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Miller LVC, Papa G, Vaysburd M, Cheng S, Sweeney PW, Smith A, Franco C, Katsinelos T, Huang M, Sanford SAI, Benn J, Farnsworth J, Higginson K, Joyner H, McEwan WA, James LC. Co-opting templated aggregation to degrade pathogenic tau assemblies and improve motor function. Cell 2024:S0092-8674(24)00912-7. [PMID: 39276772 DOI: 10.1016/j.cell.2024.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/14/2024] [Accepted: 08/12/2024] [Indexed: 09/17/2024]
Abstract
Protein aggregation causes a wide range of neurodegenerative diseases. Targeting and removing aggregates, but not the functional protein, is a considerable therapeutic challenge. Here, we describe a therapeutic strategy called "RING-Bait," which employs an aggregating protein sequence combined with an E3 ubiquitin ligase. RING-Bait is recruited into aggregates, whereupon clustering dimerizes the RING domain and activates its E3 function, resulting in the degradation of the aggregate complex. We exemplify this concept by demonstrating the specific degradation of tau aggregates while sparing soluble tau. Unlike immunotherapy, RING-Bait is effective against both seeded and cell-autonomous aggregation. RING-Bait removed tau aggregates seeded from Alzheimer's disease (AD) and progressive supranuclear palsy (PSP) brain extracts and was also effective in primary neurons. We used a brain-penetrant adeno-associated virus (AAV) to treat P301S tau transgenic mice, reducing tau pathology and improving motor function. A RING-Bait strategy could be applied to other neurodegenerative proteinopathies by replacing the Bait sequence to match the target aggregate.
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Affiliation(s)
- Lauren V C Miller
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Guido Papa
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Marina Vaysburd
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Shi Cheng
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate, Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Paul W Sweeney
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
| | - Annabel Smith
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Catarina Franco
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Taxiarchis Katsinelos
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Melissa Huang
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Sophie A I Sanford
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Jonathan Benn
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Jasmine Farnsworth
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Katie Higginson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Holly Joyner
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - William A McEwan
- UK Dementia Research Institute at the University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK.
| | - Leo C James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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2
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Moezpoor MR, Stevenson M. Help or Hinder: Protein Host Factors That Impact HIV-1 Replication. Viruses 2024; 16:1281. [PMID: 39205255 PMCID: PMC11360189 DOI: 10.3390/v16081281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
Interactions between human immunodeficiency virus type 1 (HIV-1) and the host factors or restriction factors of its target cells determine the cell's susceptibility to, and outcome of, infection. Factors intrinsic to the cell are involved at every step of the HIV-1 replication cycle, contributing to productive infection and replication, or severely attenuating the chances of success. Furthermore, factors unique to certain cell types contribute to the differences in infection between these cell types. Understanding the involvement of these factors in HIV-1 infection is a key requirement for the development of anti-HIV-1 therapies. As the list of factors grows, and the dynamic interactions between these factors and the virus are elucidated, comprehensive and up-to-date summaries that recount the knowledge gathered after decades of research are beneficial to the field, displaying what is known so that researchers can build off the groundwork of others to investigate what is unknown. Herein, we aim to provide a review focusing on protein host factors, both well-known and relatively new, that impact HIV-1 replication in a positive or negative manner at each stage of the replication cycle, highlighting factors unique to the various HIV-1 target cell types where appropriate.
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Affiliation(s)
- Michael Rameen Moezpoor
- Department of Microbiology and Immunology, University of Miami Leonard M. Miller School of Medicine, Miami, FL 33136, USA
| | - Mario Stevenson
- Raymond F. Schinazi and Family Endowed Chair in Biomedicine; Professor of Medicine; Director, Institute of AIDS and Emerging Infectious Diseases; Department of Microbiology and Immunology, University of Miami Leonard M. Miller School of Medicine, Life Science Technology Park, 1951 NW 7th Avenue, Room 2331B, Suite 200, Miami, FL 33136, USA;
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3
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Saha B, Olsvik H, Williams GL, Oh S, Evjen G, Sjøttem E, Mandell MA. TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery. Cell Rep 2024; 43:114294. [PMID: 38814780 PMCID: PMC11216866 DOI: 10.1016/j.celrep.2024.114294] [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: 11/24/2023] [Revised: 04/05/2024] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
Ubiquitination of mitochondrial proteins provides a basis for the downstream recruitment of mitophagy machinery, yet whether ubiquitination of the machinery itself contributes to mitophagy is unknown. Here, we show that K63-linked polyubiquitination of the key mitophagy regulator TBK1 is essential for its mitophagy functions. This modification is catalyzed by the ubiquitin ligase TRIM5α and is required for TBK1 to interact with and activate a set of ubiquitin-binding autophagy adaptors including NDP52, p62/SQSTM1, and NBR1. Autophagy adaptors, along with TRIM27, enable TRIM5α to engage with TBK1 following mitochondrial damage. TRIM5α's ubiquitin ligase activity is required for the accumulation of active TBK1 on damaged mitochondria in Parkin-dependent and Parkin-independent mitophagy pathways. Our data support a model in which TRIM5α provides a mitochondria-localized, ubiquitin-based, self-amplifying assembly platform for TBK1 and mitophagy adaptors that is ultimately necessary for the recruitment of the core autophagy machinery.
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Affiliation(s)
- Bhaskar Saha
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Hallvard Olsvik
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Geneva L Williams
- Biomedical Sciences Graduate Program, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Seeun Oh
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Gry Evjen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Eva Sjøttem
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Michael A Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Autophagy, Inflammation, and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
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4
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Spada SJ, Grigg ME, Bouamr F, Best SM, Zhang P. TRIM5α: A Protean Architect of Viral Recognition and Innate Immunity. Viruses 2024; 16:997. [PMID: 39066160 PMCID: PMC11281341 DOI: 10.3390/v16070997] [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: 05/07/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
The evolutionary pressures exerted by viral infections have led to the development of various cellular proteins with potent antiviral activities, some of which are known as antiviral restriction factors. TRIpartite Motif-containing protein 5 alpha (TRIM5α) is a well-studied restriction factor of retroviruses that exhibits virus- and host-species-specific functions in protecting against cross-primate transmission of specific lentiviruses. This specificity is achieved at the level of the host gene through positive selection predominantly within its C-terminal B30.2/PRYSPRY domain, which is responsible for the highly specific recognition of retroviral capsids. However, more recent work has challenged this paradigm, demonstrating TRIM5α as a restriction factor for retroelements as well as phylogenetically distinct viral families, acting similarly through the recognition of viral gene products via B30.2/PRYSPRY. This spectrum of antiviral activity raises questions regarding the genetic and structural plasticity of this protein as a mediator of the recognition of a potentially diverse array of viral molecular patterns. This review highlights the dynamic evolutionary footprint of the B30.2/PRYSPRY domain in response to retroviruses while exploring the guided 'specificity' conferred by the totality of TRIM5α's additional domains that may account for its recently identified promiscuity.
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Affiliation(s)
- Stephanie J. Spada
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK;
- Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20894, USA; (M.E.G.); (F.B.)
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA;
| | - Michael E. Grigg
- Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20894, USA; (M.E.G.); (F.B.)
| | - Fadila Bouamr
- Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20894, USA; (M.E.G.); (F.B.)
| | - Sonja M. Best
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA;
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK;
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK
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5
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Sumner RP, Blest H, Lin M, Maluquer de Motes C, Towers GJ. HIV-1 with gag processing defects activates cGAS sensing. Retrovirology 2024; 21:10. [PMID: 38778414 PMCID: PMC11112816 DOI: 10.1186/s12977-024-00643-0] [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: 04/08/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Detection of viruses by host pattern recognition receptors induces the expression of type I interferon (IFN) and IFN-stimulated genes (ISGs), which suppress viral replication. Numerous studies have described HIV-1 as a poor activator of innate immunity in vitro. The exact role that the viral capsid plays in this immune evasion is not fully understood. RESULTS To better understand the role of the HIV-1 capsid in sensing we tested the effect of making HIV-1 by co-expressing a truncated Gag that encodes the first 107 amino acids of capsid fused with luciferase or GFP, alongside wild type Gag-pol. We found that unlike wild type HIV-1, viral particles produced with a mixture of wild type and truncated Gag fused to luciferase or GFP induced a potent IFN response in THP-1 cells and macrophages. Innate immune activation by Gag-fusion HIV-1 was dependent on reverse transcription and DNA sensor cGAS, suggesting activation of an IFN response by viral DNA. Further investigation revealed incorporation of the Gag-luciferase/GFP fusion proteins into viral particles that correlated with subtle defects in wild type Gag cleavage and a diminished capacity to saturate restriction factor TRIM5α, likely due to aberrant particle formation. We propose that expression of the Gag fusion protein disturbs the correct cleavage and maturation of wild type Gag, yielding viral particles that are unable to effectively shield viral DNA from detection by innate sensors including cGAS. CONCLUSIONS These data highlight the crucial role of capsid in innate evasion and support growing literature that disruption of Gag cleavage and capsid formation induces a viral DNA- and cGAS-dependent innate immune response. Together these data demonstrate a protective role for capsid and suggest that antiviral activity of capsid-targeting antivirals may benefit from enhanced innate and adaptive immunity in vivo.
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Affiliation(s)
- Rebecca P Sumner
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK.
- Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK.
| | - Henry Blest
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | - Meiyin Lin
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
| | | | - Greg J Towers
- Division of Infection and Immunity, University College London, 90 Gower Street, London, WC1E 6BT, UK
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6
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Twentyman J, Emerman M, Ohainle M. Capsid-dependent lentiviral restrictions. J Virol 2024; 98:e0030824. [PMID: 38497663 PMCID: PMC11019884 DOI: 10.1128/jvi.00308-24] [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] [Indexed: 03/19/2024] Open
Abstract
Host antiviral proteins inhibit primate lentiviruses and other retroviruses by targeting many features of the viral life cycle. The lentiviral capsid protein and the assembled viral core are known to be inhibited through multiple, directly acting antiviral proteins. Several phenotypes, including those known as Lv1 through Lv5, have been described as cell type-specific blocks to infection against some but not all primate lentiviruses. Here we review important features of known capsid-targeting blocks to infection together with several blocks to infection for which the genes responsible for the inhibition still remain to be identified. We outline the features of these blocks as well as how current methodologies are now well suited to find these antiviral genes and solve these long-standing mysteries in the HIV and retrovirology fields.
