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Sullender ME, Pierce LR, Annaswamy Srinivas M, Crockett SL, Dunlap BF, Rodgers R, Schriefer LA, Kennedy EA, Stewart BM, Doench JG, Baldridge MT, Orchard RC. Selective Polyprotein Processing Determines Norovirus Sensitivity to Trim7. J Virol 2022; 96:e0070722. [PMID: 35972292 PMCID: PMC9472627 DOI: 10.1128/jvi.00707-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
Noroviruses are a leading cause of gastroenteritis worldwide, yet the molecular mechanisms of how host antiviral factors restrict norovirus infection are poorly understood. Here, we present a CRISPR activation screen that identifies mouse genes which inhibit murine norovirus (MNV) replication. Detailed analysis of the major hit Trim7 demonstrates a potent inhibition of the early stages of MNV replication. Leveraging in vitro evolution, we identified MNV mutants that escape Trim7 restriction by altering the cleavage of the viral NS6-7 polyprotein precursor. NS6, but not the NS6-7 precursor, directly binds the substrate-binding domain of Trim7. Surprisingly, the selective polyprotein processing that enables Trim7 evasion inflicts a significant evolutionary burden, as viruses with decreased NS6-7 cleavage are strongly attenuated in viral replication and pathogenesis. Our data provide an unappreciated mechanism of viral evasion of cellular antiviral factors through selective polyprotein processing and highlight the evolutionary tradeoffs in acquiring resistance to host restriction factors. IMPORTANCE To maximize a limited genetic capacity, viruses encode polyproteins that can be subsequently separated into individual components by viral proteases. While classically viewed as a means of economy, recent findings have indicated that polyprotein processing can spatially and temporally coordinate the distinct phases of the viral life cycle. Here, we present a function for alternative polyprotein processing centered on immune defense. We discovered that selective polyprotein processing of the murine norovirus polyprotein shields MNV from restriction by the host antiviral protein Trim7. Trim7 can bind the viral protein NS6 but not the viral precursor protein NS6-7. Our findings provide insight into the evolutionary pressures that define patterns of viral polyprotein processing and uncover a trade-off between viral replication and immune evasion.
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Affiliation(s)
- Meagan E. Sullender
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Linley R. Pierce
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Stacey L. Crockett
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bria F. Dunlap
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rachel Rodgers
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lawrence A. Schriefer
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elizabeth A. Kennedy
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Brittany M. Stewart
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Robert C. Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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2
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The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation. PLoS Pathog 2021; 17:e1009412. [PMID: 34597346 PMCID: PMC8513853 DOI: 10.1371/journal.ppat.1009412] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 10/13/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022] Open
Abstract
Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It identified viral protein adjacency to specific host proteins whose regulatory variants are linked to COVID-19 severity, including the TRIM4 interferon signaling regulator which was found proximal to the SARS-CoV-2 M protein. Viral NSP1 protein adjacency to the EIF3 complex was associated with inhibited host protein translation whereas ORF6 localization with MAVS was associated with inhibited RIG-I 2CARD-mediated IFNB1 promoter activation. Quantitative proteomics identified candidate host targets for the NSP5 protease, with specific functional cleavage sequences in host proteins CWC22 and FANCD2. This data resource identifies host factors proximal to viral proteins in living human cells and nominates pathogenic mechanisms employed by SARS-CoV-2. SARS-CoV-2 is the latest pathogenic coronavirus to emerge as a public health threat. We create a database of proximal host proteins to 17 SARS-CoV-2 viral proteins. We validate that NSP1 is proximal to the EIF3 translation initiation complex and is a potent inhibitor of translation. We also identify ORF6 antagonism of RNA-mediate innate immune signaling. We produce a database of potential host targets of the viral protease NSP5, and create a fluorescence-based assay to screen cleavage of peptide sequences. We believe that this data will be useful for identifying roles for many of the uncharacterized SARS-CoV-2 proteins and provide insights into the pathogenicity of new or emerging coronaviruses.
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3
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Meyer B, Chiaravalli J, Gellenoncourt S, Brownridge P, Bryne DP, Daly LA, Grauslys A, Walter M, Agou F, Chakrabarti LA, Craik CS, Eyers CE, Eyers PA, Gambin Y, Jones AR, Sierecki E, Verdin E, Vignuzzi M, Emmott E. Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential. Nat Commun 2021; 12:5553. [PMID: 34548480 PMCID: PMC8455558 DOI: 10.1038/s41467-021-25796-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigens S and N: the main targets for vaccine and antibody testing efforts. We discover significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We show that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, show a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.
