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Dupont M, Krischuns T, Gianetto QG, Paisant S, Bonazza S, Brault JB, Douché T, Arragain B, Florez-Prada A, Perez-Perri JI, Hentze MW, Cusack S, Matondo M, Isel C, Courtney DG, Naffakh N. The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication. Nucleic Acids Res 2024:gkae291. [PMID: 38686810 DOI: 10.1093/nar/gkae291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Genome-wide approaches have significantly advanced our knowledge of the repertoire of RNA-binding proteins (RBPs) that associate with cellular polyadenylated mRNAs within eukaryotic cells. Recent studies focusing on the RBP interactomes of viral mRNAs, notably SARS-Cov-2, have revealed both similarities and differences between the RBP profiles of viral and cellular mRNAs. However, the RBPome of influenza virus mRNAs remains unexplored. Herein, we identify RBPs that associate with the viral mRNA encoding the nucleoprotein (NP) of an influenza A virus. Focusing on TDP-43, we show that it binds several influenza mRNAs beyond the NP-mRNA, and that its depletion results in lower levels of viral mRNAs and proteins within infected cells, and a decreased yield of infectious viral particles. We provide evidence that the viral polymerase recruits TDP-43 onto viral mRNAs through a direct interaction with the disordered C-terminal domain of TDP-43. Notably, other RBPs found to be associated with influenza virus mRNAs also interact with the viral polymerase, which points to a role of the polymerase in orchestrating the assembly of viral messenger ribonucleoproteins.
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Affiliation(s)
- Maud Dupont
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Stefano Bonazza
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Jean-Baptiste Brault
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Benoît Arragain
- European Molecular Biology Laboratory, 38042Grenoble, France
| | | | | | | | - Stephen Cusack
- European Molecular Biology Laboratory, 38042Grenoble, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - David G Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
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2
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Boghdeh NA, McGraw B, Barrera MD, Anderson C, Baha H, Risner KH, Ogungbe IV, Alem F, Narayanan A. Inhibitors of the Ubiquitin-Mediated Signaling Pathway Exhibit Broad-Spectrum Antiviral Activities against New World Alphaviruses. Viruses 2023; 15:v15030655. [PMID: 36992362 PMCID: PMC10059822 DOI: 10.3390/v15030655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/09/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
New World alphaviruses including Venezuelan Equine Encephalitis Virus (VEEV) and Eastern Equine Encephalitis Virus (EEEV) are mosquito-transmitted viruses that cause disease in humans and equines. There are currently no FDA-approved therapeutics or vaccines to treat or prevent exposure-associated encephalitic disease. The ubiquitin proteasome system (UPS)-associated signaling events are known to play an important role in the establishment of a productive infection for several acutely infectious viruses. The critical engagement of the UPS-associated signaling mechanisms by many viruses as host–pathogen interaction hubs led us to hypothesize that small molecule inhibitors that interfere with these signaling pathways will exert broad-spectrum inhibitory activity against alphaviruses. We queried eight inhibitors of the UPS signaling pathway for antiviral outcomes against VEEV. Three of the tested inhibitors, namely NSC697923 (NSC), bardoxolone methyl (BARM) and omaveloxolone (OMA) demonstrated broad-spectrum antiviral activity against VEEV and EEEV. Dose dependency and time of addition studies suggest that BARM and OMA exhibit intracellular and post-entry viral inhibition. Cumulatively, our studies indicate that inhibitors of the UPS-associated signaling pathways exert broad-spectrum antiviral outcomes in the context of VEEV and EEEV infection, supporting their translational application as therapeutic candidates to treat alphavirus infections.
