The SARS-CoV-2 proteins NSP1 and NSP13 inhibit interferon activation through distinct mechanisms

Abstract

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic, infecting over 100 million people and claiming over 2 million lives globally. This drastically highlights the need for understanding the host-virus protein-protein interactions and immune evasion strategies governing SARS-CoV-2 pathogenesis. Our overall aim was to identify antiviral immune targeting during SARS-CoV-2 infection and protein overexpression. To understand if SARS-CoV-2 can block immune signaling, we first examined nuclear translocation of the transcription factors, IRF3 and NF-κB, as nuclear translocation is one step in interferon induction, during SARS-CoV-2 infection of the human airway epithelial cells. We found that in infected cells, there was limited IRF3 and NF-κB nuclear translocation, suggesting SARS-CoV-2 can limit immune activation. Additionally, through promoter luciferase signaling assays, the viral proteins NSP1, the host translation shutoff factor, and NSP13, the RNA helicase, can block signaling to the IFN-β and NF-κB promoters. To further investigate this reduction in promoter signaling, we examined nuclear translocation of NF-κB in the context of NSP1 and NSP13 plasmid overexpression. Surprisingly, we found that while NSP13 reduced NF-κB nuclear translocation, NSP1 was unable to despite its ability to limit promoter signaling. Instead, we found, utilizing Click-it chemistry, that NSP1 reduces host protein synthesis. Last, we found NSP13 targets TBK1 activation by limiting its phosphorylation in a dose-dependent manner. Collectively, our data illustrate that SARS-CoV-2 can block multiple innate immune signaling pathways through distinct mechanisms.