1
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Kmiec D, Kirchhoff F. Antiviral factors and their counteraction by HIV-1: many uncovered and more to be discovered. J Mol Cell Biol 2024; 16:mjae005. [PMID: 38318650 PMCID: PMC11334937 DOI: 10.1093/jmcb/mjae005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 02/04/2024] [Indexed: 02/07/2024] Open
Abstract
Extensive studies on HIV-1 have led to the discovery of a variety of structurally and functionally diverse innate defense factors that target various steps of the retroviral replication cycle. Some of them, such as APOBEC3, tetherin, and SERINC5, are well established. Their importance is evident from the fact that HIV-1 uses its accessory proteins Vif, Vpu, and Nef to counteract them. However, the list of antiviral factors is constantly increasing, and accumulating evidence suggests that innate defense mechanisms, which restrict HIV-1 and/or are counteracted by viral proteins, remain to be discovered. These antiviral factors are relevant to diseases other than HIV/AIDS, since they are commonly active against various viral pathogens. In this review, we provide an overview of recently reported antiretroviral factors and viral countermeasures, present the evidence suggesting that more innate defense mechanisms remain to be discovered, and discuss why this is a challenging but rewarding task.
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Affiliation(s)
- Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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2
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Konno Y, Uriu K, Chikata T, Takada T, Kurita JI, Ueda MT, Islam S, Yang Tan BJ, Ito J, Aso H, Kumata R, Williamson C, Iwami S, Takiguchi M, Nishimura Y, Morita E, Satou Y, Nakagawa S, Koyanagi Y, Sato K. Two-step evolution of HIV-1 budding system leading to pandemic in the human population. Cell Rep 2024; 43:113697. [PMID: 38294901 DOI: 10.1016/j.celrep.2024.113697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/19/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
The pandemic HIV-1, HIV-1 group M, emerged from a single spillover event of its ancestral lentivirus from a chimpanzee. During human-to-human spread worldwide, HIV-1 diversified into multiple subtypes. Here, our interdisciplinary investigation mainly sheds light on the evolutionary scenario of the viral budding system of HIV-1 subtype C (HIV-1C), a most successfully spread subtype. Of the two amino acid motifs for HIV-1 budding, the P(T/S)AP and YPxL motifs, HIV-1C loses the YPxL motif. Our data imply that HIV-1C might lose this motif to evade immune pressure. Additionally, the P(T/S)AP motif is duplicated dependently of the level of HIV-1 spread in the human population, and >20% of HIV-1C harbored the duplicated P(T/S)AP motif. We further show that the duplication of the P(T/S)AP motif is caused by the expansion of the CTG triplet repeat. Altogether, our results suggest that HIV-1 has experienced a two-step evolution of the viral budding process during human-to-human spread worldwide.
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Affiliation(s)
- Yoriyuki Konno
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Takayuki Chikata
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Toru Takada
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Saiful Islam
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Benjy Jek Yang Tan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Hirofumi Aso
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Ryuichi Kumata
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan; MIRAI, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Yorifumi Satou
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan; CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan.
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3
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Abstract
Human and simian immunodeficiency viruses (HIVs and SIVs, respectively) encode several small proteins (Vif, Vpr, Nef, Vpu, and Vpx) that are called accessory because they are not generally required for viral replication in cell culture. However, they play complex and important roles for viral immune evasion and spread in vivo. Here, we discuss the diverse functions and the relevance of the viral protein U (Vpu) that is expressed from a bicistronic RNA during the late stage of the viral replication cycle and found only in HIV-1 and closely related SIVs. It is well established that Vpu counteracts the restriction factor tetherin, mediates degradation of the primary viral CD4 receptors, and inhibits activation of the transcription factor nuclear factor kappa B. Recent studies identified additional activities and provided new insights into the sophisticated mechanisms by which Vpu enhances and prolongs the release of fully infectious viral particles. In addition, it has been shown that Vpu prevents superinfection not only by degrading CD4 but also by modulating DNA repair mechanisms to promote degradation of nuclear viral complementary DNA in cells that are already productively infected.
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Affiliation(s)
- Meta Volcic
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany;
| | - Lisa Wiesmüller
- Division of Gynecological Oncology, Department of Obstetrics and Gynecology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany;
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4
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Marchitto L, Benlarbi M, Prévost J, Laumaea A, Descôteaux-Dinelle J, Medjahed H, Bourassa C, Gendron-Lepage G, Kirchhoff F, Sauter D, Hahn BH, Finzi A, Richard J. Impact of HIV-1 Vpu-mediated downregulation of CD48 on NK-cell-mediated antibody-dependent cellular cytotoxicity. mBio 2023; 14:e0078923. [PMID: 37404017 PMCID: PMC10470595 DOI: 10.1128/mbio.00789-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/18/2023] [Indexed: 07/06/2023] Open
Abstract
HIV-1 evades antibody-dependent cellular cytotoxicity (ADCC) responses not only by controlling Env conformation and quantity at the cell surface but also by altering NK cell activation via the downmodulation of several ligands of activating and co-activating NK cell receptors. The signaling lymphocyte activation molecule (SLAM) family of receptors, which includes NTB-A and 2B4, act as co-activating receptors to sustain NK cell activation and cytotoxic responses. These receptors cooperate with CD16 (FcγRIII) and other activating receptors to trigger NK cell effector functions. In that context, Vpu-mediated downregulation of NTB-A on HIV-1-infected CD4 T cells was shown to prevent NK cell degranulation via an homophilic interaction, thus contributing to ADCC evasion. However, less is known on the capacity of HIV-1 to evade 2B4-mediated NK cell activation and ADCC. Here, we show that HIV-1 downregulates the ligand of 2B4, CD48, from the surface of infected cells in a Vpu-dependent manner. This activity is conserved among Vpu proteins from the HIV-1/SIVcpz lineage and depends on conserved residues located in its transmembrane domain and dual phosphoserine motif. We show that NTB-A and 2B4 stimulate CD16-mediated NK cell degranulation and contribute to ADCC responses directed to HIV-1-infected cells to the same extent. Our results suggest that HIV-1 has evolved to downmodulate the ligands of both SLAM receptors to evade ADCC. IMPORTANCE Antibody-dependent cellular cytotoxicity (ADCC) can contribute to the elimination of HIV-1-infected cells and HIV-1 reservoirs. An in-depth understanding of the mechanisms used by HIV-1 to evade ADCC might help develop novel approaches to reduce the viral reservoirs. Members of the signaling lymphocyte activation molecule (SLAM) family of receptors, such as NTB-A and 2B4, play a key role in stimulating NK cell effector functions, including ADCC. Here, we show that Vpu downmodulates CD48, the ligand of 2B4, and this contributes to protect HIV-1-infected cells from ADCC. Our results highlight the importance of the virus to prevent the triggering of the SLAM receptors to evade ADCC.
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Affiliation(s)
- Lorie Marchitto
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Annemarie Laumaea
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jade Descôteaux-Dinelle
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | | | | | | | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Beatrice H. Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Quebec, Canada
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5
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Hussein M, Molina MA, Berkhout B, Herrera-Carrillo E. A CRISPR-Cas Cure for HIV/AIDS. Int J Mol Sci 2023; 24:1563. [PMID: 36675077 PMCID: PMC9863116 DOI: 10.3390/ijms24021563] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Human immunodeficiency virus (HIV) infections and HIV-induced acquired immunodeficiency syndrome (AIDS) continue to represent a global health burden. There is currently no effective vaccine, nor any cure, for HIV infections; existing antiretroviral therapy can suppress viral replication, but only as long as antiviral drugs are taken. HIV infects cells of the host immune system, and it can establish a long-lived viral reservoir, which can be targeted and edited through gene therapy. Gene editing platforms based on the clustered regularly interspaced palindromic repeat-Cas system (CRISPR-Cas) have been recognized as promising tools in the development of gene therapies for HIV infections. In this review, we evaluate the current landscape of CRISPR-Cas-based therapies against HIV, with an emphasis on the infection biology of the virus as well as the activity of host restriction factors. We discuss the potential of a combined CRISPR-Cas approach that targets host and viral genes to activate antiviral host factors and inhibit viral replication simultaneously. Lastly, we focus on the challenges and potential solutions of CRISPR-Cas gene editing approaches in achieving an HIV cure.
