1
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Blest HTW, Redmond A, Avissar J, Barker J, Bridgeman A, Fowler G, Chauveau L, Hertzog J, Vendrell I, Fischer R, Iversen MB, Jing L, Koelle DM, Paludan SR, Kessler BM, Crump CM, Rehwinkel J. HSV-1 employs UL56 to antagonize expression and function of cGAMP channels. Cell Rep 2024; 43:114122. [PMID: 38652659 DOI: 10.1016/j.celrep.2024.114122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/21/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
DNA sensing is important for antiviral immunity. The DNA sensor cGAS synthesizes 2'3'-cyclic GMP-AMP (cGAMP), a second messenger that activates STING, which induces innate immunity. cGAMP not only activates STING in the cell where it is produced but cGAMP also transfers to other cells. Transporters, channels, and pores (including SLC19A1, SLC46A2, P2X7, ABCC1, and volume-regulated anion channels (VRACs)) release cGAMP into the extracellular space and/or import cGAMP. We report that infection with multiple human viruses depletes some of these cGAMP conduits. This includes herpes simplex virus 1 (HSV-1) that targets SLC46A2, P2X7, and the VRAC subunits LRRC8A and LRRC8C for degradation. The HSV-1 protein UL56 is necessary and sufficient for these effects that are mediated at least partially by proteasomal turnover. UL56 thereby inhibits cGAMP uptake via VRAC, SLC46A2, and P2X7. Taken together, HSV-1 antagonizes intercellular cGAMP transfer. We propose that this limits innate immunity by reducing cell-to-cell communication via the immunotransmitter cGAMP.
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Affiliation(s)
- Henry T W Blest
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Alexander Redmond
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jed Avissar
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jake Barker
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, UK
| | - Anne Bridgeman
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Gerissa Fowler
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Lise Chauveau
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jonny Hertzog
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marie B Iversen
- Department of Biomedicine, Aarhus University, Aarhus Aarhus C, Denmark
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus Aarhus C, Denmark
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Colin M Crump
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, UK
| | - Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK.
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2
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Gonzalez MM, Vizoso-Pinto MG, Erra-Balsells R, Gensch T, Cabrerizo FM. In Vitro Effect of 9,9'-Norharmane Dimer against Herpes Simplex Viruses. Int J Mol Sci 2024; 25:4966. [PMID: 38732185 PMCID: PMC11084892 DOI: 10.3390/ijms25094966] [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: 02/21/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Herpes simplex virus (HSV) infections are highly widespread among humans, producing symptoms ranging from ulcerative lesions to severe diseases such as blindness and life-threatening encephalitis. At present, there are no vaccines available, and some existing antiviral treatments can be ineffective or lead to adverse effects. As a result, there is a need for new anti-HSV drugs. In this report, the in vitro anti-HSV effect of 9,9'-norharmane dimer (nHo-dimer), which belongs to the β-carboline (βC) alkaloid family, was evaluated. The dimer exhibited no virucidal properties and did not impede either the attachment or penetration steps of viral particles. The antiviral effect was only exerted under the constant presence of the dimer in the incubation media, and the mechanism of action was found to involve later events of virus infection. Analysis of fluorescence lifetime imaging data showed that the nHo-dimer internalized well into the cells when present in the extracellular incubation medium, with a preferential accumulation into perinuclear organelles including mitochondria. After washing the host cells with fresh medium free of nHo-dimer, the signal decreased, suggesting the partial release of the compound from the cells. This agrees with the observation that the antiviral effect is solely manifested when the alkaloid is consistently present in the incubation media.
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Affiliation(s)
- María Micaela Gonzalez
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, CC 164 (B7130IWA), Chascomús 7130, Argentina;
- Escuela de Bio y Nanotecnologías (UNSAM), San Martín 1650, Argentina
| | - Maria Guadalupe Vizoso-Pinto
- Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU, D-80336 Munich, Germany;
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán 4000, Argentina
- Laboratorio Central de Cs. Básicas, Facultad de Medicina, Universidad Nacional de Tucumán, Tucumán 4000, Argentina
| | - Rosa Erra-Balsells
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II, 3er P., Ciudad Universitaria, Buenos Aires 1428, Argentina;
- Centro de Investigación en Hidratos de Carbono (CIHIDECAR), CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Naturales Pabellón II, 3er P. Ciudad Universitaria, Buenos Aires 1428, Argentina
| | - Thomas Gensch
- Institute of Biological Information Processing 1 (IBI-1; Molecular and Cellular Physiology), Forschungszentrum Jülich, Wilhelm-Jonen-Straße, 52428 Jülich, Germany
| | - Franco M. Cabrerizo
- Instituto Tecnológico de Chascomús (CONICET-UNSAM), Av. Intendente Marino Km 8.2, CC 164 (B7130IWA), Chascomús 7130, Argentina;
- Escuela de Bio y Nanotecnologías (UNSAM), San Martín 1650, Argentina
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3
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Banerjee S, Gadpayle MP, Samanta S, Dutta P, Das S, Datta R, Maiti S. Role of Macrophage PIST Protein in Regulating Leishmania major Infection. ACS Infect Dis 2024; 10:1414-1428. [PMID: 38556987 DOI: 10.1021/acsinfecdis.4c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PDZ protein interacting specifically with Tc10 or PIST is a mammalian trans-Golgi resident protein that regulates subcellular sorting of plasma membrane receptors. PIST has recently emerged as a key player in regulating viral pathogenesis. Nevertheless, the involvement of PIST in parasitic infections remains unexplored. Leishmania parasites infiltrate their host macrophage cells through phagocytosis, where they subsequently multiply within the parasitophorous vacuole (PV). Host cell autophagy has been found to be important in regulating this parasite infection. Since PIST plays a pivotal role in triggering autophagy through the Beclin 1-PI3KC3 pathway, it becomes interesting to identify the status of PIST during Leishmania infection. We found that while macrophage cells are infected with Leishmania major (L. major), the expression of PIST protein remains unaltered; however, it traffics from the Golgi compartment to PV. Further, we identified that in L. major-infected macrophage cells, PIST associates with the autophagy regulatory protein Beclin 1 within the PVs; however, PIST does not interact with LC3. Reduction in PIST protein through siRNA silencing significantly increased parasite burden, whereas overexpression of PIST in macrophages restricted L. major infectivity. Together, our study reports that the macrophage PIST protein is essential in regulating L. major infectivity.