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Affiliation(s)
- Joy Twentyman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Molly Ohainle
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California Berkeley, Berkeley, California, USA
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7
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Saha B, Olsvik H, Williams GL, Oh S, Evjen G, Sjøttem E, Mandell MA. TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563195. [PMID: 37905089 PMCID: PMC10614974 DOI: 10.1101/2023.10.19.563195] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ubiquitination of mitochondrial proteins provides a basis for the downstream recruitment of mitophagy machinery, yet whether ubiquitination of the machinery itself contributes to mitophagy is unknown. Here, we show that K63-linked polyubiquitination of the key mitophagy regulator TBK1 is essential for its mitophagy functions. This modification is catalyzed by the ubiquitin ligase TRIM5α. Mitochondrial damage triggers TRIM5α's auto-ubiquitination and its interaction with ubiquitin-binding autophagy adaptors including NDP52, optineurin, and NBR1. Autophagy adaptors, along with TRIM27, enable TRIM5α to engage with TBK1. TRIM5α with intact ubiquitination function is required for the proper accumulation of active TBK1 on damaged mitochondria in Parkin-dependent and Parkin-independent mitophagy pathways. Additionally, we show that TRIM5α can directly recruit autophagy initiation machinery to damaged mitochondria. Our data support a model in which TRIM5α provides a self-amplifying, mitochondria-localized, ubiquitin-based, assembly platform for TBK1 and mitophagy adaptors that is ultimately required to recruit the core autophagy machinery.
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Affiliation(s)
- Bhaskar Saha
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 USA
| | - Hallvard Olsvik
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Geneva L Williams
- Biomedical Sciences Graduate Program, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 USA
| | - Seeun Oh
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 USA
| | - Gry Evjen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Eva Sjøttem
- Autophagy Research Group, Department of Medical Biology, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Michael A Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131 USA
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center
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8
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Mello-Vieira J, Bopp T, Dikic I. Ubiquitination and cell-autonomous immunity. Curr Opin Immunol 2023; 84:102368. [PMID: 37451128 DOI: 10.1016/j.coi.2023.102368] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
Cell-autonomous immunity is the first line of defense by which cells recognize and contribute to eliminating invasive pathogens. It is composed of immune signaling networks that sense microbial pathogens, promote pathogen restriction, and stimulate their elimination, including host cell death. Ubiquitination is a pivotal orchestrator of these pathways, by changing the activity of signal transducers and effector proteins in an efficient way. In this review, we will focus on how ubiquitin connects the pathways that sense pathogens to the cellular responses to invaders and shed light on how ubiquitination impacts the microenvironment around the infected cell, stimulating the appropriate immune response. Finally, we discuss therapeutic options directed at favoring cell-autonomous immune responses to infection.
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Affiliation(s)
- João Mello-Vieira
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Tobias Bopp
- Institute for Immunology, University Medical Center, Johannes Gutenberg University, Mainz, Germany.
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany; Max Planck Institute for Biophysics, Frankfurt am Main, Germany.
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9
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Beilinson HA, Sevilleja A, Spring J, Benavides F, Beilinson V, Neokosmidis N, Golovkina T. A single dominant locus restricts retrovirus replication in YBR/Ei mice. J Virol 2023; 97:e0068523. [PMID: 37578238 PMCID: PMC10506465 DOI: 10.1128/jvi.00685-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/28/2023] [Indexed: 08/15/2023] Open
Abstract
Differential responses to viral infections are influenced by the genetic makeup of the host. Studies of resistance to retroviruses in human populations are complicated due to the inability to conduct proof-of-principle studies. Inbred mouse lines, which have a range of susceptible phenotypes to retroviruses, are an ideal tool to identify and characterize mechanisms of resistance and define their genetic underpinnings. YBR/Ei mice become infected with Mouse Mammary Tumor Virus, a mucosally transmitted murine retrovirus, but eliminate the virus from their pedigrees. Virus elimination correlates with a lack of virus-specific neonatal oral tolerance, which is a major mechanism for blocking the anti-virus response in susceptible mice. Virus control is unrelated to virus-neutralizing antibodies, cytotoxic CD8+ T cells, NK cells, and NK T cells, which are the best characterized mechanisms of resistance to retroviruses. We identified a single, dominant locus that controls the resistance mechanism, which we provisionally named attenuation of virus titers (Avt) and mapped to the distal region of chromosome 18. IMPORTANCE Elucidation of the mechanism that mediates resistance to retroviruses is of fundamental importance to human health, as it will ultimately lead to knowledge of the genetic differences among individuals in susceptibility to microbial infections.
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Affiliation(s)
- Helen A. Beilinson
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Amanda Sevilleja
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| | - Jessica Spring
- Committee on Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Fernando Benavides
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Vera Beilinson
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | | | - Tatyana Golovkina
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
- Committee on Microbiology, University of Chicago, Chicago, Illinois, USA
- Committee on Genetics, Genomics and System Biology, University of Chicago, Chicago, Illinois, USA
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10
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Twentyman J, Khalifeh A, Felton AL, Emerman M, Ohainle M. Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor. Retrovirology 2023; 20:15. [PMID: 37608289 PMCID: PMC10464172 DOI: 10.1186/s12977-023-00629-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/08/2023] [Indexed: 08/24/2023] Open
Abstract
Human immunodeficiency virus (HIV) and other lentiviruses adapt to new hosts by evolving to evade host-specific innate immune proteins that differ in sequence and often viral recognition between host species. Understanding how these host antiviral proteins, called restriction factors, constrain lentivirus replication and transmission is key to understanding the emergence of pandemic viruses like HIV-1. Human TRIM34, a paralogue of the well-characterized lentiviral restriction factor TRIM5α, was previously identified by our lab via CRISPR-Cas9 screening as a restriction factor of certain HIV and SIV capsids. Here, we show that diverse primate TRIM34 orthologues from non-human primates can restrict a range of Simian Immunodeficiency Virus (SIV) capsids including SIVAGM-SAB, SIVAGM-TAN and SIVMAC capsids, which infect sabaeus monkeys, tantalus monkeys, and rhesus macaques, respectively. All primate TRIM34 orthologues tested, regardless of species of origin, were able to restrict this same subset of viral capsids. However, in all cases, this restriction also required the presence of TRIM5α. We demonstrate that TRIM5α is necessary, but not sufficient, for restriction of these capsids, and that human TRIM5α functionally interacts with TRIM34 from different species. Finally, we find that both the TRIM5α SPRY v1 loop and the TRIM34 SPRY domain are essential for TRIM34-mediated restriction. These data support a model in which TRIM34 is a broadly-conserved primate lentiviral restriction factor that acts in tandem with TRIM5α, such that together, these proteins can restrict capsids that neither can restrict alone.
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Affiliation(s)
- Joy Twentyman
- Department of Global Health, University of Washington, Seattle, WA, USA
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anthony Khalifeh
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California -Berkeley, Berkeley, CA, USA
| | - Abby L Felton
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Molly Ohainle
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California -Berkeley, Berkeley, CA, USA.
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11
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Horns F, Martinez JA, Fan C, Haque M, Linton JM, Tobin V, Santat L, Maggiolo AO, Bjorkman PJ, Lois C, Elowitz MB. Engineering RNA export for measurement and manipulation of living cells. Cell 2023; 186:3642-3658.e32. [PMID: 37437570 PMCID: PMC10528933 DOI: 10.1016/j.cell.2023.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/08/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
A system for programmable export of RNA molecules from living cells would enable both non-destructive monitoring of cell dynamics and engineering of cells capable of delivering executable RNA programs to other cells. We developed genetically encoded cellular RNA exporters, inspired by viruses, that efficiently package and secrete cargo RNA molecules from mammalian cells within protective nanoparticles. Exporting and sequencing RNA barcodes enabled non-destructive monitoring of cell population dynamics with clonal resolution. Further, by incorporating fusogens into the nanoparticles, we demonstrated the delivery, expression, and functional activity of exported mRNA in recipient cells. We term these systems COURIER (controlled output and uptake of RNA for interrogation, expression, and regulation). COURIER enables measurement of cell dynamics and establishes a foundation for hybrid cell and gene therapies based on cell-to-cell delivery of RNA.
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Affiliation(s)
- Felix Horns
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Joe A Martinez
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mehernaz Haque
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - James M Linton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Victoria Tobin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leah Santat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ailiena O Maggiolo
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carlos Lois
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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12
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Zhao Y, Lu Y, Richardson S, Sreekumar M, Albarnaz JD, Smith GL. TRIM5α restricts poxviruses and is antagonized by CypA and the viral protein C6. Nature 2023; 620:873-880. [PMID: 37558876 PMCID: PMC10447239 DOI: 10.1038/s41586-023-06401-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/04/2023] [Indexed: 08/11/2023]
Abstract
Human tripartite motif protein 5α (TRIM5α) is a well-characterized restriction factor for some RNA viruses, including HIV1-5; however, reports are limited for DNA viruses6,7. Here we demonstrate that TRIM5α also restricts orthopoxviruses and, via its SPRY domain, binds to the orthopoxvirus capsid protein L3 to diminish virus replication and activate innate immunity. In response, several orthopoxviruses, including vaccinia, rabbitpox, cowpox, monkeypox, camelpox and variola viruses, deploy countermeasures. First, the protein C6 binds to TRIM5 via the RING domain to induce its proteasome-dependent degradation. Second, cyclophilin A (CypA) is recruited via interaction with the capsid protein L3 to virus factories and virions to antagonize TRIM5α; this interaction is prevented by cyclosporine A (CsA) and the non-immunosuppressive derivatives alisporivir and NIM811. Both the proviral effect of CypA and the antiviral effect of CsA are dependent on TRIM5α. CsA, alisporivir and NIM811 have antiviral activity against orthopoxviruses, and because these drugs target a cellular protein, CypA, the emergence of viral drug resistance is difficult. These results warrant testing of CsA derivatives against orthopoxviruses, including monkeypox and variola.
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Affiliation(s)
- Yiqi Zhao
- Department of Pathology, University of Cambridge, Cambridge, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Yongxu Lu
- Department of Pathology, University of Cambridge, Cambridge, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | | | - Jonas D Albarnaz
- Department of Pathology, University of Cambridge, Cambridge, UK.
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Cambridge, UK.
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Pirbright Institute, Surrey, UK.
- Chinese Academy of Medical Sciences-Oxford Institute, University of Oxford, Oxford, UK.
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13
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Ran XH, Zhu JW, Ni RZ, Zheng YT, Chen YY, Zheng WH, Mu D. TRIM5α recruits HDAC1 to p50 and Sp1 and promotes H3K9 deacetylation at the HIV-1 LTR. Nat Commun 2023; 14:3343. [PMID: 37291137 PMCID: PMC10250300 DOI: 10.1038/s41467-023-39056-6] [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: 10/27/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Tripartite motif-containing protein 5α (TRIM5α) is generally known to block the postentry events of HIV-1. Here, we report an uncharacterized role for TRIM5α in the maintenance of viral latency. Knockdown of TRIM5α potentiates the transcription of HIV-1 in multiple latency models, which is reversed by shRNA-resistant TRIM5α. TRIM5α suppresses TNFα-activated HIV-1 LTR-driven as well as NF-κB- and Sp1-driven gene expression, with the RING and B-box 2 domains being the essential determinants. Mechanistically, TRIM5α binds to and enhances the recruitment of histone deacetylase 1 (HDAC1) to NF-κB p50 and Sp1. ChIP‒qPCR analyses further reveal that the association of TRIM5α with HIV-1 LTR induces HDAC1 recruitment and local H3K9 deacetylation. Conserved suppression effects of TRIM5α orthologs from multiple species on both HIV-1 and endo-retroelement HERV-K LTR activities have also been demonstrated. These findings provide new insights into the molecular mechanisms by which proviral latency is initially established and activatable proviruses are resilenced by histone deacetylase recruitment.