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Affiliation(s)
| | | | | | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
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6
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Aso H, Ito J, Ozaki H, Kashima Y, Suzuki Y, Koyanagi Y, Sato K. Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections. Gigascience 2022; 12:giad086. [PMID: 37848618 PMCID: PMC10580374 DOI: 10.1093/gigascience/giad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/12/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Bats harbor various viruses without severe symptoms and act as their natural reservoirs. The tolerance of bats against viral infections is assumed to originate from the uniqueness of their immune system. However, how immune responses vary between primates and bats remains unclear. Here, we characterized differences in the immune responses by peripheral blood mononuclear cells to various pathogenic stimuli between primates (humans, chimpanzees, and macaques) and bats (Egyptian fruit bats) using single-cell RNA sequencing. RESULTS We show that the induction patterns of key cytosolic DNA/RNA sensors and antiviral genes differed between primates and bats. A novel subset of monocytes induced by pathogenic stimuli specifically in bats was identified. Furthermore, bats robustly respond to DNA virus infection even though major DNA sensors are dampened in bats. CONCLUSIONS Overall, our data suggest that immune responses are substantially different between primates and bats, presumably underlying the difference in viral pathogenicity among the mammalian species tested.
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Affiliation(s)
- Hirofumi Aso
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
- Department of AI Systems Medicine, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo 1138510, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Haruka Ozaki
- Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba 3050821, Japan
- Center for Artificial Intelligence Research, University of Tsukuba, Tsukuba 3058577, Japan
| | - Yukie Kashima
- Laboratory of Systems Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan
| | - Yoshio Koyanagi
- Institute for Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 1130033, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
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7
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Prévost J, Anand SP, Rajashekar JK, Zhu L, Richard J, Goyette G, Medjahed H, Gendron-Lepage G, Chen HC, Chen Y, Horwitz JA, Grunst MW, Zolla-Pazner S, Haynes BF, Burton DR, Flavell RA, Kirchhoff F, Hahn BH, Smith AB, Pazgier M, Nussenzweig MC, Kumar P, Finzi A. HIV-1 Vpu restricts Fc-mediated effector functions in vivo. Cell Rep 2022; 41:111624. [PMID: 36351384 PMCID: PMC9703018 DOI: 10.1016/j.celrep.2022.111624] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/02/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
Non-neutralizing antibodies (nnAbs) can eliminate HIV-1-infected cells via antibody-dependent cellular cytotoxicity (ADCC) and were identified as a correlate of protection in the RV144 vaccine trial. Fc-mediated effector functions of nnAbs were recently shown to alter the course of HIV-1 infection in vivo using a vpu-defective virus. Since Vpu is known to downregulate cell-surface CD4, which triggers conformational changes in the viral envelope glycoprotein (Env), we ask whether the lack of Vpu expression was linked to the observed nnAbs activity. We find that restoring Vpu expression greatly reduces nnAb recognition of infected cells, rendering them resistant to ADCC. Moreover, administration of nnAbs in humanized mice reduces viral loads only in animals infected with a vpu-defective but not with a wild-type virus. CD4-mimetics administration, known to "open" Env and expose nnAb epitopes, renders wild-type viruses sensitive to nnAbs Fc-effector functions. This work highlights the importance of Vpu-mediated evasion of humoral responses.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada.
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jyothi Krishnaswamy Rajashekar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Li Zhu
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | | | | | | | - Hung-Ching Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Yaozong Chen
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Joshua A Horwitz
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michael W Grunst
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Susan Zolla-Pazner
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Departments of Medicine and Immunology, Duke University School of Medicine, Durham, NC 27710, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), Duke University, Durham, NC 27710, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, Harvard University, Cambridge, MA 02139, USA
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Marzena Pazgier
- Infectious Diseases Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.
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8
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Kumata R, Iwanami S, Mar KB, Kakizoe Y, Misawa N, Nakaoka S, Koyanagi Y, Perelson AS, Schoggins JW, Iwami S, Sato K. Antithetic effect of interferon-α on cell-free and cell-to-cell HIV-1 infection. PLoS Comput Biol 2022; 18:e1010053. [PMID: 35468127 PMCID: PMC9037950 DOI: 10.1371/journal.pcbi.1010053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/23/2022] [Indexed: 01/23/2023] Open
Abstract
In HIV-1-infected individuals, transmitted/founder (TF) virus contributes to establish new infection and expands during the acute phase of infection, while chronic control (CC) virus emerges during the chronic phase of infection. TF viruses are more resistant to interferon-alpha (IFN-α)-mediated antiviral effects than CC virus, however, its virological relevance in infected individuals remains unclear. Here we perform an experimental-mathematical investigation and reveal that IFN-α strongly inhibits cell-to-cell infection by CC virus but only weakly affects that by TF virus. Surprisingly, IFN-α enhances cell-free infection of HIV-1, particularly that of CC virus, in a virus-cell density-dependent manner. We further demonstrate that LY6E, an IFN-stimulated gene, can contribute to the density-dependent enhancement of cell-free HIV-1 infection. Altogether, our findings suggest that the major difference between TF and CC viruses can be explained by their resistance to IFN-α-mediated inhibition of cell-to-cell infection and their sensitivity to IFN-α-mediated enhancement of cell-free infection.
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Affiliation(s)
- Ryuichi Kumata
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Faculty of Science, Kyoto University, Kyoto, Japan
| | - Shoya Iwanami
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Katrina B. Mar
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yusuke Kakizoe
- Mathematical Biology Laboratory, Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Naoko Misawa
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shinji Nakaoka
- Laboratory of Mathematical Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
- PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Alan S. Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - John W. Schoggins
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Shingo Iwami
- interdisciplinary Biology Laboratory (iBLab), Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- MIRAI, Japan Science and Technology Agency, Saitama, Japan
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- NEXT-Ganken Program, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
- Science Groove Inc., Fukuoka, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
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9
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Comprehensive Investigation on the Interplay between Feline APOBEC3Z3 Proteins and Feline Immunodeficiency Virus Vif Proteins. J Virol 2021; 95:e0017821. [PMID: 33762419 PMCID: PMC8437355 DOI: 10.1128/jvi.00178-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As the hosts of lentiviruses, almost 40 species of felids (family Felidae) are distributed around the world, and more than 20 feline species test positive for feline immunodeficiency virus (FIV), a lineage of lentiviruses. These observations suggest that FIVs globally infected a variety of feline species through multiple cross-species transmission events during a million-year history. Cellular restriction factors potentially inhibit lentiviral replication and limit cross-species lentiviral transmission, and cellular APOBEC3 deaminases are known as a potent restriction factor. In contrast, lentiviruses have evolutionary-acquired viral infectivity factor (Vif) to neutralize the APOBEC3-mediated antiviral effect. Because the APOBEC3-Vif interaction is strictly specific for viruses and their hosts, a comprehensive investigation focusing on Vif-APOBEC3 interplay can provide clues that will elucidate the roles of this virus-host interplay on cross-species transmission of lentiviruses. Here, we performed a comprehensive investigation with 144 patterns of a round robin test using 18 feline APOBEC3Z3 genes, an antiviral APOBEC3 gene in felid, and 8 FIV Vifs and derived a matrix showing the interplay between feline APOBEC3Z3 and FIV Vif. We particularly focused on the interplay between the APOBEC3Z3 of three felids (domestic cat, ocelot, and Asian golden cat) and an FIV Vif (strain Petaluma), and revealed that residues 65 and 66 of the APOBEC3Z3 protein of multiple felids are responsible for the counteraction triggered by FIV Petaluma Vif. Altogether, our findings can be a clue to elucidate not only the scenarios of the cross-species transmissions of FIVs in felids but also the evolutionary interaction between mammals and lentiviruses. IMPORTANCE Most of the emergences of new virus infections originate from the cross-species transmission of viruses. The fact that some virus infections are strictly specific for the host species indicates that certain “species barriers” in the hosts restrict cross-species jump of viruses, while viruses have evolutionary acquired their own “arms” to overcome/antagonize/neutralize these hurdles. Therefore, understanding of the molecular mechanism leading to successful cross-species viral transmission is crucial for considering the menus of the emergence of novel pathogenic viruses. In the field of retrovirology, APOBEC3-Vif interaction is a well-studied example of the battles between hosts and viruses. Here, we determined the sequences of 11 novel feline APOBEC3Z3 genes and demonstrated that all 18 different feline APOBEC3Z3 proteins tested exhibit anti-feline immunodeficiency virus (FIV) activity. Our comprehensive investigation focusing on the interplay between feline APOBEC3 and FIV Vif can be a clue to elucidate the scenarios of the cross-species transmissions of FIVs in felids.
