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Taylor IA, Fassati A. The capsid revolution. J Mol Cell Biol 2024; 15:mjad076. [PMID: 38037430 PMCID: PMC11193064 DOI: 10.1093/jmcb/mjad076] [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: 07/25/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023] Open
Abstract
Lenacapavir, targeting the human immunodeficiency virus type-1 (HIV-1) capsid, is the first-in-class antiretroviral drug recently approved for clinical use. The development of Lenacapavir is attributed to the remarkable progress in our understanding of the capsid protein made during the last few years. Considered little more than a component of the virus shell to be shed early during infection, the capsid has been found to be a key player in the HIV-1 life cycle by interacting with multiple host factors, entering the nucleus, and directing integration. Here, we describe the key advances that led to this 'capsid revolution'.
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Affiliation(s)
- Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ariberto Fassati
- Division of Infection and Immunity, University College London, London WC1E 6JF, UK
- Institute of Immunity and Transplantation, University College London, London NW3 2PP, UK
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2
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Kambol R, Gatseva A, Gifford RJ. An endogenous lentivirus in the germline of a rodent. Retrovirology 2022; 19:30. [PMID: 36539757 PMCID: PMC9768972 DOI: 10.1186/s12977-022-00615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Lentiviruses (genus Lentivirus) are complex retroviruses that infect a broad range of mammals, including humans. Unlike many other retrovirus genera, lentiviruses have only rarely been incorporated into the mammalian germline. However, a small number of endogenous retrovirus (ERV) lineages have been identified, and these rare genomic "fossils" can provide crucial insights into the long-term history of lentivirus evolution. Here, we describe a previously unreported endogenous lentivirus lineage in the genome of the South African springhare (Pedetes capensis), demonstrating that the host range of lentiviruses has historically extended to rodents (order Rodentia). Furthermore, through comparative and phylogenetic analysis of lentivirus and ERV genomes, considering the biogeographic and ecological characteristics of host species, we reveal broader insights into the long-term evolutionary history of the genus.
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Affiliation(s)
- Roziah Kambol
- grid.412259.90000 0001 2161 1343School of Biological Sciences, Faculty of Applied Sciences, University Teknologi MARA, 40450 Shah Alam, Selangor Malaysia
| | - Anna Gatseva
- grid.301713.70000 0004 0393 3981MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, G61 1QH Glasgow UK
| | - Robert J. Gifford
- grid.301713.70000 0004 0393 3981MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, G61 1QH Glasgow UK
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3
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Long M, Cantrelle FX, Robert X, Boll E, Sierra N, Gouet P, Hanoulle X, Alvarez GI, Guillon C. Identification of a Potential Inhibitor of the FIV p24 Capsid Protein and Characterization of Its Binding Site. Biochemistry 2021; 60:1896-1908. [PMID: 34096272 DOI: 10.1021/acs.biochem.1c00228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Feline immunodeficiency virus (FIV) is a veterinary infective agent for which there is currently no efficient drug available. Drugs targeting the lentivirus capsid are currently under development for the treatment of human immunodeficiency virus 1 (HIV-1). Here we describe a lead compound that interacts with the FIV capsid. This compound, 696, modulates the in vitro assembly of and stabilizes the assembled capsid protein. To decipher the mechanism of binding of this compound to the protein, we performed the first nuclear magnetic resonance (NMR) assignment of the FIV p24 capsid protein. Experimental NMR chemical shift perturbations (CSPs) observed after the addition of 696 enabled the characterization of a specific binding site for 696 on p24. This site was further analyzed by molecular modeling of the protein:compound interaction, demonstrating a strong similarity with the binding sites of existing drugs targeting the HIV-1 capsid protein. Taken together, we characterized a promising capsid-interacting compound with a low cost of synthesis, for which derivatives could lead to the development of efficient treatments for FIV infection. More generally, our strategy combining the NMR assignment of FIV p24 with NMR CSPs and molecular modeling will be useful for the analysis of future compounds targeting p24 in the quest to identify an efficient treatment for FIV.
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Affiliation(s)
- Mathieu Long
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - François-Xavier Cantrelle
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Xavier Robert
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - Emmanuelle Boll
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Natalia Sierra
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, 60000 Paysandú, Uruguay
| | - Patrice Gouet
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
| | - Xavier Hanoulle
- CNRS, ERL9002, Integrative Structural Biology, F-59000 Lille, France.,Univ. Lille, INSERM, CHU Lille University Hospital, Institut Pasteur de Lille, UMR1167-RID-AGE-Risk factors and molecular determinants of aging-related, F-59000 Lille, France
| | - Guzmán I Alvarez
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, 60000 Paysandú, Uruguay
| | - Christophe Guillon
- UMR 5086, Molecular Microbiology and Structural Biochemistry, CNRS/Université Lyon 1, 69367 Lyon, France
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4
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Tabasi M, Nombela I, Janssens J, Lahousse AP, Christ F, Debyser Z. Role of Transportin-SR2 in HIV-1 Nuclear Import. Viruses 2021; 13:829. [PMID: 34064404 PMCID: PMC8147801 DOI: 10.3390/v13050829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/14/2022] Open
Abstract
The HIV replication cycle depends on the interaction of viral proteins with proteins of the host. Unraveling host-pathogen interactions during the infection is of great importance for understanding the pathogenesis and the development of antiviral therapies. To date HIV uncoating and nuclear import are the most debated steps of the HIV-1 replication cycle. Despite numerous studies during past decades, there is still much controversy with respect to the identity and the role of viral and host factors involved in these processes. In this review, we provide a comprehensive overview on the role of transportin-SR2 as a host cell factor during active nuclear transport.
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Affiliation(s)
| | | | | | | | | | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium; (M.T.); (I.N.); (J.J.); (A.P.L.); (F.C.)
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5
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Toccafondi E, Lener D, Negroni M. HIV-1 Capsid Core: A Bullet to the Heart of the Target Cell. Front Microbiol 2021; 12:652486. [PMID: 33868211 PMCID: PMC8046902 DOI: 10.3389/fmicb.2021.652486] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
The first step of the intracellular phase of retroviral infection is the release of the viral capsid core in the cytoplasm. This structure contains the viral genetic material that will be reverse transcribed and integrated into the genome of infected cells. Up to recent times, the role of the capsid core was considered essentially to protect this genetic material during the earlier phases of this process. However, increasing evidence demonstrates that the permanence inside the cell of the capsid as an intact, or almost intact, structure is longer than thought. This suggests its involvement in more aspects of the infectious cycle than previously foreseen, particularly in the steps of viral genomic material translocation into the nucleus and in the phases preceding integration. During the trip across the infected cell, many host factors are brought to interact with the capsid, some possessing antiviral properties, others, serving as viral cofactors. All these interactions rely on the properties of the unique component of the capsid core, the capsid protein CA. Likely, the drawback of ensuring these multiple functions is the extreme genetic fragility that has been shown to characterize this protein. Here, we recapitulate the busy agenda of an HIV-1 capsid in the infectious process, in particular in the light of the most recent findings.
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Affiliation(s)
| | - Daniela Lener
- CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Matteo Negroni
- CNRS, Architecture et Réactivité de l’ARN, UPR 9002, Université de Strasbourg, Strasbourg, France
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6
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Human TRIM5α: Autophagy Connects Cell-Intrinsic HIV-1 Restriction and Innate Immune Sensor Functioning. Viruses 2021; 13:v13020320. [PMID: 33669846 PMCID: PMC7923229 DOI: 10.3390/v13020320] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/12/2021] [Accepted: 02/13/2021] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus-1 (HIV-1) persists as a global health concern, with an incidence rate of approximately 2 million, and estimated global prevalence of over 35 million. Combination antiretroviral treatment is highly effective, but HIV-1 patients that have been treated still suffer from chronic inflammation and residual viral replication. It is therefore paramount to identify therapeutically efficacious strategies to eradicate viral reservoirs and ultimately develop a cure for HIV-1. It has been long accepted that the restriction factor tripartite motif protein 5 isoform alpha (TRIM5α) restricts HIV-1 infection in a species-specific manner, with rhesus macaque TRIM5α strongly restricting HIV-1, and human TRIM5α having a minimal restriction capacity. However, several recent studies underscore human TRIM5α as a cell-dependent HIV-1 restriction factor. Here, we present an overview of the latest research on human TRIM5α and propose a novel conceptualization of TRIM5α as a restriction factor with a varied portfolio of antiviral functions, including mediating HIV-1 degradation through autophagy- and proteasome-mediated mechanisms, and acting as a viral sensor and effector of antiviral signaling. We have also expanded on the protective antiviral roles of autophagy and outline the therapeutic potential of autophagy modulation to intervene in chronic HIV-1 infection.
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7
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Tandon H, de Brevern AG, Srinivasan N. Transient association between proteins elicits alteration of dynamics at sites far away from interfaces. Structure 2020; 29:371-384.e3. [PMID: 33306961 DOI: 10.1016/j.str.2020.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022]
Abstract
Proteins are known to undergo structural changes upon binding to partner proteins. However, the prevalence, extent, location, and function of change in protein dynamics due to transient protein-protein interactions is not well documented. Here, we have analyzed a dataset of 58 protein-protein complexes of known three-dimensional structure and structures of their corresponding unbound forms to evaluate dynamics changes induced by binding. Fifty-five percent of cases showed significant dynamics change away from the interfaces. This change is not always accompanied by an observed structural change. Binding of protein partner is found to alter inter-residue communication within the tertiary structure in about 90% of cases. Also, residue motions accessible to proteins in unbound form were not always maintained in the bound form. Further analyses revealed functional roles for the distant site where dynamics change was observed. Overall, the results presented here strongly suggest that alteration of protein dynamics due to binding of a partner protein commonly occurs.
