1
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Yi D, An N, Li Q, Liu Q, Shao H, Zhou R, Wang J, Zhang Y, Ma L, Guo F, Li X, Liu Z, Cen S. Interferon-induced MXB protein restricts vimentin-dependent viral infection. Acta Pharm Sin B 2024; 14:2520-2536. [PMID: 38828143 PMCID: PMC11143536 DOI: 10.1016/j.apsb.2024.03.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/16/2024] [Accepted: 03/14/2024] [Indexed: 06/05/2024] Open
Abstract
Type I interferon (IFN) inhibits a wide spectrum of viruses through stimulating the expression of antiviral proteins. As an IFN-induced protein, myxovirus resistance B (MXB) protein was reported to inhibit multiple highly pathogenic human viruses. It remains to be determined whether MXB employs a common mechanism to restrict different viruses. Here, we find that IFN alters the subcellular localization of hundreds of host proteins, and this IFN effect is partially lost upon MXB depletion. The results of our mechanistic study reveal that MXB recognizes vimentin (VIM) and recruits protein kinase B (AKT) to phosphorylate VIM at amino acid S38, which leads to reorganization of the VIM network and impairment of intracellular trafficking of virus protein complexes, hence causing a restriction of virus infection. These results highlight a new function of MXB in modulating VIM-mediated trafficking, which may lead towards a novel broad-spectrum antiviral strategy to control a large group of viruses that depend on VIM for successful replication.
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Affiliation(s)
- Dongrong Yi
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Ni An
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Quanjie Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Qian Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Huihan Shao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Rui Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Jing Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Yongxin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Fei Guo
- Institute of Pathogen Biology, Chinese Academy of Medical Science, Beijing 100730, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
| | - Zhenlong Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing 100050, China
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2
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Warger J, Gaudieri S. On the Evolutionary Trajectory of SARS-CoV-2: Host Immunity as a Driver of Adaptation in RNA Viruses. Viruses 2022; 15:70. [PMID: 36680110 PMCID: PMC9866609 DOI: 10.3390/v15010070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Host immunity can exert a complex array of selective pressures on a pathogen, which can drive highly mutable RNA viruses towards viral escape. The plasticity of a virus depends on its rate of mutation, as well as the balance of fitness cost and benefit of mutations, including viral adaptations to the host's immune response. Since its emergence, SARS-CoV-2 has diversified into genetically distinct variants, which are characterised often by clusters of mutations that bolster its capacity to escape human innate and adaptive immunity. Such viral escape is well documented in the context of other pandemic RNA viruses such as the human immunodeficiency virus (HIV) and influenza virus. This review describes the selection pressures the host's antiviral immunity exerts on SARS-CoV-2 and other RNA viruses, resulting in divergence of viral strains into more adapted forms. As RNA viruses obscure themselves from host immunity, they uncover weak points in their own armoury that can inform more comprehensive, long-lasting, and potentially cross-protective vaccine coverage.
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Affiliation(s)
- Jacob Warger
- School of Medicine and Pharmacology, University of Western Australia, Crawley, WA 6009, Australia
| | - Silvana Gaudieri
- School of Human Sciences, University of Western Australia, Crawley, WA 6009, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Mandurah, WA 6150, Australia
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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3
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Morizako N, Butlertanaka EP, Tanaka YL, Shibata H, Okabayashi T, Mekata H, Saito A. Generation of a bovine cell line for gene engineering using an HIV-1-based lentiviral vector. Sci Rep 2022; 12:16952. [PMID: 36258028 PMCID: PMC9579131 DOI: 10.1038/s41598-022-20970-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/21/2022] [Indexed: 12/29/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1)-based lentiviral vectors are indispensable tools for gene engineering in mammalian cells. Conversely, lentiviral vector transduction is severely inhibited in bovine cells. Previous studies demonstrated that this inhibition is caused by the anti-lentiviral host factor tripartite motif containing 5 (TRIM5), which targets incoming HIV-1 virions by interacting with the viral capsid. In this study, we investigated several methods for overcoming the limited applicability of lentiviral vectors in bovine cells. First, we demonstrated that the SPRY domain of bovine TRIM5 is the major determinant of anti-viral activity. Second, we found that mutations that allow the capsid to evade rhesus macaque TRIM5α minimally rescued HIV-1 infectivity in bovine-derived MDBK cells. Third, we found that cyclosporine A, which relieves the inhibition of HIV-1 infection in monkey cells, significantly rescued the impaired HIV-1 infectivity in MDBK cells. Lastly, we successfully generated a bovine cell line lacking intact TRIM5 using the CRISPR/Cas9 technique. This TRIM5 knockout cell line displayed significantly higher susceptibility to an HIV-1-based lentiviral vector. In conclusion, our findings provide a promising gene engineering strategy for bovine cells, thereby contributing to innovations in agriculture and improvements in animal health.
