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Sun J, Qin F, Sun F, He P, Wei E, Wang R, Zhu F, Wang Q, Tang X, Zhang Y, Shen Z. Identification and subcellular colocalization of protein transport protein Sec61α and Sec61γ in Nosema bombycis. Gene X 2023; 851:146971. [DOI: 10.1016/j.gene.2022.146971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
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2
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Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Wang P, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H. A comprehensive SARS-CoV-2-human protein-protein interactome reveals COVID-19 pathobiology and potential host therapeutic targets. Nat Biotechnol 2023; 41:128-139. [PMID: 36217030 PMCID: PMC9851973 DOI: 10.1038/s41587-022-01474-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/15/2022] [Indexed: 01/25/2023]
Abstract
Studying viral-host protein-protein interactions can facilitate the discovery of therapies for viral infection. We use high-throughput yeast two-hybrid experiments and mass spectrometry to generate a comprehensive SARS-CoV-2-human protein-protein interactome network consisting of 739 high-confidence binary and co-complex interactions, validating 218 known SARS-CoV-2 host factors and revealing 361 novel ones. Our results show the highest overlap of interaction partners between published datasets and of genes differentially expressed in samples from COVID-19 patients. We identify an interaction between the viral protein ORF3a and the human transcription factor ZNF579, illustrating a direct viral impact on host transcription. We perform network-based screens of >2,900 FDA-approved or investigational drugs and identify 23 with significant network proximity to SARS-CoV-2 host factors. One of these drugs, carvedilol, shows clinical benefits for COVID-19 patients in an electronic health records analysis and antiviral properties in a human lung cell line infected with SARS-CoV-2. Our study demonstrates the value of network systems biology to understand human-virus interactions and provides hits for further research on COVID-19 therapeutics.
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Affiliation(s)
- Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yuan Liu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
| | - Shagun Gupta
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Mauricio I Paramo
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Chengsheng Mao
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Shayne Wierbowski
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Marta Bertolotti
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA
| | - Mriganka Nerkar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Lara Jehi
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Nir Drayman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Haley Gula
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL, USA
| | - Peihui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
- Center for Advanced Proteomics, Cornell University, Ithaca, NY, USA.
- Department of Computational Biology, Cornell University, Ithaca, NY, USA.
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3
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Zhou Y, Liu Y, Gupta S, Paramo MI, Hou Y, Mao C, Luo Y, Judd J, Wierbowski S, Bertolotti M, Nerkar M, Jehi L, Drayman N, Nicolaescu V, Gula H, Tay S, Randall G, Lis JT, Feschotte C, Erzurum SC, Cheng F, Yu H. A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19. RESEARCH SQUARE 2022:rs.3.rs-1354127. [PMID: 35677070 PMCID: PMC9176654 DOI: 10.21203/rs.3.rs-1354127/v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Physical interactions between viral and host proteins are responsible for almost all aspects of the viral life cycle and the host's immune response. Studying viral-host protein-protein interactions is thus crucial for identifying strategies for treatment and prevention of viral infection. Here, we use high-throughput yeast two-hybrid and affinity purification followed by mass spectrometry to generate a comprehensive SARS-CoV-2-human protein-protein interactome network consisting of both binary and co-complex interactions. We report a total of 739 high-confidence interactions, showing the highest overlap of interaction partners among published datasets as well as the highest overlap with genes differentially expressed in samples (such as upper airway and bronchial epithelial cells) from patients with SARS-CoV-2 infection. Showcasing the utility of our network, we describe a novel interaction between the viral accessory protein ORF3a and the host zinc finger transcription factor ZNF579 to illustrate a SARS-CoV-2 factor mediating a direct impact on host transcription. Leveraging our interactome, we performed network-based drug screens for over 2,900 FDA-approved/investigational drugs and obtained a curated list of 23 drugs that had significant network proximities to SARS-CoV-2 host factors, one of which, carvedilol, showed promising antiviral properties. We performed electronic health record-based validation using two independent large-scale, longitudinal COVID-19 patient databases and found that carvedilol usage was associated with a significantly lowered probability (17%-20%, P < 0.001) of obtaining a SARS-CoV-2 positive test after adjusting various confounding factors. Carvedilol additionally showed anti-viral activity against SARS-CoV-2 in a human lung epithelial cell line [half maximal effective concentration (EC 50 ) value of 4.1 µM], suggesting a mechanism for its beneficial effect in COVID-19. Our study demonstrates the value of large-scale network systems biology approaches for extracting biological insight from complex biological processes.