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Affiliation(s)
- Himani Tandon
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, 75739 Paris, France; Univ Paris, UMR_S 1134, 75739 Paris, France; Institut National de la Transfusion Sanguine (INTS), 75739 Paris, France; Laboratoire d'Excellence GR-Ex, 75739 Paris, France
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8
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Yap MW, Young GR, Varnaite R, Morand S, Stoye JP. Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli allows protection from multiple retroviruses. PLoS Genet 2020; 16:e1008471. [PMID: 32525879 PMCID: PMC7313476 DOI: 10.1371/journal.pgen.1008471] [Citation(s) in RCA: 5] [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: 10/08/2019] [Revised: 06/23/2020] [Accepted: 05/13/2020] [Indexed: 12/29/2022] Open
Abstract
Viruses and their hosts are locked in an evolutionary race where resistance to infection is acquired by the hosts while viruses develop strategies to circumvent these host defenses. Forming one arm of the host defense armory are cell autonomous restriction factors like Fv1. Originally described as protecting laboratory mice from infection by murine leukemia virus (MLV), Fv1s from some wild mice have also been found to restrict non-MLV retroviruses, suggesting an important role in the protection against viruses in nature. We surveyed the Fv1 genes of wild mice trapped in Thailand and characterized their restriction activities against a panel of retroviruses. An extra copy of the Fv1 gene, named Fv7, was found on chromosome 6 of three closely related Asian species of mice: Mus caroli, M. cervicolor, and M. cookii. The presence of flanking repeats suggested it arose by LINE-mediated retroduplication within their most recent common ancestor. A high degree of natural variation was observed in both Fv1 and Fv7 and, on top of positive selection at certain residues, insertions and deletions were present that changed the length of the reading frames. These genes exhibited a range of restriction phenotypes, with activities directed against gamma-, spuma-, and lentiviruses. It seems likely, at least in the case of M. caroli, that the observed gene duplication may expand the breadth of restriction beyond the capacity of Fv1 alone and that one or more such viruses have recently driven or continue to drive the evolution of the Fv1 and Fv7 genes.
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Affiliation(s)
| | | | | | - Serge Morand
- Centre National de la Recherche Scientifique-Centre de coopération
Internationale en Recherche Agronomique pour le Développement Animal et Gestion
Intégrée des Risques, Faculty of Veterinary Technology, Kasetsart University,
Bangkok, Thailand
| | - Jonathan P. Stoye
- The Francis Crick Institute, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United
Kingdom
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9
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Abstract
Retroviruses infect a broad range of vertebrate hosts that includes amphibians, reptiles, fish, birds and mammals. In addition, a typical vertebrate genome contains thousands of loci composed of ancient retroviral sequences known as endogenous retroviruses (ERVs). ERVs are molecular remnants of ancient retroviruses and proof that the ongoing relationship between retroviruses and their vertebrate hosts began hundreds of millions of years ago. The long-term impact of retroviruses on vertebrate evolution is twofold: first, as with other viruses, retroviruses act as agents of selection, driving the evolution of host genes that block viral infection or that mitigate pathogenesis, and second, through the phenomenon of endogenization, retroviruses contribute an abundance of genetic novelty to host genomes, including unique protein-coding genes and cis-acting regulatory elements. This Review describes ERV origins, their diversity and their relationships to retroviruses and discusses the potential for ERVs to reveal virus-host interactions on evolutionary timescales. It also describes some of the many examples of cellular functions, including protein-coding genes and regulatory elements, that have evolved from ERVs.
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10
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Kim K, Dauphin A, Komurlu S, McCauley SM, Yurkovetskiy L, Carbone C, Diehl WE, Strambio-De-Castillia C, Campbell EM, Luban J. Cyclophilin A protects HIV-1 from restriction by human TRIM5α. Nat Microbiol 2019; 4:2044-2051. [PMID: 31636416 PMCID: PMC6879858 DOI: 10.1038/s41564-019-0592-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/12/2019] [Indexed: 12/20/2022]
Abstract
The HIV-1 capsid (CA) protein lattice encases viral genomic RNA and regulates steps essential to target cell invasion1. Cyclophilin A (CypA) has interacted with the CA of lentiviruses related to HIV-1 for millions of years2–7. Disruption of the CA-CypA interaction decreases HIV-1 infectivity in human cells8–12, but stimulates infectivity in non-human primate cells13–15. Genetic and biochemical data suggest that CypA protects HIV-1 from a CA-specific restriction factor in human cells16–20. Discovery of the CA-specific restriction factor tripartite-containing motif 5α (TRIM5α)21, and of multiple, independently-derived, TRIM5-CypA fusion genes4,5,15,22–26, pointed to human TRIM5α as the CypA-sensitive restriction factor. However, HIV-1 restriction by human TRIM5α in tumor cell lines is minimal21, and inhibition of such activity by CypA has not been detected27. Here, exploiting reverse genetic tools optimized for primary human blood cells, we demonstrate that disruption of the CA-CypA interaction renders HIV-1 susceptible to potent restriction by human TRIM5α, with the block occurring before reverse transcription. Endogenous TRIM5α associated with virion cores as they entered the cytoplasm, but only when the CA-CypA interaction was disrupted. These experiments resolve the long-standing mystery of the role of CypA in HIV-1 replication by demonstrating that this ubiquitous cellular protein shields HIV-1 from previously inapparent restriction by human TRIM5α.
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Affiliation(s)
- Kyusik Kim
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sevnur Komurlu
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Sean M McCauley
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Leonid Yurkovetskiy
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Claudia Carbone
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - William E Diehl
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Edward M Campbell
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.,Infectious Disease and Immunology Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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11
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The HIV-1 Capsid: More than Just a Delivery Package. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:69-83. [PMID: 31317496 DOI: 10.1007/978-3-030-14741-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Productive HIV infection requires integration of viral genes into the host genome. But how viral DNA gets to the nucleus in the first place remains one of the most controversial yet deceptively simple questions in HIV post-entry biology. This is illustrated in cartoons of viral entry, which often depict the entry process as an 'explosion' of the HIV capsid in the cytosol and independent movement of viral DNA through nuclear pores and into the nucleus. HIV enters the cell cytosol with two encapsidated RNA strands and must undergo reverse transcription (RT) to synthesise DNA. Even here there is no consensus for where, when or how RT happens. HIV must get into the nucleus, which in a non-dividing cell requires transport through the nuclear pore. Finally, the virus must 'uncoat': shed its protein capsid to allow its DNA to be spliced with that of the host. Where the virus uncoats and whether this is a single or multi-step process are similarly hotly debated. Understanding these processes is further complicated by three broad factors. First, that there are inter-relationships between these processes that may ensure HIV undergoes the right step at the right place at the right time. Second, the host has cofactors which the virus is dependent upon and must recruit but also immune factors that can sense and inhibit virus and so must be avoided. Third, HIV post-entry biology is cell-type dependent-meaning that factors which are essential in one cell type can be redundant in another.
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12
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Gifford RJ, Blomberg J, Coffin JM, Fan H, Heidmann T, Mayer J, Stoye J, Tristem M, Johnson WE. Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology 2018; 15:59. [PMID: 30153831 PMCID: PMC6114882 DOI: 10.1186/s12977-018-0442-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 08/20/2018] [Indexed: 11/10/2022] Open
Abstract
Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. There is an immediate need for a unified system of nomenclature for ERV loci, not only to assist genome annotation, but also to facilitate research on ERVs and their impact on genome biology and evolution. In this review, we examine how ERV nomenclatures have developed, and consider the possibilities for the implementation of a systematic approach for naming ERV loci. We propose that such a nomenclature should not only provide unique identifiers for individual loci, but also denote orthologous relationships between ERVs in different species. In addition, we propose that-where possible-mnemonic links to previous, well-established names for ERV loci and groups should be retained. We show how this approach can be applied and integrated into existing taxonomic and nomenclature schemes for retroviruses, ERVs and transposable elements.
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Affiliation(s)
- Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA
| | - Hung Fan
- Department of Molecular Biology and Biochemistry and Cancer Research Institute, University of California, Irvine, CA, 92697, USA
| | - Thierry Heidmann
- Department of Molecular Physiology and Pathology of Infectious and Endogenous Retroviruses, CNRS UMR 9196, Institut Gustave Roussy, 94805, Villejuif, France
| | - Jens Mayer
- Department of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, Homburg, Germany
| | - Jonathan Stoye
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, UK
| | - Michael Tristem
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | - Welkin E Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts, 02467, USA.
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Abstract
Human immunodeficiency virus (HIV) is one of the most studied of all human pathogens. One strain-HIV-1 group M-is responsible for a global pandemic that has infected >60 million people and killed >20 million. Understanding the stages of HIV infection has led to highly effective therapeutics in the form of antiviral drugs that target the viral enzymes reverse transcriptase, integrase, and protease as well as biotechnological developments in the form of retroviral and lentiviral vectors for the transduction of cells in tissue culture and, potentially, gene therapy. However, despite considerable research focus in this area, there is much we still do not understand about the HIV replicative cycle, particularly the first steps that are crucial to establishing a productive infection. One especially enigmatic player has been the HIV capsid. In this review, we discuss three aspects of the HIV capsid: its function as a structural shell, its role in mediating host interactions, and its vulnerability to antiviral activity.
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Affiliation(s)
- Leo C James
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - David A Jacques
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales Sydney, Randwick NSW 2031, Australia;
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14
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Blanco-Melo D, Gifford RJ, Bieniasz PD. Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. Retrovirology 2018; 15:34. [PMID: 29716624 PMCID: PMC5930517 DOI: 10.1186/s12977-018-0416-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND About 10% of the mouse genome is composed of endogenous retroviruses (ERVs) that represent a molecular fossil record of past retroviral infections. One such retrovirus, murine ERV-L (MuERV-L) is an env-deficient ERV that has undergone episodic proliferation, with the most recent amplification occurring ~ 2 million years ago. MuERV-L related sequences have been co-opted by mice for antiretroviral defense, and possibly as promoters for some genes that regulate totipotency in early mouse embryos. However, MuERV-L sequences present in modern mouse genomes have not been observed to replicate. RESULTS Here, we describe the reconstruction of an ancestral MuERV-L (ancML) sequence through paleovirological analyses of MuERV-L elements in the modern mouse genome. The resulting MuERV-L (ancML) sequence was synthesized and a reporter gene embedded. The reconstructed MuERV-L (ancML) could replicate in a manner that is dependent on reverse transcription and generated de novo integrants. Notably, MuERV-L (ancML) exhibited a narrow host range. Interferon-α could reduce MuERV-L (ancML) replication, suggesting the existence of interferon-inducible genes that could inhibit MuERV-L replication. While mouse APOBEC3 was able to restrict the replication of MuERV-L (ancML), inspection of endogenous MuERV-L sequences suggested that the impact of APOBEC3 mediated hypermutation on MuERV-L has been minimal. CONCLUSION The reconstruction of an ancestral MuERV-L sequence highlights the potential for the retroviral fossil record to illuminate ancient events and enable studies of the impact of retroviral elements on animal evolution.
