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Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential

Bjoern MeyerViral Populations and Pathogenesis Unit, CNRS, UMR 3569, Institut Pasteur, CEDEX 15, Paris, FranceJeanne ChiaravalliChemogenomic and Biological Screening Core Facility, C2RT, Departments of Cell Biology & Infection and of Structural Biology & Chemistry, Institut Pasteur, CEDEX 15, Paris, FranceStacy GellenoncourtCIVIC Group, Virus & Immunity Unit, Institut Pasteur and CNRS, UMR 3569, Paris, FrancePhilip BrownridgeCentre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UKDominic P. BryneDepartment of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UKLeonard A. DalyCentre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UKArturas GrauslysComputational Biology Facility, LIV-SRF, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UKMarius WalterBuck Institute for Research on Aging, Novato, CA, 94945, USAFabrice AgouChemogenomic and Biological Screening Core Facility, C2RT, Departments of Cell Biology & Infection and of Structural Biology & Chemistry, Institut Pasteur, CEDEX 15, Paris, FranceLisa A. ChakrabartiCIVIC Group, Virus & Immunity Unit, Institut Pasteur and CNRS, UMR 3569, Paris, FranceCharles S. CraikDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USAClaire E. EyersCentre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UKPatrick A. EyersDepartment of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UKYann GambinEMBL Australia Node for Single Molecule Sciences, and School of Medical Sciences, Botany Road, The University of New South Wales, Sydney, NSW, 2052, AustraliaAndrew R. JonesDepartment of Biochemistry & Systems Biology, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UKEmma SiereckiEMBL AustraliaEric VerdinBuck Institute for Research on Aging, Novato, CA, 94945, USAMarco VignuzziViral Populations and Pathogenesis Unit, CNRS, UMR 3569, Institut Pasteur, CEDEX 15, Paris, FranceEdward EmmottCentre 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. [email protected]

2021en

ABI

Annotatsiya

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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Identifikatorlar

DOI: 10.1038/s41467-021-25796-w

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