stronger than the interaction between CRM1 and its export substrates. Two NUP98 fusions, NUP98-HOXA9 and NUP98-DDX10, whose fusion partners are structurally and functionally unrelated, interacted with endogenous CRM1 in myeloid cells as shown by co-immunoprecipitation. These leukemogenic NUP98 fusion proteins interacted with CRM1, Ran, and the nucleoporin NUP214 in a manner fundamentally different from that of wild-type NUP98. NUP98-HOXA9 and NUP98-DDX10 formed characteristic aggregates within the nuclei of a myeloid cell line and primary human CD34+ cells and caused aberrant localization of CRM1 to these aggregates. These NUP98 fusions caused nuclear accumulation of two transcription factors, NFAT and NFkappaB, that are regulated by CRM1-mediated export. The nuclear entrapment of NFAT and NFkappaB correlated with enhanced transcription from promoters responsive to these transcription factors. Taken together, the results suggest a new mechanism by which NUP98 fusions dysregulate transcription and cause leukemia, namely, inhibition of CRM1-mediated nuclear export with aberrant nuclear retention of transcriptional regulators.
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MESH Headings
- Active Transport, Cell Nucleus/genetics
- Amino Acid Motifs
- Antigens, CD34
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cell Nucleus/pathology
- Guanosine Triphosphate/genetics
- Guanosine Triphosphate/metabolism
- HIV-1/genetics
- HIV-1/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- K562 Cells
- Karyopherins/genetics
- Karyopherins/metabolism
- Leukemia/genetics
- Leukemia/metabolism
- Leukemia/pathology
- Mutation
- NF-kappa B/genetics
- NF-kappa B/metabolism
- NFATC Transcription Factors/genetics
- NFATC Transcription Factors/metabolism
- Nuclear Pore Complex Proteins/genetics
- Nuclear Pore Complex Proteins/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Promoter Regions, Genetic/genetics
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Transcription, Genetic/genetics
- ran GTP-Binding Protein/genetics
- ran GTP-Binding Protein/metabolism
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- Exportin 1 Protein
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Affiliation(s)
- Akiko Takeda
- From the Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Nayan J. Sarma
- From the Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Anmaar M. Abdul-Nabi
- From the Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Nabeel R. Yaseen
- From the Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110
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43
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Liu ZL, Li XY, Zhang Q, Jia PP, Yang L, Wei XL, Jiang JD, Cen S. [Establishment and application of a screening anti-HIV-1 drug model targeted nuclear trafficking of virus RNA]. Yao Xue Xue Bao 2010; 45:257-62. [PMID: 21351437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The HIV-1 Rev protein facilitates nuclear export of unspliced and singly spliced viral transcripts containing RRE RNA through the CRM1 export pathway. Inhibition of Rev-mediated RNA nuclear export can arrest HIV-1 transcriptional process, which clearly, reveals a target for anti-HIV drug development. In this work, a cell-based assay has been established for screening anti-HIV compounds targeting the Rev-mediated RNA nuclear export. This assay utilized a codon-optimized green fluorescent protein (GFP) as reporter gene, which expression is in a Rev-dependent manner. Any compound that inhibits the Rev-mediated RNA nuclear export is identified by reducing emission of GFP. The Z' score of this model is 0.8220. Three thousands compounds were screened and the positive rate was 9.3% with a cutoff at 50% inhibition. IMB7C7, one of the positive compounds, efficiently inhibits viral production from HIV-1 infected cells.
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Affiliation(s)
- Zhen-long Liu
- Department of Immunology, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Vallejos M, Ramdohr P, Valiente-Echeverría F, Tapia K, Rodriguez FE, Lowy F, Huidobro-Toro JP, Dangerfield JA, López-Lastra M. The 5'-untranslated region of the mouse mammary tumor virus mRNA exhibits cap-independent translation initiation. Nucleic Acids Res 2010; 38:618-32. [PMID: 19889724 PMCID: PMC2811009 DOI: 10.1093/nar/gkp890] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 09/19/2009] [Accepted: 10/05/2009] [Indexed: 01/04/2023] Open
Abstract
In this study, we demonstrate the identification of an internal ribosome entry site (IRES) within the 5'-untranslated region (5'-UTR) of the mouse mammary tumor virus (MMTV). The 5'-UTR of the full-length mRNA derived from the infectious, complete MMTV genome was cloned into a dual luciferase reporter construct containing an upstream Renilla luciferase gene (RLuc) and a downstream firefly luciferase gene (FLuc). In rabbit reticulocyte lysate, the MMTV 5'-UTR was capable of driving translation of the second cistron. In vitro translational activity from the MMTV 5'-UTR was resistant to the addition of m(7)GpppG cap-analog and cleavage of eIF4G by foot-and-mouth disease virus (FMDV) L-protease. IRES activity was also demonstrated in the Xenopus laevis oocyte by micro-injection of capped and polyadenylated bicistronic RNAs harboring the MMTV-5'-UTR. Finally, transfection assays showed that the MMTV-IRES exhibits cell type-dependent translational activity, suggesting a requirement for as yet unidentified cellular factors for its optimal function.
