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Martin MF, Bonaventure B, McCray NE, Peersen OB, Rozen-Gagnon K, Stapleford KA. Distinct chikungunya virus polymerase palm subdomains contribute to virus replication and virion assembly. bioRxiv 2024:2024.01.15.575630. [PMID: 38293111 PMCID: PMC10827052 DOI: 10.1101/2024.01.15.575630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Alphaviruses encode an error-prone RNA-dependent RNA polymerase (RdRp), nsP4, required for genome synthesis, yet how the RdRp functions in the complete alphavirus life cycle is not well-defined. Previous work using chikungunya virus (CHIKV) has established the importance of the nsP4 residue cysteine 483 in maintaining viral genetic fidelity. Given the location of residue C483 in the nsP4 palm domain, we hypothesized that other residues within this domain and surrounding subdomains would also contribute to polymerase function. To test this hypothesis, we designed a panel of nsP4 variants via homology modeling based on the Coxsackievirus B3 3 polymerase. We rescued each variant in both mammalian and mosquito cells and discovered that the palm domain and ring finger subdomain contribute to polymerase host-specific replication and genetic stability. Surprisingly, in mosquito cells, these variants in the ring finger and palm domain were replication competent and produced viral structural proteins, but they were unable to produce infectious progeny, indicating a yet uncharacterized role for the polymerase in viral assembly. Finally, we have identified additional residues in the nsP4 palm domain that influence the genetic diversity of the viral progeny, potentially via an alteration in NTP binding and/or discrimination by the polymerase. Taken together, these studies highlight that distinct nsP4 subdomains regulate multiple processes of the alphavirus life cycle, placing nsP4 in a central role during the switch from RNA synthesis to packaging and assembly.
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Affiliation(s)
- Marie-France Martin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nia E. McCray
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Olve B. Peersen
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Kenneth A. Stapleford
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
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2
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Higgins CA, Nilsson-Payant BE, Bonaventure B, Kurland AP, Ye C, Yaron TM, Johnson JL, Adhikary P, Golynker I, Panis M, Danziger O, Rosenberg BR, Cantley LC, Martínez-Sobrido L, tenOever B, Johnson JR. SARS-CoV-2 hijacks p38β/MAPK11 to promote virus replication. mBio 2023; 14:e0100723. [PMID: 37345956 PMCID: PMC10470746 DOI: 10.1128/mbio.01007-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19) pandemic, drastically modifies infected cells to optimize virus replication. One such modification is the activation of the host p38 mitogen-activated protein kinase (MAPK) pathway, which plays a major role in inflammatory cytokine production, a hallmark of severe COVID-19. We previously demonstrated that inhibition of p38/MAPK activity in SARS-CoV-2-infected cells reduced both cytokine production and viral replication. Here, we combined quantitative genetic screening, genomics, proteomics, and phosphoproteomics to better understand mechanisms underlying the dependence of SARS-CoV-2 on the p38 pathway. We found that p38β is a critical host factor for SARS-CoV-2 replication in multiple relevant cell lines and that it functions at a step after viral mRNA expression. We identified putative host and viral p38β substrates in the context of SARS-CoV-2 infection and found that most host substrates have intrinsic antiviral activities. Taken together, this study reveals a unique proviral function for p38β and supports exploring p38β inhibitor development as a strategy toward creating a new class of COVID-19 therapies. IMPORTANCE SARS-CoV-2 is the causative agent of the COVID-19 pandemic that has claimed millions of lives since its emergence in 2019. SARS-CoV-2 infection of human cells requires the activity of several cellular pathways for successful replication. One such pathway, the p38 MAPK pathway, is required for virus replication and disease pathogenesis. Here, we applied systems biology approaches to understand how MAPK pathways benefit SARS-CoV-2 replication to inform the development of novel COVID-19 drug therapies.