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Affiliation(s)
- Nanami Morizako
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Erika P. Butlertanaka
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Yuri L. Tanaka
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Honoka Shibata
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Tamaki Okabayashi
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan ,grid.410849.00000 0001 0657 3887Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan ,grid.410849.00000 0001 0657 3887Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Miyazaki 8891692 Japan
| | - Hirohisa Mekata
- grid.410849.00000 0001 0657 3887Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan
| | - Akatsuki Saito
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan ,grid.410849.00000 0001 0657 3887Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki 8892192 Japan ,grid.410849.00000 0001 0657 3887Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Miyazaki 8891692 Japan
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4
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Yoh SM, Mamede JI, Lau D, Ahn N, Sánchez-Aparicio MT, Temple J, Tuckwell A, Fuchs NV, Cianci GC, Riva L, Curry H, Yin X, Gambut S, Simons LM, Hultquist JF, König R, Xiong Y, García-Sastre A, Böcking T, Hope TJ, Chanda SK. Recognition of HIV-1 capsid by PQBP1 licenses an innate immune sensing of nascent HIV-1 DNA. Mol Cell 2022; 82:2871-2884.e6. [PMID: 35809572 PMCID: PMC9552964 DOI: 10.1016/j.molcel.2022.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/22/2022] [Accepted: 06/07/2022] [Indexed: 12/21/2022]
Abstract
We have previously described polyglutamine-binding protein 1 (PQBP1) as an adapter required for the cyclic GMP-AMP synthase (cGAS)-mediated innate response to the human immunodeficiency virus 1 (HIV-1) and other lentiviruses. Cytoplasmic HIV-1 DNA is a transient and low-abundance pathogen-associated molecular pattern (PAMP), and the mechanism for its detection and verification is not fully understood. Here, we show a two-factor authentication strategy by the innate surveillance machinery to selectively respond to the low concentration of HIV-1 DNA, while distinguishing these species from extranuclear DNA molecules. We find that, upon HIV-1 infection, PQBP1 decorates the intact viral capsid, and this serves as a primary verification step for the viral nucleic acid cargo. As reverse transcription and capsid disassembly initiate, cGAS is recruited to the capsid in a PQBP1-dependent manner. This positions cGAS at the site of PAMP generation and sanctions its response to a low-abundance DNA PAMP.
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Affiliation(s)
- Sunnie M Yoh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA.
| | - João I Mamede
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
| | - Derrick Lau
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Narae Ahn
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Maria T Sánchez-Aparicio
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua Temple
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Andrew Tuckwell
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Nina V Fuchs
- Host-Pathogen Interaction, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Gianguido C Cianci
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Laura Riva
- Calibr, a Division of The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Heather Curry
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Xin Yin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, P.R. China
| | - Stéphanie Gambut
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL 60612, USA
| | - Lacy M Simons
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Renate König
- Host-Pathogen Interaction, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Thomas J Hope
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sumit K Chanda
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA.