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Affiliation(s)
- Sourav Banerjee
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Mandip Pratham Gadpayle
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Suman Samanta
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Priyanka Dutta
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Swagata Das
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Rupak Datta
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Sankar Maiti
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
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4
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Hunter LM, Kite J, Fletcher-Etherington A, Nightingale K, Nobre L, Antrobus R, Fielding CA, Stanton RJ, Weekes MP. HCMV US2 co-opts TRC8 to degrade the endoplasmic reticulum-resident protein LMAN2L. J Gen Virol 2024; 105:001980. [PMID: 38687323 PMCID: PMC11083459 DOI: 10.1099/jgv.0.001980] [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: 02/06/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
The human cytomegalovirus (HCMV) pUS2 glycoprotein exploits the host's endoplasmic reticulum (ER)-associated degradation (ERAD) pathway to degrade major histocompatibility complex class I (MHC-I) and prevent antigen presentation. Beyond MHC-I, pUS2 has been shown to target a range of cellular proteins for degradation, preventing their cell surface expression. Here we have identified a novel pUS2 target, ER-resident protein lectin mannose binding 2 like (LMAN2L). pUS2 expression was both necessary and sufficient for the downregulation of LMAN2L, which was dependent on the cellular E3 ligase TRC8. Given the hypothesized role of LMAN2L in the trafficking of glycoproteins, we employed proteomic plasma membrane profiling to measure LMAN2L-dependent changes at the cell surface. A known pUS2 target, integrin alpha-6 (ITGA6), was downregulated from the surface of LMAN2L-deficient cells, but not other integrins. Overall, these results suggest a novel strategy of pUS2-mediated protein degradation whereby pUS2 targets LMAN2L to impair trafficking of ITGA6. Given that pUS2 can directly target other integrins, we propose that this single viral protein may exhibit both direct and indirect mechanisms to downregulate key cell surface molecules.
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Affiliation(s)
- Leah M. Hunter
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Hills Road, Cambridge, CB2 2QQ, UK
| | - Joanne Kite
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Hills Road, Cambridge, CB2 2QQ, UK
| | - Alice Fletcher-Etherington
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Hills Road, Cambridge, CB2 2QQ, UK
| | - Katie Nightingale
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Hills Road, Cambridge, CB2 2QQ, UK
| | - Luis Nobre
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Hills Road, Cambridge, CB2 2QQ, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Hills Road, Cambridge, CB2 2QQ, UK
| | - Ceri A. Fielding
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Richard J. Stanton
- Cardiff University School of Medicine, Division of Infection and Immunity, Henry Wellcome Building, Heath Park, Cardiff CF14 4XN, UK
| | - Michael P. Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
- Department of Medicine, University of Cambridge, Hills Road, Cambridge, CB2 2QQ, UK
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5
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Song MS, Lee DK, Lee CY, Park SC, Yang J. Host Subcellular Organelles: Targets of Viral Manipulation. Int J Mol Sci 2024; 25:1638. [PMID: 38338917 PMCID: PMC10855258 DOI: 10.3390/ijms25031638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Viruses have evolved sophisticated mechanisms to manipulate host cell processes and utilize intracellular organelles to facilitate their replication. These complex interactions between viruses and cellular organelles allow them to hijack the cellular machinery and impair homeostasis. Moreover, viral infection alters the cell membrane's structure and composition and induces vesicle formation to facilitate intracellular trafficking of viral components. However, the research focus has predominantly been on the immune response elicited by viruses, often overlooking the significant alterations that viruses induce in cellular organelles. Gaining a deeper understanding of these virus-induced cellular changes is crucial for elucidating the full life cycle of viruses and developing potent antiviral therapies. Exploring virus-induced cellular changes could substantially improve our understanding of viral infection mechanisms.
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Affiliation(s)
- Min Seok Song
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Dong-Kun Lee
- Department of Physiology and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
| | - Chung-Young Lee
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Sang-Cheol Park
- Artificial Intelligence and Robotics Laboratory, Myongji Hospital, Goyang 10475, Republic of Korea
| | - Jinsung Yang
- Department of Biochemistry and Convergence Medical Science, Institute of Medical Science, College of Medicine, Gyeongsang National University, Jinju 52727, Republic of Korea
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6
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Albarnaz JD, Kite J, Oliveira M, Li H, Di Y, Christensen MH, Paulo JA, Antrobus R, Gygi SP, Schmidt FI, Huttlin EL, Smith GL, Weekes MP. Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection. Nat Commun 2023; 14:8134. [PMID: 38065956 PMCID: PMC10709566 DOI: 10.1038/s41467-023-43299-8] [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: 12/21/2022] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
Modified vaccinia Ankara (MVA) virus does not replicate in human cells and is the vaccine deployed to curb the current outbreak of mpox. Here, we conduct a multiplexed proteomic analysis to quantify >9000 cellular and ~80% of viral proteins throughout MVA infection of human fibroblasts and macrophages. >690 human proteins are down-regulated >2-fold by MVA, revealing a substantial remodelling of the host proteome. >25% of these MVA targets are not shared with replication-competent vaccinia. Viral intermediate/late gene expression is necessary for MVA antagonism of innate immunity, and suppression of interferon effectors such as ISG20 potentiates virus gene expression. Proteomic changes specific to infection of macrophages indicate modulation of the inflammatory response, including inflammasome activation. Our approach thus provides a global view of the impact of MVA on the human proteome and identifies mechanisms that may underpin its abortive infection. These discoveries will prove vital to design future generations of vaccines.