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Affiliation(s)
- Xiang-Hong Ran
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Jia-Wu Zhu
- School of Basic Medical Sciences, Kunming Medical University, Kunming, Yunnan, China
| | - Run-Ze Ni
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ya-Yun Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Wei-Hua Zheng
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Dan Mu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.
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14
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Papa G, Albecka A, Mallery D, Vaysburd M, Renner N, James LC. IP6-stabilised HIV capsids evade cGAS/STING-mediated host immune sensing. EMBO Rep 2023; 24:e56275. [PMID: 36970882 PMCID: PMC10157305 DOI: 10.15252/embr.202256275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
HIV-1 uses inositol hexakisphosphate (IP6) to build a metastable capsid capable of delivering its genome into the host nucleus. Here, we show that viruses that are unable to package IP6 lack capsid protection and are detected by innate immunity, resulting in the activation of an antiviral state that inhibits infection. Disrupting IP6 enrichment results in defective capsids that trigger cytokine and chemokine responses during infection of both primary macrophages and T-cell lines. Restoring IP6 enrichment with a single mutation rescues the ability of HIV-1 to infect cells without being detected. Using a combination of capsid mutants and CRISPR-derived knockout cell lines for RNA and DNA sensors, we show that immune sensing is dependent upon the cGAS-STING axis and independent of capsid detection. Sensing requires the synthesis of viral DNA and is prevented by reverse transcriptase inhibitors or reverse transcriptase active-site mutation. These results demonstrate that IP6 is required to build capsids that can successfully transit the cell and avoid host innate immune sensing.
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Affiliation(s)
- Guido Papa
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Anna Albecka
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Donna Mallery
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Marina Vaysburd
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Nadine Renner
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
| | - Leo C James
- MRC Laboratory of Molecular Biology, Protein & Nucleic Acid DivisionCambridgeUK
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15
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Lagisquet J, Conrad M, Wittmann S, Volkmann B, Weissinger H, Sticht H, Gramberg T. A frequent SNP in TRIM5α strongly enhances the innate immune response against LINE-1 elements. Front Immunol 2023; 14:1168589. [PMID: 37180175 PMCID: PMC10169663 DOI: 10.3389/fimmu.2023.1168589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/29/2023] [Indexed: 05/15/2023] Open
Abstract
The intracellular restriction factor TRIM5α inhibits endogenous LINE-1 retroelements. It induces innate immune signaling cascades upon sensing of cytoplasmic LINE-1 complexes, thereby underlining its importance for protecting the human genome from harmful retrotransposition events. Here, we show that a frequent SNP within the RING domain of TRIM5α, resulting in the variant H43Y, blocks LINE-1 retrotransposition with higher efficiency compared to TRIM5α WT. Upon sensing of LINE-1 complexes in the cytoplasm, TRIM5α H43Y activates both NF-κB and AP-1 signaling pathways more potently than TRIM5α WT, triggering a strong block of the LINE-1 promoter. Interestingly, the H43Y allele lost its antiviral function suggesting that its enhanced activity against endogenous LINE-1 elements is the driving force behind its maintenance within the population. Thus, our study suggests that the H43Y variant of the restriction factor and sensor TRIM5α persists within the human population since it preserves our genome from uncontrolled LINE-1 retrotransposition with higher efficiency.
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Affiliation(s)
- Justine Lagisquet
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Marcus Conrad
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sabine Wittmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bianca Volkmann
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hannah Weissinger
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Gramberg
- Institute of Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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16
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Orlova OV, Glazkova DV, Mintaev RR, Tsyganova GM, Urusov FA, Shipulin GA, Bogoslovskaya EV. Comparative Evaluation of the Activity of Various Lentiviral Vectors Containing Three Anti-HIV Genes. Microorganisms 2023; 11:microorganisms11041053. [PMID: 37110476 PMCID: PMC10141122 DOI: 10.3390/microorganisms11041053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/14/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
A promising direction in the treatment of HIV infection is a gene therapy approach based on the insertion of antiviral genes aimed at inhibiting HIV replication into the genome of host cells. We obtained six constructs of lentiviral vectors with different arrangements of three antiviral genes: microRNAs against the CCR5 gene, the gene encoding the C-peptide, and the gene encoding the modified human TRIM5a protein. We found that despite containing the same genes, these vectors were produced at different titers and had different effects on cell viability, transduction efficiency, and expression stability. Comparative evaluation of the antiviral activity of three of the six developed vectors that showed stable expression was carried out using the continuous SupT1 lymphocytic cell line. All of the vectors protected cells from HIV infection: the viral load was several orders of magnitude lower than in control cells, and with one vector, complete cessation of virus growth in modified cells was achieved.
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Affiliation(s)
- Olga Vladimirovna Orlova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Dina Viktorovna Glazkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Ramil Rafailovich Mintaev
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Galina Mikhailovna Tsyganova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Felix Anatolevich Urusov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - German Alexandrovich Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Elena Vladimirovna Bogoslovskaya
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
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17
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Kiss L, Rhinesmith T, Luptak J, Dickson CF, Weidenhausen J, Smyly S, Yang JC, Maslen SL, Sinning I, Neuhaus D, Clift D, James LC. Trim-Away ubiquitinates and degrades lysine-less and N-terminally acetylated substrates. Nat Commun 2023; 14:2160. [PMID: 37061529 PMCID: PMC10105713 DOI: 10.1038/s41467-023-37504-x] [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: 06/29/2022] [Accepted: 03/20/2023] [Indexed: 04/17/2023] Open
Abstract
TRIM proteins are the largest family of E3 ligases in mammals. They include the intracellular antibody receptor TRIM21, which is responsible for mediating targeted protein degradation during Trim-Away. Despite their importance, the ubiquitination mechanism of TRIM ligases has remained elusive. Here we show that while Trim-Away activation results in ubiquitination of both ligase and substrate, ligase ubiquitination is not required for substrate degradation. N-terminal TRIM21 RING ubiquitination by the E2 Ube2W can be inhibited by N-terminal acetylation, but this doesn't prevent substrate ubiquitination nor degradation. Instead, uncoupling ligase and substrate degradation prevents ligase recycling and extends functional persistence in cells. Further, Trim-Away degrades substrates irrespective of whether they contain lysines or are N-terminally acetylated, which may explain the ability of TRIM21 to counteract fast-evolving pathogens and degrade diverse substrates.
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Affiliation(s)
- Leo Kiss
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Tyler Rhinesmith
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jakub Luptak
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Claire F Dickson
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging School of Medical Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Jonas Weidenhausen
- Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany
- EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Shannon Smyly
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Irmgard Sinning
- Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Leo C James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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18
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Twentyman J, Khalifeh A, Felton AL, Emerman M, OhAinle M. Primate TRIM34 is a broadly-acting, TRIM5-dependent lentiviral restriction factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534139. [PMID: 36993223 PMCID: PMC10055373 DOI: 10.1101/2023.03.24.534139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Human immunodeficiency virus (HIV) and other lentiviruses adapt to new hosts by evolving to evade host-specific innate immune proteins that differ in sequence and often viral recognition between host species. Understanding how these host antiviral proteins, called restriction factors, constrain lentivirus replication and transmission is key to understanding the emergence of pandemic viruses like HIV-1. Human TRIM34, a paralogue of the well-characterized lentiviral restriction factor TRIM5α, was previously identified by our lab via CRISPR-Cas9 screening as a restriction factor of certain HIV and SIV capsids. Here, we show that diverse primate TRIM34 orthologues from non-human primates can restrict a range of Simian Immunodeficiency Virus (SIV) capsids including SIV AGM-SAB , SIV AGM-TAN and SIV MAC capsids, which infect sabaeus monkeys, tantalus monkeys, and rhesus macaques, respectively. All primate TRIM34 orthologues tested, regardless of species of origin, were able to restrict this same subset of viral capsids. However, in all cases, this restriction also required the presence of TRIM5α. We demonstrate that TRIM5α is necessary, but not sufficient, for restriction of these capsids, and that human TRIM5α functionally interacts with TRIM34 from different species. Finally, we find that both the TRIM5α SPRY v1 loop and the TRIM34 SPRY domain are essential for TRIM34-mediated restriction. These data support a model in which TRIM34 is a broadly-conserved primate lentiviral restriction factor that acts in tandem with TRIM5α, such that together, these proteins can restrict capsids that neither can restrict alone.
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Affiliation(s)
- Joy Twentyman
- Department of Global Health, University of Washington, Seattle, WA, United States
- Divisions of Human Biology and Basic Sciences, Fred Hutch Cancer Center, Seattle, WA, United States
| | - Anthony Khalifeh
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California –Berkeley, Berkeley, CA, United States
| | - Abby L. Felton
- Divisions of Human Biology and Basic Sciences, Fred Hutch Cancer Center, Seattle, WA, United States
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutch Cancer Center, Seattle, WA, United States
| | - Molly OhAinle
- Divisions of Human Biology and Basic Sciences, Fred Hutch Cancer Center, Seattle, WA, United States
- Department of Molecular and Cell Biology, Division of Immunology and Molecular Medicine, University of California –Berkeley, Berkeley, CA, United States
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19
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Li J, Zhang Z, Gu J, Amini R, Mansfield AG, Xia J, White D, Stacey HD, Ang JC, Panesar G, Capretta A, Filipe CDM, Mossman K, Salena BJ, Gubbay JB, Balion C, Soleymani L, Miller MS, Yamamura D, Brennan JD, Li Y. Three on Three: Universal and High-Affinity Molecular Recognition of the Symmetric Homotrimeric Spike Protein of SARS-CoV-2 with a Symmetric Homotrimeric Aptamer. J Am Chem Soc 2022; 144:23465-23473. [PMID: 36520671 PMCID: PMC9762500 DOI: 10.1021/jacs.2c09870] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Indexed: 12/23/2022]
Abstract
Our previously discovered monomeric aptamer for SARS-CoV-2 (MSA52) possesses a universal affinity for COVID-19 spike protein variants but is ultimately limited by its ability to bind only one subunit of the spike protein. The symmetrical shape of the homotrimeric SARS-CoV-2 spike protein presents the opportunity to create a matching homotrimeric molecular recognition element that is perfectly complementary to its structural scaffold, causing enhanced binding affinity. Here, we describe a branched homotrimeric aptamer with three-fold rotational symmetry, named TMSA52, that not only possesses excellent binding affinity but is also capable of binding several SARS-CoV-2 spike protein variants with picomolar affinity, as well as pseudotyped lentiviruses expressing SARS-CoV-2 spike protein variants with femtomolar affinity. Using Pd-Ir nanocubes as nanozymes in an enzyme-linked aptamer binding assay (ELABA), TMSA52 was capable of sensitively detecting diverse pseudotyped lentiviruses in pooled human saliva with a limit of detection as low as 6.3 × 103 copies/mL. The ELABA was also used to test 50 SARS-CoV-2-positive and 60 SARS-CoV-2-negative patient saliva samples, providing sensitivity and specificity values of 84.0 and 98.3%, respectively, thus highlighting the potential of TMSA52 for the development of future rapid tests.