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Affiliation(s)
- Christina A Higgins
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Department of Microbiology, New York University Langone Health , New York, New York, USA
- Vilcek Graduate School for Biomedical Sciences, New York University Langone Health , New York, New York, USA
| | | | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute , San Antonio, Texas, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine Weill Cornell Medicine , New York, New York, USA
- Columbia University Vagelos College of Physicians and Surgeons , New York, New York, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Harvard Medical School , Boston, Massachusetts, USA
| | - Prithy Adhikary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Ilona Golynker
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Maryline Panis
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Oded Danziger
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Brad R Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine , New York, New York, USA
- Department of Cell Biology, Harvard Medical School , Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Harvard Medical School , Boston, Massachusetts, USA
| | | | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health , New York, New York, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai , New York, New York, USA
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3
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Kurland AP, Bonaventure B, Johnson JR. A Chemical Proteomics Approach to Discover Regulators of Innate Immune Signaling. Viruses 2023; 15:v15051112. [PMID: 37243198 DOI: 10.3390/v15051112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/26/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Innate immune pathways are tightly regulated to balance an appropriate response to infectious agents and tolerable levels of inflammation. Dysregulation of innate immune pathways can lead to severe autoinflammatory disorders or susceptibility to infections. Here, we aimed to identify kinases in common cellular pathways that regulate innate immune pathways by combining small-scale kinase inhibitor screening with quantitative proteomics. We found that inhibitors of kinases ATM, ATR, AMPK, and PLK1 reduced the induction of interferon-stimulated gene expression in response to innate immune pathway activation by poly(I:C) transfection. However, siRNA depletion of these kinases did not validate findings with kinase inhibitors, suggesting that off-target effects may explain their activities. We mapped the effects of kinase inhibitors to various stages in innate immune pathways. Determining the mechanisms by which kinase inhibitors antagonize these pathways may illuminate novel mechanisms of innate immune pathway control.
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Affiliation(s)
- Andrew P Kurland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Boris Bonaventure
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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4
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Bonaventure B, Goujon C. [The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses]. Med Sci (Paris) 2023; 39:322-325. [PMID: 37094262 DOI: 10.1051/medsci/2023039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Affiliation(s)
- Boris Bonaventure
- Institut de recherche en infectiologie de Montpellier, CNRS, université de Montpellier, Montpellier, France - Adresse actuelle : Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, États-Unis
| | - Caroline Goujon
- Institut de recherche en infectiologie de Montpellier, CNRS, université de Montpellier, Montpellier, France
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5
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Bonaventure B, Rebendenne A, Chaves Valadão AL, Arnaud‐Arnould M, Gracias S, Garcia de Gracia F, McKellar J, Labaronne E, Tauziet M, Vivet‐Boudou V, Bernard E, Briant L, Gros N, Djilli W, Courgnaud V, Parrinello H, Rialle S, Blaise M, Lacroix L, Lavigne M, Paillart J, Ricci EP, Schulz R, Jouvenet N, Moncorgé O, Goujon C. The
DEAD
box
RNA
helicase
DDX42
is an intrinsic inhibitor of positive‐strand
RNA
viruses. EMBO Rep 2022; 23:e54061. [PMID: 36161446 PMCID: PMC9638865 DOI: 10.15252/embr.202154061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/29/2022] Open
Abstract
Genome‐wide screens are powerful approaches to unravel regulators of viral infections. Here, a CRISPR screen identifies the RNA helicase DDX42 as an intrinsic antiviral inhibitor of HIV‐1. Depletion of endogenous DDX42 increases HIV‐1 DNA accumulation and infection in cell lines and primary cells. DDX42 overexpression inhibits HIV‐1 infection, whereas expression of a dominant‐negative mutant increases infection. Importantly, DDX42 also restricts LINE‐1 retrotransposition and infection with other retroviruses and positive‐strand RNA viruses, including CHIKV and SARS‐CoV‐2. However, DDX42 does not impact the replication of several negative‐strand RNA viruses, arguing against an unspecific effect on target cells, which is confirmed by RNA‐seq analysis. Proximity ligation assays show DDX42 in the vicinity of viral elements, and cross‐linking RNA immunoprecipitation confirms a specific interaction of DDX42 with RNAs from sensitive viruses. Moreover, recombinant DDX42 inhibits HIV‐1 reverse transcription in vitro. Together, our data strongly suggest a direct mode of action of DDX42 on viral ribonucleoprotein complexes. Our results identify DDX42 as an intrinsic viral inhibitor, opening new perspectives to target the life cycle of numerous RNA viruses.