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Affiliation(s)
- Niloufar A. Boghdeh
- Biomedical Research Laboratory, George Mason University, Manassas, VA 20110, USA
| | - Brittany McGraw
- School of Systems Biology, College of Science, George Mason University, Manassas, VA 20110, USA
| | - Michael D. Barrera
- Biomedical Research Laboratory, George Mason University, Manassas, VA 20110, USA
- School of Systems Biology, College of Science, George Mason University, Manassas, VA 20110, USA
| | - Carol Anderson
- Biomedical Research Laboratory, George Mason University, Manassas, VA 20110, USA
- School of Systems Biology, College of Science, George Mason University, Manassas, VA 20110, USA
| | - Haseebullah Baha
- Biomedical Research Laboratory, George Mason University, Manassas, VA 20110, USA
- School of Systems Biology, College of Science, George Mason University, Manassas, VA 20110, USA
| | - Kenneth H. Risner
- Biomedical Research Laboratory, George Mason University, Manassas, VA 20110, USA
- School of Systems Biology, College of Science, George Mason University, Manassas, VA 20110, USA
| | - Ifedayo V. Ogungbe
- Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA
| | - Farhang Alem
- Biomedical Research Laboratory, George Mason University, Manassas, VA 20110, USA
- School of Systems Biology, College of Science, George Mason University, Manassas, VA 20110, USA
| | - Aarthi Narayanan
- Biomedical Research Laboratory, George Mason University, Manassas, VA 20110, USA
- Department of Biology, College of Science, George Mason University, Fairfax, VA 22030, USA
- Correspondence:
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3
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The ubiquitination landscape of the influenza A virus polymerase. Nat Commun 2023; 14:787. [PMID: 36774438 PMCID: PMC9922279 DOI: 10.1038/s41467-023-36389-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/30/2023] [Indexed: 02/13/2023] Open
Abstract
During influenza A virus (IAV) infections, viral proteins are targeted by cellular E3 ligases for modification with ubiquitin. Here, we decipher and functionally explore the ubiquitination landscape of the IAV polymerase proteins during infection of human alveolar epithelial cells by applying mass spectrometry analysis of immuno-purified K-ε-GG (di-glycyl)-remnant-bearing peptides. We have identified 59 modified lysines across the three subunits, PB2, PB1 and PA of the viral polymerase of which 17 distinctively affect mRNA transcription, vRNA replication and the generation of recombinant viruses via non-proteolytic mechanisms. Moreover, further functional and in silico analysis indicate that ubiquitination at K578 in the PB1 thumb domain is mechanistically linked to dynamic structural transitions of the viral polymerase that are required for vRNA replication. Mutations K578A and K578R differentially affect the generation of recombinant viruses by impeding cRNA and vRNA synthesis, NP binding as well as polymerase dimerization. Collectively, our results demonstrate that the ubiquitin-mediated charge neutralization at PB1-K578 disrupts the interaction to an unstructured loop in the PB2 N-terminus that is required to coordinate polymerase dimerization and facilitate vRNA replication. This provides evidence that IAV exploits the cellular ubiquitin system to modulate the activity of the viral polymerase for viral replication.