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Affiliation(s)
- Jiuxing Li
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Zijie Zhang
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jimmy Gu
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Ryan Amini
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Alexandria G. Mansfield
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jianrun Xia
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Dawn White
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
| | - Hannah D. Stacey
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jann C. Ang
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Gurpreet Panesar
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Alfredo Capretta
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Carlos D. M. Filipe
- Department
of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Karen Mossman
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Bruno J. Salena
- Department
of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | | | - Cynthia Balion
- Department
of Pathology and Molecular Medicine, McMaster
University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Leyla Soleymani
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- School
of Biomedical Engineering, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Matthew S. Miller
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- McMaster
Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Deborah Yamamura
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Department
of Pathology and Molecular Medicine, McMaster
University, 1280 Main
Street West, Hamilton, Ontario L8S 4K1, Canada
| | - John D. Brennan
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
| | - Yingfu Li
- Department
of Biochemistry and Biomedical Sciences, McMaster University,1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- Biointerfaces
Institute, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4O3, Canada
- Michael
G. DeGroote Institute of Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- School
of Biomedical Engineering, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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20
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Regulation of Epstein-Barr Virus Minor Capsid Protein BORF1 by TRIM5α. Int J Mol Sci 2022; 23:ijms232315340. [PMID: 36499678 PMCID: PMC9735550 DOI: 10.3390/ijms232315340] [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: 05/06/2022] [Revised: 11/16/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
TRIM5α is a host anti-retroviral restriction factor that destroys human immunodeficiency virus (HIV) virions and triggers innate immune signaling. TRIM5α also mediates the autophagic degradation of target proteins via TRIMosome formation. We previously showed that TRIM5α promotes Epstein-Barr virus (EBV) Rta ubiquitination and attenuates EBV lytic progression. In this study, we sought to elucidate whether TRIM5α can interact with and induce the degradation of EBV capsid proteins. Glutathione S-transferase (GST) pulldown and immunoprecipitation assays were conducted to identify interacting proteins, and mutants were generated to investigate key binding domains and ubiquitination sites. Results showed that TRIM5α binds directly with BORF1, an EBV capsid protein with a nuclear localization signal (NLS) that enables the transport of EBV capsid proteins into the host nucleus to facilitate capsid assembly. TRIM5α promotes BORF1 ubiquitination, which requires the surface patch region in the TRIM5α PRY/SPRY domain. TRIM5α expression also decreases the stability of BORF1(6KR), a mutant with all lysine residues mutated to arginine. However, chloroquine treatment restores the stability of BORF1(6KR), suggesting that TRIM5α destabilizes BORF1 via direct recognition of its substrate for autophagic degradation. These results reveal novel insights into the antiviral impact of TRIM5α beyond retroviruses.
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21
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Zhang T, Tamman H, Coppieters 't Wallant K, Kurata T, LeRoux M, Srikant S, Brodiazhenko T, Cepauskas A, Talavera A, Martens C, Atkinson GC, Hauryliuk V, Garcia-Pino A, Laub MT. Direct activation of a bacterial innate immune system by a viral capsid protein. Nature 2022; 612:132-140. [PMID: 36385533 PMCID: PMC9712102 DOI: 10.1038/s41586-022-05444-z] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022]
Abstract
Bacteria have evolved diverse immunity mechanisms to protect themselves against the constant onslaught of bacteriophages1-3. Similar to how eukaryotic innate immune systems sense foreign invaders through pathogen-associated molecular patterns4 (PAMPs), many bacterial immune systems that respond to bacteriophage infection require phage-specific triggers to be activated. However, the identities of such triggers and the sensing mechanisms remain largely unknown. Here we identify and investigate the anti-phage function of CapRelSJ46, a fused toxin-antitoxin system that protects Escherichia coli against diverse phages. Using genetic, biochemical and structural analyses, we demonstrate that the C-terminal domain of CapRelSJ46 regulates the toxic N-terminal region, serving as both antitoxin and phage infection sensor. Following infection by certain phages, newly synthesized major capsid protein binds directly to the C-terminal domain of CapRelSJ46 to relieve autoinhibition, enabling the toxin domain to pyrophosphorylate tRNAs, which blocks translation to restrict viral infection. Collectively, our results reveal the molecular mechanism by which a bacterial immune system directly senses a conserved, essential component of phages, suggesting a PAMP-like sensing model for toxin-antitoxin-mediated innate immunity in bacteria. We provide evidence that CapRels and their phage-encoded triggers are engaged in a 'Red Queen conflict'5, revealing a new front in the intense coevolutionary battle between phages and bacteria. Given that capsid proteins of some eukaryotic viruses are known to stimulate innate immune signalling in mammalian hosts6-10, our results reveal a deeply conserved facet of immunity.
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Affiliation(s)
- Tong Zhang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hedvig Tamman
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, (ULB), Brussels, Belgium
| | - Kyo Coppieters 't Wallant
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Michele LeRoux
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sriram Srikant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Albinas Cepauskas
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, (ULB), Brussels, Belgium
| | - Ariel Talavera
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, (ULB), Brussels, Belgium
| | - Chloe Martens
- Centre for Structural Biology and Bioinformatics, Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
- Institute of Technology, University of Tartu, Tartu, Estonia.
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, (ULB), Brussels, Belgium.
- WELBIO, Brussels, Belgium.
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
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22
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Structural and functional asymmetry of RING trimerization controls priming and extension events in TRIM5α autoubiquitylation. Nat Commun 2022; 13:7104. [PMID: 36402777 PMCID: PMC9675739 DOI: 10.1038/s41467-022-34920-3] [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: 01/10/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022] Open
Abstract
TRIM5α is an E3 ubiquitin ligase of the TRIM family that binds to the capsids of primate immunodeficiency viruses and blocks viral replication after cell entry. Here we investigate how synthesis of K63-linked polyubiquitin is upregulated by transient proximity of three RING domains in honeycomb-like assemblies formed by TRIM5α on the surface of the retroviral capsid. Proximity of three RINGs creates an asymmetric arrangement, in which two RINGs form a catalytic dimer that activates E2-ubiquitin conjugates and the disordered N-terminus of the third RING acts as the substrate for N-terminal autoubiquitylation. RING dimerization is required for activation of the E2s that contribute to the antiviral function of TRIM5α, UBE2W and heterodimeric UBE2N/V2, whereas the proximity of the third RING enhances the rate of each of the two distinct steps in the autoubiquitylation process: the initial N-terminal monoubiquitylation (priming) of TRIM5α by UBE2W and the subsequent extension of the K63-linked polyubiquitin chain by UBE2N/V2. The mechanism we describe explains how recognition of infection-associated epitope patterns by TRIM proteins initiates polyubiquitin-mediated downstream events in innate immunity.
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23
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Zuliani-Alvarez L, Govasli ML, Rasaiyaah J, Monit C, Perry SO, Sumner RP, McAlpine-Scott S, Dickson C, Rifat Faysal KM, Hilditch L, Miles RJ, Bibollet-Ruche F, Hahn BH, Boecking T, Pinotsis N, James LC, Jacques DA, Towers GJ. Evasion of cGAS and TRIM5 defines pandemic HIV. Nat Microbiol 2022; 7:1762-1776. [PMID: 36289397 PMCID: PMC9613477 DOI: 10.1038/s41564-022-01247-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022]
Abstract
Of the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.
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Affiliation(s)
- Lorena Zuliani-Alvarez
- Division of Infection and Immunity, UCL, London, UK
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | | | | | - Chris Monit
- Division of Infection and Immunity, UCL, London, UK
- Carnall Farrar, London, UK
| | - Stephen O Perry
- Division of Infection and Immunity, UCL, London, UK
- Quell Therapeutics Ltd, Translation & Innovation Hub, London, UK
| | | | | | - Claire Dickson
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - K M Rifat Faysal
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Laura Hilditch
- Division of Infection and Immunity, UCL, London, UK
- Nucleus Global, London, UK
| | | | - Frederic Bibollet-Ruche
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Till Boecking
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Leo C James
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - David A Jacques
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia.
| | - Greg J Towers
- Division of Infection and Immunity, UCL, London, UK.
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24
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Niemeyer D, Stenzel S, Veith T, Schroeder S, Friedmann K, Weege F, Trimpert J, Heinze J, Richter A, Jansen J, Emanuel J, Kazmierski J, Pott F, Jeworowski LM, Olmer R, Jaboreck MC, Tenner B, Papies J, Walper F, Schmidt ML, Heinemann N, Möncke-Buchner E, Baumgardt M, Hoffmann K, Widera M, Thao TTN, Balázs A, Schulze J, Mache C, Jones TC, Morkel M, Ciesek S, Hanitsch LG, Mall MA, Hocke AC, Thiel V, Osterrieder K, Wolff T, Martin U, Corman VM, Müller MA, Goffinet C, Drosten C. SARS-CoV-2 variant Alpha has a spike-dependent replication advantage over the ancestral B.1 strain in human cells with low ACE2 expression. PLoS Biol 2022; 20:e3001871. [PMID: 36383605 PMCID: PMC9710838 DOI: 10.1371/journal.pbio.3001871] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/30/2022] [Accepted: 10/06/2022] [Indexed: 11/17/2022] Open
Abstract
Epidemiological data demonstrate that Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) Alpha and Delta are more transmissible, infectious, and pathogenic than previous variants. Phenotypic properties of VOC remain understudied. Here, we provide an extensive functional study of VOC Alpha replication and cell entry phenotypes assisted by reverse genetics, mutational mapping of spike in lentiviral pseudotypes, viral and cellular gene expression studies, and infectivity stability assays in an enhanced range of cell and epithelial culture models. In almost all models, VOC Alpha spread less or equally efficiently as ancestral (B.1) SARS-CoV-2. B.1. and VOC Alpha shared similar susceptibility to serum neutralization. Despite increased relative abundance of specific sgRNAs in the context of VOC Alpha infection, immune gene expression in infected cells did not differ between VOC Alpha and B.1. However, inferior spreading and entry efficiencies of VOC Alpha corresponded to lower abundance of proteolytically cleaved spike products presumably linked to the T716I mutation. In addition, we identified a bronchial cell line, NCI-H1299, which supported 24-fold increased growth of VOC Alpha and is to our knowledge the only cell line to recapitulate the fitness advantage of VOC Alpha compared to B.1. Interestingly, also VOC Delta showed a strong (595-fold) fitness advantage over B.1 in these cells. Comparative analysis of chimeric viruses expressing VOC Alpha spike in the backbone of B.1, and vice versa, showed that the specific replication phenotype of VOC Alpha in NCI-H1299 cells is largely determined by its spike protein. Despite undetectable ACE2 protein expression in NCI-H1299 cells, CRISPR/Cas9 knock-out and antibody-mediated blocking experiments revealed that multicycle spread of B.1 and VOC Alpha required ACE2 expression. Interestingly, entry of VOC Alpha, as opposed to B.1 virions, was largely unaffected by treatment with exogenous trypsin or saliva prior to infection, suggesting enhanced resistance of VOC Alpha spike to premature proteolytic cleavage in the extracellular environment of the human respiratory tract. This property may result in delayed degradation of VOC Alpha particle infectivity in conditions typical of mucosal fluids of the upper respiratory tract that may be recapitulated in NCI-H1299 cells closer than in highly ACE2-expressing cell lines and models. Our study highlights the importance of cell model evaluation and comparison for in-depth characterization of virus variant-specific phenotypes and uncovers a fine-tuned interrelationship between VOC Alpha- and host cell-specific determinants that may underlie the increased and prolonged virus shedding detected in patients infected with VOC Alpha.
