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Taha TY, Suryawanshi RK, Chen IP, Correy GJ, McCavitt-Malvido M, O’Leary PC, Jogalekar MP, Diolaiti ME, Kimmerly GR, Tsou CL, Gascon R, Montano M, Martinez-Sobrido L, Krogan NJ, Ashworth A, Fraser JS, Ott M. A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication in vivo. PLoS Pathog 2023; 19:e1011614. [PMID: 37651466 PMCID: PMC10499221 DOI: 10.1371/journal.ppat.1011614] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/13/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the role of Mac1 catalytic activity in viral replication, we generated recombinant viruses and replicons encoding a catalytically inactive NSP3 Mac1 domain by mutating a critical asparagine in the active site. While substitution to alanine (N40A) reduced catalytic activity by ~10-fold, mutations to aspartic acid (N40D) reduced activity by ~100-fold relative to wild-type. Importantly, the N40A mutation rendered Mac1 unstable in vitro and lowered expression levels in bacterial and mammalian cells. When incorporated into SARS-CoV-2 molecular clones, the N40D mutant only modestly affected viral fitness in immortalized cell lines, but reduced viral replication in human airway organoids by 10-fold. In mice, the N40D mutant replicated at >1000-fold lower levels compared to the wild-type virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection. Our data validate the critical role of SARS-CoV-2 NSP3 Mac1 catalytic activity in viral replication and as a promising therapeutic target to develop antivirals.
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Affiliation(s)
- Taha Y. Taha
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Rahul K. Suryawanshi
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Irene P. Chen
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
| | - Galen J. Correy
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Maria McCavitt-Malvido
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
| | - Patrick C. O’Leary
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Manasi P. Jogalekar
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Morgan E. Diolaiti
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - Gabriella R. Kimmerly
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Chia-Lin Tsou
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Ronnie Gascon
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Mauricio Montano
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
| | - Luis Martinez-Sobrido
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, United States of America
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Alan Ashworth
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California, United States of America
| | - James S. Fraser
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, United States of America
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California, United States of America
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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