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5
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The role of cyclophilins in viral infec and the immune response. J Infect 2022; 85:365-373. [DOI: 10.1016/j.jinf.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022]
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6
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Gruenke PR, Aneja R, Welbourn S, Ukah OB, Sarafianos SG, Burke DH, Lange MJ. Selection and identification of an RNA aptamer that specifically binds the HIV-1 capsid lattice and inhibits viral replication. Nucleic Acids Res 2022; 50:1701-1717. [PMID: 35018437 PMCID: PMC8860611 DOI: 10.1093/nar/gkab1293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/23/2021] [Accepted: 12/16/2021] [Indexed: 01/25/2023] Open
Abstract
The HIV-1 capsid core participates in several replication processes. The mature capsid core is a lattice composed of capsid (CA) monomers thought to assemble first into CA dimers, then into ∼250 CA hexamers and 12 CA pentamers. CA assembly requires conformational flexibility of each unit, resulting in the presence of unique, solvent-accessible surfaces. Significant advances have improved our understanding of the roles of the capsid core in replication; however, the contributions of individual CA assembly forms remain unclear and there are limited tools available to evaluate these forms in vivo. Here, we have selected aptamers that bind CA lattice tubes. We describe aptamer CA15-2, which selectively binds CA lattice, but not CA monomer or CA hexamer, suggesting that it targets an interface present and accessible only on CA lattice. CA15-2 does not compete with PF74 for binding, indicating that it likely binds a non-overlapping site. Furthermore, CA15-2 inhibits HIV-1 replication when expressed in virus producer cells, but not target cells, suggesting that it binds a biologically-relevant site during virus production that is either not accessible during post-entry replication steps or is accessible but unaltered by aptamer binding. Importantly, CA15-2 represents the first aptamer that specifically recognizes the HIV-1 CA lattice.
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Affiliation(s)
- Paige R Gruenke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Rachna Aneja
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Sarah Welbourn
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Obiaara B Ukah
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Margaret J Lange
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
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7
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Saito A, Irie T, Suzuki R, Maemura T, Nasser H, Uriu K, Kosugi Y, Shirakawa K, Sadamasu K, Kimura I, Ito J, Wu J, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Loeber S, Tsuda M, Wang L, Ozono S, Butlertanaka EP, Tanaka YL, Shimizu R, Shimizu K, Yoshimatsu K, Kawabata R, Sakaguchi T, Tokunaga K, Yoshida I, Asakura H, Nagashima M, Kazuma Y, Nomura R, Horisawa Y, Yoshimura K, Takaori-Kondo A, Imai M, Tanaka S, Nakagawa S, Ikeda T, Fukuhara T, Kawaoka Y, Sato K. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature 2022; 602:300-306. [PMID: 34823256 PMCID: PMC8828475 DOI: 10.1038/s41586-021-04266-9] [Citation(s) in RCA: 351] [Impact Index Per Article: 175.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022]
Abstract
During the current coronavirus disease 2019 (COVID-19) pandemic, a variety of mutations have accumulated in the viral genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and, at the time of writing, four variants of concern are considered to be potentially hazardous to human society1. The recently emerged B.1.617.2/Delta variant of concern is closely associated with the COVID-19 surge that occurred in India in the spring of 2021 (ref. 2). However, the virological properties of B.1.617.2/Delta remain unclear. Here we show that the B.1.617.2/Delta variant is highly fusogenic and notably more pathogenic than prototypic SARS-CoV-2 in infected hamsters. The P681R mutation in the spike protein, which is highly conserved in this lineage, facilitates cleavage of the spike protein and enhances viral fusogenicity. Moreover, we demonstrate that the P681R-bearing virus exhibits higher pathogenicity compared with its parental virus. Our data suggest that the P681R mutation is a hallmark of the virological phenotype of the B.1.617.2/Delta variant and is associated with enhanced pathogenicity.
