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Despite the odds: formation of the SARS-CoV-2 methylation complex

Alex Matsuda, View ORCID ProfileJacek Plewka, Yuliya Chykunova, Alisha N. Jones, Magdalena Pachota, View ORCID ProfileMichał Rawski, André Mourão, Abdulkarim Karim, Leanid Kresik, Kinga Lis, Igor Minia, Kinga Hartman, Ravi Sonani, View ORCID ProfileGrzegorz Dubin, View ORCID ProfileMichael Sattler, Piotr Suder, Paweł Mak, Grzegorz M. Popowicz, View ORCID ProfileKrzysztof Pyrć, View ORCID ProfileAnna Czarna
doi: https://doi.org/10.1101/2022.01.25.477673
Alex Matsuda
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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Jacek Plewka
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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Yuliya Chykunova
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
2Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
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Alisha N. Jones
3Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
4Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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Magdalena Pachota
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
2Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
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Michał Rawski
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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André Mourão
3Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
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Abdulkarim Karim
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
5Department of Biology, College of Science, Salahaddin University-Erbil, Kirkuk Road, 44002 Erbil, Kurdistan Region, Iraq
6Department of Community Health, College of Health Technology, Cihan University-Erbil, 100 street, 44001 Erbil, Kurdistan Region, Iraq
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Leanid Kresik
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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Kinga Lis
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
7Faculty of Chemical Engineering and Technology, Cracow University of Technology, Warszawska 24, 31-155, Poland
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Igor Minia
8Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin 13125, Germany
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Kinga Hartman
9Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
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Ravi Sonani
10Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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Grzegorz Dubin
10Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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Michael Sattler
3Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
4Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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Piotr Suder
9Department of Analytical Chemistry and Biochemistry, Faculty of Materials Science and Ceramics, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
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Paweł Mak
11Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
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Grzegorz M. Popowicz
3Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
4Bavarian NMR Center, Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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  • For correspondence: k.a.pyrc@uj.edu.pl
Krzysztof Pyrć
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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  • For correspondence: k.a.pyrc@uj.edu.pl
Anna Czarna
1Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
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  • For correspondence: k.a.pyrc@uj.edu.pl
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Abstract

Coronaviruses protect their single-stranded RNA genome with a methylated cap during replication. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16 where nsp10 acts as a co-factor to both. Aditionally, nsp14 carries an exonuclease domain, which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins should be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex. This interaction is expected to encourage formation of mature capped viral mRNA, modulating the nsp14’s exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 01, 2022.
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Despite the odds: formation of the SARS-CoV-2 methylation complex
Alex Matsuda, Jacek Plewka, Yuliya Chykunova, Alisha N. Jones, Magdalena Pachota, Michał Rawski, André Mourão, Abdulkarim Karim, Leanid Kresik, Kinga Lis, Igor Minia, Kinga Hartman, Ravi Sonani, Grzegorz Dubin, Michael Sattler, Piotr Suder, Paweł Mak, Grzegorz M. Popowicz, Krzysztof Pyrć, Anna Czarna
bioRxiv 2022.01.25.477673; doi: https://doi.org/10.1101/2022.01.25.477673
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Despite the odds: formation of the SARS-CoV-2 methylation complex
Alex Matsuda, Jacek Plewka, Yuliya Chykunova, Alisha N. Jones, Magdalena Pachota, Michał Rawski, André Mourão, Abdulkarim Karim, Leanid Kresik, Kinga Lis, Igor Minia, Kinga Hartman, Ravi Sonani, Grzegorz Dubin, Michael Sattler, Piotr Suder, Paweł Mak, Grzegorz M. Popowicz, Krzysztof Pyrć, Anna Czarna
bioRxiv 2022.01.25.477673; doi: https://doi.org/10.1101/2022.01.25.477673

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