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10
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Aso H, Nagaoka S, Kawakami E, Ito J, Islam S, Tan BJY, Nakaoka S, Ashizaki K, Shiroguchi K, Suzuki Y, Satou Y, Koyanagi Y, Sato K. Multiomics Investigation Revealing the Characteristics of HIV-1-Infected Cells In Vivo. Cell Rep 2021; 32:107887. [PMID: 32668246 DOI: 10.1016/j.celrep.2020.107887] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/06/2020] [Accepted: 06/08/2020] [Indexed: 12/30/2022] Open
Abstract
For eradication of HIV-1 infection, it is important to elucidate the detailed features and heterogeneity of HIV-1-infected cells in vivo. To reveal multiple characteristics of HIV-1-producing cells in vivo, we use a hematopoietic-stem-cell-transplanted humanized mouse model infected with GFP-encoding replication-competent HIV-1. We perform multiomics experiments using recently developed technology to identify the features of HIV-1-infected cells. Genome-wide HIV-1 integration-site analysis reveals that productive HIV-1 infection tends to occur in cells with viral integration into transcriptionally active genomic regions. Bulk transcriptome analysis reveals that a high level of viral mRNA is transcribed in HIV-1-infected cells. Moreover, single-cell transcriptome analysis shows the heterogeneity of HIV-1-infected cells, including CXCL13high cells and a subpopulation with low expression of interferon-stimulated genes, which can contribute to efficient viral spread in vivo. Our findings describe multiple characteristics of HIV-1-producing cells in vivo, which could provide clues for the development of an HIV-1 cure.
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Affiliation(s)
- Hirofumi Aso
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Shumpei Nagaoka
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Eiryo Kawakami
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan; Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba 2608670, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Saiful Islam
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Benjy Jek Yang Tan
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Shinji Nakaoka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 0600810, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - Koichi Ashizaki
- RIKEN Medical Sciences Innovation Hub Program, Yokohama, Kanagawa 2300045, Japan
| | - Katsuyuki Shiroguchi
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 5650874, Japan; RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 2300045, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 2778561, Japan
| | - Yorifumi Satou
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan; Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan.
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11
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Kimura I, Konno Y, Uriu K, Hopfensperger K, Sauter D, Nakagawa S, Sato K. Sarbecovirus ORF6 proteins hamper induction of interferon signaling. Cell Rep 2021; 34:108916. [PMID: 33765414 PMCID: PMC7953434 DOI: 10.1016/j.celrep.2021.108916] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/24/2021] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
The presence of an ORF6 gene distinguishes sarbecoviruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 from other betacoronaviruses. Here we show that ORF6 inhibits induction of innate immune signaling, including upregulation of type I interferon (IFN) upon viral infection as well as type I and III IFN signaling. Intriguingly, ORF6 proteins from SARS-CoV-2 lineages are more efficient antagonists of innate immunity than their orthologs from SARS-CoV lineages. Mutational analyses identified residues E46 and Q56 as important determinants of the antagonistic activity of SARS-CoV-2 ORF6. Moreover, we show that the anti-innate immune activity of ORF6 depends on its C-terminal region and that ORF6 inhibits nuclear translocation of IRF3. Finally, we identify naturally occurring frameshift/nonsense mutations that result in an inactivating truncation of ORF6 in approximately 0.2% of SARS-CoV-2 isolates. Our findings suggest that ORF6 contributes to the poor IFN activation observed in individuals with coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yoriyuki Konno
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo 1130033, Japan
| | - Kristina Hopfensperger
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen 72076, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen 72076, Germany
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
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12
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Soper A, Koyanagi Y, Sato K. HIV-1 tracing method of systemic viremia in vivo using an artificially mutated virus pool. Microbiol Immunol 2021; 65:17-27. [PMID: 33230872 DOI: 10.1111/1348-0421.12862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/05/2020] [Accepted: 11/20/2020] [Indexed: 11/28/2022]
Abstract
The appearance of human immunodeficiency virus type 1 (HIV-1) plasma viremia is associated with progression to symptomatic disease and CD4+ T cell depletion. To locate the source of systemic viremia, this study employed a novel method to trace HIV-1 infection in vivo. We created JRCSFξnef, a pool of infectious HIV-1 (strain JR-CSF) with highly mutated nef gene regions by random mutagenesis PCR and infected this mutated virus pool into both Jurkat-CCR5 cells and hematopoietic stem cell-transplanted humanized mice. Infection resulted in systemic plasma viremia in humanized mice and viral RNA sequencing helped us to identify multiple lymphoid organs such as spleen, lymph nodes, and bone marrow but not peripheral blood cells as the source of systemic viremia. Our data suggest that this method could be useful for the tracing of viral trafficking in vivo.
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Affiliation(s)
- Andrew Soper
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kei Sato
- Department of Infectious Disease Control, Division of Systems Virology, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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13
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Site-Specific Evolutionary Rate Shifts in HIV-1 and SIV. Viruses 2020; 12:v12111312. [PMID: 33207801 PMCID: PMC7696578 DOI: 10.3390/v12111312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/28/2022] Open
Abstract
Site-specific evolutionary rate shifts are defined as protein sites, where the rate of substitution has changed dramatically across the phylogeny. With respect to a given clade, sites may either undergo a rate acceleration or a rate deceleration, reflecting a site that was conserved and became variable, or vice-versa, respectively. Sites displaying such a dramatic evolutionary change may point to a loss or gain of function at the protein site, reflecting adaptation, or they may indicate epistatic interactions among sites. Here, we analyzed full genomes of HIV and SIV-1 and identified 271 rate-shifting sites along the HIV-1/SIV phylogeny. The majority of rate shifts occurred at long branches, often corresponding to cross-species transmission branches. We noted that in most proteins, the number of rate accelerations and decelerations was equal, and we suggest that this reflects epistatic interactions among sites. However, several accessory proteins were enriched for either accelerations or decelerations, and we suggest that this may be a signature of adaptation to new hosts. Interestingly, the non-pandemic HIV-1 group O clade exhibited a substantially higher number of rate-shift events than the pandemic group M clade. We propose that this may be a reflection of the height of the species barrier between gorillas and humans versus chimpanzees and humans. Our results provide a genome-wide view of the constraints operating on proteins of HIV-1 and SIV.