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Affiliation(s)
| | | | | | | | - Ségolène Gracias
- Virus Sensing and Signaling Unit, Department of Virology, Institut Pasteur Université de Paris Cité, CNRS UMR 3569 Paris France
| | | | | | | | | | - Valérie Vivet‐Boudou
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002 Strasbourg France
| | | | | | - Nathalie Gros
- CEMIPAI, CNRS Université de Montpellier Montpellier France
| | | | | | - Hugues Parrinello
- Montpellier GenomiX (MGX), Biocampus, CNRS, INSERM Université de Montpellier Montpellier France
| | - Stéphanie Rialle
- Montpellier GenomiX (MGX), Biocampus, CNRS, INSERM Université de Montpellier Montpellier France
| | | | - Laurent Lacroix
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL Paris France
| | - Marc Lavigne
- Department of Virology Institut Pasteur Paris France
| | | | | | - Reiner Schulz
- Department of Medical & Molecular Genetics King's College London London UK
| | - Nolwenn Jouvenet
- Virus Sensing and Signaling Unit, Department of Virology, Institut Pasteur Université de Paris Cité, CNRS UMR 3569 Paris France
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6
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Abstract
DExH/D-box helicases are essential nucleic acid and ribonucleoprotein remodelers involved in all aspects of nucleic acid metabolism including replication, gene expression and post-transcriptional modifications. In parallel to their importance in basic cellular functions, DExH/D-box helicases play multiple roles in viral life cycles, with some of them highjacked by viruses or negatively regulating innate immune activation. However, other DExH/D-box helicases have recurrently been highlighted as direct antiviral effectors or as positive regulators of innate immune activation. Innate immunity relies on the ability of Pathogen Recognition Receptors to recognize viral signatures and trigger the production of interferons (IFNs) and pro-inflammatory cytokines. Secreted IFNs interact with their receptors to establish antiviral cellular reprogramming via expression regulation of the interferon-stimulated genes (ISGs). Several DExH/D-box helicases have been reported to act as viral sensors (DDX3, DDX41, DHX9, DDX1/DDX21/DHX36 complex), and others to play roles in innate immune activation (DDX60, DDX60L, DDX23). In contrast, the DDX39A, DDX46, DDX5 and DDX24 helicases act as negative regulators and impede IFN production upon viral infection. Beyond their role in viral sensing, the ISGs DDX60 and DDX60L act as viral inhibitors. Interestingly, the constitutively expressed DEAD-box helicases DDX56, DDX17, DDX42 intrinsically restrict viral replication. Hence, DExH/D-box helicases appear to form a multilayer network of primary and secondary factors involved in both intrinsic and innate antiviral immunity. In this review, we highlight recent findings on the extent of antiviral defences played by helicases and emphasize the need to better understand their immune functions as well as their complex interplay.
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Affiliation(s)
- Boris Bonaventure
- IRIM, CNRS, Montpellier University, France.,Present address: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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7
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Rebendenne A, Roy P, Bonaventure B, Chaves Valadão AL, Desmarets L, Arnaud-Arnould M, Rouillé Y, Tauziet M, Giovannini D, Touhami J, Lee Y, DeWeirdt P, Hegde M, Urbach S, Koulali KE, de Gracia FG, McKellar J, Dubuisson J, Wencker M, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs. Nat Genet 2022; 54:1090-1102. [PMID: 35879413 DOI: 10.1038/s41588-022-01110-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 05/26/2022] [Indexed: 12/23/2022]
Abstract
CRISPR knockout (KO) screens have identified host factors regulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Here, we conducted a meta-analysis of these screens, which showed a high level of cell-type specificity of the identified hits, highlighting the necessity of additional models to uncover the full landscape of host factors. Thus, we performed genome-wide KO and activation screens in Calu-3 lung cells and KO screens in Caco-2 colorectal cells, followed by secondary screens in four human cell lines. This revealed host-dependency factors, including AP1G1 adaptin and ATP8B1 flippase, as well as inhibitors, including mucins. Interestingly, some of the identified genes also modulate Middle East respiratory syndrome coronavirus (MERS-CoV) and seasonal human coronavirus (HCoV) (HCoV-NL63 and HCoV-229E) replication. Moreover, most genes had an impact on viral entry, with AP1G1 likely regulating TMPRSS2 activity at the plasma membrane. These results demonstrate the value of multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential targets for therapeutic interventions.
