Molecular Mechanism of SARS-CoVs Orf6 Targeting the Rae1-Nup98 Complex to Compete With mRNA Nuclear Export.

Tinghan Li,Xiaoyun Ji,Haitao Yang,Hangtian Guo,Tingting Yang,Yibo Wen

doi:10.3389/fmolb.2021.813248

Abstract

The accessory protein Orf6 is uniquely expressed in sarbecoviruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which is an ongoing pandemic. SARS-CoV-2 Orf6 antagonizes host interferon signaling by inhibition of mRNA nuclear export through its interactions with the ribonucleic acid export 1 (Rae1)–nucleoporin 98 (Nup98) complex. Here, we confirmed the direct tight binding of Orf6 to the Rae1-Nup98 complex, which competitively inhibits RNA binding. We determined the crystal structures of both SARS-CoV-2 and SARS-CoV-1 Orf6 C-termini in complex with the Rae1–Nup98 heterodimer. In each structure, SARS-CoV Orf6 occupies the same potential mRNA-binding groove of the Rae1–Nup98 complex, comparable to the previously reported structures of other viral proteins complexed with Rae1-Nup98, indicating that the Rae1–Nup98 complex is a common target for different viruses to impair the nuclear export pathway. Structural analysis and biochemical studies highlight the critical role of the highly conserved methionine (M58) of SARS-CoVs Orf6. Altogether our data unravel a mechanistic understanding of SARS-CoVs Orf6 targeting the mRNA-binding site of the Rae1–Nup98 complex to compete with the nuclear export of host mRNA, which further emphasizes that Orf6 is a critical virulence factor of SARS-CoVs.

Highlights

Coronavirus disease 2019 (COVID-19) (Berlin et al, 2020; Zhu et al, 2020), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Zhang and Holmes, 2020), has brought global pandemic since March 2020
Coimmunoprecipitation and pull-down experiments have shown that SARS-CoV-2 Orf6 can directly interact with the ribonucleic acid export 1 (Rae1)–nucleoporin 98 (Nup98) complex through its C-terminal tail (Miorin et al, 2020)
Given that Orf6 from SARS-CoV-1 has high sequence similarity with SARS-CoV-2 (∼85.7%), we anticipated that Orf6 from both viruses could interact with the Rae1–Nup98 complex

Summary

Introduction

Coronavirus disease 2019 (COVID-19) (Berlin et al, 2020; Zhu et al, 2020), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Zhang and Holmes, 2020), has brought global pandemic since March 2020. Upon entry into host cells, SARS-CoV-2 produces two polyproteins that are subsequently proteolytically processed into 16 non-structural proteins (Nsp1-Nsp16) which further form viral replicase–transcriptase complex in double-membrane vesicles (V’Kovski et al, 2021). SARS-CoV-2 genome encodes four structural proteins including spike (S), envelope (E), membrane (M) and nucleocapsid (N), and nine accessory proteins including Orf3a, 3b, 6, 7a, 7b, 8, 9b, 9c, and 10 (Chan et al, 2020). Orf3b and Orf from SARS-CoV-1 were found to antagonize with type-I interferon signaling during SARS-CoV-1 infection (Liu et al, 2014)

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Conclusion