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14
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Nakano Y, Yamamoto K, Ueda MT, Soper A, Konno Y, Kimura I, Uriu K, Kumata R, Aso H, Misawa N, Nagaoka S, Shimizu S, Mitsumune K, Kosugi Y, Juarez-Fernandez G, Ito J, Nakagawa S, Ikeda T, Koyanagi Y, Harris RS, Sato K. A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans. PLoS Pathog 2020; 16:e1008812. [PMID: 32913367 PMCID: PMC7482973 DOI: 10.1371/journal.ppat.1008812] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
The APOBEC3 deaminases are potent inhibitors of virus replication and barriers to cross-species transmission. For simian immunodeficiency virus (SIV) to transmit to a new primate host, as happened multiple times to seed the ongoing HIV-1 epidemic, the viral infectivity factor (Vif) must be capable of neutralizing the APOBEC3 enzymes of the new host. Although much is known about current interactions of HIV-1 Vif and human APOBEC3s, the evolutionary changes in SIV Vif required for transmission from chimpanzees to gorillas and ultimately to humans are poorly understood. Here, we demonstrate that gorilla APOBEC3G is a factor with the potential to hamper SIV transmission from chimpanzees to gorillas. Gain-of-function experiments using SIVcpzPtt Vif revealed that this barrier could be overcome by a single Vif acidic amino acid substitution (M16E). Moreover, degradation of gorilla APOBEC3F is induced by Vif through a mechanism that is distinct from that of human APOBEC3F. Thus, our findings identify virus adaptations in gorillas that preceded and may have facilitated transmission to humans. Humans are exposed continuously to a menace of viral diseases such as Ebola virus and coronaviruses. Such emerging/re-emerging viral outbreaks can be triggered by cross-species viral transmission from wild animals to humans. HIV-1, the causative agent of AIDS, most likely originated from related precursors found in chimpanzees and gorillas (SIVcpzPtt or SIVgor), approximately 100 years ago. Additionally, SIVgor most likely emerged through the cross-species jump of SIVcpzPtt from chimpanzees to gorillas. However, it remains unclear how primate lentiviruses successfully transmitted among different species. To limit cross-species lentiviral transmission, cellular "restriction factors", including tetherin, SAMHD1, and APOBEC3 proteins potentially inhibit lentiviral replication. In contrast, primate lentiviruses have evolutionary acquired their own "arms" to antagonize the antiviral effect of restriction factors. Here we show that gorilla APOBEC3G potentially plays a role in inhibiting SIVcpzPtt replication. To our knowledge, this is the first report suggesting that a great ape APOBEC3 protein can potentially restrict the cross-species transmission of great ape lentiviruses and how lentiviruses overcame this species barrier.
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Affiliation(s)
- Yusuke Nakano
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Keisuke Yamamoto
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Andrew Soper
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoriyuki Konno
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Izumi Kimura
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Ryuichi Kumata
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Faculty of Science, Kyoto University, Kyoto, Japan
| | - Hirofumi Aso
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Naoko Misawa
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shumpei Nagaoka
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Soma Shimizu
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Keito Mitsumune
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Kosugi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Guillermo Juarez-Fernandez
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jumpei Ito
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Terumasa Ikeda
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kei Sato
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- * E-mail:
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15
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Konno Y, Kimura I, Uriu K, Fukushi M, Irie T, Koyanagi Y, Sauter D, Gifford RJ, Nakagawa S, Sato K. SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant. Cell Rep 2020; 32:108185. [PMID: 32941788 PMCID: PMC7473339 DOI: 10.1016/j.celrep.2020.108185] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/22/2020] [Accepted: 09/01/2020] [Indexed: 01/25/2023] Open
Abstract
One of the features distinguishing SARS-CoV-2 from its more pathogenic counterpart SARS-CoV is the presence of premature stop codons in its ORF3b gene. Here, we show that SARS-CoV-2 ORF3b is a potent interferon antagonist, suppressing the induction of type I interferon more efficiently than its SARS-CoV ortholog. Phylogenetic analyses and functional assays reveal that SARS-CoV-2-related viruses from bats and pangolins also encode truncated ORF3b gene products with strong anti-interferon activity. Furthermore, analyses of approximately 17,000 SARS-CoV-2 sequences identify a natural variant in which a longer ORF3b reading frame was reconstituted. This variant was isolated from two patients with severe disease and further increased the ability of ORF3b to suppress interferon induction. Thus, our findings not only help to explain the poor interferon response in COVID-19 patients but also describe the emergence of natural SARS-CoV-2 quasispecies with an extended ORF3b gene that may potentially affect COVID-19 pathogenesis.
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Affiliation(s)
- Yoriyuki Konno
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo 1088639, Japan
| | - Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan
| | - Masaya Fukushi
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7398511, Japan
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima 7398511, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK
| | | | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, the University of Tokyo, Tokyo 1088639, Japan.
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16
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Schouest B, Leslie GJ, Hoxie JA, Maness NJ. Tetherin downmodulation by SIVmac Nef lost with the H196Q escape variant is restored by an upstream variant. PLoS One 2020; 15:e0225420. [PMID: 32764749 PMCID: PMC7413475 DOI: 10.1371/journal.pone.0225420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 07/13/2020] [Indexed: 01/17/2023] Open
Abstract
The H196 residue in SIVmac239 Nef is conserved across the majority of HIV and SIV isolates, lies immediately adjacent to the AP-2 (adaptor protein 2) binding di-leucine domain (ExxxLM195), and is critical for several described AP-2 dependent Nef functions, including the downregulation of tetherin (BST-2/CD317), CD4, and others. Surprisingly, many stocks of the closely related SIVmac251 swarm virus harbor a nef allele encoding a Q196. In SIVmac239, this variant is associated with loss of multiple AP-2 dependent functions. Publicly available sequences for SIVmac251 stocks were mined for variants linked to Q196 that might compensate for functional defects associated with this residue. Variants were engineered into the SIVmac239 backbone and in Nef expression plasmids and flow cytometry was used to examine surface tetherin expression in primary CD4 T cells and surface CD4 expression in SupT1 cells engineered to express rhesus CD4. We found that SIVmac251 stocks that encode a Q196 residue in Nef uniformly also encode an upstream R191 residue. We show that R191 restores the ability of Nef to downregulate tetherin in the presence of Q196 and has a similar but less pronounced impact on CD4 expression. However, a published report showed Q196 commonly evolves to H196 in vivo, suggesting a fitness cost. R191 may represent compensatory evolution to restore the ability to downregulate tetherin lost in viruses harboring Q196.