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Affiliation(s)
- Daniel Blanco-Melo
- Laboratory of Retrovirology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Paul D Bieniasz
- Laboratory of Retrovirology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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15
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Reed JC, Westergreen N, Barajas BC, Ressler DTB, Phuong DJ, Swain JV, Lingappa VR, Lingappa JR. Formation of RNA Granule-Derived Capsid Assembly Intermediates Appears To Be Conserved between Human Immunodeficiency Virus Type 1 and the Nonprimate Lentivirus Feline Immunodeficiency Virus. J Virol 2018; 92:e01761-17. [PMID: 29467316 PMCID: PMC5899207 DOI: 10.1128/jvi.01761-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/14/2018] [Indexed: 01/18/2023] Open
Abstract
During immature capsid assembly in cells, human immunodeficiency virus type 1 (HIV-1) Gag co-opts a host RNA granule, forming a pathway of intracellular assembly intermediates containing host components, including two cellular facilitators of assembly, ABCE1 and DDX6. A similar assembly pathway has been observed for other primate lentiviruses. Here we asked whether feline immunodeficiency virus (FIV), a nonprimate lentivirus, also forms RNA granule-derived capsid assembly intermediates. First, we showed that the released FIV immature capsid and a large FIV Gag-containing intracellular complex are unstable during analysis, unlike for HIV-1. We identified harvest conditions, including in situ cross-linking, that overcame this problem, revealing a series of FIV Gag-containing complexes corresponding in size to HIV-1 assembly intermediates. Previously, we showed that assembly-defective HIV-1 Gag mutants are arrested at specific assembly intermediates; here we identified four assembly-defective FIV Gag mutants, including three not previously studied, and demonstrated that they appear to be arrested at the same intermediate as the cognate HIV-1 mutants. Further evidence that these FIV Gag-containing complexes correspond to assembly intermediates came from coimmunoprecipitations demonstrating that endogenous ABCE1 and the RNA granule protein DDX6 are associated with FIV Gag, as shown previously for HIV-1 Gag, but are not associated with a ribosomal protein, at steady state. Additionally, we showed that FIV Gag associates with another RNA granule protein, DCP2. Finally, we validated the FIV Gag-ABCE1 and FIV Gag-DCP2 interactions with proximity ligation assays demonstrating colocalization in situ Together, these data support a model in which primate and nonprimate lentiviruses form intracellular capsid assembly intermediates derived from nontranslating host RNA granules.IMPORTANCE Like HIV-1 Gag, FIV Gag assembles into immature capsids; however, it is not known whether FIV Gag progresses through a pathway of immature capsid assembly intermediates derived from host RNA granules, as shown for HIV-1 Gag. Here we showed that FIV Gag forms complexes that resemble HIV-1 capsid assembly intermediates in size and in their association with ABCE1 and DDX6, two host facilitators of HIV-1 immature capsid assembly that are found in HIV-1 assembly intermediates. Our studies also showed that known and novel assembly-defective FIV Gag mutants fail to progress past putative intermediates in a pattern resembling that observed for HIV-1 Gag mutants. Finally, we used imaging to demonstrate colocalization of FIV Gag with ABCE1 and with the RNA granule protein DCP2. Thus, we conclude that formation of assembly intermediates derived from host RNA granules is likely conserved between primate and nonprimate lentiviruses and could provide targets for future antiviral strategies.
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Affiliation(s)
| | | | - Brook C Barajas
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - Daryl J Phuong
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - John V Swain
- Prosetta Biosciences, San Francisco, California, USA
| | | | - Jaisri R Lingappa
- Department of Global Health, University of Washington, Seattle, Washington, USA
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16
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Folio C, Sierra N, Dujardin M, Alvarez G, Guillon C. Crystal Structure of the Full-Length Feline Immunodeficiency Virus Capsid Protein Shows an N-Terminal β-Hairpin in the Absence of N-Terminal Proline. Viruses 2017; 9:v9110335. [PMID: 29120364 PMCID: PMC5707542 DOI: 10.3390/v9110335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/03/2017] [Accepted: 11/08/2017] [Indexed: 12/31/2022] Open
Abstract
Feline immunodeficiency virus (FIV) is a member of the Retroviridae family. It is the causative agent of an acquired immunodeficiency syndrome (AIDS) in cats and wild felines. Its capsid protein (CA) drives the assembly of the viral particle, which is a critical step in the viral replication cycle. Here, the first atomic structure of full-length FIV CA to 1.67 Å resolution is determined. The crystallized protein exhibits an original tetrameric assembly, composed of dimers which are stabilized by an intermolecular disulfide bridge induced by the crystallogenesis conditions. The FIV CA displays a standard α-helical CA topology with two domains, separated by a linker shorter than other retroviral CAs. The β-hairpin motif at its amino terminal end, which interacts with nucleotides in HIV-1, is unusually long in FIV CA. Interestingly, this functional β-motif is formed in this construct in the absence of the conserved N-terminal proline. The FIV CA exhibits a cis Arg–Pro bond in the CypA-binding loop, which is absent in known structures of lentiviral CAs. This structure represents the first tri-dimensional structure of a functional, full-length FIV CA.
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Affiliation(s)
- Christelle Folio
- Equipe Rétrovirus et Biochimie Structurale, Université de Lyon, CNRS, MMSB, UMR 5086 CNRS/Université de Lyon, IBCP, Lyon 69367 CEDEX 07, France.
| | - Natalia Sierra
- Laboratorio de Moléculas Bioactivas, Centro Universitario Regional Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay.
| | - Marie Dujardin
- Equipe Rétrovirus et Biochimie Structurale, Université de Lyon, CNRS, MMSB, UMR 5086 CNRS/Université de Lyon, IBCP, Lyon 69367 CEDEX 07, France.
| | - Guzman Alvarez
- Laboratorio de Moléculas Bioactivas, Centro Universitario Regional Litoral Norte, Universidad de la República, Paysandú 60000, Uruguay.
| | - Christophe Guillon
- Equipe Rétrovirus et Biochimie Structurale, Université de Lyon, CNRS, MMSB, UMR 5086 CNRS/Université de Lyon, IBCP, Lyon 69367 CEDEX 07, France.
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17
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Geis FK, Galla M, Hoffmann D, Kuehle J, Zychlinski D, Maetzig T, Schott JW, Schwarzer A, Goffinet C, Goff SP, Schambach A. Potent and reversible lentiviral vector restriction in murine induced pluripotent stem cells. Retrovirology 2017; 14:34. [PMID: 28569216 PMCID: PMC5452410 DOI: 10.1186/s12977-017-0358-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/23/2017] [Indexed: 12/12/2022] Open
Abstract
Background Retroviral vectors are derived from wild-type retroviruses, can be used to study retrovirus-host interactions and are effective tools in gene and cell therapy. However, numerous cell types are resistant or less permissive to retrovirus infection due to the presence of active defense mechanisms, or the absence of important cellular host co-factors. In contrast to multipotent stem cells, pluripotent stem cells (PSC) have potential to differentiate into all three germ layers. Much remains to be elucidated in the field of anti-viral immunity in stem cells, especially in PSC. Results In this study, we report that transduction with HIV-1-based, lentiviral vectors (LV) is impaired in murine PSC. Analyses of early retroviral events in induced pluripotent stem cells (iPSC) revealed that the restriction is independent of envelope choice and does not affect reverse transcription, but perturbs nuclear entry and proviral integration. Proteasomal inhibition by MG132 could not circumvent the restriction. However, prevention of cyclophilin A (CypA) binding to the HIV-1 capsid via use of either a CypA inhibitor (cyclosporine A) or CypA-independent capsid mutants improved transduction. In addition, application of higher vector doses also increased transduction. Our data revealed a CypA mediated restriction in iPSC, which was acquired during reprogramming, associated with pluripotency and relieved upon subsequent differentiation. Conclusions We showed that murine PSC and iPSC are less susceptible to LV. The block observed in iPSC was CypA-dependent and resulted in reduced nuclear entry of viral DNA and proviral integration. Our study helps to improve transduction of murine pluripotent cells with HIV-1-based vectors and contributes to our understanding of retrovirus-host interactions in PSC. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0358-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Franziska K Geis
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Dirk Hoffmann
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Johannes Kuehle
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Daniela Zychlinski
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Tobias Maetzig
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Juliane W Schott
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Adrian Schwarzer
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Christine Goffinet
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infections Research, Hannover, Germany
| | - Stephen P Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany. .,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany. .,Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA.