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Affiliation(s)
- Yadi Zhou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
| | - Yuan Liu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
| | - Shagun Gupta
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, US
| | - Mauricio I. Paramo
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Yuan Hou
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
| | - Chengsheng Mao
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, US
| | - Yuan Luo
- Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, US
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Shayne Wierbowski
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, US
| | - Marta Bertolotti
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
| | - Mriganka Nerkar
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Lara Jehi
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
| | - Nir Drayman
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, US
| | - Vlad Nicolaescu
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL 60637, US
| | - Haley Gula
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL 60637, US
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, US
| | - Glenn Randall
- Department of Microbiology, Ricketts Laboratory, University of Chicago, Chicago, IL 60637, US
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, US
| | - Serpil C. Erzurum
- Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, US
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, US
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, US
| | - Haiyuan Yu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, US
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, US
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Zhu L, Gao T, Huang Y, Jin J, Wang D, Zhang L, Jin Y, Li P, Hu Y, Wu Y, Liu H, Dong Q, Wang G, Zheng T, Song C, Bai Y, Zhang X, Liu Y, Yang W, Xu K, Zou G, Zhao L, Cao R, Zhong W, Xia X, Xiao G, Liu X, Cao C. Ebola virus VP35 hijacks the PKA-CREB1 pathway for replication and pathogenesis by AKIP1 association. Nat Commun 2022; 13:2256. [PMID: 35474062 PMCID: PMC9042921 DOI: 10.1038/s41467-022-29948-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/06/2022] [Indexed: 12/17/2022] Open
Abstract
Ebola virus (EBOV), one of the deadliest viruses, is the cause of fatal Ebola virus disease (EVD). The underlying mechanism of viral replication and EBOV-related hemorrhage is not fully understood. Here, we show that EBOV VP35, a cofactor of viral RNA-dependent RNA polymerase, binds human A kinase interacting protein (AKIP1), which consequently activates protein kinase A (PKA) and the PKA-downstream transcription factor CREB1. During EBOV infection, CREB1 is recruited into EBOV ribonucleoprotein complexes in viral inclusion bodies (VIBs) and employed for viral replication. AKIP1 depletion or PKA-CREB1 inhibition dramatically impairs EBOV replication. Meanwhile, the transcription of several coagulation-related genes, including THBD and SERPINB2, is substantially upregulated by VP35-dependent CREB1 activation, which may contribute to EBOV-related hemorrhage. The finding that EBOV VP35 hijacks the host PKA-CREB1 signal axis for viral replication and pathogenesis provides novel potential therapeutic approaches against EVD. Ebola virus virion protein 35 (VP35) is a cofactor of the viral RNA-dependent RNA polymerase, required for viral assembly and IFN antagonist. Here, Zhu et al. provide evidence that EBOV VP35 induces an AKIP1-mediated (human A kinase interacting protein) activation of the PKA-CREB1 signaling pathway and contributes to viral replication and pathogenesis in vitro and in vivo.
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Affiliation(s)
- Lin Zhu
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Ting Gao
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Yi Huang
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan, Hubei, 430020, China
| | - Jing Jin
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Di Wang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Leike Zhang
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan, Hubei, 430020, China
| | - Yanwen Jin
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Yong Hu
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Yan Wu
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan, Hubei, 430020, China
| | - Hainan Liu
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Qincai Dong
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Guangfei Wang
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Tong Zheng
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Caiwei Song
- Beijing Institute of Biotechnology, Beijing, 100039, China
| | - Yu Bai
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Xun Zhang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Yaoning Liu
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Weihong Yang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Ke Xu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Gang Zou
- Insitut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lei Zhao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Ruiyuan Cao
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Wu Zhong
- National Engineering Research Center for the Emergency Drug, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xianzhu Xia
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130000, China
| | - Gengfu Xiao
- National Biosafety Laboratory, Chinese Academy of Sciences, Wuhan, Hubei, 430020, China.
| | - Xuan Liu
- Beijing Institute of Biotechnology, Beijing, 100039, China.