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Affiliation(s)
- Blake Schouest
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA, United States of America
| | - George J. Leslie
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - James A. Hoxie
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Nicholas J. Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, LA, United States of America
- Department of Microbiology and Immunology, School of Medicine, Tulane University Health Sciences Center, New Orleans, LA, United States of America
- * E-mail:
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17
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Vpu modulates DNA repair to suppress innate sensing and hyper-integration of HIV-1. Nat Microbiol 2020; 5:1247-1261. [PMID: 32690953 DOI: 10.1038/s41564-020-0753-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/11/2020] [Indexed: 12/19/2022]
Abstract
To avoid innate sensing and immune control, human immunodeficiency virus type 1 (HIV-1) has to prevent the accumulation of viral complementary DNA species. Here, we show that the late HIV-1 accessory protein Vpu hijacks DNA repair mechanisms to promote degradation of nuclear viral cDNA in cells that are already productively infected. Vpu achieves this by interacting with RanBP2-RanGAP1*SUMO1-Ubc9 SUMO E3-ligase complexes at the nuclear pore to reprogramme promyelocytic leukaemia protein nuclear bodies and reduce SUMOylation of Bloom syndrome protein, unleashing end degradation of viral cDNA. Concomitantly, Vpu inhibits RAD52-mediated homologous repair of viral cDNA, preventing the generation of dead-end circular forms of single copies of the long terminal repeat and permitting sustained nucleolytic attack. Our results identify Vpu as a key modulator of the DNA repair machinery. We show that Bloom syndrome protein eliminates nuclear HIV-1 cDNA and thereby suppresses immune sensing and proviral hyper-integration. Therapeutic targeting of DNA repair may facilitate the induction of antiviral immunity and suppress proviral integration replenishing latent HIV reservoirs.
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18
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Hopfensperger K, Richard J, Stürzel CM, Bibollet-Ruche F, Apps R, Leoz M, Plantier JC, Hahn BH, Finzi A, Kirchhoff F, Sauter D. Convergent Evolution of HLA-C Downmodulation in HIV-1 and HIV-2. mBio 2020; 11:e00782-20. [PMID: 32665270 PMCID: PMC7360927 DOI: 10.1128/mbio.00782-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
HLA-C-mediated antigen presentation induces the killing of human immunodeficiency virus (HIV)-infected CD4+ T cells by cytotoxic T lymphocytes (CTLs). To evade killing, many HIV-1 group M strains decrease HLA-C surface levels using their accessory protein Vpu. However, some HIV-1 group M isolates lack this activity, possibly to prevent the activation of natural killer (NK) cells. Analyzing diverse primate lentiviruses, we found that Vpu-mediated HLA-C downregulation is not limited to pandemic group M but is also found in HIV-1 groups O and P as well as several simian immunodeficiency viruses (SIVs). We show that Vpu targets HLA-C primarily at the protein level, independently of its ability to suppress NF-κB-driven gene expression, and that in some viral lineages, HLA-C downregulation may come at the cost of efficient counteraction of the restriction factor tetherin. Remarkably, HIV-2, which does not carry a vpu gene, uses its accessory protein Vif to decrease HLA-C surface expression. This Vif activity requires intact binding sites for the Cullin5/Elongin ubiquitin ligase complex but is separable from its ability to counteract APOBEC3G. Similar to HIV-1 Vpu, the degree of HIV-2 Vif-mediated HLA-C downregulation varies considerably among different virus isolates. In agreement with opposing selection pressures in vivo, we show that the reduction of HLA-C surface levels by HIV-2 Vif is accompanied by increased NK cell-mediated killing. In summary, our results highlight the complex role of HLA-C in lentiviral infections and demonstrate that HIV-1 and HIV-2 have evolved at least two independent mechanisms to decrease HLA-C levels on infected cells.IMPORTANCE Genome-wide association studies suggest that HLA-C expression is a major determinant of viral load set points and CD4+ T cell counts in HIV-infected individuals. On the one hand, efficient HLA-C expression enables the killing of infected cells by cytotoxic T lymphocytes (CTLs). On the other hand, HLA-C sends inhibitory signals to natural killer (NK) cells and enhances the infectivity of newly produced HIV particles. HIV-1 group M viruses modulate HLA-C expression using the accessory protein Vpu, possibly to balance CTL- and NK cell-mediated immune responses. Here, we show that the second human immunodeficiency virus, HIV-2, can use its accessory protein Vif to evade HLA-C-mediated restriction. Furthermore, our mutational analyses provide insights into the underlying molecular mechanisms. In summary, our results reveal how the two human AIDS viruses modulate HLA-C, a key component of the antiviral immune response.
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Affiliation(s)
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, Maryland, USA
| | - Marie Leoz
- Normandie Université, UNIROUEN, UNICAEN, GRAM 2.0, Rouen, France
| | - Jean-Christophe Plantier
- Normandie Université, UNIROUEN, UNICAEN, GRAM 2.0, Rouen University Hospital, Department of Virology, Laboratory Associated with the National Reference Center on HIV, Rouen, France
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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19
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Zadeh VR, Urata S, Sakaguchi M, Yasuda J. Human BST-2/tetherin inhibits Junin virus release from host cells and its inhibition is partially counteracted by viral nucleoprotein. J Gen Virol 2020; 101:573-586. [PMID: 32375950 DOI: 10.1099/jgv.0.001414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Bone marrow stromal cell antigen-2 (BST-2), also known as tetherin, is an interferon-inducible membrane-associated protein. It effectively targets enveloped viruses at the release step of progeny viruses from host cells, thereby restricting the further spread of viral infection. Junin virus (JUNV) is a member of Arenaviridae, which causes Argentine haemorrhagic fever that is associated with a high rate of mortality. In this study, we examined the effect of human BST-2 on the replication and propagation of JUNV. The production of JUNV Z-mediated virus-like particles (VLPs) was significantly inhibited by over-expression of BST-2. Electron microscopy analysis revealed that BST-2 functions by forming a physical link that directly retains VLPs on the cell surface. Infection using JUNV showed that infectious JUNV production was moderately inhibited by endogenous or exogenous BST-2. We also observed that JUNV infection triggers an intense interferon response, causing an upregulation of BST-2, in infected cells. However, the expression of cell surface BST-2 was reduced upon infection. Furthermore, the expression of JUNV nucleoprotein (NP) partially recovered VLP production from BST-2 restriction, suggesting that the NP functions as an antagonist against antiviral effect of BST-2. We further showed that JUNV NP also rescued the production of Ebola virus VP40-mediated VLP from BST-2 restriction as a broad spectrum BST-2 antagonist. To our knowledge, this is the first report showing that an arenavirus protein counteracts the antiviral function of BST-2.
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Affiliation(s)
- Vahid Rajabali Zadeh
- Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Shuzo Urata
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan.,Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Miako Sakaguchi
- Central Laboratory, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Jiro Yasuda
- National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan.,Program for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.,Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
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20
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Tavakoli-Tameh A, Janaka SK, Zarbock K, O’Connor S, Crosno K, Capuano S, Uno H, Lifson JD, Evans DT. Loss of tetherin antagonism by Nef impairs SIV replication during acute infection of rhesus macaques. PLoS Pathog 2020; 16:e1008487. [PMID: 32302364 PMCID: PMC7190186 DOI: 10.1371/journal.ppat.1008487] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/29/2020] [Accepted: 03/21/2020] [Indexed: 12/13/2022] Open
Abstract
Most simian immunodeficiency viruses use Nef to counteract the tetherin proteins of their nonhuman primate hosts. Nef also downmodulates cell-surface CD4 and MHC class I (MHC I) molecules and enhances viral infectivity by counteracting SERINC5. We previously demonstrated that tetherin antagonism by SIV Nef is genetically separable from CD4- and MHC I-downmodulation. Here we show that disruption of tetherin antagonism by Nef impairs virus replication during acute SIV infection of rhesus macaques. A combination of mutations was introduced into the SIVmac239 genome resulting in three amino acid substitutions in Nef that impair tetherin antagonism, but not CD3-, CD4- or MHC I-downmodulation. Further characterization of this mutant (SIVmac239AAA) revealed that these changes also result in partial sensitivity to SERINC5. Separate groups of four rhesus macaques were infected with either wild-type SIVmac239 or SIVmac239AAA, and viral RNA loads in plasma and sequence changes in the viral genome were monitored. Viral loads were significantly lower during acute infection in animals infected with SIVmac239AAA than in animals infected with wild-type SIVmac239. Sequence analysis of the virus population in plasma confirmed that the substitutions in Nef were retained during acute infection; however, changes were observed by week 24 post-infection that fully restored anti-tetherin activity and partially restored anti-SERINC5 activity. These observations reveal overlap in the residues of SIV Nef required for counteracting tetherin and SERINC5 and selective pressure to overcome these restriction factors in vivo.