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Affiliation(s)
- Bjoern Meyer
- Viral Populations and Pathogenesis Unit, CNRS, UMR 3569, Institut Pasteur, CEDEX 15, Paris, France
| | - Jeanne Chiaravalli
- Chemogenomic and Biological Screening Core Facility, C2RT, Departments of Cell Biology & Infection and of Structural Biology & Chemistry, Institut Pasteur, CEDEX 15, Paris, France
| | - Stacy Gellenoncourt
- CIVIC Group, Virus & Immunity Unit, Institut Pasteur and CNRS, UMR 3569, Paris, France
| | - Philip Brownridge
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Dominic P Bryne
- Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Leonard A Daly
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Arturas Grauslys
- Computational Biology Facility, LIV-SRF, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Marius Walter
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Fabrice Agou
- Chemogenomic and Biological Screening Core Facility, C2RT, Departments of Cell Biology & Infection and of Structural Biology & Chemistry, Institut Pasteur, CEDEX 15, Paris, France
| | - Lisa A Chakrabarti
- CIVIC Group, Virus & Immunity Unit, Institut Pasteur and CNRS, UMR 3569, Paris, France
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Claire E Eyers
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Patrick A Eyers
- Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Yann Gambin
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Andrew R Jones
- Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Emma Sierecki
- EMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, NSW, 2052, Australia
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, 94945, USA
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS, UMR 3569, Institut Pasteur, CEDEX 15, Paris, France
| | - Edward Emmott
- Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK.
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4
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Dycke JV, Rymenants J, Neyts J, Rocha-Pereira J. Assessment of the anti-norovirus activity in cell culture using the mouse norovirus: Early mechanistic studies. Antivir Chem Chemother 2021; 29:20402066211025175. [PMID: 34525875 PMCID: PMC8450984 DOI: 10.1177/20402066211025175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Human norovirus is the main cause of viral gastroenteritis, resulting annually in ∼ 700 million infections and 200,000 deaths, of whom most are children <5 years. Mouse norovirus-infected macrophages are the most widely used in vitro system to screen and characterize the antiviral effect of norovirus-targeting small molecules. We have previously established antiviral assays using this system, identified novel inhibitors and performed additional studies in order to have a first insight into their mechanism of action. After the identification of novel small molecules with anti-norovirus activity (part 1 of this protocol), we here describe the logical next step which entails the generation of early information of their mode of action. This information together with a continuous improvement of the potency of compounds will contribute to the optimization of a compound class towards in vivo efficacy and a successful preclinical development.
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Affiliation(s)
- Jana Van Dycke
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Jasper Rymenants
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Johan Neyts
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Joana Rocha-Pereira
- KU Leuven - Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Leuven, Belgium
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5
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Van Dycke J, Dai W, Stylianidou Z, Li J, Cuvry A, Roux E, Li B, Rymenants J, Bervoets L, de Witte P, Liu H, Neyts J, Rocha-Pereira J. A Novel Class of Norovirus Inhibitors Targeting the Viral Protease with Potent Antiviral Activity In Vitro and In Vivo. Viruses 2021; 13:v13091852. [PMID: 34578432 PMCID: PMC8472913 DOI: 10.3390/v13091852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 12/15/2022] Open
Abstract
Human noroviruses (HuNoVs) are the most common cause of viral gastroenteritis resulting annually in ~219,000 deaths and a societal cost of ~USD 60 billion, and no antivirals or vaccines are available. Here, we assess the anti-norovirus activity of new peptidomimetic aldehydes related to the protease inhibitor rupintrivir. The early hit compound 4 inhibited the replication of murine norovirus (MNV) and the HuNoV GI.1 replicon in vitro (EC50 ~1 µM) and swiftly cleared the HuNoV GI.1 replicon from the cells. Compound 4 still inhibits the proteolytic activity. We selected a resistant GI.1 replicon, with a mutation (I109V) in a highly conserved region of the viral protease, conferring a low yield of resistance against compound 4 and rupintrivir. After testing new derivatives, compound 10d was the most potent (EC50 nanomolar range). Molecular docking indicated that the aldehyde group of compounds 4 and 10d bind with Cys139 in the HuNoV 3CL protease by a covalent linkage. Finally, compound 10d inhibited the replication of HuNoV GII.4 in infected zebrafish larvae, and PK studies in mice showed an adequate profile.
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Affiliation(s)
- Jana Van Dycke
- Laboratory of Virology and Chemotherapy, KU Leuven–Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium; (J.V.D.); (Z.S.); (A.C.); (E.R.); (J.R.); (L.B.); (J.N.)
| | - Wenhao Dai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (W.D.); (J.L.); (B.L.)
| | - Zoe Stylianidou
- Laboratory of Virology and Chemotherapy, KU Leuven–Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium; (J.V.D.); (Z.S.); (A.C.); (E.R.); (J.R.); (L.B.); (J.N.)
| | - Jian Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (W.D.); (J.L.); (B.L.)