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Affiliation(s)
- Akatsuki Saito
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan ,grid.410849.00000 0001 0657 3887Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan ,grid.410849.00000 0001 0657 3887Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Takashi Irie
- grid.257022.00000 0000 8711 3200Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Rigel Suzuki
- grid.39158.360000 0001 2173 7691Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Tadashi Maemura
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan ,grid.14003.360000 0001 2167 3675Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI USA
| | - Hesham Nasser
- grid.274841.c0000 0001 0660 6749Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan ,grid.33003.330000 0000 9889 5690Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Keiya Uriu
- grid.26999.3d0000 0001 2151 536XDivision of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Kosugi
- grid.26999.3d0000 0001 2151 536XDivision of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenji Sadamasu
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Izumi Kimura
- grid.26999.3d0000 0001 2151 536XDivision of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jumpei Ito
- grid.26999.3d0000 0001 2151 536XDivision of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jiaqi Wu
- grid.265061.60000 0001 1516 6626Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan ,grid.419082.60000 0004 1754 9200CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Kiyoko Iwatsuki-Horimoto
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Mutsumi Ito
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seiya Yamayoshi
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan ,grid.45203.300000 0004 0489 0290The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Samantha Loeber
- grid.28803.310000 0001 0701 8607Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI USA
| | - Masumi Tsuda
- grid.39158.360000 0001 2173 7691Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Hokkaido, Japan ,grid.39158.360000 0001 2173 7691Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Hokkaido, Japan
| | - Lei Wang
- grid.39158.360000 0001 2173 7691Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Hokkaido, Japan ,grid.39158.360000 0001 2173 7691Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Hokkaido, Japan
| | - Seiya Ozono
- grid.410795.e0000 0001 2220 1880Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Erika P. Butlertanaka
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Yuri L. Tanaka
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ryo Shimizu
- grid.274841.c0000 0001 0660 6749Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenta Shimizu
- grid.39158.360000 0001 2173 7691Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Kumiko Yoshimatsu
- grid.39158.360000 0001 2173 7691Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Ryoko Kawabata
- grid.257022.00000 0000 8711 3200Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takemasa Sakaguchi
- grid.257022.00000 0000 8711 3200Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenzo Tokunaga
- grid.410795.e0000 0001 2220 1880Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Isao Yoshida
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Hiroyuki Asakura
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Mami Nagashima
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Yasuhiro Kazuma
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Nomura
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihito Horisawa
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuhisa Yoshimura
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Akifumi Takaori-Kondo
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Imai
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan ,grid.45203.300000 0004 0489 0290The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | | | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Hokkaido, Japan. .,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Hokkaido, Japan.
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan. .,CREST, Japan Science and Technology Agency, Saitama, Japan.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan.
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan. .,Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA. .,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. .,CREST, Japan Science and Technology Agency, Saitama, Japan.
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8
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Saito A, Yamashita M. HIV-1 capsid variability: viral exploitation and evasion of capsid-binding molecules. Retrovirology 2021; 18:32. [PMID: 34702294 PMCID: PMC8549334 DOI: 10.1186/s12977-021-00577-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 11/17/2022] Open
Abstract
The HIV-1 capsid, a conical shell encasing viral nucleoprotein complexes, is involved in multiple post-entry processes during viral replication. Many host factors can directly bind to the HIV-1 capsid protein (CA) and either promote or prevent HIV-1 infection. The viral capsid is currently being explored as a novel target for therapeutic interventions. In the past few decades, significant progress has been made in our understanding of the capsid–host interactions and mechanisms of action of capsid-targeting antivirals. At the same time, a large number of different viral capsids, which derive from many HIV-1 mutants, naturally occurring variants, or diverse lentiviruses, have been characterized for their interactions with capsid-binding molecules in great detail utilizing various experimental techniques. This review provides an overview of how sequence variation in CA influences phenotypic properties of HIV-1. We will focus on sequence differences that alter capsid–host interactions and give a brief account of drug resistant mutations in CA and their mutational effects on viral phenotypes. Increased knowledge of the sequence-function relationship of CA helps us deepen our understanding of the adaptive potential of the viral capsid.
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Affiliation(s)
- Akatsuki Saito
- Department of Veterinary Medicine, Faculty of Agriculture, University of Miyazaki, Miyazaki, Miyazaki, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Miyazaki, Japan
| | - Masahiro Yamashita
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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Structure, Function, and Interactions of the HIV-1 Capsid Protein. Life (Basel) 2021; 11:life11020100. [PMID: 33572761 PMCID: PMC7910843 DOI: 10.3390/life11020100] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 11/30/2022] Open
Abstract
The capsid (CA) protein of the human immunodeficiency virus type 1 (HIV-1) is an essential structural component of a virion and facilitates many crucial life cycle steps through interactions with host cell factors. Capsid shields the reverse transcription complex from restriction factors while it enables trafficking to the nucleus by hijacking various adaptor proteins, such as FEZ1 and BICD2. In addition, the capsid facilitates the import and localization of the viral complex in the nucleus through interaction with NUP153, NUP358, TNPO3, and CPSF-6. In the later stages of the HIV-1 life cycle, CA plays an essential role in the maturation step as a constituent of the Gag polyprotein. In the final phase of maturation, Gag is cleaved, and CA is released, allowing for the assembly of CA into a fullerene cone, known as the capsid core. The fullerene cone consists of ~250 CA hexamers and 12 CA pentamers and encloses the viral genome and other essential viral proteins for the next round of infection. As research continues to elucidate the role of CA in the HIV-1 life cycle and the importance of the capsid protein becomes more apparent, CA displays potential as a therapeutic target for the development of HIV-1 inhibitors.