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Affiliation(s)
| | - Priyanka Roy
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Lowiese Desmarets
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Yves Rouillé
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Donatella Giovannini
- IGMM, CNRS, Montpellier University, Montpellier, France.,Metafora Biosystems, Paris, France
| | - Jawida Touhami
- IGMM, CNRS, Montpellier University, Montpellier, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Serge Urbach
- IGF, Montpellier University, CNRS, INSERM, Montpellier, France
| | | | | | - Joe McKellar
- IRIM, CNRS, Montpellier University, Montpellier, France
| | - Jean Dubuisson
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - Sandrine Belouzard
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | | | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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8
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Maarifi G, Lagisquet J, Hertel Q, Bonaventure B, Chamontin C, Fuchs K, Moncorgé O, Tauziet M, Mombled M, Papin L, Molès JP, Bodet C, Lévèque N, Gross A, Arhel N, Nisole S, Van de Perre P, Goujon C, Blanchet FP. Alarmin S100A9 restricts retroviral infection by limiting reverse transcription in human dendritic cells. EMBO J 2021; 40:e106540. [PMID: 34121210 DOI: 10.15252/embj.2020106540] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 11/09/2022] Open
Abstract
Dendritic cells (DC) subsets, like Langerhans cells (LC), are immune cells involved in pathogen sensing. They express specific antimicrobial cellular factors that are able to restrict infection and limit further pathogen transmission. Here, we identify the alarmin S100A9 as a novel intracellular antiretroviral factor expressed in human monocyte-derived and skin-derived LC. The intracellular expression of S100A9 is decreased upon LC maturation and inversely correlates with enhanced susceptibility to HIV-1 infection of LC. Furthermore, silencing of S100A9 in primary human LC relieves HIV-1 restriction while ectopic expression of S100A9 in various cell lines promotes intrinsic resistance to both HIV-1 and MLV infection by acting on reverse transcription. Mechanistically, the intracellular expression of S100A9 alters viral capsid uncoating and reverse transcription. S100A9 also shows potent inhibitory effect against HIV-1 and MMLV reverse transcriptase (RTase) activity in vitro in a divalent cation-dependent manner. Our findings uncover an unexpected intracellular function of the human alarmin S100A9 in regulating antiretroviral immunity in Langerhans cells.
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Affiliation(s)
- Ghizlane Maarifi
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Justine Lagisquet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Quentin Hertel
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Boris Bonaventure
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Célia Chamontin
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Kyra Fuchs
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Olivier Moncorgé
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Marine Tauziet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Margaux Mombled
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Laure Papin
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Etablissement Français du Sang, CHU Montpellier, Montpellier, France
| | - Charles Bodet
- Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Nicolas Lévèque
- Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Antoine Gross
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Nathalie Arhel
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Sébastien Nisole
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic Infections, INSERM, University of Montpellier, Etablissement Français du Sang, CHU Montpellier, Montpellier, France
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Fabien P Blanchet
- Institut de Recherche en Infectiologie de Montpellier, University of Montpellier, CNRS, Montpellier, France
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9
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Rebendenne A, Roy P, Bonaventure B, Chaves VAL, Desmarets L, Rouillé Y, Tauziet M, Arnaud-Arnould M, Giovannini D, Lee Y, DeWeirdt P, Hegde M, Garcia de GF, McKellar J, Wencker M, Dubuisson J, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal HCoVs. Res Sq 2021:rs.3.rs-555275. [PMID: 34075371 PMCID: PMC8168385 DOI: 10.21203/rs.3.rs-555275/v1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.