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Affiliation(s)
- Maricarmen Vallejos
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
| | - Pablo Ramdohr
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
| | - Fernando Valiente-Echeverría
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
| | - Karla Tapia
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
| | - Felipe E. Rodriguez
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
| | - Fernando Lowy
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
| | - J. Pablo Huidobro-Toro
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
| | - John A. Dangerfield
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Centro de Investigaciones Médicas, Pontificia Universidad Católica de Chile, Marcoleta 391, Centro de Regulación Celular y Patología, J. V. Luco e Instituto Milenio de Biología Fundamental y Aplicada, MIFAB, Departamento de Fisiología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago, Chile and Institute of Virology, University of Veterinary Sciences, Veterinaerplatz 1, A-1210 Vienna, Austria and Christian Doppler Laboratory Foreign Module for Virology-Nanotechnology, #05-518 Centros, 20 Biopolis Way, 138668 Singapore
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Levin A, Hayouka Z, Helfer M, Brack-Werner R, Friedler A, Loyter A. Peptides derived from HIV-1 integrase that bind Rev stimulate viral genome integration. PLoS One 2009; 4:e4155. [PMID: 19127291 PMCID: PMC2607543 DOI: 10.1371/journal.pone.0004155] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 12/02/2008] [Indexed: 01/05/2023] Open
Abstract
Background The human immunodeficiency virus type 1 (HIV-1) integrase protein (IN), catalyzes the integration of viral DNA into the host cell genome. IN catalyzes the first step of the integration process, namely the 3′-end processing in which IN removes a pGT dinucleotide from the 3′ end of each viral long terminal repeat (LTR). Following nuclear import of the viral preintegration complex, the host chromosomal DNA becomes accessible to the viral cDNA and the second step of the integration process, namely the strand-transfer step takes place. This ordered sequence of events, centered on integration, is mandatory for HIV replication. Methodology/Principal Findings Using an integrase peptide library, we selected two peptides, designated INr-1 and INr-2, which interact with the Rev protein and probably mediate the Rev-integrase interaction. Using an in-vitro assay system, we show that INr-1 and INr-2 are able to abrogate the inhibitory effects exerted by Rev and Rev-derived peptides on integrase activity. Both INr-1 and INr-2 were found to be cell-permeable and nontoxic, allowing a study of their effect in HIV-1-infected cultured cells. Interestingly, both INr peptides stimulated virus infectivity as estimated by production of the viral P24 protein, as well as by determination of the appearance of newly formed virus particles. Furthermore, kinetics studies revealed that the cell-permeable INr peptides enhance the integration process, as was indeed confirmed by direct determination of viral DNA integration by real-time PCR. Conclusions/Significance The results of the present study raise the possibility that in HIV-infected cells, the Rev protein may be involved in the integration of proviral DNA by controlling/regulating the activity of the integrase. Release from such inhibition leads to stimulation of IN activity and multiple viral DNA integration events.