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing, 100039, China.
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5
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Abstract
This chapter reviews our current knowledge about the spatiotemporal assembly of filoviral particles. We will follow particles from nucleocapsid entry into the cytoplasm until the nucleocapsids are enveloped at the plasma membrane. We will also highlight the currently open scientific questions surrounding filovirus assembly.
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Staufen1 Interacts with Multiple Components of the Ebola Virus Ribonucleoprotein and Enhances Viral RNA Synthesis. mBio 2018; 9:mBio.01771-18. [PMID: 30301857 PMCID: PMC6178623 DOI: 10.1128/mbio.01771-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Ebola virus (EBOV) is a negative-strand RNA virus with significant public health importance. Currently, no therapeutics are available for Ebola, which imposes an urgent need for a better understanding of EBOV biology. Here we dissected the virus-host interplay between EBOV and host RNA-binding proteins. We identified novel EBOV host factors, including Staufen1, which interacts with multiple viral factors and is required for efficient viral RNA synthesis. Ebola virus (EBOV) genome and mRNAs contain long, structured regions that could hijack host RNA-binding proteins to facilitate infection. We performed RNA affinity chromatography coupled with mass spectrometry to identify host proteins that bind to EBOV RNAs and identified four high-confidence proviral host factors, including Staufen1 (STAU1), which specifically binds both 3′ and 5′ extracistronic regions of the EBOV genome. We confirmed that EBOV infection rate and production of infectious particles were significantly reduced in STAU1-depleted cells. STAU1 was recruited to sites of EBOV RNA synthesis upon infection and enhanced viral RNA synthesis. Furthermore, STAU1 interacts with EBOV nucleoprotein (NP), virion protein 30 (VP30), and VP35; the latter two bridge the viral polymerase to the NP-coated genome, forming the viral ribonucleoprotein (RNP) complex. Our data indicate that STAU1 plays a critical role in EBOV replication by coordinating interactions between the viral genome and RNA synthesis machinery.
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Garcia-Moreno M, Järvelin AI, Castello A. Unconventional RNA-binding proteins step into the virus-host battlefront. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1498. [PMID: 30091184 PMCID: PMC7169762 DOI: 10.1002/wrna.1498] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 12/15/2022]
Abstract
The crucial participation of cellular RNA‐binding proteins (RBPs) in virtually all steps of virus infection has been known for decades. However, most of the studies characterizing this phenomenon have focused on well‐established RBPs harboring classical RNA‐binding domains (RBDs). Recent proteome‐wide approaches have greatly expanded the census of RBPs, discovering hundreds of proteins that interact with RNA through unconventional RBDs. These domains include protein–protein interaction platforms, enzymatic cores, and intrinsically disordered regions. Here, we compared the experimentally determined census of RBPs to gene ontology terms and literature, finding that 472 proteins have previous links with viruses. We discuss what these proteins are and what their roles in infection might be. We also review some of the pioneering examples of unorthodox RBPs whose RNA‐binding activity has been shown to be critical for virus infection. Finally, we highlight the potential of these proteins for host‐based therapies against viruses. This article is categorized under:
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
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Affiliation(s)
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
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8
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Martin S, Chiramel AI, Schmidt ML, Chen YC, Whitt N, Watt A, Dunham EC, Shifflett K, Traeger S, Leske A, Buehler E, Martellaro C, Brandt J, Wendt L, Müller A, Peitsch S, Best SM, Stech J, Finke S, Römer-Oberdörfer A, Groseth A, Feldmann H, Hoenen T. A genome-wide siRNA screen identifies a druggable host pathway essential for the Ebola virus life cycle. Genome Med 2018; 10:58. [PMID: 30081931 PMCID: PMC6090742 DOI: 10.1186/s13073-018-0570-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/13/2018] [Indexed: 01/01/2023] Open
Abstract
Background The 2014–2016 Ebola virus (EBOV) outbreak in West Africa highlighted the need for improved therapeutic options against this virus. Approaches targeting host factors/pathways essential for the virus are advantageous because they can potentially target a wide range of viruses, including newly emerging ones and because the development of resistance is less likely than when targeting the virus directly. However, systematic approaches for screening host factors important for EBOV have been hampered by the necessity to work with this virus at biosafety level 4 (BSL4). Methods In order to identify host factors involved in the EBOV life cycle, we performed a genome-wide siRNA screen comprising 64,755 individual siRNAs against 21,566 human genes to assess their activity in EBOV genome replication and transcription. As a screening platform, we used reverse genetics-based life cycle modelling systems that recapitulate these processes without the need for a BSL4 laboratory. Results Among others, we identified the de novo pyrimidine synthesis pathway as an essential host pathway for EBOV genome replication and transcription, and confirmed this using infectious EBOV under BSL4 conditions. An FDA-approved drug targeting this pathway showed antiviral activity against infectious EBOV, as well as other non-segmented negative-sense RNA viruses. Conclusions This study provides a minable data set for every human gene regarding its role in EBOV genome replication and transcription, shows that an FDA-approved drug targeting one of the identified pathways is highly efficacious in vitro, and demonstrates the power of life cycle modelling systems for conducting genome-wide host factor screens for BSL4 viruses. Electronic supplementary material The online version of this article (10.1186/s13073-018-0570-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Scott Martin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA.,Present address: Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Abhilash I Chiramel