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Affiliation(s)
| | - Priyanka Roy
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - Lowiese Desmarets
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | - Yves Rouillé
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | | | | | | | - Yenarae Lee
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Peter DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Mudra Hegde
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | | | - Jean Dubuisson
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | - Sandrine Belouzard
- Lille University, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, France
| | | | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, USA
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Rebendenne A, Roy P, Bonaventure B, Chaves Valadão AL, Desmarets L, Rouillé Y, Tauziet M, Arnaud-Arnould M, Giovannini D, Lee Y, DeWeirdt P, Hegde M, Garcia de Gracia F, McKellar J, Wencker M, Dubuisson J, Belouzard S, Moncorgé O, Doench JG, Goujon C. Bidirectional genome-wide CRISPR screens reveal host factors regulating SARS-CoV-2, MERS-CoV and seasonal coronaviruses. bioRxiv 2021. [PMID: 34031654 DOI: 10.1101/2021.05.19.444823] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several genome-wide CRISPR knockout screens have been conducted to identify host factors regulating SARS-CoV-2 replication, but the models used have often relied on overexpression of ACE2 receptor. Additionally, such screens have yet to identify the protease TMPRSS2, known to be important for viral entry at the plasma membrane. Here, we conducted a meta-analysis of these screens and showed a high level of cell-type specificity of the identified hits, arguing for the necessity of additional models to uncover the full landscape of SARS-CoV-2 host factors. We performed genome-wide knockout and activation CRISPR screens in Calu-3 lung epithelial cells, as well as knockout screens in Caco-2 intestinal cells. In addition to identifying ACE2 and TMPRSS2 as top hits, our study reveals a series of so far unidentified and critical host-dependency factors, including the Adaptins AP1G1 and AP1B1 and the flippase ATP8B1. Moreover, new anti-SARS-CoV-2 proteins with potent activity, including several membrane-associated Mucins, IL6R, and CD44 were identified. We further observed that these genes mostly acted at the critical step of viral entry, with the notable exception of ATP8B1, the knockout of which prevented late stages of viral replication. Exploring the pro- and anti-viral breadth of these genes using highly pathogenic MERS-CoV, seasonal HCoV-NL63 and -229E and influenza A orthomyxovirus, we reveal that some genes such as AP1G1 and ATP8B1 are general coronavirus cofactors. In contrast, Mucins recapitulated their known role as a general antiviral defense mechanism. These results demonstrate the value of considering multiple cell models and perturbational modalities for understanding SARS-CoV-2 replication and provide a list of potential new targets for therapeutic interventions.
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Siadous FA, Cantet F, Van Schaik E, Burette M, Allombert J, Lakhani A, Bonaventure B, Goujon C, Samuel J, Bonazzi M, Martinez E. Coxiella effector protein CvpF subverts RAB26-dependent autophagy to promote vacuole biogenesis and virulence. Autophagy 2020; 17:706-722. [PMID: 32116095 PMCID: PMC8032239 DOI: 10.1080/15548627.2020.1728098] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Coxiella burnetii, the etiological agent of the zoonosis Q fever, replicates inside host cells within a large vacuole displaying autolysosomal characteristics. The development of this compartment is mediated by bacterial effectors, which interfere with a number of host membrane trafficking pathways. By screening a Coxiella transposon mutant library, we observed that transposon insertions in cbu0626 led to intracellular replication and vacuole biogenesis defects. Here, we demonstrate that CBU0626 is a novel member of the Coxiella vacuolar protein (Cvp) family of effector proteins, which is translocated by the Dot/Icm secretion system and localizes to vesicles with autolysosomal features as well as Coxiella-containing vacuoles (CCVs). We thus renamed this effector CvpF for Coxiella vacuolar protein F. CvpF specifically interacts with the host small GTPase RAB26, leading to the recruitment of the autophagosomal marker MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta) to CCVs. Importantly, cvpF::Tn mutants were highly attenuated compared to wild-type bacteria in the SCID mouse model of infection, highlighting the importance of CvpF for Coxiella virulence. These results suggest that CvpF manipulates endosomal trafficking and macroautophagy/autophagy induction for optimal C. burnetii vacuole biogenesis. Abbreviations: ACCM: acidified citrate cystein medium; AP: adaptor related protein complex; CCV: Coxiella-containing vacuole; Cvp: Coxiella vacuolar protein; GDI: guanosine nucleotide dissociation inhibitor; GDF: GDI dissociation factor; GEF: guanine exchange factor; LAMP1: lysosomal associated membrane protein 1; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTORC1: mechanistic target of rapamycin kinase MTOR complex 1; PBS: phosphate-buffered saline; PMA: phorbol myristate acetate; SQSTM1/p62: sequestosome 1; WT: wild-type.