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18
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Blanco-Melo D, Gifford RJ, Bieniasz PD. Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. eLife 2017; 6. [PMID: 28397686 PMCID: PMC5388530 DOI: 10.7554/elife.22519] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/26/2017] [Indexed: 12/22/2022] Open
Abstract
Endogenous retroviral sequences provide a molecular fossil record of ancient infections whose analysis might illuminate mechanisms of viral extinction. A close relative of gammaretroviruses, HERV-T, circulated in primates for ~25 million years (MY) before apparent extinction within the past ~8 MY. Construction of a near-complete catalog of HERV-T fossils in primate genomes allowed us to estimate a ~32 MY old ancestral sequence and reconstruct a functional envelope protein (ancHTenv) that could support infection of a pseudotyped modern gammaretrovirus. Using ancHTenv, we identify monocarboxylate transporter-1 (MCT-1) as a receptor used by HERV-T for attachment and infection. A single HERV-T provirus in hominid genomes includes an env gene (hsaHTenv) that has been uniquely preserved. This apparently exapted HERV-T env could not support virion infection but could block ancHTenv mediated infection, by causing MCT-1 depletion from cell surfaces. Thus, hsaHTenv may have contributed to HERV-T extinction, and could also potentially regulate cellular metabolism. DOI:http://dx.doi.org/10.7554/eLife.22519.001 Over millions of years, viruses and the animals that they infect have been locked in a battle for survival, where each has needed to evolve ways to counteract the effects of the other. While the evolution of ancient animals can be studied by looking at the fossilized remains of their extinct relatives, studying how ancient viruses have evolved is more difficult as they usually do not leave behind physical traces of their existence. However, a family of viruses called retroviruses is a notable exception to this rule. Retroviruses have a step in their life cycle in which their genetic material is integrated into the genome (the name for an organism’s complete set of genetic material) of the cell that they have infected. In rare cases, when that cell is a precursor of a sperm or egg cell, then the viral genes may then be passed on to the animal’s offspring, ultimately leaving genetic traces that can be studied in modern animals. This acts as a genetic ‘fossil record’ of extinct viruses. HERV-T was a retrovirus that spread among our primate ancestors for about 25 million years before its extinction roughly 11 million years ago. Blanco-Melo et al. have now analyzed the genetic remains left by HERV-T in the genomes of humans and related primates, and were able to use this information to recreate a protein that made up the outer envelope that surrounded the virus. Further experiments showed that this viral protein helped HERV-T to infect human cells by interacting with a protein called MCT1 on the cell surface. Blanco-Melo et al. also found a particular HERV-T gene that was unexpectedly well preserved in the human genome. The gene retained its ability to produce an envelope protein for about 13 to 19 million years. It is likely that ancient primates ‘hijacked’ the viral gene and used the protein it produced to remove the MCT1 protein from the surface of their own cells. Without MCT1 on the surface, HERV-T was unable to infect the cells. Thus, these findings present an example of how viruses themselves can provide the genetic material that animals use to combat them, potentially leading to their extinction. DOI:http://dx.doi.org/10.7554/eLife.22519.002
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Affiliation(s)
- Daniel Blanco-Melo
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, United States.,Laboratory of Retrovirology, The Rockefeller University, New York, United States
| | - Robert J Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Paul D Bieniasz
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, United States.,Laboratory of Retrovirology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, The Rockefeller University, New York, United States
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19
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Taylor WR, Stoye JP, Taylor IA. A comparative analysis of the foamy and ortho virus capsid structures reveals an ancient domain duplication. BMC STRUCTURAL BIOLOGY 2017; 17:3. [PMID: 28372592 PMCID: PMC5379526 DOI: 10.1186/s12900-017-0073-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/10/2017] [Indexed: 01/28/2023]
Abstract
BACKGROUND The Spumaretrovirinae (foamy viruses) and the Orthoretrovirinae (e.g. HIV) share many similarities both in genome structure and the sequences of the core viral encoded proteins, such as the aspartyl protease and reverse transcriptase. Similarity in the gag region of the genome is less obvious at the sequence level but has been illuminated by the recent solution of the foamy virus capsid (CA) structure. This revealed a clear structural similarity to the orthoretrovirus capsids but with marked differences that left uncertainty in the relationship between the two domains that comprise the structure. METHODS We have applied protein structure comparison methods in order to try and resolve this ambiguous relationship. These included both the DALI method and the SAP method, with rigorous statistical tests applied to the results of both methods. For this, we employed collections of artificial fold 'decoys' (generated from the pair of native structures being compared) to provide a customised background distribution for each comparison, thus allowing significance levels to be estimated. RESULTS We have shown that the relationship of the two domains conforms to a simple linear correspondence rather than a domain transposition. These similarities suggest that the origin of both viral capsids was a common ancestor with a double domain structure. In addition, we show that there is also a significant structural similarity between the amino and carboxy domains in both the foamy and ortho viruses. CONCLUSIONS These results indicate that, as well as the duplication of the double domain capsid, there may have been an even more ancient gene-duplication that preceded the double domain structure. In addition, our structure comparison methodology demonstrates a general approach to problems where the components have a high intrinsic level of similarity.
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Affiliation(s)
- William R. Taylor
- Computational Cell and Molecular Biology Laboratory, Francis Crick Institute, Midland Road, London, NW1 1AT UK
| | - Jonathan P. Stoye
- Retrovirus-Host Interactions Laboratory, Francis Crick Institute, Midland Road, London, NW1 1AT UK
| | - Ian A. Taylor
- Macromolecular Structure Laboratory, Francis Crick Institute, Midland Road, London, NW1 1AT UK
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20
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Li W, Yap MW, Voss V, Stoye JP. Expression levels of Fv1: effects on retroviral restriction specificities. Retrovirology 2016; 13:42. [PMID: 27342974 PMCID: PMC4921018 DOI: 10.1186/s12977-016-0276-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The mouse protein Fv1 is a factor that can confer resistance to retroviral infection. The two major Fv1 alleles from laboratory mice, Fv1 (n) and Fv1 (b) , restrict infection by different murine leukaemia viruses (MLVs). Fv1(n) restricts B-tropic MLV, but not N-tropic MLV or NB-tropic MLV. In cells expressing Fv1(b) at natural levels, only N-MLV is restricted, however restriction of NB-MLV and partial restriction of B-MLV were observed when recombinant Fv1(b) was expressed from an MLV promoter in Fv1 null Mus dunni tail fibroblast cells. To investigate the relationship between expression level and restriction specificity we have developed new retroviral delivery vectors which allow inducible expression of Fv1, and yet allow sufficient production of fluorescent reporter proteins for analysis in our FACS-based restriction assay. RESULTS We demonstrated that at concentrations close to the endogenous expression level, Fv1(b) specifically restricts only N-MLV, but restriction of NB-MLV, and to a lesser extent B-MLV, could be gained by increasing the protein level of Fv1(b). By contrast, we found that even when Fv1(n) is expressed at very high levels, no significant inhibition of N-MLV or NB-MLV could be observed. Study of Fv1 mutants using this assay led to the identification of determinants for N/B tropism at an expression level close to that of endogenous Fv1(n) and Fv1(b). We also compared the recently described restriction activities of wild mice Fv1 proteins directed against non-MLV retroviruses when expressed at different levels. Fv1 from M. spretus restricted N-MLV, B-MLV and equine infectious anaemia virus equally even at low concentrations, while Fv1 from M. macedonicus showed even stronger restriction against equine infectious anaemia virus than to N-MLV. Restriction of feline foamy virus by Fv1 of M. caroli occurred at levels equivalent to MLV restriction. CONCLUSIONS Our data indicate that for some but not all Fv1 proteins, gain of restriction activities could be achieved by increasing the expression level of Fv1. However such a concentration dependent effect is not seen with most Fv1s and cannot explain the recently reported activities against non-MLVs. It will be interesting to examine whether overexpression of other capsid binding restriction factors such as TRIM5α or Mx2 result in novel restriction specificities.
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Affiliation(s)
- Wilson Li
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Melvyn W Yap
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Vicky Voss
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
| | - Jonathan P Stoye
- Retrovirus-Host Interactions Laboratory, The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK. .,Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK.
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21
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Lahaye X, Satoh T, Gentili M, Cerboni S, Silvin A, Conrad C, Ahmed-Belkacem A, Rodriguez EC, Guichou JF, Bosquet N, Piel M, Le Grand R, King MC, Pawlotsky JM, Manel N. Nuclear Envelope Protein SUN2 Promotes Cyclophilin-A-Dependent Steps of HIV Replication. Cell Rep 2016; 15:879-892. [PMID: 27149839 PMCID: PMC4850421 DOI: 10.1016/j.celrep.2016.03.074] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 02/12/2016] [Accepted: 03/20/2016] [Indexed: 12/01/2022] Open
Abstract
During the early phase of replication, HIV reverse transcribes its RNA and crosses the nuclear envelope while escaping host antiviral defenses. The host factor Cyclophilin A (CypA) is essential for these steps and binds the HIV capsid; however, the mechanism underlying this effect remains elusive. Here, we identify related capsid mutants in HIV-1, HIV-2, and SIVmac that are restricted by CypA. This antiviral restriction of mutated viruses is conserved across species and prevents nuclear import of the viral cDNA. Importantly, the inner nuclear envelope protein SUN2 is required for the antiviral activity of CypA. We show that wild-type HIV exploits SUN2 in primary CD4+ T cells as an essential host factor that is required for the positive effects of CypA on reverse transcription and infection. Altogether, these results establish essential CypA-dependent functions of SUN2 in HIV infection at the nuclear envelope. HIV capsid mutants reveal that Cyclophilin A can restrict viral nuclear import Nuclear envelope protein SUN2 is implicated in the restriction of HIV mutants SUN2 is essential for wild-type HIV infection in CD4+ T cells and dendritic cells In CD4+ T cells, the activities of CypA on HIV-1 infection require SUN2
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Affiliation(s)
- Xavier Lahaye
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Takeshi Satoh
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Matteo Gentili
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Silvia Cerboni
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Aymeric Silvin
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | - Cécile Conrad
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France
| | | | - Elisa C Rodriguez
- Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520-8002, USA
| | - Jean-François Guichou
- CNRS UMR5048, INSERM U1054 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France
| | - Nathalie Bosquet
- Université Paris Sud, INSERM, CEA, DRF-Immunology of Viral Infections and Autoimmune Diseases department (IMVA), UMR1184, IDMIT Infrastructure, iMETI, 92260 Fontenay-aux-Roses, France
| | - Matthieu Piel
- Subcellular Structure and Cellular Dynamics Department, Institut Curie, PSL Research University, CNRS UMR144, 75005 Paris, France; Institut Pierre-Gilles de Gennes, PSL Research University, 75005 Paris, France
| | - Roger Le Grand
- Université Paris Sud, INSERM, CEA, DRF-Immunology of Viral Infections and Autoimmune Diseases department (IMVA), UMR1184, IDMIT Infrastructure, iMETI, 92260 Fontenay-aux-Roses, France
| | - Megan C King
- Yale School of Medicine, 333 Cedar Street, New Haven, CT 06520-8002, USA
| | - Jean-Michel Pawlotsky
- INSERM U955, 94010 Créteil, France; Department of Virology, National Reference Center for Viral Hepatitis B, C and D, Hôpital Henri Mondor, Université Paris-Est, 94010 Créteil, France
| | - Nicolas Manel
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, 75005 Paris, France.
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22
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Perilla JR, Gronenborn AM. Molecular Architecture of the Retroviral Capsid. Trends Biochem Sci 2016; 41:410-420. [PMID: 27039020 DOI: 10.1016/j.tibs.2016.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/21/2016] [Accepted: 02/26/2016] [Indexed: 12/13/2022]
Abstract
Retroviral capsid cores are proteinaceous containers that self-assemble to encase the viral genome and a handful of proteins that promote infection. Their function is to protect and aid in the delivery of viral genes to the nucleus of the host, and, in many cases, infection pathways are influenced by capsid-cellular interactions. From a mathematical perspective, capsid cores are polyhedral cages and, as such, follow well-defined geometric rules. However, marked morphological differences in shapes exist, depending on virus type. Given the specific roles of capsid in the viral life cycle, the availability of detailed molecular structures, particularly at assembly interfaces, opens novel avenues for targeted drug development against these pathogens. Here, we summarize recent advances in the structure and understanding of retroviral capsid, with particular emphasis on assemblies and the capsid cores.
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Affiliation(s)
- Juan R Perilla
- Beckman Institute for Advanced Science and Technology and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, and Pittsburgh Center for HIV Protein Interactions, Pittsburgh, PA 15260, USA.