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Qixia District, Nanjing 210023, China
| | - Arno Cuvry
- Laboratory of Virology and Chemotherapy, KU Leuven–Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium; (J.V.D.); (Z.S.); (A.C.); (E.R.); (J.R.); (L.B.); (J.N.)
| | - Emma Roux
- Laboratory of Virology and Chemotherapy, KU Leuven–Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium; (J.V.D.); (Z.S.); (A.C.); (E.R.); (J.R.); (L.B.); (J.N.)
| | - Bingqian Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (W.D.); (J.L.); (B.L.)
| | - Jasper Rymenants
- Laboratory of Virology and Chemotherapy, KU Leuven–Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium; (J.V.D.); (Z.S.); (A.C.); (E.R.); (J.R.); (L.B.); (J.N.)
| | - Lindsey Bervoets
- Laboratory of Virology and Chemotherapy, KU Leuven–Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium; (J.V.D.); (Z.S.); (A.C.); (E.R.); (J.R.); (L.B.); (J.N.)
| | - Peter de Witte
- Laboratory for Molecular Biodiscovery, KU Leuven–Department of Pharmaceutical and Pharmacological Sciences, 3000 Leuven, Belgium;
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China; (W.D.); (J.L.); (B.L.)
- Correspondence: (H.L.); (J.R.-P.)
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, KU Leuven–Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium; (J.V.D.); (Z.S.); (A.C.); (E.R.); (J.R.); (L.B.); (J.N.)
| | - Joana Rocha-Pereira
- Laboratory of Virology and Chemotherapy, KU Leuven–Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium; (J.V.D.); (Z.S.); (A.C.); (E.R.); (J.R.); (L.B.); (J.N.)
- Correspondence: (H.L.); (J.R.-P.)
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6
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Borg C, Jahun AS, Thorne L, Sorgeloos F, Bailey D, Goodfellow IG. Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection. J Gen Virol 2021; 102. [PMID: 34491891 PMCID: PMC8567427 DOI: 10.1099/jgv.0.001651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Murine norovirus (MNV) is widely used as a model for studying norovirus biology. While MNV isolates vary in their pathogenesis, infection of immunocompetent mice mostly results in persistent infection. The ability of a virus to establish a persistent infection is dependent on its ability to subvert or avoid the host immune response. Previously, we described the identification and characterization of virulence factor 1 (VF1) in MNV, and demonstrated its role as an innate immune antagonist. Here, we explore the role of VF1 during persistent MNV infection in an immunocompetent host. Using reverse genetics, we generated MNV-3 viruses carrying a single or a triple termination codon inserted in the VF1 ORF. VF1-deleted MNV-3 replicated to comparable levels to the wildtype virus in tissue culture. Comparative studies between MNV-3 and an acute MNV-1 strain show that MNV-3 VF1 exerts the same functions as MNV-1 VF1, but with reduced potency. C57BL/6 mice infected with VF1-deleted MNV-3 showed significantly reduced replication kinetics during the acute phase of the infection, but viral loads rapidly reached the levels seen in mice infected with wildtype virus after phenotypic restoration of VF1 expression. Infection with an MNV-3 mutant that had three termination codons inserted into VF1, in which reversion was suppressed, resulted in consistently lower replication throughout a 3 month persistent infection in mice, suggesting a role for VF1 in viral fitness in vivo. Our results indicate that VF1 expressed by a persistent strain of MNV also functions to antagonize the innate response to infection. We found that VF1 is not essential for viral persistence, but instead contributes to viral fitness in mice. These data fit with the hypothesis that noroviruses utilize multiple mechanisms to avoid and/or control the host response to infection and that VF1 is just one component of this.
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Affiliation(s)
- Constantina Borg
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, Cambridge, CB2 0QQ, UK
| | - Aminu S Jahun
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, Cambridge, CB2 0QQ, UK
| | - Lucy Thorne
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, Cambridge, CB2 0QQ, UK.,Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Frédéric Sorgeloos
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, Cambridge, CB2 0QQ, UK.,Université catholique de Louvain, de Duve Institute, MIPA-VIRO 74-49, 74 Avenue Hippocrate, B-1200 Brussels, Belgium
| | - Dalan Bailey
- The Pirbright Institute, Pirbright, Woking, GU24 0NF, UK
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, Cambridge, CB2 0QQ, UK
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7
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The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33655243 PMCID: PMC7924263 DOI: 10.1101/2021.02.23.432450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Viral proteins localize within subcellular compartments to subvert host machinery and promote pathogenesis. To study SARS-CoV-2 biology, we generated an atlas of 2422 human proteins vicinal to 17 SARS-CoV-2 viral proteins using proximity proteomics. This identified viral proteins at specific intracellular locations, such as association of accessary proteins with intracellular membranes, and projected SARS-CoV-2 impacts on innate immune signaling, ER-Golgi transport, and protein translation. It identified viral protein adjacency to specific host proteins whose regulatory variants are linked to COVID-19 severity, including the TRIM4 interferon signaling regulator which was found proximal to the SARS-CoV-2 M protein. Viral NSP1 protein adjacency to the EIF3 complex was associated with inhibited host protein translation whereas ORF6 localization with MAVS was associated with inhibited RIG-I 2CARD-mediated IFNB1 promoter activation. Quantitative proteomics identified candidate host targets for the NSP5 protease, with specific functional cleavage sequences in host proteins CWC22 and FANCD2. This data resource identifies host factors proximal to viral proteins in living human cells and nominates pathogenic mechanisms employed by SARS-CoV-2. Author Summary SARS-CoV-2 is the latest pathogenic coronavirus to emerge as a public health threat. We create a database of proximal host proteins to 17 SARS-CoV-2 viral proteins. We validate that NSP1 is proximal to the EIF3 translation initiation complex and is a potent inhibitor of translation. We also identify ORF6 antagonism of RNA-mediate innate immune signaling. We produce a database of potential host targets of the viral protease NSP5, and create a fluorescence-based assay to screen cleavage of peptide sequences. We believe that this data will be useful for identifying roles for many of the uncharacterized SARS-CoV-2 proteins and provide insights into the pathogenicity of new or emerging coronaviruses.