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Affiliation(s)
- Daniela Niemeyer
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Saskia Stenzel
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Talitha Veith
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Simon Schroeder
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Kirstin Friedmann
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Friderike Weege
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
| | - Julian Heinze
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Anja Richter
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jenny Jansen
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Jackson Emanuel
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Kazmierski
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Fabian Pott
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Lara M. Jeworowski
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Ruth Olmer
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Mark-Christian Jaboreck
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Beate Tenner
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Papies
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Walper
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Marie L. Schmidt
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Nicolas Heinemann
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Elisabeth Möncke-Buchner
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Morris Baumgardt
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Karen Hoffmann
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Marek Widera
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | | | - Anita Balázs
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jessica Schulze
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Christin Mache
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Terry C. Jones
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Morkel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, Berlin, Germany
- BIH Bioportal Single Cells, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Sandra Ciesek
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
- German Center for Infection Research, DZIF, Braunschweig, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch Translational Medicine and Pharmacology, Frankfurt am Main, Germany
| | - Leif G. Hanitsch
- Institute of Medical Immunology, Charité — Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Marcus A. Mall
- Institut für Virologie, Freie Universität Berlin, Berlin, Germany
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Lung Research (DZL), associated partner Charité, Berlin, Germany
| | - Andreas C. Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité — Universitätsmedizin Berlin, Berlin, Germany
| | - Volker Thiel
- Institute of Virology and Immunology, Bern, Switzerland
| | - Klaus Osterrieder
- Berlin Institute of Health, Berlin, Germany
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Thorsten Wolff
- Unit 17 “Influenza and other Respiratory Viruses", Robert Koch Institute, Berlin, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH — Center for Translational Regenerative Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany
| | - Victor M. Corman
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
| | - Marcel A. Müller
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Campus Charité Mitte, Charité — Universitätsmedizin Berlin, Berlin, Germany
- German Center for Infection Research, associated partner Charité, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- Labor Berlin – Charité Vivantes GmbH, Berlin, Germany
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25
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Zhang Y, Zhang W, Zheng L, Guo Q. The roles and targeting options of TRIM family proteins in tumor. Front Pharmacol 2022; 13:999380. [PMID: 36249749 PMCID: PMC9561884 DOI: 10.3389/fphar.2022.999380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Tripartite motif (TRIM) containing proteins are a class of E3 ubiquitin ligases, which are critically implicated in the occurrence and development of tumors. They can function through regulating various aspects of tumors, such as tumor proliferation, metastasis, apoptosis and the development of drug resistance during tumor therapy. Some members of TRIM family proteins can mediate protein ubiquitination and chromosome translocation via modulating several signaling pathways, like p53, NF-κB, AKT, MAPK, Wnt/β-catenin and other molecular regulatory mechanisms. The multi-domain nature/multi-functional biological role of TRIMs implies that blocking just one function or one domain might not be sufficient to obtain the desired therapeutic outcome, therefore, a detailed and systematic understanding of the biological functions of the individual domains of TRIMs is required. This review mainly described their roles and underlying mechanisms in tumorigenesis and progression, and it might shade light on a potential targeting strategy for TRIMs in tumor treatment, especially using PROTACs.
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Affiliation(s)
- Yuxin Zhang
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
| | - Wenzhou Zhang
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
- *Correspondence: Lufeng Zheng, ; Qianqian Guo,
| | - Qianqian Guo
- Department of Pharmacy, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, China
- *Correspondence: Lufeng Zheng, ; Qianqian Guo,
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26
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Tozawa T, Matsunaga K, Izumi T, Shigehisa N, Uekita T, Taoka M, Ichimura T. Ubiquitination-coupled liquid phase separation regulates the accumulation of the TRIM family of ubiquitin ligases into cytoplasmic bodies. PLoS One 2022; 17:e0272700. [PMID: 35930602 PMCID: PMC9355226 DOI: 10.1371/journal.pone.0272700] [Citation(s) in RCA: 8] [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: 03/17/2022] [Accepted: 07/25/2022] [Indexed: 12/02/2022] Open
Abstract
Many members of the tripartite motif (TRIM) family of ubiquitin ligases localize in spherical, membrane-free structures collectively referred to as cytoplasmic bodies (CBs) in a concentration-dependent manner. These CBs may function as aggresome precursors or storage compartments that segregate potentially harmful excess TRIM molecules from the cytosolic milieu. However, the manner in which TRIM proteins accumulate into CBs is unclear. In the present study, using TRIM32, TRIM5α and TRIM63 as examples, we demonstrated that CBs are in a liquid droplet state, resulting from liquid-liquid phase separation (LLPS). This finding is based on criteria that defines phase-separated structures, such as recovery after photobleaching, sensitivity to hexanediol, and the ability to undergo fusion. CB droplets, which contain cyan fluorescent protein (CFP)-fused TRIM32, were purified from HEK293 cells using a fluorescence-activated cell sorter and analyzed by LC-MS/MS. We found that in addition to TRIM32, these droplets contain a variety of endogenous proteins and enzymes including ubiquitin. Localization of ubiquitin within CBs was further verified by fluorescence microscopy. We also found that the activation of the intracellular ubiquitination cascade promotes the assembly of TRIM32 molecules into CBs, whereas inhibition causes suppression. Regulation is dependent on the intrinsic E3 ligase activity of TRIM32. Similar regulation by ubiquitination on the TRIM assembly was also observed with TRIM5α and TRIM63. Our findings provide a novel mechanical basis for the organization of CBs that couples compartmentalization through LLPS with ubiquitination.
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Affiliation(s)
- Takafumi Tozawa
- Department of Applied Chemistry, National Defense Academy, Yokosuka, Kanagawa, Japan
| | - Kohichi Matsunaga
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Tetsuro Izumi
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Naotake Shigehisa
- Department of Applied Chemistry, National Defense Academy, Yokosuka, Kanagawa, Japan
| | - Takamasa Uekita
- Department of Applied Chemistry, National Defense Academy, Yokosuka, Kanagawa, Japan
| | - Masato Taoka
- Department of Chemistry, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Tohru Ichimura
- Department of Applied Chemistry, National Defense Academy, Yokosuka, Kanagawa, Japan
- * E-mail:
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27
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Luptak J, Mallery DL, Jahun AS, Albecka A, Clift D, Ather O, Slodkowicz G, Goodfellow I, James LC. TRIM7 Restricts Coxsackievirus and Norovirus Infection by Detecting the C-Terminal Glutamine Generated by 3C Protease Processing. Viruses 2022; 14:1610. [PMID: 35893676 PMCID: PMC9394474 DOI: 10.3390/v14081610] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/14/2022] [Accepted: 07/20/2022] [Indexed: 12/04/2022] Open
Abstract
TRIM7 catalyzes the ubiquitination of multiple substrates with unrelated biological functions. This cross-reactivity is at odds with the specificity usually displayed by enzymes, including ubiquitin ligases. Here we show that TRIM7's extreme substrate promiscuity is due to a highly unusual binding mechanism, in which the PRYSPRY domain captures any ligand with a C-terminal helix that terminates in a hydrophobic residue followed by a glutamine. Many of the non-structural proteins found in RNA viruses contain C-terminal glutamines as a result of polyprotein cleavage by 3C protease. This viral processing strategy generates novel substrates for TRIM7 and explains its ability to inhibit Coxsackie virus and norovirus replication. In addition to viral proteins, cellular proteins such as glycogenin have evolved C-termini that make them a TRIM7 substrate. The 'helix-ΦQ' degron motif recognized by TRIM7 is reminiscent of the N-end degron system and is found in ~1% of cellular proteins. These features, together with TRIM7's restricted tissue expression and lack of immune regulation, suggest that viral restriction may not be its physiological function.
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Affiliation(s)
- Jakub Luptak
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | - Donna L. Mallery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | - Aminu S. Jahun
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (A.S.J.); (I.G.)
| | - Anna Albecka
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | - Osaid Ather
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
| | | | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK; (A.S.J.); (I.G.)
| | - Leo C. James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; (J.L.); (D.L.M.); (A.A.); (D.C.); (O.A.)
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Saha B, Salemi M, Williams GL, Oh S, Paffett ML, Phinney B, Mandell MA. Interactomic analysis reveals a homeostatic role for the HIV restriction factor TRIM5α in mitophagy. Cell Rep 2022; 39:110797. [PMID: 35545034 PMCID: PMC9136943 DOI: 10.1016/j.celrep.2022.110797] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/16/2022] [Accepted: 04/15/2022] [Indexed: 12/13/2022] Open
Abstract
The protein TRIM5α has multiple roles in antiretroviral defense, but the mechanisms underlying TRIM5α action are unclear. Here, we employ APEX2-based proteomics to identify TRIM5α-interacting partners. Our proteomics results connect TRIM5 to other proteins with actions in antiviral defense. Additionally, they link TRIM5 to mitophagy, an autophagy-based mode of mitochondrial quality control that is compromised in several human diseases. We find that TRIM5 is required for Parkin-dependent and -independent mitophagy pathways where TRIM5 recruits upstream autophagy regulators to damaged mitochondria. Expression of a TRIM5 mutant lacking ubiquitin ligase activity is unable to rescue mitophagy in TRIM5 knockout cells. Cells lacking TRIM5 show reduced mitochondrial function under basal conditions and are more susceptible to immune activation and death in response to mitochondrial damage than are wild-type cells. Taken together, our studies identify a homeostatic role for a protein previously recognized exclusively for its antiviral actions. The protein TRIM5α is well known for its roles in antiretroviral defense. Saha et al. show that TRIM5α also has key homeostatic functions. They report that TRIM5α helps to maintain mitochondrial quality control by enabling the autophagy-dependent removal of damaged mitochondria (mitophagy).
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Affiliation(s)
- Bhaskar Saha
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Michelle Salemi
- UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Geneva L Williams
- Biomedical Sciences Graduate Program, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Seeun Oh
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
| | - Michael L Paffett
- Fluorescence Microscopy and Cell Imaging Shared Resource, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Brett Phinney
- UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Michael A Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA; Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA.