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23
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Abstract
Endogenous retroviruses comprise millions of discrete genetic loci distributed within the genomes of extant vertebrates. These sequences, which are clearly related to exogenous retroviruses, represent retroviral infections of the deep past, and their abundance suggests that retroviruses were a near-constant presence throughout the evolutionary history of modern vertebrates. Endogenous retroviruses contribute in myriad ways to the evolution of host genomes, as mutagens and as sources of genetic novelty (both coding and regulatory) to be acted upon by the twin engines of random genetic drift and natural selection. Importantly, the richness and complexity of endogenous retrovirus data can be used to understand how viruses spread and adapt on evolutionary timescales by combining population genetics and evolutionary theory with a detailed understanding of retrovirus biology (gleaned from the study of extant retroviruses). In addition to revealing the impact of viruses on organismal evolution, such studies can help us better understand, by looking back in time, how life-history traits, as well as ecological and geological events, influence the movement of viruses within and between populations.
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Affiliation(s)
- Welkin E Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts 02467;
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24
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Qing J, Wang Y, Sun Y, Huang J, Yan W, Wang J, Su D, Ni C, Li J, Rao Z, Liu L, Lou Z. Cyclophilin A associates with enterovirus-71 virus capsid and plays an essential role in viral infection as an uncoating regulator. PLoS Pathog 2014; 10:e1004422. [PMID: 25275585 PMCID: PMC4183573 DOI: 10.1371/journal.ppat.1004422] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 08/25/2014] [Indexed: 02/05/2023] Open
Abstract
Viruses utilize host factors for their efficient proliferation. By evaluating the inhibitory effects of compounds in our library, we identified inhibitors of cyclophilin A (CypA), a known immunosuppressor with peptidyl-prolyl cis-trans isomerase activity, can significantly attenuate EV71 proliferation. We demonstrated that CypA played an essential role in EV71 entry and that the RNA interference-mediated reduction of endogenous CypA expression led to decreased EV71 multiplication. We further revealed that CypA directly interacted with and modified the conformation of H-I loop of the VP1 protein in EV71 capsid, and thus regulated the uncoating process of EV71 entry step in a pH-dependent manner. Our results aid in the understanding of how host factors influence EV71 life cycle and provide new potential targets for developing antiviral agents against EV71 infection.
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Affiliation(s)
- Jie Qing
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China
- School of Medicine, Tsinghua University, Beijing, China
| | - Yaxin Wang
- School of Medicine, Tsinghua University, Beijing, China
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Yuna Sun
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Jiaoyan Huang
- School of Medicine, Tsinghua University, Beijing, China
| | - Wenzhong Yan
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jinglan Wang
- School of Medicine, Tsinghua University, Beijing, China
| | - Dan Su
- Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Cheng Ni
- Beijing No. 4 High School, Beijing, China
| | - Jian Li
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zihe Rao
- School of Medicine, Tsinghua University, Beijing, China
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China
- * E-mail: (LL); (ZL)
| | - Zhiyong Lou
- School of Medicine, Tsinghua University, Beijing, China
- Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
- * E-mail: (LL); (ZL)
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25
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Contribution of glutamine residues in the helix 4-5 loop to capsid-capsid interactions in simian immunodeficiency virus of macaques. J Virol 2014; 88:10289-302. [PMID: 24991000 DOI: 10.1128/jvi.01388-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Following retrovirus entry, the viral capsid (CA) disassembles into its component capsid proteins. The rate of this uncoating process, which is regulated by CA-CA interactions and by the association of the capsid with host cell factors like cyclophilin A (CypA), can influence the efficiency of reverse transcription. Inspection of the CA sequences of lentiviruses reveals that several species of simian immunodeficiency viruses (SIVs) have lost the glycine-proline motif in the helix 4-5 loop important for CypA binding; instead, the helix 4-5 loop in these SIVs exhibits an increase in the number of glutamine residues. In this study, we investigated the role of these glutamine residues in SIVmac239 replication. Changes in these residues, particularly glutamine 89 and glutamine 92, resulted in a decreased efficiency of core condensation, decreased stability of the capsids in infected cells, and blocks to reverse transcription. In some cases, coexpression of two different CA mutants produced chimeric virions that exhibited higher infectivity than either parental mutant virus. For this complementation of infectivity, glutamine 89 was apparently required on one of the complementing pair of mutants and glutamine 92 on the other. Modeling suggests that glutamines 89 and 92 are located on the distal face of hexameric capsid spokes and thus are well positioned to contribute to interhexamer interactions. Requirements to evade host restriction factors like TRIMCyp may drive some SIV lineages to evolve means other than CypA binding to stabilize the capsid. One solution used by several SIV strains consists of glutamine-based bonding. IMPORTANCE The retroviral capsid is an assembly of individual capsid proteins that surrounds the viral RNA. After a retrovirus enters a cell, the capsid must disassemble, or uncoat, at a proper rate. The interactions among capsid proteins contribute to this rate of uncoating. We found that some simian immunodeficiency viruses use arrays of glutamine residues, which can form hydrogen bonds efficiently, to keep their capsids stable. This strategy may allow these viruses to forego the use of capsid-stabilizing factors from the host cell, some of which have antiviral activity.
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Structural studies of postentry restriction factors reveal antiparallel dimers that enable avid binding to the HIV-1 capsid lattice. Proc Natl Acad Sci U S A 2014; 111:9609-14. [PMID: 24979782 DOI: 10.1073/pnas.1402448111] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Restriction factors (RFs) form important components of host defenses to retroviral infection. The Fv1, Trim5α, and TrimCyp RFs contain N-terminal dimerization and C-terminal specificity domains that target assembled retroviral capsid (CA) proteins enclosing the viral core. However, the molecular detail of the interaction between RFs and their CA targets is unknown. Therefore, we have determined the crystal structure of the B-box and coiled-coil (BCC) region from Trim5α and used small-angle X-ray scattering to examine the solution structure of Trim5α BCC, the dimerization domain of Fv1 (Fv1Ntd), and the hybrid restriction factor Fv1Cyp comprising Fv1NtD fused to the HIV-1 binding protein Cyclophilin A (CypA). These data reveal that coiled-coil regions of Fv1 and Trim5α form extended antiparallel dimers. In Fv1Cyp, two CypA moieties are located at opposing ends, creating a molecule with a dumbbell appearance. In Trim5α, the B-boxes are located at either end of the coiled-coil, held in place by interactions with a helical motif from the L2 region of the opposing monomer. A comparative analysis of Fv1Cyp and CypA binding to a preformed HIV-1 CA lattice reveals how RF dimerization enhances the affinity of interaction through avidity effects. We conclude that the antiparallel organization of the NtD regions of Fv1 and Trim5α dimers correctly positions C-terminal specificity and N-terminal effector domains and facilitates stable binding to adjacent CA hexamers in viral cores.
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Yap MW, Colbeck E, Ellis SA, Stoye JP. Evolution of the retroviral restriction gene Fv1: inhibition of non-MLV retroviruses. PLoS Pathog 2014; 10:e1003968. [PMID: 24603659 PMCID: PMC3948346 DOI: 10.1371/journal.ppat.1003968] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 01/16/2014] [Indexed: 11/18/2022] Open
Abstract
Fv1 is the prototypic restriction factor that protects against infection by the murine leukemia virus (MLV). It was first identified in cells that were derived from laboratory mice and was found to be homologous to the gag gene of an endogenous retrovirus (ERV). To understand the evolution of the host restriction gene from its retroviral origins, Fv1s from wild mice were isolated and characterized. Most of these possess intact open reading frames but not all restricted N-, B-, NR-or NB-tropic MLVs, suggesting that other viruses could have played a role in the selection of the gene. The Fv1s from Mus spretus and Mus caroli were found to restrict equine infectious anemia virus (EIAV) and feline foamy virus (FFV) respectively, indicating that Fv1 could have a broader target range than previously thought, including activity against lentiviruses and spumaviruses. Analyses of the Fv1 sequences revealed a number of residues in the C-terminal region that had evolved under positive selection. Four of these selected residues were found to be involved in the novel restriction by mapping studies. These results strengthen the similarities between the two capsid binding restriction factors, Fv1 and TRIM5α, which support the hypothesis that Fv1 defended mice against waves of retroviral infection possibly including non-MLVs as well as MLVs. We have followed the evolution of the retroviral restriction gene, Fv1, by functional analysis. We show that Fv1 can recognize and restrict a wider range of retroviruses than previously thought including examples from the gammaretrovirus, lentivirus and foamy virus genera. Nearly every Fv1 tested showed a different pattern of restriction activity. We also identify several hypervariable regions in the coding sequence containing positively selected amino acids that we show to be directly involved in determining restriction specificity. Our results strengthen the analogy between Fv1 and another capsid-binding, retrovirus restriction factor, TRIM5α. Although they share no sequence identity they appear to share a similar design and appear likely to recognise different targets by a mechanism involving multiple weak interactions between a virus-binding domain containing several variable regions and the surface of the viral capsid. We also describe a pattern of constant genetic change, implying that different species of Mus have evolved in the face of ever-changing retroviral threats by viruses of different kinds.
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Affiliation(s)
- Melvyn W. Yap
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Emily Colbeck
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Scott A. Ellis
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Jonathan P. Stoye
- Division of Virology, National Institute for Medical Research, Mill Hill, London, United Kingdom
- Faculty of Medicine, Imperial College London, London, United Kingdom
- * E-mail:
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Contribution of PDZD8 to stabilization of the human immunodeficiency virus type 1 capsid. J Virol 2014; 88:4612-23. [PMID: 24554657 DOI: 10.1128/jvi.02945-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Following human immunodeficiency virus type 1 (HIV-1) entry into the host cell, the viral capsid gradually disassembles in a process called uncoating. A proper rate of uncoating is important for reverse transcription of the HIV-1 genome. Host restriction factors such as TRIM5α and TRIMCyp bind retroviral capsids and cause premature disassembly, leading to blocks in reverse transcription. Other host factors, such as cyclophilin A, stabilize the HIV-1 capsid and are required for efficient infection in some cell types. Here, we show that a heat-labile factor greater than 100 kDa in the cytoplasm of cells from multiple vertebrate species slows the spontaneous disassembly of HIV-1 capsid-nucleocapsid (CA-NC) complexes in vitro. We identified the PDZ domain-containing protein 8 (PDZD8) as a critical component of the capsid-stabilizing activity in the cytoplasmic extracts. PDZD8 has been previously reported to bind the HIV-1 Gag polyprotein and to make a positive contribution to the efficiency of HIV-1 infection (M. S. Henning, S. G. Morham, S. P. Goff, and M. H. Naghavi, J. Virol. 84:: 8990-8995, 2010, doi:10.1128/JVI.00843-10). PDZD8 knockdown accelerated the disassembly of HIV-1 capsids in infected cells, resulting in decreased reverse transcription. The PDZD8 coiled-coil domain is sufficient for HIV-1 capsid binding, but other parts of the protein, including the PDZ domain, are apparently required for stabilizing the capsid and supporting HIV-1 infection. In summary, PDZD8 interacts with and stabilizes the HIV-1 capsid and thus represents a potentially targetable host cofactor for HIV-1 infection. IMPORTANCE After human immunodeficiency virus type 1 (HIV-1) gains access to the interior of the target cell, host cell factors can influence virus infection in either a positive or negative way. HIV-1 depends upon certain host cell factors to assist processes that are required for virus replication. One example of such a host factor is PDZD8. This work shows that PDZD8 helps to stabilize the HIV-1 capsid, a huge complex of the viral RNA, enzymes, and protein. When PDZD8 is prevented from interacting with the HIV-1 capsid, the capsid becomes unstable and HIV-1 infection is inhibited. These results show that PDZD8 regulates the uncoating of the HIV-1 capsid. Interfering with the interaction of PDZD8 and capsid could prove to be a useful strategy for intervening in HIV-1 infection and transmission.