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Affiliation(s)
- Jonas D Albarnaz
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK.
| | - Joanne Kite
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Marisa Oliveira
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Hanqi Li
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Ying Di
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Florian I Schmidt
- Institute of Innate Immunity, University of Bonn, 53127, Bonn, Germany
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA
| | - Geoffrey L Smith
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
- Department of Medicine, University of Cambridge, Cambridge, CB2 0XY, UK.
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7
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Albarnaz JD, Weekes MP. Proteomic analysis of antiviral innate immunity. Curr Opin Virol 2023; 58:101291. [PMID: 36529073 DOI: 10.1016/j.coviro.2022.101291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/03/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022]
Abstract
The capacity of host cells to detect and restrict an infecting virus rests on an array of cell-autonomous antiviral effectors and innate immune receptors that can trigger inflammatory processes at tissue and organismal levels. Dynamic changes in protein abundance, subcellular localisation, post-translational modifications and interactions with other biomolecules govern these processes. Proteomics is therefore an ideal experimental tool to discover novel mechanisms of host antiviral immunity. Additional information can be gleaned both about host and virus by systematic analysis of viral immune evasion strategies. In this review, we summarise recent advances in proteomic technologies and their application to antiviral innate immunity.
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Affiliation(s)
- Jonas D Albarnaz
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB2 0XY Cambridge, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB2 0XY Cambridge, UK.
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8
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Dremel SE, Jimenez AR, Tucker JM. "Transfer" of power: The intersection of DNA virus infection and tRNA biology. Semin Cell Dev Biol 2023; 146:31-39. [PMID: 36682929 PMCID: PMC10101907 DOI: 10.1016/j.semcdb.2023.01.011] [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: 12/01/2022] [Revised: 01/17/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023]
Abstract
Transfer RNAs (tRNAs) are at the heart of the molecular biology central dogma, functioning to decode messenger RNAs into proteins. As obligate intracellular parasites, viruses depend on the host translation machinery, including host tRNAs. Thus, the ability of a virus to fine-tune tRNA expression elicits the power to impact the outcome of infection. DNA viruses commonly upregulate the output of RNA polymerase III (Pol III)-dependent transcripts, including tRNAs. Decades after these initial discoveries we know very little about how mature tRNA pools change during viral infection, as tRNA sequencing methodology has only recently reached proficiency. Here, we review perturbation of tRNA biogenesis by DNA virus infection, including an emerging player called tRNA-derived fragments (tRFs). We discuss how tRNA dysregulation shifts the power landscape between the host and virus, highlighting the potential for tRNA-based antivirals as a future therapeutic.
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Affiliation(s)
- Sarah E Dremel
- HIV and AIDS Malignancy Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ariana R Jimenez
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, USA
| | - Jessica M Tucker
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
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9
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Mohnke J, Stark I, Fischer M, Fischer PM, Schlosser A, Grothey A, O’Hare P, Sodeik B, Erhard F, Dölken L, Hennig T. pUL36 Deubiquitinase Activity Augments Both the Initiation and the Progression of Lytic Herpes Simplex Virus Infection in IFN-Primed Cells. J Virol 2022; 96:e0096322. [PMID: 36314822 PMCID: PMC9683058 DOI: 10.1128/jvi.00963-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/15/2022] [Indexed: 11/24/2022] Open
Abstract
The evolutionarily conserved, structural HSV-1 tegument protein pUL36 is essential for both virus entry and assembly. While its N-terminal deubiquitinase (DUB) activity is dispensable for infection in cell culture, it is required for efficient virus spread in vivo, as it acts as a potent viral immune evasin. Interferon (IFN) induces the expression of hundreds of antiviral factors, including many ubiquitin modulators, which HSV-1 needs to neutralize to efficiently initiate a productive infection. Herein, we discover two functions of the conserved pUL36 DUB during lytic replication in cell culture in an understudied but equally important scenario of HSV-1 infection in IFN-treated cells. Our data indicate that the pUL36 DUB contributes to overcoming the IFN-mediated suppression of productive infection in both the early and late phases of HSV-1 infection. We show that incoming tegument-derived pUL36 DUB activity contributes to the IFN resistance of HSV-1 in IFN-primed cells to efficiently initiate lytic virus replication. Subsequently, the de novo expressed DUB augmented the efficiency of virus replication and increased the output of infectious virus. Notably, the DUB defect was only apparent when IFN was applied prior to infection. Our data indicate that IFN-induced defense mechanisms exist and that they work to both neutralize infectivity early on and slow the progression of HSV-1 replication in the late stages of infection. Also, our data indicate that pUL36 DUB activity contributes to the disarming of these host responses. IMPORTANCE HSV-1 is a ubiquitous human pathogen that is responsible for common cold sores and may also cause life-threatening disease. pUL36 is an essential, conserved herpesvirus protein with N-terminal deubiquitinating (DUB) activity. The DUB is dispensable for HSV-1 replication in cell culture but represents an important viral immune evasin in vivo. IFN plays a pivotal role in HSV-1 infection and suppresses viral replication both in vitro and in vivo. Here, we show that DUB activity contributes to overcoming IFN-induced cellular resistance in order to more efficiently initiate lytic replication and produce infectious virions. As such, DUB activity in the incoming virions increases their infectivity, while the de novo synthesized DUB augments productive infection. Thus, the HSV-1 DUB antagonizes the activity of IFN-inducible effector proteins to facilitate productive infection at multiple levels. Our findings underscore the importance of using more challenging cell culture systems to fully understand virus protein functions.