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8
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Weihs F, Anderson A, Trowell S, Caron K. Resonance Energy Transfer-Based Biosensors for Point-of-Need Diagnosis-Progress and Perspectives. SENSORS (BASEL, SWITZERLAND) 2021; 21:660. [PMID: 33477883 PMCID: PMC7833371 DOI: 10.3390/s21020660] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
The demand for point-of-need (PON) diagnostics for clinical and other applications is continuing to grow. Much of this demand is currently serviced by biosensors, which combine a bioanalytical sensing element with a transducing device that reports results to the user. Ideally, such devices are easy to use and do not require special skills of the end user. Application-dependent, PON devices may need to be capable of measuring low levels of analytes very rapidly, and it is often helpful if they are also portable. To date, only two transduction modalities, colorimetric lateral flow immunoassays (LFIs) and electrochemical assays, fully meet these requirements and have been widely adopted at the point-of-need. These modalities are either non-quantitative (LFIs) or highly analyte-specific (electrochemical glucose meters), therefore requiring considerable modification if they are to be co-opted for measuring other biomarkers. Förster Resonance Energy Transfer (RET)-based biosensors incorporate a quantitative and highly versatile transduction modality that has been extensively used in biomedical research laboratories. RET-biosensors have not yet been applied at the point-of-need despite its advantages over other established techniques. In this review, we explore and discuss recent developments in the translation of RET-biosensors for PON diagnoses, including their potential benefits and drawbacks.
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Affiliation(s)
- Felix Weihs
- CSIRO Health & Biosecurity, Parkville, 343 Royal Parade, Melbourne, VIC 3030, Australia;
| | - Alisha Anderson
- CSIRO Health & Biosecurity, Black Mountain, Canberra, ACT 2600, Australia;
| | - Stephen Trowell
- PPB Technology Pty Ltd., Centre for Entrepreneurial Agri-Technology, Australian National University, Canberra, ACT 2601, Australia;
| | - Karine Caron
- CSIRO Health & Biosecurity, Black Mountain, Canberra, ACT 2600, Australia;
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9
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Kiss B, Mudra D, Török G, Mártonfalvi Z, Csík G, Herényi L, Kellermayer M. Single-particle virology. Biophys Rev 2020; 12:1141-1154. [PMID: 32880826 PMCID: PMC7471434 DOI: 10.1007/s12551-020-00747-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/18/2020] [Indexed: 01/02/2023] Open
Abstract
The development of advanced experimental methodologies, such as optical tweezers, scanning-probe and super-resolved optical microscopies, has led to the evolution of single-molecule biophysics, a field of science that allows direct access to the mechanistic detail of biomolecular structure and function. The extension of single-molecule methods to the investigation of particles such as viruses permits unprecedented insights into the behavior of supramolecular assemblies. Here we address the scope of viral exploration at the level of individual particles. In an era of increased awareness towards virology, single-particle approaches are expected to facilitate the in-depth understanding, and hence combating, of viral diseases.
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Affiliation(s)
- Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Dorottya Mudra
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - György Török
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Mártonfalvi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Gabriella Csík
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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10
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Liang KH, Chang TJ, Wang ML, Tsai PH, Lin TH, Wang CT, Yang DM. Novel biosensor platforms for the detection of coronavirus infection and severe acute respiratory syndrome coronavirus 2. J Chin Med Assoc 2020; 83:701-703. [PMID: 32349033 PMCID: PMC7493778 DOI: 10.1097/jcma.0000000000000337] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022] Open
Abstract
The recent outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been causing respiratory diseases globally, damaging wide ranges of social-economic activities. This virus is transmitted through personal contact and possibly also through ambient air. Effective biosensor platforms for the detection of this virus and the related host response are in urgent demand. These platforms can facilitate routine diagnostic assays in certified clinical laboratories. They can also be integrated into point-of-care products. Furthermore, environmental biosensors can be designed to detect SARS-CoV-2 in the ambient air or in the intensive care ventilators. Here, we evaluate technical components of biosensors, including the biological targets of recognition, the recognition methods, and the signal amplification and transduction systems. Effective SARS-CoV-2 detectors can be designed by an adequate combination of these technologies.