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Marie Luisa Schmidt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Yu-Chi Chen
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Nadia Whitt
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Ari Watt
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Eric C Dunham
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Kyle Shifflett
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Shelby Traeger
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Anne Leske
- Junior Research Group Arenavirus Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Eugen Buehler
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, 31 Center Drive, Bethesda, MD, 20892, USA
| | - Cynthia Martellaro
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Janine Brandt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Lisa Wendt
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Andreas Müller
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Stephanie Peitsch
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Sonja M Best
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Jürgen Stech
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Stefan Finke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Angela Römer-Oberdörfer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Allison Groseth
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA.,Junior Research Group Arenavirus Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA
| | - Thomas Hoenen
- Laboratory of Virology, Division of Intramural Research, National Institute for Allergy and Infectious Diseases, National Institutes of Health, 903 S 4th St., Hamilton, MT, 59840, USA. .,Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald, Insel Riems, Germany.
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9
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10
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Heaton NS, Moshkina N, Fenouil R, Gardner TJ, Aguirre S, Shah PS, Zhao N, Manganaro L, Hultquist JF, Noel J, Sachs D, Hamilton J, Leon PE, Chawdury A, Tripathi S, Melegari C, Campisi L, Hai R, Metreveli G, Gamarnik AV, García-Sastre A, Greenbaum B, Simon V, Fernandez-Sesma A, Krogan NJ, Mulder LCF, van Bakel H, Tortorella D, Taunton J, Palese P, Marazzi I. Targeting Viral Proteostasis Limits Influenza Virus, HIV, and Dengue Virus Infection. Immunity 2016; 44:46-58. [PMID: 26789921 DOI: 10.1016/j.immuni.2015.12.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/22/2022]
Abstract
Viruses are obligate parasites and thus require the machinery of the host cell to replicate. Inhibition of host factors co-opted during active infection is a strategy hosts use to suppress viral replication and a potential pan-antiviral therapy. To define the cellular proteins and processes required for a virus during infection is thus crucial to understanding the mechanisms of virally induced disease. In this report, we generated fully infectious tagged influenza viruses and used infection-based proteomics to identify pivotal arms of cellular signaling required for influenza virus growth and infectivity. Using mathematical modeling and genetic and pharmacologic approaches, we revealed that modulation of Sec61-mediated cotranslational translocation selectively impaired glycoprotein proteostasis of influenza as well as HIV and dengue viruses and led to inhibition of viral growth and infectivity. Thus, by studying virus-human protein-protein interactions in the context of active replication, we have identified targetable host factors for broad-spectrum antiviral therapies.
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Affiliation(s)
- Nicholas S Heaton
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Natasha Moshkina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Romain Fenouil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Thomas J Gardner
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Sebastian Aguirre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Priya S Shah
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Nan Zhao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Lara Manganaro
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Justine Noel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - David Sachs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Jennifer Hamilton
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Paul E Leon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Amit Chawdury
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Camilla Melegari
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Laura Campisi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Rong Hai
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Giorgi Metreveli
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Andrea V Gamarnik
- Fundación Instituto Leloir-CONICET, Avenida Patricias Argentinas 435, Buenos Aires 1405, Argentina
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Benjamin Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Division of Hematology and Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Lubbertus C F Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Domenico Tortorella
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158-2140, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA.