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Affiliation(s)
- Jonas Mohnke
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Irmgard Stark
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Mara Fischer
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Patrick M. Fischer
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Arnhild Grothey
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Peter O’Hare
- Department of Virology, Imperial College London, Norfolk Place, London, United Kingdom
| | - Beate Sodeik
- Institut für Virologie, Medizinische Hochschule Hannover, Hannover, Germany
- RESIST Exzellenzcluster, Medizinische Hochschule Hannover, Hannover, Germany
| | - Florian Erhard
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Thomas Hennig
- Institut für Virologie und Immunbiologie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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10
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Benedyk TH, Connor V, Caroe ER, Shamin M, Svergun DI, Deane JE, Jeffries CM, Crump CM, Graham SC. Herpes simplex virus 1 protein pUL21 alters ceramide metabolism by activating the interorganelle transport protein CERT. J Biol Chem 2022; 298:102589. [PMID: 36243114 PMCID: PMC9668737 DOI: 10.1016/j.jbc.2022.102589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
Herpes simplex virus (HSV)-1 dramatically alters the architecture and protein composition of cellular membranes during infection, but its effects upon membrane lipid composition remain unclear. HSV-1 pUL21 is a virus-encoded protein phosphatase adaptor that promotes dephosphorylation of multiple cellular and virus proteins, including the cellular ceramide (Cer) transport protein CERT. CERT mediates nonvesicular Cer transport from the endoplasmic reticulum to the trans-Golgi network, whereupon Cer is converted to sphingomyelin (SM) and other sphingolipids that play important roles in cellular proliferation, signaling, and membrane trafficking. Here, we use click chemistry to profile the kinetics of sphingolipid metabolism, showing that pUL21-mediated dephosphorylation activates CERT and accelerates Cer-to-SM conversion. Purified pUL21 and full-length CERT interact with submicromolar affinity, and we solve the solution structure of the pUL21 C-terminal domain in complex with the CERT Pleckstrin homology and steroidogenic acute regulatory-related lipid transfer domains using small-angle X-ray scattering. We identify a single amino acid mutation on the surface of pUL21 that disrupts CERT binding in vitro and in cultured cells. This residue is highly conserved across the genus Simplexvirus. In addition, we identify a pUL21 residue essential for binding to HSV-1 pUL16. Sphingolipid profiling demonstrates that Cer-to-SM conversion is severely diminished in the context of HSV-1 infection, a defect that is compounded when infecting with a virus encoding the mutated form of pUL21 that lacks the ability to activate CERT. However, virus replication and spread in cultured keratinocytes or epithelial cells is not significantly altered when pUL21-mediated CERT dephosphorylation is abolished. Collectively, we demonstrate that HSV-1 modifies sphingolipid metabolism via specific protein-protein interactions.
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Affiliation(s)
| | - Viv Connor
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Eve R Caroe
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Maria Shamin
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Site, Hamburg, Germany
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Site, Hamburg, Germany
| | - Colin M Crump
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Stephen C Graham
- Department of Pathology, University of Cambridge, Cambridge, UK.
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11
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Fielding CA, Sabberwal P, Williamson JC, Greenwood EJD, Crozier TWM, Zelek W, Seow J, Graham C, Huettner I, Edgeworth JD, Price DA, Morgan PB, Ladell K, Eberl M, Humphreys IR, Merrick B, Doores K, Wilson SJ, Lehner PJ, Wang ECY, Stanton RJ. SARS-CoV-2 host-shutoff impacts innate NK cell functions, but antibody-dependent NK activity is strongly activated through non-spike antibodies. eLife 2022; 11:e74489. [PMID: 35587364 PMCID: PMC9239683 DOI: 10.7554/elife.74489] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
The outcome of infection is dependent on the ability of viruses to manipulate the infected cell to evade immunity, and the ability of the immune response to overcome this evasion. Understanding this process is key to understanding pathogenesis, genetic risk factors, and both natural and vaccine-induced immunity. SARS-CoV-2 antagonises the innate interferon response, but whether it manipulates innate cellular immunity is unclear. An unbiased proteomic analysis determined how cell surface protein expression is altered on SARS-CoV-2-infected lung epithelial cells, showing downregulation of activating NK ligands B7-H6, MICA, ULBP2, and Nectin1, with minimal effects on MHC-I. This occurred at the level of protein synthesis, could be mediated by Nsp1 and Nsp14, and correlated with a reduction in NK cell activation. This identifies a novel mechanism by which SARS-CoV-2 host-shutoff antagonises innate immunity. Later in the disease process, strong antibody-dependent NK cell activation (ADNKA) developed. These responses were sustained for at least 6 months in most patients, and led to high levels of pro-inflammatory cytokine production. Depletion of spike-specific antibodies confirmed their dominant role in neutralisation, but these antibodies played only a minor role in ADNKA compared to antibodies to other proteins, including ORF3a, Membrane, and Nucleocapsid. In contrast, ADNKA induced following vaccination was focussed solely on spike, was weaker than ADNKA following natural infection, and was not boosted by the second dose. These insights have important implications for understanding disease progression, vaccine efficacy, and vaccine design.