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Affiliation(s)
- Fernande Ayenoue Siadous
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
| | - Franck Cantet
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
| | - Erin Van Schaik
- Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center College of Medicine, Bryan, TX, USA
| | - Mélanie Burette
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
| | - Julie Allombert
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
| | - Anissa Lakhani
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
| | - Boris Bonaventure
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
| | - Caroline Goujon
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
| | - James Samuel
- Department of Microbial and Molecular Pathogenesis, Texas A&M Health Science Center College of Medicine, Bryan, TX, USA
| | - Matteo Bonazzi
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
| | - Eric Martinez
- Institut de Recherche en Infectiologie de Montpellier (IRIM) UMR 9004 CNRS, Université de Montpellier, Montpellier, France
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Doyle T, Moncorgé O, Bonaventure B, Pollpeter D, Lussignol M, Tauziet M, Apolonia L, Catanese MT, Goujon C, Malim MH. Author Correction: The interferon-inducible isoform of NCOA7 inhibits endosome-mediated viral entry. Nat Microbiol 2019; 4:539. [PMID: 30670794 DOI: 10.1038/s41564-019-0366-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of Supplementary Fig. 5a originally published with this Letter, the authors mistakenly duplicated images of LAMP1 staining in place of CD63 staining; this has now been amended to the correct version shown below.
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Affiliation(s)
- Tomas Doyle
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.,GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | | | | | - Darja Pollpeter
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Marion Lussignol
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Marine Tauziet
- IRIM, CNRS, Université de Montpellier, Montpellier, France
| | - Luis Apolonia
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Maria-Teresa Catanese
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
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Doyle T, Moncorgé O, Bonaventure B, Pollpeter D, Lussignol M, Tauziet M, Apolonia L, Catanese MT, Goujon C, Malim MH. The interferon-inducible isoform of NCOA7 inhibits endosome-mediated viral entry. Nat Microbiol 2018; 3:1369-1376. [PMID: 30478388 PMCID: PMC6329445 DOI: 10.1038/s41564-018-0273-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/24/2018] [Indexed: 12/19/2022]
Abstract
Interferons (IFNs) mediate cellular defence against viral pathogens by upregulation of interferon-stimulated genes (ISGs) whose products interact with viral components or alter cellular physiology to suppress viral replication (1–3). Among the ISGs that can inhibit influenza A virus (IAV) (4) are the myxovirus resistance 1 (MX1) GTPase (5) and IFN-induced transmembrane protein 3 (IFITM3) (6, 7). Here we use ectopic expression and gene knock-out to demonstrate that the IFN-inducible 219 amino acid short isoform of human nuclear receptor coactivator 7 (NCOA7) is an inhibitor of IAV as well as other viruses that enter the cell by endocytosis, including hepatitis C virus (HCV). NCOA7 interacts with the vacuolar H+-ATPase (V-ATPase) and its expression promotes cytoplasmic vesicle acidification, lysosomal protease activity and the degradation of endocytosed antigen. Step-wise dissection of the IAV entry pathway demonstrates that NCOA7 inhibits fusion of the viral and endosomal membranes and subsequent nuclear translocation of viral ribonucleoproteins (vRNPs). NCOA7, therefore, provides a mechanism for immune regulation of endo-lysosomal physiology that not only suppresses viral entry into the cytosol from this compartment but may also regulate other V-ATPase-associated cellular processes such as physiological adjustments to nutritional status, or the maturation and function of antigen presenting cells.
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Affiliation(s)
- Tomas Doyle
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.,GlaxoSmithKline Medicines Research Centre, Stevenage, UK
| | | | | | - Darja Pollpeter
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Marion Lussignol
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Marine Tauziet
- IRIM, CNRS, Université de Montpellier, Montpellier, France
| | - Luis Apolonia
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Maria-Teresa Catanese
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Michael H Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London, UK.
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