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29
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Feng G, Feng H, Qi Y, Wang T, Ni N, Wu J, Yuan H. Interaction analysis between germline genetic variants and somatic mutations in head and neck cancer. Oral Oncol 2022; 128:105859. [DOI: 10.1016/j.oraloncology.2022.105859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/24/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
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30
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Foss S, Jonsson A, Bottermann M, Watkinson R, Lode HE, McAdam MB, Michaelsen TE, Sandlie I, James LC, Andersen JT. Potent TRIM21 and complement-dependent intracellular antiviral immunity requires the IgG3 hinge. Sci Immunol 2022; 7:eabj1640. [PMID: 35486676 PMCID: PMC7614286 DOI: 10.1126/sciimmunol.abj1640] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Humans have four IgG antibody subclasses that selectively or differentially engage immune effector molecules to protect against infections. Although IgG1 has been studied in detail and is the subclass of most approved antibody therapeutics, increasing evidence indicates that IgG3 is associated with enhanced protection against pathogens. Here, we report that IgG3 has superior capacity to mediate intracellular antiviral immunity compared with the other subclasses due to its uniquely extended and flexible hinge region, which facilitates improved recruitment of the cytosolic Fc receptor TRIM21, independently of Fc binding affinity. TRIM21 may also synergize with complement C1/C4-mediated lysosomal degradation via capsid inactivation. We demonstrate that this process is potentiated by IgG3 in a hinge-dependent manner. Our findings reveal differences in how the four IgG subclasses mediate intracellular immunity, knowledge that may guide IgG subclass selection and engineering of antiviral antibodies for prophylaxis and therapy.
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Affiliation(s)
- Stian Foss
- Centre for Immune Regulation (CIR) and Department of Biosciences, University of Oslo, N-0371 Oslo, Norway.,CIR and Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, P.O. Box 4956, N-0424 Oslo, Norway.,Institute of Clinical Medicine and Department of Pharmacology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Alexandra Jonsson
- Centre for Immune Regulation (CIR) and Department of Biosciences, University of Oslo, N-0371 Oslo, Norway.,CIR and Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, P.O. Box 4956, N-0424 Oslo, Norway.,Institute of Clinical Medicine and Department of Pharmacology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Maria Bottermann
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2-0QH, UK
| | - Ruth Watkinson
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2-0QH, UK
| | - Heidrun E Lode
- Centre for Immune Regulation (CIR) and Department of Biosciences, University of Oslo, N-0371 Oslo, Norway.,CIR and Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, P.O. Box 4956, N-0424 Oslo, Norway.,Institute of Clinical Medicine and Department of Pharmacology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Martin B McAdam
- Centre for Immune Regulation (CIR) and Department of Biosciences, University of Oslo, N-0371 Oslo, Norway.,CIR and Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, P.O. Box 4956, N-0424 Oslo, Norway
| | - Terje E Michaelsen
- Department of Chemical Pharmacy, School of Pharmacy, University of Oslo, N-0371 Oslo, Norway.,Infection Immunology, Norwegian Institute of Public Health, N-0213 Oslo, Norway
| | - Inger Sandlie
- Centre for Immune Regulation (CIR) and Department of Biosciences, University of Oslo, N-0371 Oslo, Norway.,CIR and Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, P.O. Box 4956, N-0424 Oslo, Norway.,Institute of Clinical Medicine and Department of Pharmacology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - Leo C James
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2-0QH, UK
| | - Jan Terje Andersen
- CIR and Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, P.O. Box 4956, N-0424 Oslo, Norway.,Institute of Clinical Medicine and Department of Pharmacology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
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31
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Kiss L, James LC. The molecular mechanisms that drive intracellular neutralization by the antibody-receptor and RING E3 ligase TRIM21. Semin Cell Dev Biol 2021; 126:99-107. [PMID: 34823983 DOI: 10.1016/j.semcdb.2021.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022]
Abstract
The cytosolic antibody receptor and RING E3 ligase TRIM21 targets intracellular, antibody-coated immune complexes for degradation and activates the immune system. Here we review how TRIM21 degrades diverse targets and how this activity can be exploited in molecular biology and for the development of new therapeutics. In addition, we compare what is known about TRIM21's mechanism to other TRIM proteins and RING E3 ligases.
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Affiliation(s)
- Leo Kiss
- MRC Laboratory of Molecular Biology, UK.
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32
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Shen Q, Wu C, Freniere C, Tripler TN, Xiong Y. Nuclear Import of HIV-1. Viruses 2021; 13:2242. [PMID: 34835048 PMCID: PMC8619967 DOI: 10.3390/v13112242] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 11/01/2021] [Indexed: 12/12/2022] Open
Abstract
The delivery of the HIV-1 genome into the nucleus is an indispensable step in retroviral infection of non-dividing cells, but the mechanism of HIV-1 nuclear import has been a longstanding debate due to controversial experimental evidence. It was commonly believed that the HIV-1 capsid would need to disassemble (uncoat) in the cytosol before nuclear import because the capsid is larger than the central channel of nuclear pore complexes (NPCs); however, increasing evidence demonstrates that intact, or nearly intact, HIV-1 capsid passes through the NPC to enter the nucleus. With the protection of the capsid, the HIV-1 core completes reverse transcription in the nucleus and is translocated to the integration site. Uncoating occurs while, or after, the viral genome is released near the integration site. These independent discoveries reveal a compelling new paradigm of this important step of the HIV-1 life cycle. In this review, we summarize the recent studies related to HIV-1 nuclear import, highlighting the spatial-temporal relationship between the nuclear entry of the virus core, reverse transcription, and capsid uncoating.
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Affiliation(s)
| | | | | | | | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA; (Q.S.); (C.W.); (C.F.); (T.N.T.)
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33
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Regulation of Viral Restriction by Post-Translational Modifications. Viruses 2021; 13:v13112197. [PMID: 34835003 PMCID: PMC8618861 DOI: 10.3390/v13112197] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/17/2022] Open
Abstract
Intrinsic immunity is orchestrated by a wide range of host cellular proteins called restriction factors. They have the capacity to interfere with viral replication, and most of them are tightly regulated by interferons (IFNs). In addition, their regulation through post-translational modifications (PTMs) constitutes a major mechanism to shape their action positively or negatively. Following viral infection, restriction factor modification can be decisive. Palmitoylation of IFITM3, SUMOylation of MxA, SAMHD1 and TRIM5α or glycosylation of BST2 are some of those PTMs required for their antiviral activity. Nonetheless, for their benefit and by manipulating the PTMs machinery, viruses have evolved sophisticated mechanisms to counteract restriction factors. Indeed, many viral proteins evade restriction activity by inducing their ubiquitination and subsequent degradation. Studies on PTMs and their substrates are essential for the understanding of the antiviral defense mechanisms and provide a global vision of all possible regulations of the immune response at a given time and under specific infection conditions. Our aim was to provide an overview of current knowledge regarding the role of PTMs on restriction factors with an emphasis on their impact on viral replication.
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34
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Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases. Biochem Soc Trans 2021; 48:2615-2624. [PMID: 33170204 PMCID: PMC7752041 DOI: 10.1042/bst20200383] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022]
Abstract
TRIM proteins form a protein family that is characterized by a conserved tripartite motif domain comprising a RING domain, one or two B-box domains and a coiled-coil region. Members of this large protein family are important regulators of numerous cellular functions including innate immune responses, transcriptional regulation and apoptosis. Key to their cellular role is their E3 ligase activity which is conferred by the RING domain. Self-association is an important characteristic of TRIM protein activity and is mediated by homodimerization via the coiled-coil region, and in some cases higher order association via additional domains of the tripartite motif. In many of the TRIM family proteins studied thus far, RING dimerization is an important prerequisite for E3 ligase enzymatic activity though the propensity of RING domains to dimerize differs significantly between different TRIMs and can be influenced by other regions of the protein.
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35
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Bauby H, Ward CC, Hugh-White R, Swanson CM, Schulz R, Goujon C, Malim MH. HIV-1 Vpr Induces Widespread Transcriptomic Changes in CD4 + T Cells Early Postinfection. mBio 2021; 12:e0136921. [PMID: 34154423 PMCID: PMC8263007 DOI: 10.1128/mbio.01369-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
The interactions between a virus and its host are complex but can be broadly categorized as either viral manipulation of cellular functions or cellular responses to infection. These processes begin at the earliest point of contact between virus and cell and frequently result in changes to cellular gene expression, making genome-wide transcriptomics a useful tool to study them. Several previous studies have used transcriptomics to evaluate the cellular responses to human immunodeficiency virus type 1 (HIV-1) infection; however, none have examined events in primary CD4+ T cells during the first 24 h of infection. Here, we analyzed CD4+ T cells at 4.5, 8, 12, 24, and 48 h following infection. We describe global changes to host gene expression commencing at 4.5 h postinfection and evolving over the ensuing time points. We identify upregulation of genes related to innate immunity, cytokine production, and apoptosis and downregulation of those involved in transcription and translation. We further demonstrate that the viral accessory protein Vpr is necessary for almost all gene expression changes seen at 12 h postinfection and the majority of those seen at 48 h. Identifying this new role for Vpr not only provides fresh perspective on its possible function but also adds further insight into the interplay between HIV-1 and its host at the cellular level. IMPORTANCE HIV-1, while now treatable, remains an important human pathogen causing significant morbidity and mortality globally. The virus predominantly infects CD4+ T cells and, if not treated with medication, ultimately causes their depletion, resulting in AIDS and death. Further refining our understanding of the interaction between HIV-1 and these cells has the potential to inform further therapeutic development. Previous studies have used transcriptomics to assess gene expression changes in CD4+ T cells following HIV-1 infection; here, we provide a detailed examination of changes occurring in the first 24 h of infection. Importantly, we define the viral protein Vpr as essential for the changes observed at this early stage. This finding has significance for understanding the role of Vpr in infection and pathogenesis and also for interpreting previous transcriptomic analyses of HIV-1 infection.
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Affiliation(s)
- Hélène Bauby
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Christopher C. Ward
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rupert Hugh-White
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Reiner Schulz
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Caroline Goujon
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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36
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D'Amico F, Mukhopadhyay R, Ovaa H, Mulder MPC. Targeting TRIM Proteins: A Quest towards Drugging an Emerging Protein Class. Chembiochem 2021; 22:2011-2031. [PMID: 33482040 PMCID: PMC8251876 DOI: 10.1002/cbic.202000787] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/22/2021] [Indexed: 02/06/2023]
Abstract
The ubiquitylation machinery regulates several fundamental biological processes from protein homeostasis to a wide variety of cellular signaling pathways. As a consequence, its dysregulation is linked to diseases including cancer, neurodegeneration, and autoimmunity. With this review, we aim to highlight the therapeutic potential of targeting E3 ligases, with a special focus on an emerging class of RING ligases, named tri-partite motif (TRIM) proteins, whose role as targets for drug development is currently gaining pharmaceutical attention. TRIM proteins exert their catalytic activity as scaffolds involved in many protein-protein interactions, whose multidomains and adapter-like nature make their druggability very challenging. Herein, we give an overview of the current understanding of this class of single polypeptide RING E3 ligases and discuss potential targeting options.