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Affiliation(s)
- Aidin Tavakoli-Tameh
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Sanath Kumar Janaka
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Katie Zarbock
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Shelby O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kristin Crosno
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Saverio Capuano
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Hajime Uno
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Jeffrey D. Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - David T. Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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21
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Kmiec D, Nchioua R, Sherrill-Mix S, Stürzel CM, Heusinger E, Braun E, Gondim MVP, Hotter D, Sparrer KMJ, Hahn BH, Sauter D, Kirchhoff F. CpG Frequency in the 5' Third of the env Gene Determines Sensitivity of Primary HIV-1 Strains to the Zinc-Finger Antiviral Protein. mBio 2020; 11:e02903-19. [PMID: 31937644 PMCID: PMC6960287 DOI: 10.1128/mbio.02903-19] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
CpG dinucleotide suppression has been reported to allow HIV-1 to evade inhibition by the zinc-finger antiviral protein (ZAP). Here, we show that primate lentiviruses display marked differences in CpG frequencies across their genome, ranging from 0.44% in simian immunodeficiency virus SIVwrc from Western red colobus to 2.3% in SIVmon infecting mona monkeys. Moreover, functional analyses of a large panel of human and simian immunodeficiency viruses revealed that the magnitude of CpG suppression does not correlate with their susceptibility to ZAP. However, we found that the number of CpG dinucleotides within a region of ∼700 bases at the 5' end of the env gene determines ZAP sensitivity of primary HIV-1 strains but not of HIV-2. Increased numbers of CpGs in this region were associated with reduced env mRNA expression and viral protein production. ZAP sensitivity profiles of chimeric simian-human immunodeficiency viruses (SHIVs) expressing different HIV-1 env genes were highly similar to those of the corresponding HIV-1 strains. The frequency of CpGs in the identified env region correlated with differences in clinical progression rates. Thus, the CpG frequency in a specific part of env, rather than the overall genomic CpG content, governs the susceptibility of HIV-1 to ZAP and might affect viral pathogenicity in vivoIMPORTANCE Evasion of the zinc-finger antiviral protein (ZAP) may drive CpG dinucleotide suppression in HIV-1 and many other viral pathogens but the viral determinants of ZAP sensitivity are poorly defined. Here, we examined CpG suppression and ZAP sensitivity in a large number of primate lentiviruses and demonstrate that their genomic frequency of CpGs varies substantially and does not correlate with ZAP sensitivity. We further show that the number of CpG residues in a defined region at the 5' end of the env gene together with structural features plays a key role in HIV-1 susceptibility to ZAP and correlates with differences in clinical progression rates in HIV-1-infected individuals. Our identification of a specific part of env as a major determinant of HIV-1 susceptibility to ZAP restriction provides a basis for future studies of the underlying inhibitory mechanisms and their potential relevance in the pathogenesis of AIDS.
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Affiliation(s)
- Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Elena Heusinger
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Elisabeth Braun
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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22
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Prévost J, Pickering S, Mumby MJ, Medjahed H, Gendron-Lepage G, Delgado GG, Dirk BS, Dikeakos JD, Stürzel CM, Sauter D, Kirchhoff F, Bibollet-Ruche F, Hahn BH, Dubé M, Kaufmann DE, Neil SJD, Finzi A, Richard J. Upregulation of BST-2 by Type I Interferons Reduces the Capacity of Vpu To Protect HIV-1-Infected Cells from NK Cell Responses. mBio 2019; 10:e01113-19. [PMID: 31213558 PMCID: PMC6581860 DOI: 10.1128/mbio.01113-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/09/2019] [Indexed: 01/03/2023] Open
Abstract
The HIV-1 accessory protein Vpu enhances viral release by counteracting the restriction factor BST-2. Furthermore, Vpu promotes NK cell evasion by downmodulating cell surface NTB-A and PVR, known ligands of the NK cell receptors NTB-A and DNAM-1, respectively. While it has been established that Vpu's transmembrane domain (TMD) is required for the interaction and intracellular sequestration of BST-2, NTB-A, and PVR, it remains unclear how Vpu manages to target these proteins simultaneously. In this study, we show that upon upregulation, BST-2 is preferentially downregulated by Vpu over its other TMD substrates. We found that type I interferon (IFN)-mediated BST-2 upregulation greatly impairs the ability of Vpu to downregulate NTB-A and PVR. Our results suggest that occupation of Vpu by BST-2 affects its ability to downregulate other TMD substrates. Accordingly, knockdown of BST-2 increases Vpu's potency to downmodulate NTB-A and PVR in the presence of type I IFN treatment. Moreover, we show that expression of human BST-2, but not that of the macaque orthologue, decreases Vpu's capacity to downregulate NTB-A. Importantly, we show that type I IFNs efficiently sensitize HIV-1-infected cells to NTB-A- and DNAM-1-mediated direct and antibody-dependent NK cell responses. Altogether, our results reveal that type I IFNs decrease Vpu's polyfunctionality, thus reducing its capacity to protect HIV-1-infected cells from NK cell responses.IMPORTANCE The restriction factor BST-2 and the NK cell ligands NTB-A and PVR are among a growing list of membrane proteins found to be downregulated by HIV-1 Vpu. BST-2 antagonism enhances viral release, while NTB-A and PVR downmodulation contributes to NK cell evasion. However, it remains unclear how Vpu can target multiple cellular factors simultaneously. Here we provide evidence that under physiological conditions, BST-2 is preferentially targeted by Vpu over NTB-A and PVR. Specifically, we show that type I IFNs decrease Vpu's polyfunctionality by upregulating BST-2, thus reducing its capacity to protect HIV-1-infected cells from NK cell responses. This indicates that there is a hierarchy of Vpu substrates upon IFN treatment, revealing that for the virus, targeting BST-2 as part of its resistance to IFN takes precedence over evading NK cell responses. This reveals a potential weakness in HIV-1's immunoevasion mechanisms that may be exploited therapeutically to harness NK cell responses against HIV-1.
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Affiliation(s)
- Jérémie Prévost
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec, Canada
| | - Suzanne Pickering
- Department of Infectious Disease, King's College London School of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom
| | - Mitchell J Mumby
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | | | | | | | - Brennan S Dirk
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frederic Bibollet-Ruche
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mathieu Dubé
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California, USA
| | - Stuart J D Neil
- Department of Infectious Disease, King's College London School of Life Sciences and Medicine, Guy's Hospital, London, United Kingdom
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Jonathan Richard
- Centre de Recherche du CHUM, Montreal, Quebec, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, Québec, Canada
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23
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Zheng W, Wang D, Zou X. Control of multilayer biological networks and applied to target identification of complex diseases. BMC Bioinformatics 2019; 20:271. [PMID: 31138124 PMCID: PMC6540418 DOI: 10.1186/s12859-019-2841-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/22/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Networks have been widely used to model the structures of various biological systems. The ultimate aim of research on biological networks is to steer biological system structures to desired states by manipulating signals. Despite great advances in the linear control of single-layer networks, it has been observed that many complex biological systems have a multilayer networked structure and extremely complicated nonlinear processes. RESULT In this study, we propose a general framework for controlling nonlinear dynamical systems with multilayer networked structures by formulating the problem as a minimum union optimization problem. In particular, we offer a novel approach for identifying the minimal driver nodes that can steer a multilayered nonlinear dynamical system toward any desired dynamical attractor. Three disease-related biology multilayer networks are used to demonstrate the effectiveness of our approaches. Moreover, in the set of minimum driver nodes identified by the algorithm we proposed, we confirmed that some nodes can act as drug targets in the biological experiments. Other nodes have not been reported as drug targets; however, they are also involved in important biological processes from existing literature. CONCLUSIONS The proposed method could be a promising tool for determining higher drug target enrichment or more meaningful steering nodes for studying complex diseases.