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C910 chemical compound inhibits the traffiking of several bacterial AB toxins with cross-protection against influenza virus. iScience 2022; 25:104537. [PMID: 35769882 PMCID: PMC9234246 DOI: 10.1016/j.isci.2022.104537] [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: 11/04/2021] [Revised: 04/20/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022] Open
Abstract
The development of anti-infectives against a large range of AB-like toxin-producing bacteria includes the identification of compounds disrupting toxin transport through both the endolysosomal and retrograde pathways. Here, we performed a high-throughput screening of compounds blocking Rac1 proteasomal degradation triggered by the Cytotoxic Necrotizing Factor-1 (CNF1) toxin, which was followed by orthogonal screens against two toxins that hijack the endolysosomal (diphtheria toxin) or retrograde (Shiga-like toxin 1) pathways to intoxicate cells. This led to the identification of the molecule C910 that induces the enlargement of EEA1-positive early endosomes associated with sorting defects of CNF1 and Shiga toxins to their trafficking pathways. C910 protects cells against eight bacterial AB toxins and the CNF1-mediated pathogenic Escherichia coli invasion. Interestingly, C910 reduces influenza A H1N1 and SARS-CoV-2 viral infection in vitro. Moreover, parenteral administration of C910 to mice resulted in its accumulation in lung tissues and a reduction in lethal influenza infection. Screen for inhibitors disrupting bacterial AB toxins vesicular trafficking pathways C910 affects EEA1/Rab5-positive early endosome morphology and sorting functions C910 protects cells against eight AB toxins, SARS-CoV-2 and influenza A virus C910 accumulates in lung tissues and protects mice against influenza A virus
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5
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Park ES, Dezhbord M, Lee AR, Kim KH. The Roles of Ubiquitination in Pathogenesis of Influenza Virus Infection. Int J Mol Sci 2022; 23:ijms23094593. [PMID: 35562987 PMCID: PMC9105177 DOI: 10.3390/ijms23094593] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 01/14/2023] Open
Abstract
The ubiquitin system denotes a potent post-translational modification machinery that is capable of activation or deactivation of target proteins through reversible linkage of a single ubiquitin or ubiquitin chains. Ubiquitination regulates major cellular functions such as protein degradation, trafficking and signaling pathways, innate immune response, antiviral defense, and virus replication. The RNA sensor RIG-I ubiquitination is specifically induced by influenza A virus (IAV) to activate type I IFN production. Influenza virus modulates the activity of major antiviral proteins in the host cell to complete its full life cycle. Its structural and non-structural proteins, matrix proteins and the polymerase complex can regulate host immunity and antiviral response. The polymerase PB1-F2 of mutated 1918 IAV, adapts a novel IFN antagonist function by sending the DDX3 into proteasomal degradation. Ultimately the fate of virus is determined by the outcome of interplay between viral components and host antiviral proteins and ubiquitination has a central role in the encounter of virus and its host cell.
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Affiliation(s)
- Eun-Sook Park
- Institute of Biomedical Science and Technology, School of Medicine, Konkuk University, Seoul 05029, Korea;
| | - Mehrangiz Dezhbord
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
| | - Ah Ram Lee
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
| | - Kyun-Hwan Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (M.D.); (A.R.L.)
- Correspondence: ; Tel.: +82-31-299-6126
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Wang Q, Zhang Q, Zheng M, Wen J, Li Q, Zhao G. Viral-Host Interactome Analysis Reveals Chicken STAU2 Interacts With Non-structural Protein 1 and Promotes the Replication of H5N1 Avian Influenza Virus. Front Immunol 2021; 12:590679. [PMID: 33968009 PMCID: PMC8098808 DOI: 10.3389/fimmu.2021.590679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 02/22/2021] [Indexed: 12/29/2022] Open
Abstract
As a highly pathogenic influenza virus, H5N1 avian influenza virus (AIV) poses a great threat to poultry production and public health. H5N1 AIV has a small genome and, therefore, relies heavily on its host cellular machinery to replicate. To develop a comprehensive understanding of how H5N1 AIV rewires host cellular machinery during the course of infection, it is crucial to identify which host proteins and complexes come into physical contact with the viral proteins. Here, we utilized affinity purification mass spectrometry (AP-MS) to systematically determine the physical interactions of 11 H5N1 AIV proteins with host proteins in chicken DF1 cells. We identified with high confidence 1,043 H5N1 AIV–chicken interactions involving 621 individual chicken proteins and uncovered a number of host proteins and complexes that were targeted by the viral proteins. Specifically, we revealed that chicken Staufen double-stranded RNA-binding protein 2 interacts with AIV non-structural protein 1 (NS1) and promotes the replication of the virus by enhancing the nuclear export of NS1 mRNA. This dataset facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of H5N1 AIV infection.
