The nucleotide addition cycle of the SARS-CoV-2 polymerase

Subhas Chandra Bera; Mona Seifert; Robert N. Kirchdoerfer; Pauline van Nies; Yibulayin Wubulikasimu; Salina Quack; Flávia S. Papini; Jamie J. Arnold; Bruno Canard; Craig E. Cameron; Martin Depken; David Dulin

doi:10.1016/j.celrep.2021.109650

The nucleotide addition cycle of the SARS-CoV-2 polymerase

Subhas Chandra Bera, Mona Seifert, Robert N. Kirchdoerfer, Pauline van Nies, Yibulayin Wubulikasimu, Salina Quack, Flávia S. Papini, Jamie J. Arnold, Bruno Canard, Craig E. Cameron, Martin Depken^*, David Dulin

^*Corresponding author for this work

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

Coronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We use a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core polymerase. The core polymerase exists in at least three catalytically distinct conformations, one being kinetically consistent with incorporation of incorrect nucleotides. We provide evidence that the RNA-dependent RNA polymerase (RdRp) uses a thermal ratchet instead of a power stroke to transition from the pre- to post-translocated state. Ultra-stable magnetic tweezers enable the direct observation of coronavirus polymerase deep and long-lived backtracking that is strongly stimulated by secondary structures in the template. The framework we present here elucidates one of the most important structure-dynamics-function relationships in human health today and will form the grounds for understanding the regulation of this complex.

Original language	English
Article number	109650
Pages (from-to)	1-23
Number of pages	23
Journal	Cell Reports
Volume	36
Issue number	9
Early online date	17 Aug 2021
DOIs	https://doi.org/10.1016/j.celrep.2021.109650
Publication status	Published - 31 Aug 2021

Bibliographical note

Funding Information:
D.D. thanks OICE for hosting his lab. D.D. was supported by the Interdisciplinary Center for Clinical Research (IZKF) at the University Hospital of the University of Erlangen-Nuremberg, the German Research Foundation ( DFG-DU-1872/3-1 ), the Netherlands Ministry of Education, Culture and Science (OCW) BaSyC (Building a Synthetic Cell) Gravitation grant ( 024.003.019 ), and the Netherlands Organisation for Scientific Research (NWO). R.N.K. was supported by NIAID NIH ( AI123498 ). B.C. acknowledge grants by the Fondation pour la Recherche Médicale (Aide aux équipes), the SCORE project H2020 SC1-PHE-Coronavirus-2020 ( 101003627 ), and the REACTing initiative (REsearch and ACTion targeting emerging infectious diseases). J.J.A. and C.E.C. were supported by NIAID NIH ( AI045818 ).

Publisher Copyright:
© 2021 The Author(s)

Keywords

backtracking
high-throughput/ultra-stable magnetic tweezers
nucleotide addition cycle
polymerase mechanochemistry
SARS-CoV-2 polymerase
single-molecule biophysics

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title = "The nucleotide addition cycle of the SARS-CoV-2 polymerase",

abstract = "Coronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We use a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core polymerase. The core polymerase exists in at least three catalytically distinct conformations, one being kinetically consistent with incorporation of incorrect nucleotides. We provide evidence that the RNA-dependent RNA polymerase (RdRp) uses a thermal ratchet instead of a power stroke to transition from the pre- to post-translocated state. Ultra-stable magnetic tweezers enable the direct observation of coronavirus polymerase deep and long-lived backtracking that is strongly stimulated by secondary structures in the template. The framework we present here elucidates one of the most important structure-dynamics-function relationships in human health today and will form the grounds for understanding the regulation of this complex.",

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AU - Wubulikasimu, Yibulayin

AU - Quack, Salina

AU - Papini, Flávia S.

AU - Arnold, Jamie J.

AU - Canard, Bruno

AU - Cameron, Craig E.

AU - Depken, Martin

AU - Dulin, David

N1 - Funding Information: D.D. thanks OICE for hosting his lab. D.D. was supported by the Interdisciplinary Center for Clinical Research (IZKF) at the University Hospital of the University of Erlangen-Nuremberg, the German Research Foundation ( DFG-DU-1872/3-1 ), the Netherlands Ministry of Education, Culture and Science (OCW) BaSyC (Building a Synthetic Cell) Gravitation grant ( 024.003.019 ), and the Netherlands Organisation for Scientific Research (NWO). R.N.K. was supported by NIAID NIH ( AI123498 ). B.C. acknowledge grants by the Fondation pour la Recherche Médicale (Aide aux équipes), the SCORE project H2020 SC1-PHE-Coronavirus-2020 ( 101003627 ), and the REACTing initiative (REsearch and ACTion targeting emerging infectious diseases). J.J.A. and C.E.C. were supported by NIAID NIH ( AI045818 ). Publisher Copyright: © 2021 The Author(s)

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N2 - Coronaviruses have evolved elaborate multisubunit machines to replicate and transcribe their genomes. Central to these machines are the RNA-dependent RNA polymerase subunit (nsp12) and its intimately associated cofactors (nsp7 and nsp8). We use a high-throughput magnetic-tweezers approach to develop a mechanochemical description of this core polymerase. The core polymerase exists in at least three catalytically distinct conformations, one being kinetically consistent with incorporation of incorrect nucleotides. We provide evidence that the RNA-dependent RNA polymerase (RdRp) uses a thermal ratchet instead of a power stroke to transition from the pre- to post-translocated state. Ultra-stable magnetic tweezers enable the direct observation of coronavirus polymerase deep and long-lived backtracking that is strongly stimulated by secondary structures in the template. The framework we present here elucidates one of the most important structure-dynamics-function relationships in human health today and will form the grounds for understanding the regulation of this complex.

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The nucleotide addition cycle of the SARS-CoV-2 polymerase

Abstract

Bibliographical note

Keywords

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