Coupling of N7-methyltransferase and 3′-5′ exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading

• Published in: Cell 2021-06, Vol.184 (13), p.3474-3485.e11
• Main Authors: Yan, Liming, Yang, Yunxiang, Li, Mingyu, Zhang, Ying, Zheng, Litao, Ge, Ji, Huang, Yucen C., Liu, Zhenyu, Wang, Tao, Gao, Shan, Zhang, Ran, Huang, Yuanyun Y., Guddat, Luke W., Gao, Yan, Rao, Zihe, Lou, Zhiyong
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Coronavirus RNA-Dependent RNA Polymerase - genetics; COVID-19 - virology; cryo-EM; Exoribonucleases - genetics; Humans; Methyltransferases - genetics; mRNA capping; proofreading; replication-transcription complex; RNA, Messenger - genetics; RNA, Viral - genetics; SARS-CoV-2; SARS-CoV-2 - genetics; Sequence Alignment; Transcription, Genetic - genetics; Virus Replication - genetics
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2021.05.033

The capping of mRNA and the proofreading play essential roles in SARS-CoV-2 replication and transcription. Here, we present the cryo-EM structure of the SARS-CoV-2 replication-transcription complex (RTC) in a form identified as Cap(0)-RTC, which couples a co-transcriptional capping complex (CCC) composed of nsp12 NiRAN, nsp9, the bifunctional nsp14 possessing an N-terminal exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), and nsp10 as a cofactor of nsp14. Nsp9 and nsp12 NiRAN recruit nsp10/nsp14 into the Cap(0)-RTC, forming the N7-CCC to yield cap(0) (7MeGpppA) at 5′ end of pre-mRNA. A dimeric form of Cap(0)-RTC observed by cryo-EM suggests an in trans backtracking mechanism for nsp14 ExoN to facilitate proofreading of the RNA in concert with polymerase nsp12. These results not only provide a structural basis for understanding co-transcriptional modification of SARS-CoV-2 mRNA but also shed light on how replication fidelity in SARS-CoV-2 is maintained. [Display omitted] •Structure of SARS-CoV-2 Cap(0)-RTC is determined•Cap(0)-RTC couples a co-transcriptional capping complex bearing nsp10/nsp14•The third action for mRNA capping occurs in Cap(0)-RTC•The dimeric Cap(0)-RTC suggests an in trans backtracking proofreading mechanism Structures of the capping machinery and the polymerase super-complex of SARS-CoV-2 provides insights into virus replication, mRNA capping, and proofreading.