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Affiliation(s)
- Qiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qinghe Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Malausse N, van der Werf S, Naffakh N, Munier S. Influenza B Virus Infection Is Enhanced Upon Heterotypic Co-infection With Influenza A Virus. Front Microbiol 2021; 12:631346. [PMID: 33717023 PMCID: PMC7947630 DOI: 10.3389/fmicb.2021.631346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022] Open
Abstract
Homotypic co-infections with influenza viruses are described to increase genetic population diversity, to drive viral evolution and to allow genetic complementation. Less is known about heterotypic co-infections between influenza A (IAV) and influenza B (IBV) viruses. Previous publications showed that IAV replication was suppressed upon co-infection with IBV. However, the effect of heterotypic co-infections on IBV replication was not investigated. To do so, we produced by reverse genetics a pair of replication-competent recombinant IAV (A/WSN/33) and IBV (B/Brisbane/60/2008) expressing a GFP and mCherry fluorescent reporter, respectively. A549 cells were infected simultaneously or 1 h apart at a high MOI with IAV-GFP or IBV-mCherry and the fluorescence was measured at 6 h post-infection by flow cytometry. Unexpectedly, we observed that IBV-mCherry infection was enhanced upon co-infection with IAV-GFP, and more strongly so when IAV was added 1 h prior to IBV. The same effect was observed with wild-type viruses and with various strains of IAV. Using UV-inactivated IAV or type-specific antiviral compounds, we showed that the enhancing effect of IAV infection on IBV infection was dependent on transcription/replication of the IAV genome. Our results, taken with available data in the literature, support the hypothesis that the presence of IAV proteins can enhance IBV genome expression and/or complement IBV defective particles.
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Affiliation(s)
- Nicolas Malausse
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France
| | - Nadia Naffakh
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France
| | - Sandie Munier
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, CNRS UMR 3569, Université de Paris, Paris, France
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8
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Schaack GA, Mehle A. Experimental Approaches to Identify Host Factors Important for Influenza Virus. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a038521. [PMID: 31871241 DOI: 10.1101/cshperspect.a038521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An ever-expanding toolkit of experimental methods provides the means to discover and characterize host factors important for influenza virus. Here, we describe common methods for investigating genetic relationships and physical interactions between virus and host. A comprehensive knowledge of host:virus interactions is key to understanding how influenza virus exploits the host cell and to potentially identify vulnerabilities that may be manipulated to prevent or treat disease.
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Affiliation(s)
- Grace A Schaack
- Department of Medical Microbiology and Immunology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin Madison, Madison, Wisconsin 53706, USA
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9
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Declercq M, Biquand E, Karim M, Pietrosemoli N, Jacob Y, Demeret C, Barbezange C, van der Werf S. Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription. Nucleic Acids Res 2020; 48:10428-10440. [PMID: 32960265 PMCID: PMC7544206 DOI: 10.1093/nar/gkaa771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/18/2020] [Accepted: 09/10/2020] [Indexed: 12/25/2022] Open
Abstract
Cellular exonucleases involved in the processes that regulate RNA stability and quality control have been shown to restrict or to promote the multiplication cycle of numerous RNA viruses. Influenza A viruses are major human pathogens that are responsible for seasonal epidemics, but the interplay between viral proteins and cellular exonucleases has never been specifically studied. Here, using a stringent interactomics screening strategy and an siRNA-silencing approach, we identified eight cellular factors among a set of 75 cellular proteins carrying exo(ribo)nuclease activities or involved in RNA decay processes that support influenza A virus multiplication. We show that the exoribonuclease ERI1 interacts with the PB2, PB1 and NP components of the viral ribonucleoproteins and is required for viral mRNA transcription. More specifically, we demonstrate that the protein-protein interaction is RNA dependent and that both the RNA binding and exonuclease activities of ERI1 are required to promote influenza A virus transcription. Finally, we provide evidence that during infection, the SLBP protein and histone mRNAs co-purify with vRNPs alongside ERI1, indicating that ERI1 is most probably recruited when it is present in the histone pre-mRNA processing complex in the nucleus.