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Affiliation(s)
- Ceri Alan Fielding
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Pragati Sabberwal
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - James C Williamson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Edward JD Greenwood
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Thomas WM Crozier
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Wioleta Zelek
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Jeffrey Seow
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Carl Graham
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Isabella Huettner
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Jonathan D Edgeworth
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation TrustLondonUnited Kingdom
| | - David A Price
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Paul B Morgan
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Matthias Eberl
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Ian R Humphreys
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Blair Merrick
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
- Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation TrustLondonUnited Kingdom
| | - Katie Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College LondonLondonUnited Kingdom
| | - Sam J Wilson
- MRC - University of Glasgow Centre for Virus ResearchGlasgowUnited Kingdom
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of CambridgeCambridgeUnited Kingdom
| | - Eddie CY Wang
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
| | - Richard J Stanton
- Division of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUnited Kingdom
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12
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Kennedy MA, Tyl MD, Betsinger CN, Federspiel JD, Sheng X, Arbuckle JH, Kristie TM, Cristea IM. A TRUSTED targeted mass spectrometry assay for pan-herpesvirus protein detection. Cell Rep 2022; 39:110810. [PMID: 35545036 PMCID: PMC9245836 DOI: 10.1016/j.celrep.2022.110810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 02/11/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022] Open
Abstract
The presence and abundance of viral proteins within host cells are part of the essential signatures of the cellular stages of viral infections. However, methods that can comprehensively detect and quantify these proteins are still limited, particularly for viruses with large protein coding capacity. Here, we design and experimentally validate a mass spectrometry-based Targeted herpesviRUS proTEin Detection (TRUSTED) assay for monitoring human viruses representing the three Herpesviridae subfamilies—herpes simplex virus type 1, human cytomegalovirus (HCMV), and Kaposi sarcoma-associated herpesvirus. We demonstrate assay applicability for (1) capturing the temporal cascades of viral replication, (2) detecting proteins throughout a range of virus concentrations and in in vivo models of infection, (3) assessing the effects of clinical therapeutic agents and sirtuin-modulating compounds, (4) studies using different laboratory and clinical viral strains, and (5) discovering a role for carbamoyl phosphate synthetase 1 in supporting HCMV replication. Herpesviruses encode many proteins, making it difficult to comprehensively monitor viral protein levels by traditional approaches. Kennedy et al. develop a set of targeted mass spectrometry-based assays for measuring herpesvirus protein levels spanning all virus subfamilies (α, β, and γ) and demonstrate their usefulness for a wide range of applications.
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Affiliation(s)
- Michelle A Kennedy
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Matthew D Tyl
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Cora N Betsinger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Joel D Federspiel
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Jesse H Arbuckle
- Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas M Kristie
- Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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13
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Abstract
Herpesviruses assemble new viral particles in the nucleus. These nucleocapsids bud through the inner nuclear membrane to produce enveloped viral particles in the perinuclear space before fusing with the outer nuclear membrane to reach the cytoplasm. This unusual route is necessary since viral capsids are too large to pass through nuclear pores. However, the transient perinuclear nucleocapsids (250 nm in diameter) are also larger than the width of the perinuclear space (30 to 50 nm). Interestingly, linker of the nucleoskeleton and cytoskeleton (LINC) components SUN and KASH connect the inner and outer nuclear membranes and regulate their spacing. Previous work by others on the related pseudorabies virus and human cytomegalovirus showed that they functionally interact with SUN proteins. To clarify the role of SUN proteins, we explored their impact on herpes simplex virus 1 (HSV-1), another herpesvirus. Using dominant negative SUN mutants and RNA interference, we show that HSV-1 propagation is dependent on the LINC complex. In contrast to pseudorabies virus, SUN2 disruption by either approach led to increased HSV-1 extracellular viral yields. This SUN2 dependency may be linked to its greater impact on perinuclear spacing in infected cells compared to SUN1. Finally, the virus itself seems to modulate perinuclear spacing. IMPORTANCE The large size of herpesviruses prevents them from travelling across the nuclear pores, and they instead egress across the two nuclear membranes, generating short-lived enveloped perinuclear virions. This poses a challenge as the perinuclear space is smaller than the virions. This implies the separation (unzipping) of the two nuclear membranes to accommodate the viral particles. The LINC complex bridges the two nuclear membranes and is an important regulator of perinuclear spacing. Work by others hint at its functional implication during pseudorabies virus and cytomegalovirus propagation. The present study probes the importance for HSV-1 of the SUN proteins, the LINC components found in the inner nuclear membrane. Using dominant negative constructs and RNA interference (RNAi), the data reveal that SUN2 exhibits antiviral propriety toward HSV-1, as disrupting the protein leads to increased viral yields. This is in contrast with that reported for pseudorabies and suggests that differences among herpesviruses may, once again, prevail.