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Affiliation(s)
- Francesca D'Amico
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Rishov Mukhopadhyay
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Monique P. C. Mulder
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
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37
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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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38
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Rose KM, Spada SJ, Broeckel R, McNally KL, Hirsch VM, Best SM, Bouamr F. From Capsids to Complexes: Expanding the Role of TRIM5α in the Restriction of Divergent RNA Viruses and Elements. Viruses 2021; 13:v13030446. [PMID: 33801908 PMCID: PMC7998678 DOI: 10.3390/v13030446] [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: 01/26/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 01/26/2023] Open
Abstract
An evolutionary arms race has been ongoing between retroviruses and their primate hosts for millions of years. Within the last century, a zoonotic transmission introduced the Human Immunodeficiency Virus (HIV-1), a retrovirus, to the human population that has claimed the lives of millions of individuals and is still infecting over a million people every year. To counteract retroviruses such as this, primates including humans have evolved an innate immune sensor for the retroviral capsid lattice known as TRIM5α. Although the molecular basis for its ability to restrict retroviruses is debated, it is currently accepted that TRIM5α forms higher-order assemblies around the incoming retroviral capsid that are not only disruptive for the virus lifecycle, but also trigger the activation of an antiviral state. More recently, it was discovered that TRIM5α restriction is broader than previously thought because it restricts not only the human retroelement LINE-1, but also the tick-borne flaviviruses, an emergent group of RNA viruses that have vastly different strategies for replication compared to retroviruses. This review focuses on the underlying mechanisms of TRIM5α-mediated restriction of retroelements and flaviviruses and how they differ from the more widely known ability of TRIM5α to restrict retroviruses.
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Affiliation(s)
- Kevin M. Rose
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Rockville, MD 20894, USA; (K.M.R.); (S.J.S.); (V.M.H.)
| | - Stephanie J. Spada
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Rockville, MD 20894, USA; (K.M.R.); (S.J.S.); (V.M.H.)
| | - Rebecca Broeckel
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, MT 59840, USA; (R.B.); (K.L.M.); (S.M.B.)
| | - Kristin L. McNally
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, MT 59840, USA; (R.B.); (K.L.M.); (S.M.B.)
| | - Vanessa M. Hirsch
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Rockville, MD 20894, USA; (K.M.R.); (S.J.S.); (V.M.H.)
| | - Sonja M. Best
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, MT 59840, USA; (R.B.); (K.L.M.); (S.M.B.)
| | - Fadila Bouamr
- Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Rockville, MD 20894, USA; (K.M.R.); (S.J.S.); (V.M.H.)
- Correspondence:
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39
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Zhuang S, Torbett BE. Interactions of HIV-1 Capsid with Host Factors and Their Implications for Developing Novel Therapeutics. Viruses 2021; 13:417. [PMID: 33807824 PMCID: PMC8001122 DOI: 10.3390/v13030417] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 12/11/2022] Open
Abstract
The Human Immunodeficiency Virus type 1 (HIV-1) virion contains a conical shell, termed capsid, encasing the viral RNA genome. After cellular entry of the virion, the capsid is released and ensures the protection and delivery of the HIV-1 genome to the host nucleus for integration. The capsid relies on many virus-host factor interactions which are regulated spatiotemporally throughout the course of infection. In this paper, we will review the current understanding of the highly dynamic HIV-1 capsid-host interplay during the early stages of viral replication, namely intracellular capsid trafficking after viral fusion, nuclear import, uncoating, and integration of the viral genome into host chromatin. Conventional anti-retroviral therapies primarily target HIV-1 enzymes. Insights of capsid structure have resulted in a first-in-class, long-acting capsid-targeting inhibitor, GS-6207 (Lenacapavir). This inhibitor binds at the interface between capsid protein subunits, a site known to bind host factors, interferes with capsid nuclear import, HIV particle assembly, and ordered assembly. Our review will highlight capsid structure, the host factors that interact with capsid, and high-throughput screening techniques, specifically genomic and proteomic approaches, that have been and can be used to identify host factors that interact with capsid. Better structural and mechanistic insights into the capsid-host factor interactions will significantly inform the understanding of HIV-1 pathogenesis and the development of capsid-centric antiretroviral therapeutics.
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Affiliation(s)
- Shentian Zhuang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA;
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Bruce E. Torbett
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA;
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA
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40
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Zeng J, Santos AF, Mukadam AS, Osswald M, Jacques DA, Dickson CF, McLaughlin SH, Johnson CM, Kiss L, Luptak J, Renner N, Vaysburd M, McEwan WA, Morais-de-Sá E, Clift D, James LC. Target-induced clustering activates Trim-Away of pathogens and proteins. Nat Struct Mol Biol 2021; 28:278-289. [PMID: 33633400 PMCID: PMC7611929 DOI: 10.1038/s41594-021-00560-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/13/2021] [Indexed: 01/31/2023]
Abstract
Trim-Away is a recently developed technology that exploits off-the-shelf antibodies and the RING E3 ligase and cytosolic antibody receptor TRIM21 to carry out rapid protein depletion. How TRIM21 is catalytically activated upon target engagement, either during its normal immune function or when repurposed for targeted protein degradation, is unknown. Here we show that a mechanism of target-induced clustering triggers intermolecular dimerization of the RING domain to switch on the ubiquitination activity of TRIM21 and induce virus neutralization or drive Trim-Away. We harness this mechanism for selective degradation of disease-causing huntingtin protein containing long polyglutamine tracts and expand the Trim-Away toolbox with highly active TRIM21-nanobody chimeras that can also be controlled optogenetically. This work provides a mechanism for cellular activation of TRIM RING ligases and has implications for targeted protein degradation technologies.
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Affiliation(s)
- Jingwei Zeng
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Ana Filipa Santos
- i3S - Instituto de Investigação e Inovação em Saúde and IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Aamir S. Mukadam
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mariana Osswald
- i3S - Instituto de Investigação e Inovação em Saúde and IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - David A. Jacques
- EMBL Australia Node, Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Claire F. Dickson
- EMBL Australia Node, Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | | | | | - Leo Kiss
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Jakub Luptak
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Nadine Renner
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Marina Vaysburd
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - William A. McEwan
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK,Correspondence: William McEwan (); Eurico Morais-de-Sá (); Dean Clift (); Leo C. James ()
| | - Eurico Morais-de-Sá
- i3S - Instituto de Investigação e Inovação em Saúde and IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal,Correspondence: William McEwan (); Eurico Morais-de-Sá (); Dean Clift (); Leo C. James ()
| | - Dean Clift
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK,Correspondence: William McEwan (); Eurico Morais-de-Sá (); Dean Clift (); Leo C. James ()
| | - Leo C. James
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK,Correspondence: William McEwan (); Eurico Morais-de-Sá (); Dean Clift (); Leo C. James ()
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41
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Wang HT, Hur S. Substrate recognition by TRIM and TRIM-like proteins in innate immunity. Semin Cell Dev Biol 2021; 111:76-85. [PMID: 33092958 PMCID: PMC7572318 DOI: 10.1016/j.semcdb.2020.09.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/28/2020] [Indexed: 12/23/2022]
Abstract
TRIM (Tripartite motif) and TRIM-like proteins have emerged as an important class of E3 ligases in innate immunity. Their functions range from activation or regulation of innate immune signaling pathway to direct detection and restriction of pathogens. Despite the importance, molecular mechanisms for many TRIM/TRIM-like proteins remain poorly characterized, in part due to challenges of identifying their substrates. In this review, we discuss several TRIM/TRIM-like proteins in RNA sensing pathways and viral restriction functions. We focus on those containing PRY-SPRY, the domain most frequently used for substrate recognition, and discuss emerging mechanisms that are commonly utilized by several TRIM/TRIM-like proteins to tightly control their interaction with the substrates.
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Affiliation(s)
- Hai-Tao Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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42
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Kiss L, Clift D, Renner N, Neuhaus D, James LC. RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination. Nat Commun 2021; 12:1220. [PMID: 33619271 PMCID: PMC7900206 DOI: 10.1038/s41467-021-21443-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/26/2021] [Indexed: 12/24/2022] Open
Abstract
Attachment of ubiquitin (Ub) to proteins is one of the most abundant and versatile of all posttranslational modifications and affects outcomes in essentially all physiological processes. RING E3 ligases target E2 Ub-conjugating enzymes to the substrate, resulting in its ubiquitination. However, the mechanism by which a ubiquitin chain is formed on the substrate remains elusive. Here we demonstrate how substrate binding can induce a specific RING topology that enables self-ubiquitination. By analyzing a catalytically trapped structure showing the initiation of TRIM21 RING-anchored ubiquitin chain elongation, and in combination with a kinetic study, we illuminate the chemical mechanism of ubiquitin conjugation. Moreover, biochemical and cellular experiments show that the topology found in the structure can be induced by substrate binding. Our results provide insights into ubiquitin chain formation on a structural, biochemical and cellular level with broad implications for targeted protein degradation.
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Affiliation(s)
- Leo Kiss
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Leo C James
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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43
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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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44
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Retroviral Restriction Factors and Their Viral Targets: Restriction Strategies and Evolutionary Adaptations. Microorganisms 2020; 8:microorganisms8121965. [PMID: 33322320 PMCID: PMC7764263 DOI: 10.3390/microorganisms8121965] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022] Open
Abstract
The evolutionary conflict between retroviruses and their vertebrate hosts over millions of years has led to the emergence of cellular innate immune proteins termed restriction factors as well as their viral antagonists. Evidence accumulated in the last two decades has substantially increased our understanding of the elaborate mechanisms utilized by these restriction factors to inhibit retroviral replication, mechanisms that either directly block viral proteins or interfere with the cellular pathways hijacked by the viruses. Analyses of these complex interactions describe patterns of accelerated evolution for these restriction factors as well as the acquisition and evolution of their virus-encoded antagonists. Evidence is also mounting that many restriction factors identified for their inhibition of specific retroviruses have broader antiviral activity against additional retroviruses as well as against other viruses, and that exposure to these multiple virus challenges has shaped their adaptive evolution. In this review, we provide an overview of the restriction factors that interfere with different steps of the retroviral life cycle, describing their mechanisms of action, adaptive evolution, viral targets and the viral antagonists that evolved to counter these factors.