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Affiliation(s)
- Kung-Hao Liang
- Laboratory of Systems Biomedical Science, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei, Taiwan, ROC
- Institute of Biomedical Informatics, School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Tai-Jay Chang
- Laboratory of Genome Research, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- School of Biomedical science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Mong-Lien Wang
- Institute of Food Safety and Health Risk Assessment, National Yang-Ming University, Taipei, Taiwan, ROC
- Laboratory of Molecular Oncology, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Ping-Hsing Tsai
- Laboratory of Stem Cell Research II, Division of Basic Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Ta-Hsien Lin
- Institute of Biomedical Informatics, School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
- Laboratory of Nuclear Magnetic Resonance, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
| | - Chin-Tien Wang
- Laboratory of Molecular Virology, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan, ROC
| | - De-Ming Yang
- Microscopy Service Laboratory, Basic Research Division, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan, ROC
- Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC
- Biophotonics and Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei, Taiwan, ROC
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11
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Koehler M, Delguste M, Sieben C, Gillet L, Alsteens D. Initial Step of Virus Entry: Virion Binding to Cell-Surface Glycans. Annu Rev Virol 2020; 7:143-165. [PMID: 32396772 DOI: 10.1146/annurev-virology-122019-070025] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virus infection is an intricate process that requires the concerted action of both viral and host cell components. Entry of viruses into cells is initiated by interactions between viral proteins and cell-surface receptors. Various cell-surface glycans function as initial, usually low-affinity attachment factors, providing a first anchor of the virus to the cell surface, and further facilitate high-affinity binding to virus-specific cell-surface receptors, while other glycans function as specific entry receptors themselves. It is now possible to rapidly identify specific glycan receptors using different techniques, define atomic-level structures of virus-glycan complexes, and study these interactions at the single-virion level. This review provides a detailed overview of the role of glycans in viral infection and highlights experimental approaches to study virus-glycan binding along with specific examples. In particular, we highlight the development of the atomic force microscope to investigate interactions with glycans at the single-virion level directly on living mammalian cells, which offers new perspectives to better understand virus-glycan interactions in physiologically relevant conditions.
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Affiliation(s)
- Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium;
| | - Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium;
| | - Christian Sieben
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Laurent Gillet
- Immunology-Vaccinology Laboratory, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals and Health center (FARAH), University of Liège, 4000 Liège, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; .,Walloon Excellence in Life sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
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12
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Norovirus infection results in eIF2α independent host translation shut-off and remodels the G3BP1 interactome evading stress granule formation. PLoS Pathog 2020; 16:e1008250. [PMID: 31905230 PMCID: PMC6964919 DOI: 10.1371/journal.ppat.1008250] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 01/16/2020] [Accepted: 12/04/2019] [Indexed: 12/14/2022] Open
Abstract
Viral infections impose major stress on the host cell. In response, stress pathways can rapidly deploy defence mechanisms by shutting off the protein synthesis machinery and triggering the accumulation of mRNAs into stress granules to limit the use of energy and nutrients. Because this threatens viral gene expression, viruses need to evade these pathways to propagate. Human norovirus is responsible for gastroenteritis outbreaks worldwide. Here we examined how norovirus interacts with the eIF2α signaling axis controlling translation and stress granules. While norovirus infection represses host cell translation, our mechanistic analyses revealed that eIF2α signaling mediated by the stress kinase GCN2 is uncoupled from translational stalling. Moreover, infection results in a redistribution of the RNA-binding protein G3BP1 to replication complexes and remodelling of its interacting partners, allowing the avoidance from canonical stress granules. These results define novel strategies by which norovirus undergo efficient replication whilst avoiding the host stress response and manipulating the G3BP1 interactome. Viruses have evolved elegant strategies to evade host responses that restrict viral propagation by targeting the protein synthesis machinery and stress granules, which are membrane-less RNA granules with antiviral properties. Previous studies have unravelled how viruses, including norovirus the leading cause of gastroenteritis, regulate the activity of translation factors to affect the antiviral response. Furthermore, stress granules evasion strategies have been linked to targeting the scaffolding protein G3BP1. Here we dissect how murine norovirus, the main model for norovirus, evades the cellular stress responses. Our work challenges the dogma that translational control during infection is mainly mediated by eIF2α and demonstrate that norovirus evades this stress pathway. We further show that norovirus evades the stress granule response in a novel way by isolating and characterising the G3BP1 interactome for the first time in the context of a viral infection. We conclude that norovirus infection results in a redistribution of G3BP1 and its cellular partners to replication complexes, thereby preventing the assembly of stress granules. Overall, we define a novel evasion strategy by which norovirus escapes stress granule formation by rewiring the G3BP1 interactome.