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14
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Zheng ZQ, Fu YZ, Wang SY, Xu ZS, Zou HM, Wang YY. Herpes simplex virus protein UL56 inhibits cGAS-Mediated DNA sensing to evade antiviral immunity. CELL INSIGHT 2022; 1:100014. [PMID: 37193132 PMCID: PMC10120305 DOI: 10.1016/j.cellin.2022.100014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 05/18/2023]
Abstract
After herpes simplex virus type 1 (HSV-1) infection, the cytosolic sensor cyclic GMP-AMP synthase (cGAS) recognizes DNA and catalyzes synthesis of the second messenger 2'3'-cGAMP. cGAMP binds to the ER-localized adaptor protein MITA (also known as STING) to activate downstream antiviral responses. Conversely, HSV-1-encoded proteins evade antiviral immune responses via a wide variety of delicate mechanisms, promoting viral replication and pathogenesis. Here, we identified HSV-1 envelop protein UL56 as a negative regulator of cGAS-mediated innate immune responses. Overexpression of UL56 inhibited double-stranded DNA-triggered antiviral responses, whereas UL56-deficiency increased HSV-1-triggered induction of downstream antiviral genes. UL56-deficiency inhibited HSV-1 replication in wild-type but not MITA-deficient cells. UL56-deficient HSV-1 showed reduced replication in the brain of infected mice and was less lethal to infected mice. Mechanistically, UL56 interacted with cGAS and inhibited its DNA binding and enzymatic activity. Furthermore, we found that UL56 homologous proteins from different herpesviruses had similar roles in antagonizing cGAS-mediated innate immune responses. Our findings suggest that UL56 is a component of HSV-1 evasion of host innate immune responses by antagonizing the DNA sensor cGAS, which contributes to our understanding of the comprehensive mechanisms of immune evasion by herpesviruses.
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Affiliation(s)
- Zhou-Qin Zheng
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Zhi Fu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Su-Yun Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Zhi-Sheng Xu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hong-Mei Zou
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan-Yi Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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15
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Phan QV, Bogdanow B, Wyler E, Landthaler M, Liu F, Hagemeier C, Wiebusch L. Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus. PLoS Pathog 2022; 18:e1010193. [PMID: 34982803 PMCID: PMC8759705 DOI: 10.1371/journal.ppat.1010193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/14/2022] [Accepted: 12/09/2021] [Indexed: 11/19/2022] Open
Abstract
The chimpanzee cytomegalovirus (CCMV) is the closest relative of human CMV (HCMV). Because of the high conservation between these two species and the ability of human cells to fully support CCMV replication, CCMV holds great potential as a model system for HCMV. To make the CCMV genome available for precise and rapid gene manipulation techniques, we captured the genomic DNA of CCMV strain Heberling as a bacterial artificial chromosome (BAC). Selected BAC clones were reconstituted to infectious viruses, growing to similar high titers as parental CCMV. DNA sequencing confirmed the integrity of our clones and led to the identification of two polymorphic loci and a deletion-prone region within the CCMV genome. To re-evaluate the CCMV coding potential, we analyzed the viral transcriptome and proteome and identified several novel ORFs, splice variants, and regulatory RNAs. We further characterized the dynamics of CCMV gene expression and found that viral proteins cluster into five distinct temporal classes. In addition, our datasets revealed that the host response to CCMV infection and the de-regulation of cellular pathways are in line with known hallmarks of HCMV infection. In a first functional experiment, we investigated a proposed frameshift mutation in UL128 that was suspected to restrict CCMV's cell tropism. In fact, repair of this frameshift re-established productive CCMV infection in endothelial and epithelial cells, expanding the options of CCMV as an infection model. Thus, BAC-cloned CCMV can serve as a powerful tool for systematic approaches in comparative functional genomics, exploiting the close phylogenetic relationship between CCMV and HCMV.
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Affiliation(s)
- Quang Vinh Phan
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Boris Bogdanow
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Christian Hagemeier
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Lüder Wiebusch
- Department of Pediatric Oncology/Hematology, Charité—Universitätsmedizin Berlin, Berlin, Germany
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16
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Braspenning SE, Verjans GMGM, Mehraban T, Messaoudi I, Depledge DP, Ouwendijk WJD. The architecture of the simian varicella virus transcriptome. PLoS Pathog 2021; 17:e1010084. [PMID: 34807956 PMCID: PMC8648126 DOI: 10.1371/journal.ppat.1010084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/06/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Primary infection with varicella-zoster virus (VZV) causes varicella and the establishment of lifelong latency in sensory ganglion neurons. In one-third of infected individuals VZV reactivates from latency to cause herpes zoster, often complicated by difficult-to-treat chronic pain. Experimental infection of non-human primates with simian varicella virus (SVV) recapitulates most features of human VZV disease, thereby providing the opportunity to study the pathogenesis of varicella and herpes zoster in vivo. However, compared to VZV, the transcriptome and the full coding potential of SVV remains incompletely understood. Here, we performed nanopore direct RNA sequencing to annotate the SVV transcriptome in lytically SVV-infected African green monkey (AGM) and rhesus macaque (RM) kidney epithelial cells. We refined structures of canonical SVV transcripts and uncovered numerous RNA isoforms, splicing events, fusion transcripts and non-coding RNAs, mostly unique to SVV. We verified the expression of canonical and newly identified SVV transcripts in vivo, using lung samples from acutely SVV-infected cynomolgus macaques. Expression of selected transcript isoforms, including those located in the unique left-end of the SVV genome, was confirmed by reverse transcription PCR. Finally, we performed detailed characterization of the SVV homologue of the VZV latency-associated transcript (VLT), located antisense to ORF61. Analogous to VZV VLT, SVV VLT is multiply spliced and numerous isoforms are generated using alternative transcription start sites and extensive splicing. Conversely, low level expression of a single spliced SVV VLT isoform defines in vivo latency. Notably, the genomic location of VLT core exons is highly conserved between SVV and VZV. This work thus highlights the complexity of lytic SVV gene expression and provides new insights into the molecular biology underlying lytic and latent SVV infection. The identification of the SVV VLT homolog further underlines the value of the SVV non-human primate model to develop new strategies for prevention of herpes zoster. Varicella-zoster virus (VZV)–a ubiquitous human pathogen–infects most individuals during childhood, leading to chickenpox, after which the virus persists in the host for decades. Later in life, VZV reactivates to cause shingles, frequently associated with difficult-to-treat chronic pain. Our limited understanding of the viral life-cycle hampers the development of more effective treatment options. Simian varicella virus (SVV) is the non-human primate homologue of VZV and causes a natural disease in Old World monkeys with clinical, pathological, and immunological features resembling human VZV infection. However, it is unclear how similar both viruses are at the molecular level. Here, we have revisited the genome-wide transcriptional activity of SVV during lytic infection of kidney epithelial cells derived from two non-human primate species and validated expression of newly identified viral transcripts in lung tissue from SVV-infected animals. Together, this has led to the identification of numerous alternative RNA isoforms, mostly unique to SVV, and some of which may have functional implications for the virus. Notably, we defined the SVV latency-associated transcript, which is highly similar to its VZV counterpart. In conclusion, our study shows the value of understanding the molecular biology of a given animal model and identifies potentially conserved mechanism of latency.
