1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Adachi A, Koma T, Doi N, Nomaguchi M. Commentary: Derivation of Simian Tropic HIV-1 Infectious Clone Reveals Virus Adaptation to a New Host. Front Cell Infect Microbiol 2020; 10:235. [PMID: 32500043 PMCID: PMC7243179 DOI: 10.3389/fcimb.2020.00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/23/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
- Akio Adachi
- Department of Microbiology, Kansai Medical University, Osaka, Japan
| | - Takaaki Koma
- Department of Microbiology, Tokushima University Graduate School of Medical Science, Tokushima, Japan
| | - Naoya Doi
- Department of Microbiology, Tokushima University Graduate School of Medical Science, Tokushima, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Tokushima University Graduate School of Medical Science, Tokushima, Japan
| |
Collapse
|
3
|
Sii-Felice K, Castillo Padilla J, Relouzat F, Cheuzeville J, Tantawet S, Maouche L, Le Grand R, Leboulch P, Payen E. Enhanced Transduction of Macaca fascicularis Hematopoietic Cells with Chimeric Lentiviral Vectors. Hum Gene Ther 2019; 30:1306-1323. [DOI: 10.1089/hum.2018.179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Karine Sii-Felice
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
| | - Javier Castillo Padilla
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Francis Relouzat
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
| | - Joëlle Cheuzeville
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- bluebird bio France, Fontenay aux Roses, France
| | - Siriporn Tantawet
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
| | - Leïla Maouche
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- INSERM, Paris, France
| | - Roger Le Grand
- Immunology of Viral Infections and Autoimmune Diseases, UMR 1184, IDMIT Department, Institute of Biology François Jacob, INSERM, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
| | - Philippe Leboulch
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- Ramathibodi Hospital and Mahidol University, Bangkok, Thailand
- Harvard Medical School and Genetics Division, Department of Medicine, Brigham and Women's Hospital, Boston Massachusetts
| | - Emmanuel Payen
- Division of Innovative Therapies, UMR E007, Institute of Biology François Jacob, CEA, Paris-Sud University, Paris-Saclay University, Fontenay aux Roses, France
- INSERM, Paris, France
| |
Collapse
|
4
|
Allosteric Regulation of HIV-1 Capsid Structure for Gag Assembly, Virion Production, and Viral Infectivity by a Disordered Interdomain Linker. J Virol 2019; 93:JVI.00381-19. [PMID: 31189701 DOI: 10.1128/jvi.00381-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
The retroviral Gag capsid (Gag-CA) interdomain linker is an unstructured peptide segment connecting structured N-terminal and C-terminal domains. Although the region is reported to play roles in virion morphogenesis and infectivity, underlying molecular mechanisms remain unexplored. To address this issue, we determined biological and molecular phenotypes of HIV-1 CA linker mutants by experimental and in silico approaches. Among the nine linker mutants tested, eight exhibited attenuation of viral particle production to various extents mostly in parallel with a reduction in viral infectivity. Sucrose density gradient, confocal microscopy, and live-cell protein interaction analyses indicated that the defect is accompanied by attenuation of Gag-Gag interactions following Gag plasma membrane targeting in the cells. In silico analyses revealed distinct distributions of interaction-prone hydrophobic patches between immature and mature CA proteins. Molecular dynamics simulations predicted that the linker mutations can allosterically alter structural fluctuations, including the interaction surfaces apart from the mutation sites in both the immature and mature CA proteins. These results suggest that the HIV-1 CA interdomain linker is a cis-modulator of the CA interaction surfaces to optimize efficiency of Gag assembly, virion production, and viral infectivity.IMPORTANCE HIV-1 particle production and infection are highly ordered processes. Viral Gag proteins play a central role in the assembly and disassembly of viral molecules. Of these, capsid protein (CA) is a major contributor to the Gag-Gag interactions. CA consists of two structured domains, i.e., N-terminal (NTD) and C-terminal (CTD) domains, connected by an unstructured domain named the interdomain linker. While multiple regions in the NTD and CTD are reported to play roles in virion morphogenesis and infectivity, the roles of the linker region in Gag assembly and virus particle formation remain elusive. In this study, we showed by biological and molecular analyses that the linker region functions as an intramolecular modulator to tune Gag assembly, virion production, and viral infectivity. Our study thus illustrates a hitherto-unrecognized mechanism, an allosteric regulation of CA structure by the disordered protein element, for HIV-1 replication.