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13
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Emmott E, de Rougemont A, Hosmillo M, Lu J, Fitzmaurice T, Haas J, Goodfellow I. Polyprotein processing and intermolecular interactions within the viral replication complex spatially and temporally control norovirus protease activity. J Biol Chem 2019; 294:4259-4271. [PMID: 30647130 PMCID: PMC6422069 DOI: 10.1074/jbc.ra118.006780] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Indexed: 11/26/2022] Open
Abstract
Norovirus infections are a major cause of acute viral gastroenteritis and a significant burden on global human health. A vital process for norovirus replication is the processing of the nonstructural polyprotein by a viral protease into the viral components required to form the viral replication complex. This cleavage occurs at different rates, resulting in the accumulation of stable precursor forms. Here, we characterized how precursor forms of the norovirus protease accumulate during infection. Using stable forms of the protease precursors, we demonstrated that all of them are proteolytically active in vitro, but that when expressed in cells, their activities are determined by both substrate and protease localization. Although all precursors could cleave a replication complex-associated substrate, only a subset of precursors lacking the NS4 protein were capable of efficiently cleaving a cytoplasmic substrate. By mapping the full range of protein-protein interactions among murine and human norovirus proteins with the LUMIER assay, we uncovered conserved interactions between replication complex members that modify the localization of a protease precursor subset. Finally, we demonstrate that fusion to the membrane-bound replication complex components permits efficient cleavage of a fused substrate when active polyprotein-derived protease is provided in trans These findings offer a model for how norovirus can regulate the timing of substrate cleavage throughout the replication cycle. Because the norovirus protease represents a key target in antiviral therapies, an improved understanding of its function and regulation, as well as identification of interactions among the other nonstructural proteins, offers new avenues for antiviral drug design.
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Affiliation(s)
- Edward Emmott
- From the Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom,
| | - Alexis de Rougemont
- the National Reference Centre for Gastroenteritis Viruses, Labology of Biology and Pathology, University Hospital Dijon Bourgogne, Dijon 21700, France
- the AgroSup Dijon, PAM UMR A 02.102 Bourgogne Franche-Comte University, Dijon 21000, France, and
| | - Myra Hosmillo
- From the Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Jia Lu
- From the Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Timothy Fitzmaurice
- From the Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Jürgen Haas
- the Division of Infection and Pathway Medicine, University of Edinburgh Medical School, Edinburgh EH16 4SB, United Kingdom
| | - Ian Goodfellow
- From the Division of Virology, Department of Pathology, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom,
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Muzzarelli KM, Kuiper B, Spellmon N, Brunzelle J, Hackett J, Amblard F, Zhou S, Liu P, Kovari IA, Yang Z, Schinazi RF, Kovari LC. Structural and Antiviral Studies of the Human Norovirus GII.4 Protease. Biochemistry 2019; 58:900-907. [PMID: 30605321 DOI: 10.1021/acs.biochem.8b01063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Norovirus is the leading cause of acute gastroenteritis worldwide with a yearly reported 700 million cases driving a $60 billion global socioeconomic burden. With no United States Food and Drug Administration approved therapeutics and the chance for severe chronic infection and life-threatening complications, researchers have identified the protease as a potential target. However, drug development has focused on the norovirus GI.1 strain despite its accounting for less than 5% of all outbreaks. Our lab aims to change focus for norovirus drug design from GI.1 to the highly infective GII.4, responsible for more than 50% of all outbreaks worldwide. With the first published crystal structure of the norovirus GII.4 protease, we have identified several significant differences in the structure and active site that have hindered development of a potent inhibitor targeting the norovirus GII.4 protease. With these new insights, we have begun designing compounds that demonstrate increased inhibition of the clinically most relevant norovirus GII.4 strain.
