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Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease

Angel D’Oliviera, Xuhang Dai, Saba Mottaghinia, Evan P. Geissler, View ORCID ProfileLucie Etienne, View ORCID ProfileYingkai Zhang, View ORCID ProfileJeffrey S. Mugridge
doi: https://doi.org/10.1101/2023.02.20.529306
Angel D’Oliviera
1Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
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Xuhang Dai
2Department of Chemistry, New York University, New York, NY 10003
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Saba Mottaghinia
3CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
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Evan P. Geissler
1Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
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Lucie Etienne
3CIRI (Centre International de Recherche en Infectiologie), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
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Yingkai Zhang
2Department of Chemistry, New York University, New York, NY 10003
4Simons Center for Computational Physical Chemistry at New York University, New York, NY 10003
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Jeffrey S. Mugridge
1Department of Chemistry & Biochemistry, University of Delaware, Newark, DE 19716
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  • ORCID record for Jeffrey S. Mugridge
  • For correspondence: mugridge@udel.edu
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Abstract

The SARS-CoV-2 main protease (Mpro) plays a crucial role in the production of functional viral proteins during infection and, like many viral proteases, can also target and cleave host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification at the G26 position of mammalian tRNA, which promotes global protein synthesis, cellular redox homeostasis, and has links to neurological disability. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain that is required for tRNA modification activity in cells. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 may be resistant to cleavage. In primates, regions outside of the cleavage site with rapid evolution could indicate possible adaptation to ancient viral pathogens. To visualize how Mpro recognizes the TRMT1 cleavage sequence, we determined the structure of a TRMT1 peptide in complex with Mpro, which reveals a substrate binding conformation distinct from the majority of available SARS-CoV-2 Mpro-peptide complexes. Kinetic parameters for peptide cleavage showed that while TRMT1(526-536) is cleaved much slower than the Mpro nsp4/5 autoprocessing sequence, it is proteolyzed with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage that could help inform future therapeutic design and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection may impact protein translation or oxidative stress response and contribute to viral pathogenesis.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 21, 2023.
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Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease
Angel D’Oliviera, Xuhang Dai, Saba Mottaghinia, Evan P. Geissler, Lucie Etienne, Yingkai Zhang, Jeffrey S. Mugridge
bioRxiv 2023.02.20.529306; doi: https://doi.org/10.1101/2023.02.20.529306
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Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease
Angel D’Oliviera, Xuhang Dai, Saba Mottaghinia, Evan P. Geissler, Lucie Etienne, Yingkai Zhang, Jeffrey S. Mugridge
bioRxiv 2023.02.20.529306; doi: https://doi.org/10.1101/2023.02.20.529306

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