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Ramdas P, Sahu AK, Mishra T, Bhardwaj V, Chande A. From Entry to Egress: Strategic Exploitation of the Cellular Processes by HIV-1. Front Microbiol 2020; 11:559792. [PMID: 33343516 PMCID: PMC7746852 DOI: 10.3389/fmicb.2020.559792] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/05/2020] [Indexed: 01/23/2023] Open
Abstract
HIV-1 employs a rich arsenal of viral factors throughout its life cycle and co-opts intracellular trafficking pathways. This exquisitely coordinated process requires precise manipulation of the host microenvironment, most often within defined subcellular compartments. The virus capitalizes on the host by modulating cell-surface proteins and cleverly exploiting nuclear import pathways for post entry events, among other key processes. Successful virus–cell interactions are indeed crucial in determining the extent of infection. By evolving defenses against host restriction factors, while simultaneously exploiting host dependency factors, the life cycle of HIV-1 presents a fascinating montage of an ongoing host–virus arms race. Herein, we provide an overview of how HIV-1 exploits native functions of the host cell and discuss recent findings that fundamentally change our understanding of the post-entry replication events.
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Affiliation(s)
- Pavitra Ramdas
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Amit Kumar Sahu
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Tarun Mishra
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Vipin Bhardwaj
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
| | - Ajit Chande
- Molecular Virology Laboratory, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, India
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11
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Saito A, Sultana T, Ode H, Nohata K, Samune Y, Nakayama EE, Iwatani Y, Shioda T. The 4th and 112th Residues of Viral Capsid Cooperatively Modulate Capsid-CPSF6 Interactions of HIV-1. AIDS Res Hum Retroviruses 2020; 36:513-521. [PMID: 31941344 PMCID: PMC7262650 DOI: 10.1089/aid.2019.0250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Binding of HIV-1 capsid (CA) to cleavage and polyadenylation specificity factor 6 (CPSF6) is hypothesized to provide a significant fitness advantage to in vivo viral replication, explaining why CA-CPSF6 interactions are strictly conserved in primate lentiviruses. We recently identified a Q4R mutation in CA after propagation of an interferon (IFN)-β-hypersensitive CA mutant, RGDA/Q112D (H87R, A88G, P90D, P93A and Q112D) virus, in IFN-β-treated cells. The Q4R substitution conferred significant IFN-β resistance to the RGDA/Q112D virus by affecting several properties of the virus, including the sensitivity to myxovirus resistance protein B (MxB), the kinetics of reverse transcription, and the initiation of uncoating. Notably, the Q4R substitution restored the CPSF6 interaction of the RGDA/Q112D virus. To better understand how the Q4R substitution modulated the CA-CPSF6 interaction, we generated a series of CA mutants harboring substitutions at the 4th and 112th residues. In contrast to the effect in the RGDA/Q112D background, the Q4R substitution diminished CA-CPSF6 interaction in an otherwise wild-type virus. Our genetic and structural analyses revealed that while either the Q4R or Q112D substitution impaired CA-CPSF6 interaction, the combination of these substitutions restored this interaction. These results suggest that the 4th and 112th residues in HIV-1 CA cooperatively modulate CA-CPSF6 interactions, further highlighting the tremendous levels of plasticity in primate lentivirus CA, which is one of the barriers to antiretroviral therapy in HIV-1-infected individuals.