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Affiliation(s)
| | | | - Tamana Mehraban
- Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York, United States of America
- Institute of Virology, Hannover Medical School, Hannover, Germany
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17
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Benedyk TH, Muenzner J, Connor V, Han Y, Brown K, Wijesinghe KJ, Zhuang Y, Colaco S, Stoll GA, Tutt OS, Svobodova S, Svergun DI, Bryant NA, Deane JE, Firth AE, Jeffries CM, Crump CM, Graham SC. pUL21 is a viral phosphatase adaptor that promotes herpes simplex virus replication and spread. PLoS Pathog 2021; 17:e1009824. [PMID: 34398933 PMCID: PMC8389370 DOI: 10.1371/journal.ppat.1009824] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/26/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022] Open
Abstract
The herpes simplex virus (HSV)-1 protein pUL21 is essential for efficient virus replication and dissemination. While pUL21 has been shown to promote multiple steps of virus assembly and spread, the molecular basis of its function remained unclear. Here we identify that pUL21 is a virus-encoded adaptor of protein phosphatase 1 (PP1). pUL21 directs the dephosphorylation of cellular and virus proteins, including components of the viral nuclear egress complex, and we define a conserved non-canonical linear motif in pUL21 that is essential for PP1 recruitment. In vitro evolution experiments reveal that pUL21 antagonises the activity of the virus-encoded kinase pUS3, with growth and spread of pUL21 PP1-binding mutant viruses being restored in adapted strains where pUS3 activity is disrupted. This study shows that virus-directed phosphatase activity is essential for efficient herpesvirus assembly and spread, highlighting the fine balance between kinase and phosphatase activity required for optimal virus replication. Herpes simplex virus (HSV)-1 is a highly prevalent human virus that causes life-long infections. While the most common symptom of HSV-1 infection is orofacial lesions (‘cold sores’), HSV-1 infection can also cause fatal encephalitis and it is a leading cause of infectious blindness. The HSV-1 genome encodes many proteins that dramatically remodel the environment of infected cells to promote virus replication and spread, including enzymes that add phosphate groups (kinases) to cellular and viral proteins in order to fine-tune their function. Here we identify that pUL21 is an HSV-1 protein that binds directly to protein phosphatase 1 (PP1), a highly abundant cellular enzyme that removes phosphate groups from proteins. We demonstrate that pUL21 stimulates the specific dephosphorylation of both cellular and viral proteins, including a component of the viral nuclear egress complex that is essential for efficient assembly of new HSV-1 particles. Furthermore, our in vitro evolution experiments demonstrate that pUL21 antagonises the activity of the HSV-1 kinase pUS3. Our work highlights the precise control that herpesviruses exert upon the protein environment within infected cells, and specifically the careful balance of kinase and phosphatase activity that HSV-1 requires for optimal replication and spread.
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Affiliation(s)
- Tomasz H. Benedyk
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Julia Muenzner
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Viv Connor
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Yue Han
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Yunhui Zhuang
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Susanna Colaco
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Guido A. Stoll
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Owen S. Tutt
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Site, Hamburg, Germany
| | - Neil A. Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Janet E. Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Andrew E. Firth
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Site, Hamburg, Germany
| | - Colin M. Crump
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CMC); (SCG)
| | - Stephen C. Graham
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CMC); (SCG)
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18
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Abstract
The abundance, localization, modifications, and protein-protein interactions of many host cell and virus proteins can change dynamically throughout the course of any viral infection. Studying these changes is critical for a comprehensive understanding of how viruses replicate and cause disease, as well as for the development of antiviral therapeutics and vaccines. Previously, we developed a mass spectrometry-based technique called quantitative temporal viromics (QTV), which employs isobaric tandem mass tags (TMTs) to allow precise comparative quantification of host and virus proteomes through a whole time course of infection. In this review, we discuss the utility and applications of QTV, exemplified by numerous studies that have since used proteomics with a variety of quantitative techniques to study virus infection through time. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, United Kingdom;
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19
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Abstract
The cellular surfaceome and its residing extracellularly exposed proteins are involved in a multitude of molecular signaling processes across the viral infection cycle. Successful viral propagation, including viral entry, immune evasion, virion release and viral spread rely on dynamic molecular interactions with the surfaceome. Decoding of these viral-host surfaceome interactions using advanced technologies enabled the discovery of fundamental new functional insights into cellular and viral biology. In this review, we highlight recently developed experimental strategies, with a focus on spatial proteotyping technologies, aiding in the rational design of theranostic strategies to combat viral infections.