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Affiliation(s)
- Marion Declercq
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Elise Biquand
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Marwah Karim
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Natalia Pietrosemoli
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Yves Jacob
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Caroline Demeret
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Cyril Barbezange
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
| | - Sylvie van der Werf
- Unité Génétique Moléculaire des Virus à ARN, UMR3569 CNRS, Université de Paris, Département de Virologie, Institut Pasteur, Paris, France
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Kumar S, Barouch-Bentov R, Xiao F, Schor S, Pu S, Biquand E, Lu A, Lindenbach BD, Jacob Y, Demeret C, Einav S. MARCH8 Ubiquitinates the Hepatitis C Virus Nonstructural 2 Protein and Mediates Viral Envelopment. Cell Rep 2020; 26:1800-1814.e5. [PMID: 30759391 PMCID: PMC7053169 DOI: 10.1016/j.celrep.2019.01.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 11/07/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023] Open
Abstract
The mechanisms that regulate envelopment of HCV and other viruses that bud intracellularly and/or lack late-domain motifs are largely unknown. We reported that K63 polyubiquitination of the HCV nonstructural (NS) 2 protein mediates HRS (ESCRT-0 component) binding and envelopment. Nevertheless, the ubiquitin signaling that governs NS2 ubiquitination remained unknown. Here, we map the NS2 interactome with the ubiquitin proteasome system (UPS) via mammalian cell-based screens. NS2 interacts with E3 ligases, deubiquitinases, and ligase regulators, some of which are candidate proviral or antiviral factors. MARCH8, a RING-finger E3 ligase, catalyzes K63-linked NS2 polyubiquitination in vitro and in HCV-infected cells. MARCH8 is required for infection with HCV, dengue, and Zika viruses and specifically mediates HCV envelopment. Our data reveal regulation of HCV envelopment via ubiquitin signaling and both a viral protein substrate and a ubiquitin K63-linkage of the understudied MARCH8, with potential implications for cell biology, virology, and host-targeted antiviral design. The mechanisms that regulate intracellular viral envelopment are unknown. Kumar et al. report that MARCH8 catalyzes K63-linked polyubiquitination of the HCV nonstructural 2 protein and subsequently ESCRT recruitment and HCV envelopment. MARCH8 is required for infection with other Flaviviridae family members, thereby representing a potential host target for antiviral strategies.
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Affiliation(s)
- Sathish Kumar
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rina Barouch-Bentov
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fei Xiao
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stanford Schor
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Szuyuan Pu
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elise Biquand
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Albert Lu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Yves Jacob
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Caroline Demeret
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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Nonproteolytic K29-Linked Ubiquitination of the PB2 Replication Protein of Influenza A Viruses by Proviral Cullin 4-Based E3 Ligases. mBio 2020; 11:mBio.00305-20. [PMID: 32265326 PMCID: PMC7157767 DOI: 10.1128/mbio.00305-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Successful infection by influenza A virus, a pathogen of major public health importance, involves fine regulation of the multiple functions of the viral proteins, which often relies on post-translational modifications (PTMs). The PB2 protein of influenza A viruses is essential for viral replication and a key determinant of host range. While PTMs of PB2 inducing its degradation have been identified, here we show that PB2 undergoes a regulating PTM signaling detected during infection, based on an atypical K29-linked ubiquitination and mediated by two multicomponent E3 ubiquitin ligases. Recombinant viruses impaired for CRL4-mediated ubiquitination are attenuated, indicating that ubiquitination of PB2 is necessary for an optimal influenza A virus infection. The CRL4 E3 ligases are required for normal viral cycle progression and for maximal virion production. Consequently, they represent potential candidate host factors for antiviral targets. The multifunctional nature of viral proteins is essentially driven by posttranslational modifications (PTMs) and is key for the successful outcome of infection. For influenza A viruses (IAVs), a composite pattern of PTMs regulates the activity of viral proteins. However, almost none are known that target the PB2 replication protein, except for inducing its degradation. We show here that PB2 undergoes a nonproteolytic ubiquitination during infection. We identified E3 ubiquitin ligases catalyzing this ubiquitination as two multicomponent RING-E3 ligases based on cullin 4 (CRL4s), which are both contributing to the levels of ubiquitinated forms of PB2 in infected cells. The CRL4 E3 ligase activity is required for the normal progression of the viral cycle and for maximal virion production, indicating that the CRL4s mediate a ubiquitin signaling that promotes infection. The CRL4s are recruiting PB2 through an unconventional bimodal interaction with both the DDB1 adaptor and DCAF substrate receptors. While able to bind to PB2 when engaged in the viral polymerase complex, the CRL4 factors do not alter transcription and replication of the viral segments during infection. CRL4 ligases catalyze different patterns of lysine ubiquitination on PB2. Recombinant viruses mutated in the targeted lysines showed attenuated viral production, suggesting that CRL4-mediated ubiquitination of PB2 contributes to IAV infection. We identified K29-linked ubiquitin chains as main components of the nonproteolytic PB2 ubiquitination mediated by the CRL4s, providing the first example of the role of this atypical ubiquitin linkage in the regulation of a viral infection.