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Affiliation(s)
- Kendall M Muzzarelli
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Benjamin Kuiper
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Nicholas Spellmon
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Joseph Brunzelle
- Synchrotron Research Center, Life Science Collaborative Access Team , Northwestern University , Argonne , Illinois United States
| | - Justin Hackett
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Shaoman Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Peng Liu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Iulia A Kovari
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Zhe Yang
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology and Immunology , Wayne State University School of Medicine , Detroit , Michigan 48201 , United States
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15
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Kitano M, Hosmillo M, Emmott E, Lu J, Goodfellow I. Selection and Characterization of Rupintrivir-Resistant Norwalk Virus Replicon Cells In Vitro. Antimicrob Agents Chemother 2018; 62:e00201-18. [PMID: 29530860 PMCID: PMC5923142 DOI: 10.1128/aac.00201-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/02/2018] [Indexed: 12/30/2022] Open
Abstract
Human norovirus (HuNoV) is a major cause of nonbacterial gastroenteritis worldwide, yet despite its impact on society, vaccines and antivirals are currently lacking. A HuNoV replicon system has been widely applied to the evaluation of antiviral compounds and has thus accelerated the process of drug discovery against HuNoV infection. Rupintrivir, an irreversible inhibitor of the human rhinovirus 3C protease, has been reported to inhibit the replication of the Norwalk virus replicon via the inhibition of the norovirus protease. Here we report, for the first time, the generation of rupintrivir-resistant human Norwalk virus replicon cells in vitro Sequence analysis revealed that these replicon cells contained amino acid substitutions of alanine 105 to valine (A105V) and isoleucine 109 to valine (I109V) in the viral protease NS6. The application of a cell-based fluorescence resonance energy transfer (FRET) assay for protease activity demonstrated that these substitutions were involved in the enhanced resistance to rupintrivir. Furthermore, we validated the effect of these mutations using reverse genetics in murine norovirus (MNV), demonstrating that a recombinant MNV strain with a single I109V substitution in the protease also showed reduced susceptibility to rupintrivir. In summary, using a combination of different approaches, we have demonstrated that, under the correct conditions, mutations in the norovirus protease that lead to the generation of resistant mutants can rapidly occur.
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Affiliation(s)
- Mitsutaka Kitano
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Edward Emmott
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Jia Lu
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Ian Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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16
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Witte R, Andriasyan V, Georgi F, Yakimovich A, Greber UF. Concepts in Light Microscopy of Viruses. Viruses 2018; 10:E202. [PMID: 29670029 PMCID: PMC5923496 DOI: 10.3390/v10040202] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Viruses threaten humans, livestock, and plants, and are difficult to combat. Imaging of viruses by light microscopy is key to uncover the nature of known and emerging viruses in the quest for finding new ways to treat viral disease and deepening the understanding of virus–host interactions. Here, we provide an overview of recent technology for imaging cells and viruses by light microscopy, in particular fluorescence microscopy in static and live-cell modes. The review lays out guidelines for how novel fluorescent chemical probes and proteins can be used in light microscopy to illuminate cells, and how they can be used to study virus infections. We discuss advantages and opportunities of confocal and multi-photon microscopy, selective plane illumination microscopy, and super-resolution microscopy. We emphasize the prevalent concepts in image processing and data analyses, and provide an outlook into label-free digital holographic microscopy for virus research.
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Affiliation(s)
- Robert Witte
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Vardan Andriasyan
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Fanny Georgi
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| | - Artur Yakimovich
- MRC Laboratory for Molecular Cell Biology, University College London, Gower St., London WC1E 6BT, UK.
| | - Urs F Greber
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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17
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Goryashchenko AS, Khrenova MG, Savitsky AP. Detection of protease activity by fluorescent protein FRET sensors: from computer simulation to live cells. Methods Appl Fluoresc 2018; 6:022001. [DOI: 10.1088/2050-6120/aa9e47] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Yokoyama M, Oka T, Takagi H, Kojima H, Okabe T, Nagano T, Tohya Y, Sato H. A Proposal for a Structural Model of the Feline Calicivirus Protease Bound to the Substrate Peptide under Physiological Conditions. Front Microbiol 2017; 8:1383. [PMID: 28790989 PMCID: PMC5524728 DOI: 10.3389/fmicb.2017.01383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/10/2017] [Indexed: 11/30/2022] Open
Abstract
Feline calicivirus (FCV) protease functions to cleave viral precursor proteins during productive infection. Previous studies have mapped a protease-coding region and six cleavage sites in viral precursor proteins. However, how the FCV protease interacts with its substrates remains unknown. To gain insights into the interactions, we constructed a molecular model of the FCV protease bound with the octapeptide containing a cleavage site of the capsid precursor protein by homology modeling and docking simulation. The complex model was used to screen for the substrate mimic from a chemical library by pharmacophore-based in silico screening. With this structure-based approach, we identified a compound that has physicochemical features and arrangement of the P3 and P4 sites of the substrate in the protease, is predicted to bind to FCV proteases in a mode similar to that of the authentic substrate, and has the ability to inhibit viral protease activity in vitro and in the cells, and to suppress viral replication in FCV-infected cells. The complex model was further subjected to molecular dynamics simulation to refine the enzyme-substrate interactions in solution. The simulation along with a variation study predicted that the authentic substrate and anti-FCV compound share a highly conserved binding site. These results suggest the validity of our in silico model for elucidating protease-substrate interactions during FCV replication and for developing antivirals.