Collapse
|
5
|
Doi N, Miura T, Mori H, Sakawaki H, Koma T, Adachi A, Nomaguchi M. CXCR4- and CCR5-Tropic HIV-1 Clones Are Both Tractable to Grow in Rhesus Macaques. Front Microbiol 2018; 9:2510. [PMID: 30405570 PMCID: PMC6200915 DOI: 10.3389/fmicb.2018.02510] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/02/2018] [Indexed: 01/08/2023] Open
Abstract
A major issue for present HIV-1 research is to establish model systems that reflect or mimic viral replication and pathogenesis actually observed in infected humans. To this end, various strategies using macaques as infection targets have long been pursued. In particular, experimental infections of rhesus macaques by HIV-1 derivatives have been believed to be best suited, if practicable, for studies on interaction of HIV-1 and humans under various circumstances. Recently, through in vitro genetic manipulations and viral cell-adaptations, we have successfully generated a series of HIV-1 derivatives with CXCR4-tropism or CCR5-tropism that grow in macaque cells to various degrees. Of these viruses, those with best replicative potentials can grow comparably with a pathogenic SIVmac in macaque cells by counteracting major restriction factors TRIM5, APOBEC3, and tetherin proteins. In this study, rhesus macaques were challenged with CXCR4-tropic (MN4/LSDQgtu) or CCR5-tropic (gtu + A4CI1) virus. The two viruses were found to productively infect rhesus macaques, being rhesus macaque-tropic HIV-1 (HIV-1rmt). However, plasma viral RNA was reduced to be an undetectable level in infected macaques at 5–6 weeks post-infection and thereafter. While replicated similarly well in rhesus peripheral blood mononuclear cells, MN4/LSDQgtu grew much better than gtu + A4CI1 in the animals. To the best of our knowledge, this is the first report demonstrating that HIV-1 derivatives (variants) grow in rhesus macaques. These viruses certainly constitute firm bases for generating HIV-1rmt clones pathogenic for rhesus monkeys, albeit they grow more poorly than pathogenic SIVmac and SHIV clones reported to date.
Collapse
Affiliation(s)
- Naoya Doi
- Department of Microbiology, Graduate School of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Tomoyuki Miura
- Laboratory of Primate Model, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiromi Mori
- Laboratory of Primate Model, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiromi Sakawaki
- Non-human Primate Experimental Facility, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Takaaki Koma
- Department of Microbiology, Graduate School of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Akio Adachi
- Department of Microbiology, Kansai Medical University, Hirakata, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Graduate School of Medical Sciences, Tokushima University, Tokushima, Japan
| |
Collapse
|
6
|
Doi N, Sakai Y, Adachi A, Nomaguchi M. Generation and characterization of new CCR5-tropic HIV-1rmt clones. THE JOURNAL OF MEDICAL INVESTIGATION 2018; 64:272-279. [PMID: 28954995 DOI: 10.2152/jmi.64.272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
To develop effective non-human primate models for coping with numerous HIV-1/AIDS studies, rhesus macaque-tropic HIV-1 (HIV-1rmt) clones with a variety of biological properties are required. Such clones, if available, are powerful tools to experimentally elucidate HIV-1 replication and pathogenicity in host individuals, and also to develop anti-HIV-1 drugs/vaccines. However, only limited numbers of HIV-1rmt clones have been currently reported. In the present study, we generated new HIV-1rmt clones carrying various CCR5-tropic env (envelope) genes by standard recombinant DNA and intracellular homologous recombination techniques. Resultant virus clones contain the env sequences derived from an AIDS-inducible laboratory or two clinically isolated viral strains. We further constructed their variant clones bearing N160K, S304G, or G310R mutation in Env that potentially can change the viruses to better grow. Newly generated clones were analyzed for their virological properties such as Env expression, single-cycle infectivity, and multi-cycle replication ability. Out of a number of new clones examined, two were found to grow better in macaque cells than the previously constructed clone used for comparison. Our study described here constitutes the initial and essential step towards obtaining CCR5-tropic HIV-1rmt clones useful for various basic and clinical research projects on infected individuals. J. Med. Invest. 64: 272-279, August, 2017.