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Affiliation(s)
- Wei Zheng
- School of Mathematics and Statistics, Wuhan University, Wuhan, 430072, China
| | - Dingjie Wang
- School of Mathematics and Statistics, Wuhan University, Wuhan, 430072, China
| | - Xiufen Zou
- School of Mathematics and Statistics, Wuhan University, Wuhan, 430072, China.
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24
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Abstract
Latent viral reservoirs in long-living cell populations are the main obstacle to a cure of HIV/AIDS. HIV-1 latency is controlled by the activation status of infected cells and their ability to return to a resting phenotype associated with silencing of viral gene expression. These cellular features are not just determined by the host since HIV-1 has evolved sophisticated mechanisms to alter cellular activation and survival to its advantage. Especially the HIV-1 accessory proteins Nef and Vpu exert numerous activities to promote viral replication and immune evasion affecting the size and preservation of the viral reservoir. Here, we review how antagonistic and synergistic functions of Nef and Vpu might affect HIV-1 latency. We also discuss whether these two accessory factors represent suitable targets to improve the ‘shock and kill’ cure strategy.
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Affiliation(s)
- Dorota Kmiec
- Institute of Molecular Virology, ULM University Medical Center, Meyerhofstr 1, Ulm 89081, Germany
| | - Smitha Srinivasachar
- Institute of Molecular Virology, ULM University Medical Center, Meyerhofstr 1, Ulm 89081, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, ULM University Medical Center, Meyerhofstr 1, Ulm 89081, Germany
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25
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Abstract
HIV, the causative agent of AIDS, has a complex evolutionary history involving several cross-species transmissions and recombination events as well as changes in the repertoire and function of its accessory genes. Understanding these events and the adaptations to new host species provides key insights into innate defense mechanisms, viral dependencies on cellular factors, and prerequisites for the emergence of the AIDS pandemic. In addition, understanding the factors and adaptations required for the spread of HIV in the human population helps to better assess the risk of future lentiviral zoonoses and provides clues to how improved control of viral replication can be achieved. Here, we summarize our current knowledge on viral features and adaptations preceding the AIDS pandemic. We aim at providing a viral point of view, focusing on known key hurdles of each cross-species transmission and the mechanisms that HIV and its simian precursors evolved to overcome them.
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Affiliation(s)
- Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Centre, Ulm 89081, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Centre, Ulm 89081, Germany.
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26
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Aso H, Ito J, Koyanagi Y, Sato K. Comparative Description of the Expression Profile of Interferon-Stimulated Genes in Multiple Cell Lineages Targeted by HIV-1 Infection. Front Microbiol 2019; 10:429. [PMID: 30915053 PMCID: PMC6423081 DOI: 10.3389/fmicb.2019.00429] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022] Open
Abstract
Immediately after viral infections, innate immune sensors recognize viruses and lead to the production of type I interferon (IFN-I). IFN-I upregulates various genes, referred to as IFN-stimulated genes (ISGs), and some ISGs inhibit viral replication. HIV-1, the causative agent of AIDS, mainly infects CD4+ T cells and macrophages and triggers the IFN-I-mediated signaling cascade. Certain ISGs are subsequently upregulated by IFN-I stimulus and potently suppress HIV-1 replication. HIV-1 cell biology has shed light on the molecular understanding of the IFN-I production triggered by HIV-1 infection and the antiviral roles of ISGs. However, the differences in the gene expression patterns following IFN-I stimulus among HIV-1 target cell types are poorly understood. In this study, we hypothesize that the expression profiles of ISGs are different among HIV-1 target cells and address this question by utilizing public transcriptome datasets and bioinformatic techniques. We focus on three cell types intrinsically targeted by HIV-1, including CD4+ T cells, monocytes, and macrophages, and comprehensively compare the expression patterns of ISGs among these cell types. Furthermore, we use the datasets of the differentially expressed genes by HIV-1 infection and the evolutionarily conserved ISGs in mammals and perform comparative transcriptome analyses. We defined 104 ‘common ISGs’ that were upregulated by IFN-I stimulus in CD4+ T cells, monocytes, and macrophages. The ISG expression patterns were different among these three cell types, and intriguingly, both the numbers and the magnitudes of upregulated ISGs by IFN-I stimulus were greatest in macrophages. We also found that the upregulated genes by HIV-1 infection included most ‘common ISGs.’ Moreover, we determined that the ‘common ISGs,’ particularly those with antiviral activity, were evolutionarily conserved in mammals. To our knowledge, this study is the first investigation to comprehensively describe (i) the different expression patterns of ISGs among HIV-1 target cells, (ii) the overlap in the genes modulated by IFN-I stimulus and HIV-1 infection and (iii) the evolutionary conservation in mammals of the antiviral ISGs that are expressed in HIV-1 target cells. Our results will be useful for deeply understanding the relationship of the effect of IFN-I and the modulated gene expression by HIV-1 infection.
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Affiliation(s)
- Hirofumi Aso
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Jumpei Ito
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Japan
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27
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Langer S, Hammer C, Hopfensperger K, Klein L, Hotter D, De Jesus PD, Herbert KM, Pache L, Smith N, van der Merwe JA, Chanda SK, Fellay J, Kirchhoff F, Sauter D. HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses. eLife 2019; 8:41930. [PMID: 30717826 PMCID: PMC6372280 DOI: 10.7554/elife.41930] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/26/2019] [Indexed: 12/11/2022] Open
Abstract
Many viral pathogens target innate sensing cascades and/or cellular transcription factors to suppress antiviral immune responses. Here, we show that the accessory viral protein U (Vpu) of HIV-1 exerts broad immunosuppressive effects by inhibiting activation of the transcription factor NF-κB. Global transcriptional profiling of infected CD4 +T cells revealed that vpu-deficient HIV-1 strains induce substantially stronger immune responses than the respective wild type viruses. Gene set enrichment analyses and cytokine arrays showed that Vpu suppresses the expression of NF-κB targets including interferons and restriction factors. Mutational analyses demonstrated that this immunosuppressive activity of Vpu is independent of its ability to counteract the restriction factor and innate sensor tetherin. However, Vpu-mediated inhibition of immune activation required an arginine residue in the cytoplasmic domain that is critical for blocking NF-κB signaling downstream of tetherin. In summary, our findings demonstrate that HIV-1 Vpu potently suppresses NF-κB-elicited antiviral immune responses at the transcriptional level. The Human Immunodeficiency Virus (or HIV for short) has infected more than 70 million people worldwide. Although effective therapies exist to prevent the replication of the virus and the development to AIDS, there is no cure or vaccine, and the virus still spreads efficiently in human populations, infecting about 1.8 million new people every year. The unfortunate success of HIV can in part be explained by several viral proteins that trick our immune system and enable the virus to persist at high levels in the human body. For example, an HIV protein called viral protein U (Vpu) prevents infected cells from producing alarm signals such as interferons, which usually help healthy, uninfected cells to defend themselves against viruses. However, the extent to which Vpu interferes with interferons and other proteins involved in immune responses has remained unclear. To address this question, Langer, Hammer, Hopfensperger et al. compared how different variants of HIV affect immune responses in human cells. The experiments showed that cells infected with HIV variants lacking Vpu released larger amounts of interferons and other cellular proteins that are involved in immune responses compared to HIV variants with Vpu. Further experiments showed that Vpu works by inhibiting the activation of a protein called NF-κB, which usually switches on genes that encode interferons and many other proteins involved in immune responses. These findings demonstrate that Vpu has a broader impact on the human immune response than previously thought. In order to multiply efficiently, HIV initially requires the NF-κB protein to be active. Therefore, when NF-κB is inactive, HIV may adopt a dormant state that prevents current antiviral drug treatments from eradicating the virus in the human body. In the future, developing new drugs that can activate dormant HIV particles may therefore have the potential to help cure HIV infections.
