Structural and Biological Basis of Alphacoronavirus nsp1 Associated with Host Proliferation and Immune Evasion

Non-structural protein 1 (nsp1) is only characterized in alphacoronaviruses (alpha-CoVs) and betacoronaviruses (beta-CoVs). There have been extensive researches on how the beta-CoVs nsp1 regulates viral virulence by inhibiting host protein synthesis, but the regulatory mechanism of the alpha-CoVs nsp1 is still unclear. Here, we report the 2.1-angstrom full-length crystal structure of nsp1 in emerging porcine SADS-CoV and the 1.8-angstrom full-length crystal structure of nsp1 in the highly lethal cat FIPV. Although they belong to different subtypes of alpha-CoVs, these viruses all have a bucket-shaped fold composed of six beta-sheets, similar to the crystal structure of PEDV and TGEV nsp1. Comparing the above four structures, we found that the structure of alpha-CoVs nsp1 in the same subtype was more conserved. We then selected mammalian cells that were treated with SADS-CoV and FIPV nsp1 for RNA sequencing analysis and found that nsp1 had a specific inhibitory effect on interferon (IFN) and cell cycle genes. Using the Renilla luciferase (Rluc) assay and Western blotting, we confirmed that seven representative alpha-CoVs nsp1s could significantly inhibit the phosphorylation of STAT1-S727 and interfere with the effect of IFN-I. Moreover, the cell cycle experiment confirmed that alpha-CoVs nsp1 could encourage host cells to stay in the G0/G1 phase. Based on these findings, we not only greatly improved the crystal structure data on alpha-CoVs nsp1, but we also speculated that alpha-CoVs nsp1 regulated host proliferation and immune evasion-related biological functions by inhibiting the synthesis of host proteins, thus creating an environment conducive to the virus.