Collapse
Affiliation(s)
- Naoya Doi
- Department of Microbiology, Tokushima University Graduate School of Medical Science
| | - Yosuke Sakai
- Department of Microbiology, Tokushima University Graduate School of Medical Science
| | | | - Masako Nomaguchi
- Department of Microbiology, Tokushima University Graduate School of Medical Science
| |
Collapse
|
7
|
Complete Genome Sequences of Human Immunodeficiency Type 1 Viruses Genetically Engineered To Be Tropic for Rhesus Macaques. GENOME ANNOUNCEMENTS 2017; 5:5/39/e01063-17. [PMID: 28963223 PMCID: PMC5624769 DOI: 10.1128/genomea.01063-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have constructed two human immunodeficiency type 1 (HIV-1) derivatives, CXCR4 tropic and CCR5 tropic, that replicate in rhesus macaques. They are genetically engineered to be resistant to macaque restriction factors against HIV-1, including TRIM5α, APOBEC3, and tetherin proteins. The two HIV-1 variants described here are fundamental clones aiming for rhesus infection studies of HIV-1.
Collapse
|
8
|
Jimenez-Moyano E, Ruiz A, Kløverpris HN, Rodriguez-Plata MT, Peña R, Blondeau C, Selwood DL, Izquierdo-Useros N, Moris A, Clotet B, Goulder P, Towers GJ, Prado JG. Nonhuman TRIM5 Variants Enhance Recognition of HIV-1-Infected Cells by CD8+ T Cells. J Virol 2016; 90:8552-62. [PMID: 27440884 PMCID: PMC5021395 DOI: 10.1128/jvi.00819-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Tripartite motif-containing protein 5 (TRIM5) restricts human immunodeficiency virus type 1 (HIV-1) in a species-specific manner by uncoating viral particles while activating early innate responses. Although the contribution of TRIM5 proteins to cellular immunity has not yet been studied, their interactions with the incoming viral capsid and the cellular proteasome led us to hypothesize a role for them. Here, we investigate whether the expression of two nonhuman TRIM5 orthologs, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), both of which are potent restrictors of HIV-1, could enhance immune recognition of infected cells by CD8(+) T cells. We illustrate how TRIM5 restriction improves CD8(+) T-cell-mediated HIV-1 inhibition. Moreover, when TRIM5 activity was blocked by the nonimmunosuppressive analog of cyclosporine (CsA), sarcosine-3(4-methylbenzoate)-CsA (SmBz-CsA), we found a significant reduction in CD107a/MIP-1β expression in HIV-1-specific CD8(+) T cells. This finding underscores the direct link between TRIM5 restriction and activation of CD8(+) T-cell responses. Interestingly, cells expressing RhT5 induced stronger CD8(+) T-cell responses through the specific recognition of the HIV-1 capsid by the immune system. The underlying mechanism of this process may involve TRIM5-specific capsid recruitment to cellular proteasomes and increase peptide availability for loading and presentation of HLA class I antigens. In summary, we identified a novel function for nonhuman TRIM5 variants in cellular immunity. We hypothesize that TRIM5 can couple innate viral sensing and CD8(+) T-cell activation to increase species barriers against retrovirus infection. IMPORTANCE New therapeutics to tackle HIV-1 infection should aim to combine rapid innate viral sensing and cellular immune recognition. Such strategies could prevent seeding of the viral reservoir and the immune damage that occurs during acute infection. The nonhuman TRIM5 variants, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), are attractive candidates owing to their potency in sensing HIV-1 and blocking its activity. Here, we show that expression of RhT5 and TCyp in HIV-1-infected cells improves CD8(+) T-cell-mediated inhibition through the direct activation of HIV-1-specific CD8(+) T-cell responses. We found that the potency in CD8(+) activation was stronger for RhT5 variants and capsid-specific CD8(+) T cells in a mechanism that relies on TRIM5-dependent particle recruitment to cellular proteasomes. This novel mechanism couples innate viral sensing with cellular immunity in a single protein and could be exploited to develop innovative therapeutics for control of HIV-1 infection.