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Meehan AM, Saenz DT, Guevera R, Morrison JH, Peretz M, Fadel HJ, Hamada M, van Deursen J, Poeschla EM. A cyclophilin homology domain-independent role for Nup358 in HIV-1 infection. PLoS Pathog 2014; 10:e1003969. [PMID: 24586169 PMCID: PMC3930637 DOI: 10.1371/journal.ppat.1003969] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 01/15/2014] [Indexed: 12/05/2022] Open
Abstract
The large nucleoporin Nup358/RanBP2 forms eight filaments that project from the nuclear pore into the cytoplasm where they function as docking platforms for nucleocytoplasmic transport receptors. RNAi screens have implicated Nup358 in the HIV-1 life cycle. The 164 C-terminal amino acids of this 3,224 amino acid protein are a cyclophilin homology domain (Nup358Cyp), which has potential to bind the HIV-1 capsid and regulate viral progress to integration. Here we examined the virological role of Nup358 in conditional knockout mouse cells and in RNAi-depleted human CD4⁺ T cells. Cre-mediated gene knockout was toxic and diminished HIV-1 infectivity. However, cellular health and HIV-1 susceptibility were coordinately preserved if, prior to gene inactivation, a transposon was used to express all of Nup358 or only the N-terminal 1340 amino acids that contain three FG repeats and a Ran-binding domain. HIV-1, but not N74D capsid-mutant HIV-1, was markedly sensitive to TNPO3 depletion, but they infected 1-1340 segment-complemented Nup358 knockout cells equivalently. Human and mouse CypA both rescued HIV-1 in CypA gene⁻/⁻ Jurkat cells and TRIM-Nup358Cyp fusions derived from each species were equally antiviral; each also inhibited both WT and N74D virus. In the human CD4⁺T cell line SupT1, abrupt Nup358 depletion reduced viral replication but stable Nup358-depleted cells replicated HIV-1 normally. Thus, human CD4⁺ T cells can accommodate to loss of Nup358 and preserve HIV-1 susceptibility. Experiments with cylosporine, viruses with capsids that do not bind cyclophilins, and growth arrest did not uncover viral dependency on the C-terminal domains of Nup358. Our data reinforce the virological importance of TNPO3 and show that Nup358 supports nuclear transport functions important for cellular homeostasis and for HIV-1 nuclear import. However, the results do not suggest direct roles for the Nup358 cyclophilin or SUMO E3 ligase domains in engaging the HIV-1 capsid prior to nuclear translocation.
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Affiliation(s)
- Anne M. Meehan
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Dyana T. Saenz
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Rebekah Guevera
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - James H. Morrison
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Mary Peretz
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Hind J. Fadel
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Masakazu Hamada
- Department of Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Jan van Deursen
- Department of Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Eric M. Poeschla
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
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Viral and cellular requirements for the nuclear entry of retroviral preintegration nucleoprotein complexes. Viruses 2013; 5:2483-511. [PMID: 24103892 PMCID: PMC3814599 DOI: 10.3390/v5102483] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/26/2013] [Accepted: 10/03/2013] [Indexed: 02/07/2023] Open
Abstract
Retroviruses integrate their reverse transcribed genomes into host cell chromosomes as an obligate step in virus replication. The nuclear envelope separates the chromosomes from the cell cytoplasm during interphase, and different retroviral groups deal with this physical barrier in different ways. Gammaretroviruses are dependent on the passage of target cells through mitosis, where they are believed to access chromosomes when the nuclear envelope dissolves for cell division. Contrastingly, lentiviruses such as HIV-1 infect non-dividing cells, and are believed to enter the nucleus by passing through the nuclear pore complex. While numerous virally encoded elements have been proposed to be involved in HIV-1 nuclear import, recent evidence has highlighted the importance of HIV-1 capsid. Furthermore, capsid was found to be responsible for the viral requirement of various nuclear transport proteins, including transportin 3 and nucleoporins NUP153 and NUP358, during infection. In this review, we describe our current understanding of retroviral nuclear import, with emphasis on recent developments on the role of the HIV-1 capsid protein.
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Yap MW, Stoye JP. Apparent effect of rabbit endogenous lentivirus type K acquisition on retrovirus restriction by lagomorph Trim5αs. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120498. [PMID: 23938750 PMCID: PMC3758185 DOI: 10.1098/rstb.2012.0498] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To test the hypothesis that rabbit endogenous lentivirus type K (RELIK) could play a role in shaping the evolution of TRIM5α, the susceptibility of viruses containing the RELIK capsid (CA) to TRIM5 restriction was evaluated. RELIK CA-containing viruses were susceptible to the TRIM5αs from Old World monkeys but were unaffected by most ape or New World monkey factors. TRIM5αs from various lagomorph species were also isolated and tested for anti-retroviral activity. The TRIM5αs from both cottontail rabbit and pika restrict a range of retroviruses, including HIV-1, HIV-2, FIV, EIAV and N-MLV. TRIM5αs from the European and cottontail rabbit, which have previously been found to contain RELIK, also restricted RELIK CA-containing viruses, whereas a weaker restriction was observed with chimeric TRIM5α containing the B30.2 domain from the pika, which lacks RELIK. Taken together, these results could suggest that the pika had not been exposed to exogenous RELIK and that endogenized RELIK might exert a selective pressure on lagomorph TRIM5α.
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Affiliation(s)
| | - Jonathan P. Stoye
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Sanz-Ramos M, Stoye JP. Capsid-binding retrovirus restriction factors: discovery, restriction specificity and implications for the development of novel therapeutics. J Gen Virol 2013; 94:2587-2598. [PMID: 24026671 DOI: 10.1099/vir.0.058180-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The development of drugs against human immunodeficiency virus type 1 infection has been highly successful, and numerous combinational treatments are currently available. However, the risk of the emergence of resistance and the toxic effects associated with prolonged use of antiretroviral therapies have emphasized the need to consider alternative approaches. One possible area of investigation is provided by the properties of restriction factors, cellular proteins that protect organisms against retroviral infection. Many show potent viral inhibition. Here, we describe the discovery, properties and possible therapeutic uses of the group of restriction factors known to interact with the capsid core of incoming retroviruses. This group comprises Fv1, TRIM5α and TRIMCypA: proteins that all act shortly after virus entry into the target cell and block virus replication at different stages prior to integration of viral DNA into the host chromosome. They have different origins and specificities, but share general structural features required for restriction, with an N-terminal multimerization domain and a C-terminal capsid-binding domain. Their overall efficacy makes it reasonable to ask whether they might provide a framework for developing novel antiretroviral strategies.
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Affiliation(s)
- Marta Sanz-Ramos
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Jonathan P Stoye
- Department of Medicine, Imperial College London, London W2 1PG, UK.,Division of Virology, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
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Katzourakis A. Paleovirology: inferring viral evolution from host genome sequence data. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120493. [PMID: 23938747 DOI: 10.1098/rstb.2012.0493] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Aris Katzourakis
- Department of Zoology, University of Oxford, , Oxford OX1 3PS, UK
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Mamede JI, Sitbon M, Battini JL, Courgnaud V. Heterogeneous susceptibility of circulating SIV isolate capsids to HIV-interacting factors. Retrovirology 2013; 10:77. [PMID: 23883001 PMCID: PMC3751554 DOI: 10.1186/1742-4690-10-77] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/05/2013] [Indexed: 11/13/2022] Open
Abstract
Background Many species of non-human primates in Africa are naturally infected by simian immunodeficiency viruses (SIV) and humans stand at the forefront of exposure to these viruses in Sub-Saharan Africa. Cross-species transmission and adaptation of SIV to humans have given rise to human immunodeficiency viruses (HIV-1 and HIV-2) on twelve accountable, independent occasions. However, the determinants contributing to a simian-to-human lasting transmission are not fully understood. Following entry, viral cores are released into the cytoplasm and become the principal target of host cellular factors. Here, we evaluated cellular factors likely to be involved in potential new SIV cross-species transmissions. We investigated the interactions of capsids from naturally circulating SIV isolates with both HIV-1 restricting (i.e. TRIM5 proteins) and facilitating (i.e. cyclophilin A and nucleopore-associated Nup358/RanBP2 and Nup153) factors in single-round infectivity assays that reproduce early stages of the viral life-cycle. Results We show that human TRIM5α is unlikely to prevent cross-species transmission of any SIV we tested and observed that the SIV CA-CypA interaction is a widespread but not a universal feature. Moreover, entry in the nucleus of different SIV appeared to follow pathways that do not necessarily recruit Nup358/RanBP2 or Nup153, and this regardless of their interaction with CypA. Nevertheless, we found that, like HIV-1, human-adapted HIV-2 infection was dependent on Nup358/RanBP2 and Nup153 interactions for optimal infection. Furthermore, we found that, unlike HIV CA, SIV CA did not require a direct interaction with the Cyp-like domain of Nup358/RanBP2 to carry out successful infection. Conclusions Circulating SIV present a variety of phenotypes with regard to CA-interacting restricting or facilitating factors. Altogether, we unveiled unidentified pathways for SIV CA, which could also be exploited by HIV in different cellular contexts, to drive entry into the nucleus. Our findings warrant a closer evaluation of other potential defenses against circulating SIV.