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Affiliation(s)
- Akatsuki Saito
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tahmina Sultana
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Kyotaro Nohata
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yoshihiro Samune
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Emi E. Nakayama
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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12
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Ohainle M, Kim K, Komurlu Keceli S, Felton A, Campbell E, Luban J, Emerman M. TRIM34 restricts HIV-1 and SIV capsids in a TRIM5α-dependent manner. PLoS Pathog 2020; 16:e1008507. [PMID: 32282853 PMCID: PMC7179944 DOI: 10.1371/journal.ppat.1008507] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/23/2020] [Accepted: 03/29/2020] [Indexed: 02/07/2023] Open
Abstract
The HIV-1 capsid protein makes up the core of the virion and plays a critical role in early steps of HIV replication. Due to its exposure in the cytoplasm after entry, HIV capsid is a target for host cell factors that act directly to block infection such as TRIM5α and MxB. Several host proteins also play a role in facilitating infection, including in the protection of HIV-1 capsid from recognition by host cell restriction factors. Through an unbiased screening approach, called HIV-CRISPR, we show that the CPSF6-binding deficient, N74D HIV-1 capsid mutant is sensitive to restriction mediated by human TRIM34, a close paralog of the well-characterized HIV restriction factor TRIM5α. This restriction occurs at the step of reverse transcription, is independent of interferon stimulation, and limits HIV-1 infection in key target cells of HIV infection including CD4+ T cells and monocyte-derived dendritic cells. TRIM34 can also restrict some SIV capsids. TRIM34 restriction requires TRIM5α as knockout or knockdown of TRIM5α results in a loss of antiviral activity. Through immunofluorescence studies, we show that TRIM34 and TRIM5α colocalize to cytoplasmic bodies and are more frequently observed to be associated with infecting N74D capsids than with WT HIV-1 capsids. Our results identify TRIM34 as an HIV-1 CA-targeting restriction factor and highlight the potential role for heteromultimeric TRIM interactions in contributing to restriction of HIV-1 infection in human cells.
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Affiliation(s)
- Molly Ohainle
- Divisions of Human Biology and Basic Sciences, Fred Hutch, Seattle, Washington, United States of America
| | - Kyusik Kim
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sevnur Komurlu Keceli
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University, Chicago, Maywood, Illinois, United States of America
| | - Abby Felton
- Divisions of Human Biology and Basic Sciences, Fred Hutch, Seattle, Washington, United States of America
| | - Ed Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University, Chicago, Maywood, Illinois, United States of America
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutch, Seattle, Washington, United States of America
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13
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Yin X, Langer S, Zhang Z, Herbert KM, Yoh S, König R, Chanda SK. Sensor Sensibility-HIV-1 and the Innate Immune Response. Cells 2020; 9:E254. [PMID: 31968566 PMCID: PMC7016969 DOI: 10.3390/cells9010254] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 02/07/2023] Open
Abstract
Innate immunity represents the human immune system's first line of defense against a pathogenic intruder and is initiated by the recognition of conserved molecular structures known as pathogen-associated molecular patterns (PAMPs) by specialized cellular sensors, called pattern recognition receptors (PRRs). Human immunodeficiency virus type 1 (HIV-1) is a unique human RNA virus that causes acquired immunodeficiency syndrome (AIDS) in infected individuals. During the replication cycle, HIV-1 undergoes reverse transcription of its RNA genome and integrates the resulting DNA into the human genome. Subsequently, transcription of the integrated provirus results in production of new virions and spreading infection of the virus. Throughout the viral replication cycle, numerous nucleic acid derived PAMPs can be recognized by a diverse set of innate immune sensors in infected cells. However, HIV-1 has evolved efficient strategies to evade or counteract this immune surveillance and the downstream responses. Understanding the molecular underpinnings of the concerted actions of the innate immune system, as well as the corresponding viral evasion mechanisms during infection, is critical to understanding HIV-1 transmission and pathogenesis, and may provide important guidance for the design of appropriate adjuvant and vaccine strategies. Here, we summarize current knowledge of the molecular basis for sensing HIV-1 in human cells, including CD4+ T cells, dendritic cells, and macrophages. Furthermore, we discuss the underlying mechanisms by which innate sensing is regulated, and describe the strategies developed by HIV-1 to evade sensing and immune responses.
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Affiliation(s)
- Xin Yin
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
| | - Simon Langer
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
- Boehringer Ingelheim Pharma GmbH & Co. KG, 55216 Ingelheim am Rhein, Germany
| | - Zeli Zhang
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
- Division of Vaccine Discovery, La Jolla Institute for Immunology, 9420 Athena Cir, La Jolla, CA 92037, USA
| | - Kristina M. Herbert
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
| | - Sunnie Yoh
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
| | - Renate König
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Sumit K. Chanda
- Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; (X.Y.); (S.L.); (Z.Z.); (K.M.H.); (S.Y.); (R.K.)
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