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Jahan AS, Biquand E, Muñoz-Moreno R, Le Quang A, Mok CKP, Wong HH, Teo QW, Valkenburg SA, Chin AWH, Man Poon LL, Te Velthuis A, García-Sastre A, Demeret C, Sanyal S. OTUB1 Is a Key Regulator of RIG-I-Dependent Immune Signaling and Is Targeted for Proteasomal Degradation by Influenza A NS1. Cell Rep 2020; 30:1570-1584.e6. [PMID: 32023470 DOI: 10.1016/j.celrep.2020.01.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/21/2019] [Accepted: 01/02/2020] [Indexed: 12/16/2022] Open
Abstract
Deubiquitylases (DUBs) regulate critical signaling pathways at the intersection of host immunity and viral pathogenesis. Although RIG-I activation is heavily dependent on ubiquitylation, systematic analyses of DUBs that regulate this pathway have not been performed. Using a ubiquitin C-terminal electrophile, we profile DUBs that function during influenza A virus (IAV) infection and isolate OTUB1 as a key regulator of RIG-I-dependent antiviral responses. Upon infection, OTUB1 relocalizes from the nucleus to mitochondrial membranes together with RIG-I, viral PB2, and NS1. Its expression depends on competing effects of interferon stimulation and IAV-triggered degradation. OTUB1 activates RIG-I via a dual mechanism of K48 polyubiquitin hydrolysis and formation of an E2-repressive complex with UBCH5c. We reconstitute this mechanism in a cell-free system comprising [35S]IRF3, purified RIG-I, mitochondrial membranes, and cytosol expressing OTUB1 variants. A range of IAV NS1 proteins trigger proteasomal degradation of OTUB1, antagonizing the RIG-I signaling cascade and antiviral responses.
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Affiliation(s)
- Akhee Sabiha Jahan
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Elise Biquand
- Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
| | - Raquel Muñoz-Moreno
- 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
| | - Agathe Le Quang
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Chris Ka-Pun Mok
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Ho Him Wong
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Qi Wen Teo
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Sophie A Valkenburg
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Alex W H Chin
- School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Leo Lit Man Poon
- School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Artejan Te Velthuis
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Adolfo García-Sastre
- 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; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Caroline Demeret
- Molecular Genetics of RNA Viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
| | - Sumana Sanyal
- HKU-Pasteur Research Pole, University of Hong Kong, Hong Kong; School of Public Health, LKS Faculty of Medicine, University of Hong Kong, Hong Kong; School of Biomedical Sciences, LKS Faculty of Medicine, University of Hong Kong, Hong Kong.
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Biquand É, Demeret C. Interactions avec le système ubiquitine : un prérequis de l’adaptation des virus influenza à l’homme ? Med Sci (Paris) 2018; 34:509-511. [DOI: 10.1051/medsci/20183406005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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