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Affiliation(s)
- Aviad Levin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zvi Hayouka
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Markus Helfer
- Institute of Virology, Helmholtz Center Munich - German Research Center for Environmental Health, Ingolstaedter Landstr, Neuherberg, Germany
| | - Ruth Brack-Werner
- Institute of Virology, Helmholtz Center Munich - German Research Center for Environmental Health, Ingolstaedter Landstr, Neuherberg, Germany
- Clinical Cooperation Group ‘Immune-Monitoring’, Helmholtz Center Munich - German Research Center for Environmental Health, Ingolstaedter Landstr, Neuherberg, Germany
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Abraham Loyter
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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46
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Van Neck T, Pannecouque C, Vanstreels E, Stevens M, Dehaen W, Daelemans D. Inhibition of the CRM1-mediated nucleocytoplasmic transport by N-azolylacrylates: structure-activity relationship and mechanism of action. Bioorg Med Chem 2008; 16:9487-97. [PMID: 18835718 DOI: 10.1016/j.bmc.2008.09.051] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 09/12/2008] [Accepted: 09/16/2008] [Indexed: 12/01/2022]
Abstract
CRM1-mediated nucleocytoplasmic transport plays an important role in many cellular processes and diseases. To investigate the structural basis required for the inhibition of the CRM1-mediated nuclear export we have synthesized analogs of a previously identified small molecule lead compound and monitored their activity against the Rev function of the human immunodeficiency virus. Microscopy studies show that the active congeners of this series inhibit the nucleocytoplasmic transport of Rev and the co-localization between Rev and CRM1 in living cells. Mechanism of action studies show their interaction with the Cys528 residue of CRM1 involving a Michael-addition type of reaction. However, structure-activity relationship demonstrates strict constraints to the structure of the inhibitors, and shows that activity is not solely correlated to Michael-addition suggesting a more complex mechanism of action. Our results are suggestive for the existence of a well-defined interaction at the CRM1-NES binding site. In addition, the most selective congener inhibited the HIV-1 production in latently infected cells. These specific CRM1 inhibitors are of interest as tool for analyzing the mechanisms of post-transcriptional control of gene expression and provide insight in the design of new agents.
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Affiliation(s)
- Tine Van Neck
- Laboratory of Organic Synthesis, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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Furnes C, Andresen V, Szilvay AM. Functional rescue of an oligomerization-defective HIV-1 Rev mutant by fusion with an oligomeric tag. Arch Virol 2007; 153:357-62. [PMID: 18094922 DOI: 10.1007/s00705-007-1095-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 10/05/2007] [Indexed: 10/22/2022]
Abstract
The HIV-1 wild-type Rev and the negative oligomerization-defective mutant RevM4 were fused to enhanced green fluorescent protein (EGFP) and the tetrameric red fluorescent protein (DsRed1) followed by examination of their intracellular localization and Rev activity. As previously shown, fusion of EGFP to Rev and RevM4 did not affect the biological activity. Fusion of DsRed1 to Rev inhibited activity, and interestingly, fusion of DsRed1 to RevM4 restored activity. Based on these results, a model is proposed suggesting how RevM4-DsRed1 is able to rescue Rev activity through oligomerization on the viral RNA.
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Affiliation(s)
- C Furnes
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
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48
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Cao Y, Liu XY. [HIV-1 Rev and related inhibitors]. Yao Xue Xue Bao 2007; 42:347-51. [PMID: 17633198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
HIV-1 Rev is an indispensable regulatory factor of the virion protein expression. The interaction between Rev and RRE RNA accelerates the nuclear export of viral mRNA. The unspliced and singly spliced mRNA will be degraded in the absence of Rev, resulting in the interception of HIV-1 replication at the same time. The pivotal role that Rev plays in HIV-1 replication as a trans-acting factor makes it a new target in the research of AIDS drugs. In this review, the function of Rev, Rev-RRE interaction, as well as their related inhibitors are reported.
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Affiliation(s)
- Yuan Cao
- Institute of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan 250012, China
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49
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Moehle K, Athanassiou Z, Patora K, Davidson A, Varani G, Robinson JA. Design of beta-hairpin peptidomimetics that inhibit binding of alpha-helical HIV-1 Rev protein to the rev response element RNA. Angew Chem Int Ed Engl 2007; 46:9101-4. [PMID: 17893894 PMCID: PMC3809837 DOI: 10.1002/anie.200702801] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Kerstin Moehle
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland), Fax: (+41) 44-1635-6833
| | | | - Krystyna Patora
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich; (Switzerland), Fax: (+41) 44-1635-6833
| | - Amy Davidson
- Department of Chemistry, University of Washington, Seattle, WA 98195 (USA)
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195 (USA)
- Department of Biochemistry, University of Washington, Seattle, WA 98195 (USA)
| | - John A. Robinson
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland), Fax: (+41) 44-1635-6833
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