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Affiliation(s)
- Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious DiseasesTokyo, Japan
| | - Hirotaka Takagi
- Division of Biosafety Control and Research, National Institute of Infectious DiseasesTokyo, Japan
| | | | - Takayoshi Okabe
- Drug Discovery Initiative, The University of TokyoTokyo, Japan
| | - Tetsuo Nagano
- Drug Discovery Initiative, The University of TokyoTokyo, Japan
| | - Yukinobu Tohya
- Department of Veterinary Medicine, Nihon UniversityFujisawa, Japan
| | - Hironori Sato
- Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan
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19
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Design and Validation of Novel Chikungunya Virus Protease Inhibitors. Antimicrob Agents Chemother 2016; 60:7382-7395. [PMID: 27736770 DOI: 10.1128/aac.01421-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/20/2016] [Indexed: 11/20/2022] Open
Abstract
Chikungunya virus (CHIKV; genus Alphavirus) is the causative agent of chikungunya fever. CHIKV replication can be inhibited by some broad-spectrum antiviral compounds; in contrast, there is very little information about compounds specifically inhibiting the enzymatic activities of CHIKV replication proteins. These proteins are translated in the form of a nonstructural (ns) P1234 polyprotein precursor from the CHIKV positive-strand RNA genome. Active forms of replicase enzymes are generated using the autoproteolytic activity of nsP2. The available three-dimensional (3D) structure of nsP2 protease has made it a target for in silico drug design; however, there is thus far little evidence that the designed compounds indeed inhibit the protease activity of nsP2 and/or suppress CHIKV replication. In this study, a set of 12 compounds, predicted to interact with the active center of nsP2 protease, was designed using target-based modeling. The majority of these compounds were shown to inhibit the ability of nsP2 to process recombinant protein and synthetic peptide substrates. Furthermore, all compounds found to be active in these cell-free assays also suppressed CHIKV replication in cell culture, the 50% effective concentration (EC50) of the most potent inhibitor being ∼1.5 μM. Analysis of stereoisomers of one compound revealed that inhibition of both the nsP2 protease activity and CHIKV replication depended on the conformation of the inhibitor. Combining the data obtained from different assays also indicates that some of the analyzed compounds may suppress CHIKV replication using more than one mechanism.
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20
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Rocha-Pereira J, Van Dycke J, Neyts J. Norovirus genetic diversity and evolution: implications for antiviral therapy. Curr Opin Virol 2016; 20:92-98. [PMID: 27736665 DOI: 10.1016/j.coviro.2016.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/16/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023]
Abstract
Human noroviruses are the leading cause of foodborne illness causing both acute and chronic gastroenteritis. In recent years, a number of vaccine candidates entered (pre-) clinical development and the first efforts to develop antiviral therapy have been made. We here discuss aspects of norovirus genetic evolution, persistence in immunocompromised patients as well as the risk and potential consequences of resistance development toward future antiviral drugs.
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Affiliation(s)
- Joana Rocha-Pereira
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Jana Van Dycke
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Johan Neyts
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.
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Abstract
INTRODUCTION Rapid transmission of norovirus often occurs due to its low infectious dosage, high genetic diversity and its short incubation time. The viruses cause acute gastroenteritis and may lead to death. Presently, no effective vaccine or selective drugs accepted by the United States Food and Drug Administration (FDA) are available for the treatment of norovirus. Advances in the development of norovirus replicon cell lines, GII.4-Sydney HuNoV strain human B cells, and murine and gnotobiotic pig norovirus models have facilitated the discovery of effective small molecule inhibitors in vitro and in vivo. AREAS COVERED This review gives a brief discussion of the biology and replication of norovirus before highlighting the discovery of anti-norovirus molecules. The article coverage includes: an overview of the current state of norovirus drug discovery, the targeting of the norovirus life cycle, the inhibition of structural and nonstructural proteins of norovirus such as proteases and polymerase, and the blockage of virus entry into host cells. Finally, anti-norovirus drugs in the clinical development stage are described. EXPERT OPINION The current approach for the counteraction of norovirus focuses on the inhibition of viral RNA polymerase, norovirus 3C-like protease and the structural proteins VP1 as well as the blockade of norovirus entry. Broad-spectrum anti-norovirus molecules, based on the inhibition of 3C-like protease, have been developed. Other host factors and ways to overcome the development of resistance through mutation are also being examined. A dual approach in targeting viral and host factors may lead to an effective counteraction of norovirus infection. Current successes in developing norovirus replicon harboring cells and norovirus infected human cells, as well as murine norovirus models and other animal models such as piglets have facilitated the discovery of effective drugs and helped our understanding of its mechanism of action.
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Affiliation(s)
- Sahani Weerasekara
- a Department of Chemistry , Kansas State University , Manhattan , KS , USA
| | - Allan M Prior
- b Molecular Sciences Institute, School of Chemistry , University of the Witwatersrand , Johannesburg , South Africa
| | - Duy H Hua
- a Department of Chemistry , Kansas State University , Manhattan , KS , USA
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