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11
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Abstract
Ebola virus (EBOV) infects humans as well as several animal species. It can lead to a highly lethal disease, with mortality rates approaching 90% in primates. Recent advances have deepened our understanding of how this virus is able to prevent the development of protective immune responses. The EBOV genome encodes eight proteins, four of which were shown to interact with the host in ways that counteract the immune response. The viral protein 35 (VP35) is capable of capping dsRNA and interacts with IRF7 to prevent detection of the virus by immune cells. The main role of the soluble glycoprotein (sGP) is still unclear, but it is capable of subverting the anti-GP1,2 antibody response. The GP1,2 protein has shown anti-tetherin activity and the ability to hide cell-surface proteins. Finally, VP24 interferes with the production of interferons (IFNs) and with IFN signaling in infected cells. Taken together, these data point to extensive adaptation of EBOV to evade the immune system of dead end hosts. While our understanding of the interactions between the human and viral proteins increases, details of those interactions in other hosts remain largely unclear and represent a gap in our knowledge.
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Affiliation(s)
- Jonathan Audet
- 1 Department of Medical Microbiology, University of Manitoba , Winnipeg, Manitoba, Canada
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12
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García-Dorival I, Wu W, Dowall S, Armstrong S, Touzelet O, Wastling J, Barr JN, Matthews D, Carroll M, Hewson R, Hiscox JA. Elucidation of the Ebola Virus VP24 Cellular Interactome and Disruption of Virus Biology through Targeted Inhibition of Host-Cell Protein Function. J Proteome Res 2014; 13:5120-35. [DOI: 10.1021/pr500556d] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Isabel García-Dorival
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Weining Wu
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Stuart Dowall
- Public Health England, Porton
Down, Salisbury SP4 0JG, United Kingdom
| | - Stuart Armstrong
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - Olivier Touzelet
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
| | - Jonathan Wastling
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
| | - John N. Barr
- School
of Molecular and Cellular Biology, Faculty of Biological Science, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - David Matthews
- School
of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Miles Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
- Public Health England, Porton
Down, Salisbury SP4 0JG, United Kingdom
| | - Roger Hewson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
- Public Health England, Porton
Down, Salisbury SP4 0JG, United Kingdom
| | - Julian A. Hiscox
- Department
of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool L3 5RF, United Kingdom
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool L69 7BE, United Kingdom
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13
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Abstract
The VP24 protein plays an essential, albeit poorly understood role in the filovirus life cycle. VP24 is only 30% identical between Marburg virus and the ebolaviruses. Furthermore, VP24 from the ebolaviruses is immunosuppressive, while that of Marburg virus is not. The crystal structure of Marburg virus VP24, presented here, reveals that although the core is similar between the viral genera, Marburg VP24 is distinguished by a projecting β-shelf and an alternate conformation of the N-terminal polypeptide.
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14
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DNA topoisomerase 1 facilitates the transcription and replication of the Ebola virus genome. J Virol 2013; 87:8862-9. [PMID: 23658456 DOI: 10.1128/jvi.03544-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ebola virus (EBOV) protein L (EBOL) acts as a viral RNA-dependent RNA polymerase. To better understand the mechanisms underlying the transcription and replication of the EBOV genome, we sought to identify cellular factors involved in these processes via their coimmunoprecipitation with EBOL and by mass spectrometry. Of 65 candidate proteins identified, we focused on DNA topoisomerase 1 (TOP1), which localizes to the nucleus and unwinds helical DNA. We found that in the presence of EBOL, TOP1 colocalizes and interacts with EBOL in the cytoplasm, where transcription and replication of the EBOV genome occur. Knockdown of TOP1 markedly reduced virus replication and viral polymerase activity. We also found that the phosphodiester bridge-cleaving and recombination activities of TOP1 are required for the polymerase activity of EBOL. These results demonstrate that TOP1 is an important cellular factor for the transcription and replication of the EBOV genome and, as such, plays a key role in the EBOV life cycle.
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