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Affiliation(s)
- João I Mamede
- Institut de Génétique Moléculaire de Montpellier UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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McCarthy KR, Schmidt AG, Kirmaier A, Wyand AL, Newman RM, Johnson WE. Gain-of-sensitivity mutations in a Trim5-resistant primary isolate of pathogenic SIV identify two independent conserved determinants of Trim5α specificity. PLoS Pathog 2013; 9:e1003352. [PMID: 23675300 PMCID: PMC3649984 DOI: 10.1371/journal.ppat.1003352] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Accepted: 03/25/2013] [Indexed: 11/18/2022] Open
Abstract
Retroviral capsid recognition by Trim5 blocks productive infection. Rhesus macaques harbor three functionally distinct Trim5 alleles: Trim5αQ, Trim5αTFP and Trim5CypA. Despite the high degree of amino acid identity between Trim5αQ and Trim5αTFP alleles, the Q/TFP polymorphism results in the differential restriction of some primate lentiviruses, suggesting these alleles differ in how they engage these capsids. Simian immunodeficiency virus of rhesus macaques (SIVmac) evolved to resist all three alleles. Thus, SIVmac provides a unique opportunity to study a virus in the context of the Trim5 repertoire that drove its evolution in vivo. We exploited the evolved rhesus Trim5α resistance of this capsid to identify gain-of-sensitivity mutations that distinguish targets between the Trim5αQ and Trim5αTFP alleles. While both alleles recognize the capsid surface, Trim5αQ and Trim5αTFP alleles differed in their ability to restrict a panel of capsid chimeras and single amino acid substitutions. When mapped onto the structure of the SIVmac239 capsid N-terminal domain, single amino acid substitutions affecting both alleles mapped to the β-hairpin. Given that none of the substitutions affected Trim5αQ alone, and the fact that the β-hairpin is conserved among retroviral capsids, we propose that the β-hairpin is a molecular pattern widely exploited by Trim5α proteins. Mutations specifically affecting rhesus Trim5αTFP (without affecting Trim5αQ) surround a site of conservation unique to primate lentiviruses, overlapping the CPSF6 binding site. We believe targeting this site is an evolutionary innovation driven specifically by the emergence of primate lentiviruses in Africa during the last 12 million years. This modularity in targeting may be a general feature of Trim5 evolution, permitting different regions of the PRYSPRY domain to evolve independent interactions with capsid. TRIM5α is an intrinsic immunity protein that blocks retrovirus infection through a specific interaction with the viral capsid. Uniquely among primates, rhesus macaques harbor three functionally distinct kinds of Trim5 alleles: rhTrim5αTFP, rhTrim5αQ and rhTrim5CypA. SIVmac239, a simian immunodeficiency virus that causes AIDS in rhesus macaques, is resistant to all three, whereas its relative, the human AIDS virus HIV-1, is inhibited by rhTrim5αTFP and rhTrim5αQ alleles. We exploited this difference between these two retroviruses to figure out how Trim5α proteins recognize viral capsids. By combining mutagenesis, structural biology and evolutionary data we determined that both rhTrim5αTFP and rhTrim5αQ recognize a conserved structure common to all retroviral capsids. However, we also found evidence suggesting that rhTrim5αTFP evolved to recognize an additional target that is specifically conserved among primate immunodeficiency viruses. Molecular evolutionary analysis indicates that this expanded function appeared in a common ancestor of modern African monkeys sometime between 9–12 million years ago, and that it thereafter continued to be modified by strong evolutionary pressure. Our results provide insight into the evolutionary flexibility of Trim5α-capsid interactions, and support the notion that viruses related to modern HIV and SIV have been present in Africa for millions of years.
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Affiliation(s)
- Kevin R. McCarthy
- Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, United States of America
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Aaron G. Schmidt
- Laboratory of Molecular Medicine, Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrea Kirmaier
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Allison L. Wyand
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Ruchi M. Newman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Welkin E. Johnson
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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36
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RNA-mediated interference and reverse transcription control the persistence of RNA viruses in the insect model Drosophila. Nat Immunol 2013; 14:396-403. [DOI: 10.1038/ni.2542] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 01/08/2013] [Indexed: 12/13/2022]
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37
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Birth, decay, and reconstruction of an ancient TRIMCyp gene fusion in primate genomes. Proc Natl Acad Sci U S A 2013; 110:E583-92. [PMID: 23319649 DOI: 10.1073/pnas.1216542110] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
TRIM5 is a host antiviral gene with an evolutionary history of genetic conflict with retroviruses. The TRIMCyp gene encodes a protein fusion of TRIM5 effector domains with the capsid-binding ability of a retrotransposed CyclophilinA (CypA), resulting in novel antiviral specificity against lentiviruses. Previous studies have identified two independent primate TRIMCyp fusions that evolved within the past 6 My. Here, we describe an ancient primate TRIMCyp gene (that we call TRIMCypA3), which evolved in the common ancestor of simian primates 43 Mya. Gene reconstruction shows that CypA3 encoded an intact, likely active, TRIMCyp antiviral gene, which was subject to selective constraints for at least 10 My, followed by pseudogenization or loss in all extant primates. Despite its decayed status, we found TRIMCypA3 gene fusion transcripts in several primates. We found that the reconstructed "newly born" TrimCypA3 encoded robust and broad retroviral restriction activity but that this broad activity was lost via eight amino acid changes over the course of the next 10 My. We propose that TRIMCypA3 arose in response to a viral pathogen encountered by ancestral primates but was subsequently pseudogenized or lost due to a lack of selective pressure. Much like imprints of ancient viruses, fossils of decayed genes, such as TRIMCypA3, provide unique and specific insight into paleoviral infections that plagued primates deep in their evolutionary history.
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Fletcher AJ, Towers GJ. Inhibition of retroviral replication by members of the TRIM protein family. Curr Top Microbiol Immunol 2013; 371:29-66. [PMID: 23686231 DOI: 10.1007/978-3-642-37765-5_2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The TRIM protein family is emerging as a central component of mammalian antiviral innate immunity. Beginning with the identification of TRIM5α as a mammalian post-entry restriction factor against retroviruses, to the repeated observation that many TRIMs ubiquitinate and regulate signaling pathways, the past decade has witnessed an intense research effort to understand how TRIM proteins influence immunity. The list of viral families targeted directly or indirectly by TRIM proteins has grown to include adenoviruses, hepadnaviruses, picornaviruses, flaviviruses, orthomyxoviruses, paramyxoviruses, herpesviruses, rhabdoviruses and arenaviruses. We have come to appreciate how, through intense bouts of positive selection, some TRIM genes have been honed into species-specific restriction factors. Similarly, in the case of TRIMCyp, we are beginning to understand how viruses too have mutated to evade restriction, suggesting that TRIM and viruses have coevolved for millions of years of primate evolution. Recently, TRIM5α returned to the limelight when it was shown to trigger the expression of antiviral genes upon recognition of an incoming virus, a paradigm shift that demonstrated that restriction factors make excellent pathogen sensors. However, it remains unclear how many of ~100 human TRIM genes are antiviral, despite the expression of many of these genes being upregulated by interferon and upon viral infection. TRIM proteins do not conform to one type of antiviral mechanism, reflecting the diversity of viruses they target. Moreover, the cofactors of restriction remain largely enigmatic. The control of retroviral replication remains an important medical subject and provides a useful backdrop for reviewing how TRIM proteins act to repress viral replication.
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Affiliation(s)
- Adam J Fletcher
- MRC Centre for Medical Molecular Virology, University College, London, UK.
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Blanco-Melo D, Venkatesh S, Bieniasz PD. Intrinsic cellular defenses against human immunodeficiency viruses. Immunity 2012; 37:399-411. [PMID: 22999946 DOI: 10.1016/j.immuni.2012.08.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Indexed: 10/27/2022]
Abstract
Viral infections are often detrimental to host survival and reproduction. Consequently, hosts have evolved a variety of mechanisms to defend themselves against viruses. A component of this arsenal is a set of proteins, termed restriction factors, which exhibit direct antiviral activity. Among these are several classes of proteins (APOBEC3, TRIM5, Tetherin, and SAMHD1) that inhibit the replication of human and simian immunodeficiency viruses. Here, we outline the features, mechanisms, and evolution of these defense mechanisms. We also speculate on how restriction factors arose, how they might interact with the conventional innate and adaptive immune systems, and how an understanding of these intrinsic cellular defenses might be usefully exploited.
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Affiliation(s)
- Daniel Blanco-Melo
- Howard Hughes Medical Institute, Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University 455 First Avenue New York, NY, 10016
| | - Siddarth Venkatesh
- Howard Hughes Medical Institute, Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University 455 First Avenue New York, NY, 10016
| | - Paul D Bieniasz
- Howard Hughes Medical Institute, Laboratory of Retrovirology, Aaron Diamond AIDS Research Center, The Rockefeller University 455 First Avenue New York, NY, 10016
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Fassati A. Multiple roles of the capsid protein in the early steps of HIV-1 infection. Virus Res 2012; 170:15-24. [PMID: 23041358 DOI: 10.1016/j.virusres.2012.09.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 11/22/2022]
Abstract
The early steps of HIV-1 infection starting after virus entry into cells up to integration of its genome into host chromosomes are poorly understood. From seminal work showing that HIV-1 and oncoretroviruses follow different steps in the early stages post-entry, significant advances have been made in recent years and an important role for the HIV-1 capsid (CA) protein, the constituent of the viral core, has emerged. CA appears to orchestrate several events, such as virus uncoating, recognition by restriction factors and the innate immune system. It also plays a role in nuclear import and integration of HIV-1 and has become a novel target for antiretroviral drugs. Here we describe the different functions of CA and how they may be integrated into one or more coherent models that illuminate the early events in HIV-1 infection and their relations with the host cell.
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Affiliation(s)
- Ariberto Fassati
- The Wohl Virion Centre and MRC Centre for Medical & Molecular Virology, Division of Infection and Immunity, University College London, Cruciform Building, 90 Gower Street, London WC1E 6BT, UK.
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Abstract
Studies of retroviruses have been instrumental in revealing the existence of an array of antiviral proteins, or restriction factors, and the mechanisms by which they function. Some restriction factors appear to specifically inhibit retrovirus replication, while others have a broader antiviral action. Here, we briefly review current understanding of the mechanisms by which several such proteins exert antiviral activity. We also discuss how retroviruses have evolved to evade or antagonize antiviral proteins, including through the action of viral accessory proteins. Restriction factors, their viral targets and antagonists have exerted evolutionary pressure on each other, resulting in specialization and barriers to cross-species transmission. Potentially, this recently revealed intrinsic system of antiviral immunity might be mobilized for therapeutic benefit.