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20
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Scherer KM, Manton JD, Soh TK, Mascheroni L, Connor V, Crump CM, Kaminski CF. A fluorescent reporter system enables spatiotemporal analysis of host cell modification during herpes simplex virus-1 replication. J Biol Chem 2021; 296:100236. [PMID: 33380421 PMCID: PMC7948757 DOI: 10.1074/jbc.ra120.016571] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 01/12/2023] Open
Abstract
Herpesviruses are large and complex viruses that have a long history of coevolution with their host species. One important factor in the virus-host interaction is the alteration of intracellular morphology during viral replication with critical implications for viral assembly. However, the details of this remodeling event are not well understood, in part because insufficient tools are available to deconstruct this highly heterogeneous process. To provide an accurate and reliable method of investigating the spatiotemporal dynamics of virus-induced changes to cellular architecture, we constructed a dual-fluorescent reporter virus that enabled us to classify four distinct stages in the infection cycle of herpes simplex virus-1 at the single cell level. This timestamping method can accurately track the infection cycle across a wide range of multiplicities of infection. We used high-resolution fluorescence microscopy analysis of cellular structures in live and fixed cells in concert with our reporter virus to generate a detailed and chronological overview of the spatial and temporal reorganization during viral replication. The highly orchestrated and striking relocation of many organelles around the compartments of secondary envelopment during transition from early to late gene expression suggests that the reshaping of these compartments is essential for virus assembly. We furthermore find that accumulation of HSV-1 capsids in the cytoplasm is accompanied by fragmentation of the Golgi apparatus with potential impact on the late steps of viral assembly. We anticipate that in the future similar tools can be systematically applied for the systems-level analysis of intracellular morphology during replication of other viruses.
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Affiliation(s)
- Katharina M Scherer
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge, UK
| | - James D Manton
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge, UK; MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Timothy K Soh
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Luca Mascheroni
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge, UK
| | - Vivienne Connor
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Colin M Crump
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Clemens F Kaminski
- Department of Chemical Engineering & Biotechnology, University of Cambridge, Cambridge, UK.
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Howard TR, Cristea IM. Interrogating Host Antiviral Environments Driven by Nuclear DNA Sensing: A Multiomic Perspective. Biomolecules 2020; 10:biom10121591. [PMID: 33255247 PMCID: PMC7761228 DOI: 10.3390/biom10121591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/11/2022] Open
Abstract
Nuclear DNA sensors are critical components of the mammalian innate immune system, recognizing the presence of pathogens and initiating immune signaling. These proteins act in the nuclei of infected cells by binding to foreign DNA, such as the viral genomes of nuclear-replicating DNA viruses herpes simplex virus type 1 (HSV-1) and human cytomegalovirus (HCMV). Upon binding to pathogenic DNA, the nuclear DNA sensors were shown to initiate antiviral cytokines, as well as to suppress viral gene expression. These host defense responses involve complex signaling processes that, through protein–protein interactions (PPIs) and post-translational modifications (PTMs), drive extensive remodeling of the cellular transcriptome, proteome, and secretome to generate an antiviral environment. As such, a holistic understanding of these changes is required to understand the mechanisms through which nuclear DNA sensors act. The advent of omics techniques has revolutionized the speed and scale at which biological research is conducted and has been used to make great strides in uncovering the molecular underpinnings of DNA sensing. Here, we review the contribution of proteomics approaches to characterizing nuclear DNA sensors via the discovery of functional PPIs and PTMs, as well as proteome and secretome changes that define a host antiviral environment. We also highlight the value of and future need for integrative multiomic efforts to gain a systems-level understanding of DNA sensors and their influence on epigenetic and transcriptomic alterations during infection.
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Jansens RJJ, Marmiroli S, Favoreel HW. An Unbiased Approach to Mapping the Signaling Network of the Pseudorabies Virus US3 Protein. Pathogens 2020; 9:pathogens9110916. [PMID: 33167340 PMCID: PMC7694389 DOI: 10.3390/pathogens9110916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 01/18/2023] Open
Abstract
The US3 serine/threonine protein kinase is conserved among the alphaherpesvirus family and represents an important virulence factor. US3 plays a role in viral nuclear egress, induces dramatic alterations of the cytoskeleton, represses apoptosis, enhances gene expression and modulates the immune response. Although several substrates of US3 have been identified, an unbiased screen to identify US3 phosphorylation targets has not yet been described. Here, we perform a shotgun and phosphoproteomics analysis of cells expressing the US3 protein of pseudorabies virus (PRV) to identify US3 phosphorylation targets in an unbiased way. We identified several cellular proteins that are differentially phosphorylated upon US3 expression and validated the phosphorylation of lamin A/C at serine 404, both in US3-transfected and PRV-infected cells. These results provide new insights into the signaling network of the US3 protein kinase and may serve as a basis for future research into the role of the US3 protein in the viral replication cycle.
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Affiliation(s)
- Robert J. J. Jansens
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
| | - Sandra Marmiroli
- Cellular Signaling Laboratory, Department of Surgery, Medicine, Dentistry, and Morphology, University of Modena & Reggio Emilia, 41121 Modena, Italy;
| | - Herman W. Favoreel
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
- Correspondence:
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