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45
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Whiteley AM, Prado MA, de Poot SAH, Paulo JA, Ashton M, Dominguez S, Weber M, Ngu H, Szpyt J, Jedrychowski MP, Easton A, Gygi SP, Kurz T, Monteiro MJ, Brown EJ, Finley D. Global proteomics of Ubqln2-based murine models of ALS. J Biol Chem 2020; 296:100153. [PMID: 33277362 PMCID: PMC7873701 DOI: 10.1074/jbc.ra120.015960] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/21/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
Familial neurodegenerative diseases commonly involve mutations that result in either aberrant proteins or dysfunctional components of the proteolytic machinery that act on aberrant proteins. UBQLN2 is a ubiquitin receptor of the UBL/UBA family that binds the proteasome through its ubiquitin-like domain and is thought to deliver ubiquitinated proteins to proteasomes for degradation. UBQLN2 mutations result in familial amyotrophic lateral sclerosis (ALS)/frontotemporal dementia in humans through an unknown mechanism. Quantitative multiplexed proteomics was used to provide for the first time an unbiased and global analysis of the role of Ubqln2 in controlling the composition of the proteome. We studied several murine models of Ubqln2-linked ALS and also generated Ubqln2 null mutant mice. We identified impacts of Ubqln2 on diverse physiological pathways, most notably serotonergic signaling. Interestingly, we observed an upregulation of proteasome subunits, suggesting a compensatory response to diminished proteasome output. Among the specific proteins whose abundance is linked to UBQLN2 function, the strongest hits were the ubiquitin ligase TRIM32 and two retroelement-derived proteins, PEG10 and CXX1B. Cycloheximide chase studies using induced human neurons and HEK293 cells suggested that PEG10 and TRIM32 are direct clients. Although UBQLN2 directs the degradation of multiple proteins via the proteasome, it surprisingly conferred strong protection from degradation on the Gag-like protein CXX1B, which is expressed from the same family of retroelement genes as PEG10. In summary, this study charts the proteomic landscape of ALS-related Ubqln2 mutants and identifies candidate client proteins that are altered in vivo in disease models and whose degradation is promoted by UBQLN2.
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Affiliation(s)
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marissa Ashton
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara Dominguez
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Martin Weber
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Hai Ngu
- Department of Pathology, Genentech Inc, South San Francisco, California, USA
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark P Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy Easton
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Thimo Kurz
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Mervyn J Monteiro
- Center for Biomedical Engineering and Technology, Department of Anatomy and Neurobiology, University of Maryland Medical School, Baltimore, Maryland, USA
| | - Eric J Brown
- Department of Immunology and Infectious Diseases, Genentech Inc, South San Francisco, California, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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46
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Hertzog J, Rehwinkel J. Regulation and inhibition of the DNA sensor cGAS. EMBO Rep 2020; 21:e51345. [PMID: 33155371 PMCID: PMC7726805 DOI: 10.15252/embr.202051345] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Cell-autonomous sensing of nucleic acids is essential for host defence against invading pathogens by inducing antiviral and inflammatory cytokines. cGAS has emerged in recent years as a non-redundant DNA sensor important for detection of many viruses and bacteria. Upon binding to DNA, cGAS synthesises the cyclic dinucleotide 2'3'-cGAMP that binds to the adaptor protein STING and thereby triggers IRF3- and NFκB-dependent transcription. In addition to infection, the pathophysiology of an ever-increasing number of sterile inflammatory conditions in humans involves the recognition of DNA through cGAS. Consequently, the cGAS/STING signalling axis has emerged as an attractive target for pharmacological modulation. However, the development of cGAS and STING inhibitors has just begun and a need for specific and effective compounds persists. In this review, we focus on cGAS and explore how its activation by immunostimulatory DNA is regulated by cellular mechanisms, viral immune modulators and small molecules. We further use our knowledge of cGAS modulation by cells and viruses to conceptualise potential new ways of pharmacological cGAS targeting.
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Affiliation(s)
- Jonny Hertzog
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Jan Rehwinkel
- MRC Human Immunology UnitMRC Weatherall Institute of Molecular MedicineRadcliffe Department of MedicineUniversity of OxfordOxfordUK
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47
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Correlated cryogenic fluorescence microscopy and electron cryo-tomography shows that exogenous TRIM5α can form hexagonal lattices or autophagy aggregates in vivo. Proc Natl Acad Sci U S A 2020; 117:29702-29711. [PMID: 33154161 PMCID: PMC7703684 DOI: 10.1073/pnas.1920323117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
One of the most notable features of TRIM5 proteins is their ability to restrict retroviral infections by binding viral capsids. TRIM5α forms highly dynamic puncta of various sizes, and, when purified, hexagonal nets on the surface of HIV virions, but the molecular ultrastructure of the cellular bodies and the relationship of the in vitro nets to HIV restriction has remained unclear. To define the cellular ultrastructure underlying the punctate and dynamic nature of YFP-rhTRIM5α bodies, we applied cryogenic correlated light and electron microscopy combined with electron cryo-tomography to TRIM5α bodies and observed YFP-rhTRIM5α-localization to organelles found along the aggrephagy branch of the autophagy pathway. Consistent with previous work, we also found that TRIM5α forms hexagonal nets inside cells. Members of the tripartite motif (TRIM) protein family have been shown to assemble into structures in both the nucleus and cytoplasm. One TRIM protein family member, TRIM5α, has been shown to form cytoplasmic bodies involved in restricting retroviruses such as HIV-1. Here we applied cryogenic correlated light and electron microscopy, combined with electron cryo-tomography, to intact mammalian cells expressing YFP-rhTRIM5α and found the presence of hexagonal nets whose arm lengths were similar to those of the hexagonal nets formed by purified TRIM5α in vitro. We also observed YFP-rhTRIM5α within a diversity of structures with characteristics expected for organelles involved in different stages of macroautophagy, including disorganized protein aggregations (sequestosomes), sequestosomes flanked by flat double-membraned vesicles (sequestosome:phagophore complexes), sequestosomes within double-membraned vesicles (autophagosomes), and sequestosomes within multivesicular autophagic vacuoles (amphisomes or autolysosomes). Vaults were also seen in these structures, consistent with their role in autophagy. Our data 1) support recent reports that TRIM5α can form both well-organized signaling complexes and nonsignaling aggregates, 2) offer images of the macroautophagy pathway in a near-native state, and 3) reveal that vaults arrive early in macroautophagy.
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48
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Glazkova DV, Urusov FA, Bogoslovskaya EV, Shipulin GA. Retrovirus Restriction Factor TRIM5α: The Mechanism of Action and Prospects for Use in Gene Therapy of HIV Infection. Mol Biol 2020. [DOI: 10.1134/s0026893320050039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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49
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Sumner RP, Harrison L, Touizer E, Peacock TP, Spencer M, Zuliani‐Alvarez L, Towers GJ. Disrupting HIV-1 capsid formation causes cGAS sensing of viral DNA. EMBO J 2020; 39:e103958. [PMID: 32852081 PMCID: PMC7560218 DOI: 10.15252/embj.2019103958] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 07/23/2020] [Accepted: 07/27/2020] [Indexed: 01/28/2023] Open
Abstract
Detection of viral DNA by cyclic GMP-AMP synthase (cGAS) is a first line of defence leading to the production of type I interferon (IFN). As HIV-1 replication is not a strong inducer of IFN, we hypothesised that an intact capsid physically cloaks viral DNA from cGAS. To test this, we generated defective viral particles by treatment with HIV-1 protease inhibitors or by genetic manipulation of gag. These viruses had defective Gag cleavage, reduced infectivity and diminished capacity to saturate TRIM5α. Importantly, unlike wild-type HIV-1, infection with cleavage defective HIV-1 triggered an IFN response in THP-1 cells that was dependent on viral DNA and cGAS. An IFN response was also observed in primary human macrophages infected with cleavage defective viruses. Infection in the presence of the capsid destabilising small molecule PF-74 also induced a cGAS-dependent IFN response. These data demonstrate a protective role for capsid and suggest that antiviral activity of capsid- and protease-targeting antivirals may benefit from enhanced innate and adaptive immunity in vivo.
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Affiliation(s)
- Rebecca P Sumner
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Lauren Harrison
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Emma Touizer
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Thomas P Peacock
- Division of Infection and ImmunityUniversity College LondonLondonUK
- Present address:
Department of MedicineImperial College LondonLondonUK
| | - Matthew Spencer
- Division of Infection and ImmunityUniversity College LondonLondonUK
| | | | - Greg J Towers
- Division of Infection and ImmunityUniversity College LondonLondonUK
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50
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Saha B, Chisholm D, Kell AM, Mandell MA. A non-canonical role for the autophagy machinery in anti-retroviral signaling mediated by TRIM5α. PLoS Pathog 2020; 16:e1009017. [PMID: 33052966 PMCID: PMC7588057 DOI: 10.1371/journal.ppat.1009017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/26/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
TRIM5α is a key cross-species barrier to retroviral infection, with certain TRIM5 alleles conferring increased risk of HIV-1 infection in humans. TRIM5α is best known as a species-specific restriction factor that directly inhibits the viral life cycle. Additionally, it is also a pattern-recognition receptor (PRR) that activates inflammatory signaling. How TRIM5α carries out its multi-faceted actions in antiviral defense remains incompletely understood. Here, we show that proteins required for autophagy, a cellular self-digestion pathway, play an important role in TRIM5α’s function as a PRR. Genetic depletion of proteins involved in all stages of the autophagy pathway prevented TRIM5α-driven expression of NF-κB and AP1 responsive genes. One of these genes is the preeminent antiviral cytokine interferon β (IFN-β), whose TRIM5-dependent expression was lost in cells lacking the autophagy proteins ATG7, BECN1, and ULK1. Moreover, we found that the ability of TRIM5α to stimulate IFN-β expression in response to recognition of a TRIM5α-restricted HIV-1 capsid mutant (P90A) was abrogated in cells lacking autophagy factors. Stimulation of human macrophage-like cells with the P90A virus protected them against subsequent infection with an otherwise resistant wild type HIV-1 in a manner requiring TRIM5α, BECN1, and ULK1. Mechanistically, TRIM5α was attenuated in its ability to activate the kinase TAK1 in autophagy deficient cells, and both BECN1 and ATG7 contributed to the assembly of TRIM5α-TAK1 complexes. These data demonstrate a non-canonical role for the autophagy machinery in assembling antiviral signaling complexes and in establishing a TRIM5α-dependent antiviral state. TRIM5α is an antiretroviral protein that employs multiple mechanisms to protect cells against infection. Previous studies have linked TRIM5α to autophagy, a cytoplasmic quality control pathway with numerous roles in immunity, raising the possibility that TRIM5α engages autophagy in antiviral defense. This concept has been controversial, since TRIM5α’s best-known role as a directly acting antiretroviral effector is autophagy independent. However, retroviral restriction is only one aspect of TRIM5α function. We demonstrate that autophagy is crucial to another TRIM5α action: its role as a pattern-recognition receptor. We show that autophagy machinery is required for TRIM5α to transduce antiviral signaling and to establish an antiviral state. Our data indicate that autophagy provides TRIM5α with a platform upon which to activate antiviral responses.
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Affiliation(s)
- Bhaskar Saha
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Devon Chisholm
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Alison M. Kell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Michael A. Mandell
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- Autophagy, Inflammation and Metabolism Center of Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
- * E-mail:
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