Collapse
Affiliation(s)
| | - Alba Ruiz
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Henrik N Kløverpris
- KwaZulu-Natal Research Institute for TB and HIV, University of KwaZulu-Natal, Durban, South Africa
| | | | - Ruth Peña
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Caroline Blondeau
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - David L Selwood
- The Wolfson Institute for Biomedical Research, University College London, United Kingdom
| | | | - Arnaud Moris
- Sorbonne Universités, UPMC University Paris 6, INSERM U1135, CNRS ERL 8255, Center for Immunology and Microbial Infections-Paris, Paris, France
| | - Bonaventura Clotet
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Julia G Prado
- AIDS Research Institute, IrsiCaixa, Hospital Germans Trias i Pujol, Badalona, Spain
| |
Collapse
|
9
|
Sultana T, Nakayama EE, Tobita S, Yokoyama M, Seki Y, Saito A, Nomaguchi M, Adachi A, Akari H, Sato H, Shioda T. Novel mutant human immunodeficiency virus type 1 strains with high degree of resistance to cynomolgus macaque TRIMCyp generated by random mutagenesis. J Gen Virol 2016; 97:963-976. [PMID: 26795727 DOI: 10.1099/jgv.0.000408] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Old World monkey TRIM5α strongly suppresses human immunodeficiency virus type 1 (HIV-1) replication. A fusion protein comprising cynomolgus macaque (CM) TRIM5 and cyclophilin A (CM TRIMCyp) also potently suppresses HIV-1 replication. However, CM TRIMCyp fails to suppress a mutant HIV-1 that encodes a mutant capsid protein containing a SIVmac239-derived loop between α-helices 4 and 5 (L4/5). There are seven amino acid differences between L4/5 of HIV-1 and SIVmac239. Here, we investigated the minimum numbers of amino acid substitutions that would allow HIV-1 to evade CM TRIMCyp-mediated suppression. We performed random PCR mutagenesis to construct a library of HIV-1 variants containing mutations in L4/5, and then we recovered replication-competent viruses from CD4+ MT4 cells that expressed high levels of CM TRIMCyp. CM TRIMCyp-resistant viruses were obtained after three rounds of selection in MT4 cells expressing CM TRIMCyp and these were found to contain four amino acid substitutions (H87R, A88G, P90D and P93A) in L4/5. We then confirmed that these substitutions were sufficient to confer CM TRIMCyp resistance to HIV-1. In a separate experiment using a similar method, we obtained novel CM TRIM5α-resistant HIV-1 strains after six rounds of selection and rescue. Analysis of these mutants revealed that V86A and G116E mutations in the capsid region conferred partial resistance to CM TRIM5α without substantial fitness cost when propagated in MT4 cells expressing CM TRIM5α. These results confirmed and further extended the previous notion that CM TRIMCyp and CM TRIM5α recognize the HIV-1 capsid in different manners.
Collapse
Affiliation(s)
- Tahmina Sultana
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Emi E Nakayama
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Satoshi Tobita
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Yohei Seki
- Center of Human Evolution Modeling Research, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan
| | - Akatsuki Saito
- Center of Human Evolution Modeling Research, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Akio Adachi
- Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hirofumi Akari
- Center of Human Evolution Modeling Research, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan.,Laboratory of Evolutional Virology, Institute for Virus Research, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Tatsuo Shioda
- Department of Viral Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| |
Collapse
|
10
|
Abstract
HIV type 1 (HIV-1) has a very narrow host range that is limited to humans and chimpanzees. HIV-1 cannot replicate well in Old World monkey cells such as rhesus and cynomolgus monkeys. Tripartite motif (TRIM)5α is a key molecule that confers potent resistance against HIV-1 infection and is composed of really interesting new gene, B-box2, coiled-coil and PRYSPRY domains. Interaction between TRIM5α PRYSPRY domains and HIV-1 capsid core triggers the anti-HIV-1 activity of TRIM5α. Analysis of natural HIV variants and extensive mutational experiments has revealed the presence of critical amino acid residues in both the PRYSPRY domain and HIV capsid for potent HIV suppression by TRIM5α. Genetic manipulation of the human TRIM5 gene could establish human cells totally resistant to HIV-1, which may lead to a cure for HIV-1 infection in the future.
Collapse
|