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Affiliation(s)
- Theodora Hatziioannou
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, NY 10016, United States
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Abstract
The emerging field of paleovirology aims to study the evolutionary age and impact of ancient viruses (paleoviruses) on host biology. Despite a historical emphasis on retroviruses, paleoviral 'fossils' have recently been uncovered from a broad swathe of viruses. These viral imprints have upended long-held notions of the age and mutation rate of viruses. While 'direct' paleovirology relies on the insertion of viral genes in animal genomes, examination of adaptive changes in host genes that occurred in response to paleoviral infections provides a complementary strategy for making 'indirect' paleovirological inferences. Finally, viruses have also impacted host biology by providing genes hosts have domesticated for their own purpose.
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Affiliation(s)
- Maulik R Patel
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle WA USA
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Abstract
Retroviral replication involves the formation of a DNA provirus integrated into the host genome. Through this process, retroviruses can colonize the germ line to form endogenous retroviruses (ERVs). ERV inheritance can have multiple adverse consequences for the host, some resembling those resulting from exogenous retrovirus infection but others arising by mechanisms unique to ERVs. Inherited retroviruses can also confer benefits on the host. To meet the different threats posed by endogenous and exogenous retroviruses, various host defences have arisen during evolution, acting at various stages on the retrovirus life cycle. In this Review, I describe our current understanding of the distribution and architecture of ERVs, the consequences of their acquisition for the host and the emerging details of the intimate evolutionary relationship between virus and vertebrate host.
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Feschotte C, Gilbert C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet 2012; 13:283-96. [PMID: 22421730 DOI: 10.1038/nrg3199] [Citation(s) in RCA: 504] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent studies have uncovered myriad viral sequences that are integrated or 'endogenized' in the genomes of various eukaryotes. Surprisingly, it appears that not just retroviruses but almost all types of viruses can become endogenous. We review how these genomic 'fossils' offer fresh insights into the origin, evolutionary dynamics and structural evolution of viruses, which are giving rise to the burgeoning field of palaeovirology. We also examine the multitude of ways through which endogenous viruses have influenced, for better or worse, the biology of their hosts. We argue that the conflict between hosts and viruses has led to the invention and diversification of molecular arsenals, which, in turn, promote the cellular co-option of endogenous viruses.
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Affiliation(s)
- Cédric Feschotte
- Department of Biology, University of Texas, Arlington, Texas 76016, USA.
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Gifford RJ. Viral evolution in deep time: lentiviruses and mammals. Trends Genet 2011; 28:89-100. [PMID: 22197521 DOI: 10.1016/j.tig.2011.11.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/08/2011] [Accepted: 11/09/2011] [Indexed: 11/29/2022]
Abstract
Lentiviruses are a distinctive genus of retroviruses that cause chronic, persistent infections in mammals, including humans. The emergence of pandemic HIV type-1 (HIV-1) infection during the late 20th century shaped a view of lentiviruses as 'modern' viruses. However, recent research has revealed an entirely different perspective, elucidating aspects of an evolutionary relationship with mammals that extends across many millions of years. Such deep evolutionary history is likely to be typical of many host-virus systems, fundamentally underpinning their interactions in the present day. For this reason, establishing the deep history of virus and host interaction is key to developing a fully informed approach to tackling viral diseases. Here, I use the example of lentiviruses to illustrate how paleovirological, geographic and genetic calibrations allow observations of virus and host interaction across a wide range of temporal and spatial scales to be integrated into a coherent ecological and evolutionary framework.
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Affiliation(s)
- Robert J Gifford
- Aaron Diamond AIDS Research Center, 455 1st Avenue, New York, NY 10016, USA.
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de Matos AL, van der Loo W, Areal H, Lanning DK, Esteves PJ. Study of Sylvilagus rabbit TRIM5α species-specific domain: how ancient endoviruses could have shaped the antiviral repertoire in Lagomorpha. BMC Evol Biol 2011; 11:294. [PMID: 21982459 PMCID: PMC3208668 DOI: 10.1186/1471-2148-11-294] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 10/08/2011] [Indexed: 12/02/2022] Open
Abstract
Background Since the first report of the antiretroviral restriction factor TRIM5α in primates, several orthologs in other mammals have been described. Recent studies suggest that leporid retroviruses like RELIK, the first reported endogenous lentivirus ever, may have imposed positive selection in TRIM5α orthologs of the European rabbit and European brown hare. Considering that RELIK must already have been present in a common ancestor of the leporid genera Lepus, Sylvilagus and Oryctolagus, we extended the study of evolutionary patterns of TRIM5α to other members of the Leporidae family, particularly to the genus Sylvilagus. Therefore, we obtained the TRIM5α nucleotide sequences of additional subspecies and species of the three leporid genera. We also compared lagomorph TRIM5α deduced protein sequences and established TRIM5α gene and TRIM5α protein phylogenies. Results The deduced protein sequence of Iberian hare TRIM5α was 89% identical to European rabbit TRIM5α, although high divergence was observed at the PRYSPRY v1 region between rabbit and the identified alleles from this hare species (allele 1: 50% divergence; allele 2: 53% divergence). A high identity was expected between the Sylvilagus and Oryctolagus TRIM5α proteins and, in fact, the Sylvilagus TRIM5α was 91% identical to the Oryctolagus protein. Nevertheless, the PRYSPRY v1 region was only 50% similar between these genera. Selection analysis of Lagomorpha TRIM5α proteins identified 25 positively-selected codons, 11 of which are located in the PRYSPRY v1 region, responsible for species specific differences in viral capsid recognition. Conclusions By extending Lagomorpha TRIM5α studies to an additional genus known to bear RELIK, we verified that the divergent species-specific pattern observed between the Oryctolagus and Lepus PRYSPRY-domains is also present in Sylvilagus TRIM5α. This work is one of the first known studies that compare the evolution of the antiretroviral restriction factor TRIM5α in different mammalian groups, Lagomorpha and Primates.
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Affiliation(s)
- Ana Lemos de Matos
- Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
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Courgnaud V, Mamede JI. L’interaction de la cyclophiline A avec la capside lentivirale. Med Sci (Paris) 2011; 27:574-5. [DOI: 10.1051/medsci/2011276004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Ohkura S, Goldstone DC, Yap MW, Holden-Dye K, Taylor IA, Stoye JP. Novel escape mutants suggest an extensive TRIM5α binding site spanning the entire outer surface of the murine leukemia virus capsid protein. PLoS Pathog 2011; 7:e1002011. [PMID: 21483490 PMCID: PMC3068999 DOI: 10.1371/journal.ppat.1002011] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 01/28/2011] [Indexed: 12/18/2022] Open
Abstract
After entry into target cells, retroviruses encounter the host restriction
factors such as Fv1 and TRIM5α. While it is clear that these factors target
retrovirus capsid proteins (CA), recognition remains poorly defined in the
absence of structural information. To better understand the binding interaction
between TRIM5α and CA, we selected a panel of novel N-tropic murine
leukaemia virus (N-MLV) escape mutants by a serial passage of replication
competent N-MLV in rhesus macaque TRIM5α (rhTRIM5α)-positive cells using
a small percentage of unrestricted cells to allow multiple rounds of virus
replication. The newly identified mutations, many of which involve changes in
charge, are distributed over the outer ‘top’ surface of N-MLV CA,
including the N-terminal β-hairpin, and map up to 29 Ao apart.
Biological characterisation with a number of restriction factors revealed that
only one of the new mutations affects restriction by human TRIM5α,
indicating significant differences in the binding interaction between N-MLV and
the two TRIM5αs, whereas three of the mutations result in dual sensitivity
to Fv1n and Fv1b. Structural studies of two mutants show
that no major changes in the overall CA conformation are associated with escape
from restriction. We conclude that interactions involving much, if not all, of
the surface of CA are vital for TRIM5α binding. Host restriction factors such as TRIM5α are important for preventing cross
species transmission of a variety of retroviruses. They act to block viral
replication but their mode of virus recognition is poorly understood. To address
this question we have developed a procedure for isolating viruses that replicate
in the presence of restriction factors. Analysis of these viruses shows that
individual mutations across the entire surface of the viral capsid molecule can
relieve restriction. Escape from TRIM5α of one species does not necessarily
lead to escape from another. It seems likely that restriction factor recognition
involves extensive weak contacts between factor and virus. We suggest that this
represents an important design feature in a system that recognizes multiple
pathogens.
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Affiliation(s)
- Sadayuki Ohkura
- Division of Virology, MRC National Institute for Medical Research,
London, United Kingdom
| | - David C. Goldstone
- Division of Molecular Structure, MRC National Institute for Medical
Research, London, United Kingdom
| | - Melvyn W. Yap
- Division of Virology, MRC National Institute for Medical Research,
London, United Kingdom
| | - Kate Holden-Dye
- Division of Virology, MRC National Institute for Medical Research,
London, United Kingdom
| | - Ian A. Taylor
- Division of Molecular Structure, MRC National Institute for Medical
Research, London, United Kingdom
| | - Jonathan P. Stoye
- Division of Virology, MRC National Institute for Medical Research,
London, United Kingdom
- * E-mail:
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49
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Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses. J Virol 2011; 85:4173-83. [PMID: 21345948 DOI: 10.1128/jvi.00075-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lentiviruses, the genus of retrovirus that includes HIV-1, rarely endogenize. Some lemurs uniquely possess an endogenous lentivirus called PSIV ("prosimian immunodeficiency virus"). Thus, lemurs provide the opportunity to study the activity of host defense factors, such as TRIM5α, in the setting of germ line invasion. We characterized the activities of TRIM5α proteins from two distant lemurs against exogenous retroviruses and a chimeric PSIV. TRIM5α from gray mouse lemur, which carries PSIV in its genome, exhibited the narrowest restriction activity. One allelic variant of gray mouse lemur TRIM5α restricted only N-tropic murine leukemia virus (N-MLV), while a second variant restricted N-MLV and, uniquely, B-tropic MLV (B-MLV); both variants poorly blocked PSIV. In contrast, TRIM5α from ring-tailed lemur, which does not contain PSIV in its genome, revealed one of the broadest antiviral activities reported to date against lentiviruses, including PSIV. Investigation into the antiviral specificity of ring-tailed lemur TRIM5α demonstrated a major contribution of a 32-amino-acid expansion in variable region 2 (v2) of the B30.2/SPRY domain to the breadth of restriction. Data on lemur TRIM5α and the prediction of ancestral simian sequences hint at an evolutionary scenario where antiretroviral specificity is prominently defined by the lineage-specific expansion of the variable loops of B30.2/SPRY.
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