NSP1 interacts with ribosomal proteins, ribosome biogenesis factors and viral response factors. (A) Scheme for NSP1 BioID. NSP1 is fused with a promiscuous biotin ligase (birA), leading to labeling of proteins within a ∼10 nm radius. Labeled proteins are isolated on streptavidin beads and quantified by LC-MS/MS. Unfunctional mutants of NSP1 and biotin ligase alone (mock) serve as negative controls. (B) Volcano plots showing proteins enriched in SARS-CoV-2 NSP1-BioID. −log10 P-values (Y) are plotted against log2 fold change of LFQ (label-free quantification) values between NSP1-BioID and the indicated NSP1 mutant or BioID alone (mock) (X). Specific ribosomal protein (green), nuclear export factor 1 (NXF1, black), viral defense factors (referred to in the text and assigned to the GO category “defense response to virus,” red), and nucleases (orange) are shown. (C) Volcano plots showing changes in total proteome of 293T cells upon expression of SARS-CoV-2 NSP1. −log10 P-values (Y) are plotted against log2 fold change of LFQ (label-free quantification) values between NSP1 and the indicated NSP1 mutant or tag alone (mock) (X). (D) Boxplot showing changes in expression of proteins encoded by TOP genes (cyan) and all other genes (gray) upon expression of WT NSP1, compared with mock (WT/mock), KH164AA NSP1 mutant (WT/KH164AA), and RK124AA mutant (WT/RK124AA).