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Affiliation(s)
- Simon Langer
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany.,Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States
| | - Christian Hammer
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Lukas Klein
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Paul D De Jesus
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States
| | - Kristina M Herbert
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States
| | - Nikaïa Smith
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Sumit K Chanda
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, United States
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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28
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Janaka SK, Tavakoli-Tameh A, Neidermyer WJ, Serra-Moreno R, Hoxie JA, Desrosiers RC, Johnson RP, Lifson JD, Wolinsky SM, Evans DT. Polymorphisms in Rhesus Macaque Tetherin Are Associated with Differences in Acute Viremia in Simian Immunodeficiency Virus Δ nef-Infected Animals. J Virol 2018; 92:e00542-18. [PMID: 30135127 PMCID: PMC6206476 DOI: 10.1128/jvi.00542-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 08/19/2018] [Indexed: 12/19/2022] Open
Abstract
Tetherin (BST-2 or CD317) is an interferon-inducible transmembrane protein that inhibits virus release from infected cells. To determine the extent of sequence variation and the impact of polymorphisms in rhesus macaque tetherin on simian immunodeficiency virus (SIV) infection, tetherin alleles were sequenced from 146 rhesus macaques, including 68 animals infected with wild-type SIVmac239 and 47 animals infected with SIVmac239Δnef Since Nef is the viral gene product of SIV that counteracts restriction by tetherin, these groups afford a comparison of the effects of tetherin polymorphisms on SIV strains that are, and are not, resistant to tetherin. We identified 15 alleles of rhesus macaque tetherin with dimorphic residues at 9 positions. The relationship between these alleles and plasma viral loads was compared during acute infection, prior to the onset of adaptive immunity. Acute viremia did not differ significantly among the wild-type SIV-infected animals; however, differences in acute viral loads were associated with polymorphisms in tetherin among the animals infected with SIVΔnef In particular, polymorphisms at positions 43 and 111 (P43 and H111) were associated with lower acute-phase viral loads for SIVΔnef infection. These observations reveal extensive polymorphism in rhesus macaque tetherin, maintained perhaps as a consequence of variability in the selective pressure of diverse viral pathogens, and identify tetherin alleles that may have an inherently greater capacity to restrict SIV replication in the absence of Nef.IMPORTANCE As a consequence of ongoing evolutionary conflict with viral pathogens, tetherin has accumulated numerous species-specific differences that represent important barriers to the transmission of viruses between species. This study reveals extensive polymorphism in rhesus macaque tetherin and identifies specific alleles that are associated with lower viral loads during the first few weeks after infection with nef-deleted SIV. These observations suggest that the variable selective pressure of viral pathogens, in addition to driving the diversification of tetherin among species, also operates within certain species to maintain sequence variation in tetherin.
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Affiliation(s)
- Sanath Kumar Janaka
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Wisconsin, USA
| | - Aidin Tavakoli-Tameh
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Wisconsin, USA
| | - William J Neidermyer
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ruth Serra-Moreno
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - James A Hoxie
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald C Desrosiers
- Department of Pathology, Miller School of Medicine, University of Miami, Florida, USA
| | | | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - David T Evans
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, Madison, Wisconsin, USA
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29
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Abstract
Pandemic HIV-1, a human lentivirus, is the result of zoonotic transmission of SIV from chimpanzees (SIVcpz). How SIVcpz established spread in humans after spillover is an outstanding question. Lentiviral cross-species transmissions are exceptionally rare events. Nevertheless, the chimpanzee and the gorilla were part of the transmission chains that resulted in sustained infections that evolved into HIV-1. Although many restriction factors can repress the early stages of lentiviral replication, others target replication during the late phases. In some cases, viruses incorporate host proteins that interfere with subsequent rounds of replication. Though limited and small, HIVs and SIVs, including SIVcpz can use their genome products to modulate and escape some of these barriers and thus establish a chronic infection.
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Affiliation(s)
- Augustin Penda Twizerimana
- Clinic for Gastroenterology, Hepatology & Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Rachel Scheck
- Clinic for Gastroenterology, Hepatology & Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology & Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology & Infectiology, Medical Faculty, Heinrich-Heine-University, Moorenstr. 5, 40225 Düsseldorf, Germany
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30
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Preadaptation of Simian Immunodeficiency Virus SIVsmm Facilitated Env-Mediated Counteraction of Human Tetherin by Human Immunodeficiency Virus Type 2. J Virol 2018; 92:JVI.00276-18. [PMID: 29976668 DOI: 10.1128/jvi.00276-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/23/2018] [Indexed: 12/14/2022] Open
Abstract
The host restriction factor tetherin inhibits virion release from infected cells and poses a significant barrier to successful zoonotic transmission of primate lentiviruses to humans. While most simian immunodeficiency viruses (SIV), including the direct precursors of human immunodeficiency virus type 1 (HIV-1) and HIV-2, use their Nef protein to counteract tetherin in their natural hosts, they fail to antagonize the human tetherin ortholog. Pandemic HIV-1 group M and epidemic group O strains overcame this hurdle by adapting their Vpu and Nef proteins, respectively, whereas HIV-2 group A uses its envelope (Env) glycoprotein to counteract human tetherin. Whether or how the remaining eight groups of HIV-2 antagonize this antiviral factor has remained unclear. Here, we show that Nef proteins from diverse groups of HIV-2 do not or only modestly antagonize human tetherin, while their ability to downmodulate CD3 and CD4 is highly conserved. Experiments in transfected cell lines and infected primary cells revealed that not only Env proteins of epidemic HIV-2 group A but also those of a circulating recombinant form (CRF01_AB) and rare groups F and I decrease surface expression of human tetherin and significantly enhance progeny virus release. Intriguingly, we found that many SIVsmm Envs also counteract human as well as smm tetherin. Thus, Env-mediated tetherin antagonism in different groups of HIV-2 presumably stems from a preadaptation of their SIVsmm precursors to humans. In summary, we identified a phenotypic trait of SIVsmm that may have facilitated its successful zoonotic transmission to humans and the emergence of HIV-2.IMPORTANCE HIV-2 groups A to I resulted from nine independent cross-species transmission events of SIVsmm to humans and differ considerably in their prevalence and geographic spread. Thus, detailed characterization of these viruses offers a valuable means to elucidate immune evasion mechanisms and human-specific adaptations determining viral spread. In a systematic comparison of rare and epidemic HIV-2 groups and their simian SIVsmm counterparts, we found that the ability of Nef to downmodulate the primary viral entry receptor CD4 and the T cell receptor CD3 is conserved, while effects on CD28, CD74, and major histocompatibility complex class I surface expression vary considerably. Furthermore, we show that not only the Env proteins of HIV-2 groups A, AB, F, and I but also those of some SIVsmm isolates antagonize human tetherin. This finding helps to explain why SIVsmm has been able to cross the species barrier to humans on at least nine independent occasions.
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