SARS-CoV-2 Nsp1 suppresses the canonical NF-κB pathway by promoting ubiquitin-dependent degradation of TAK1 kinase
Fig 2
A pretrained protein language model identifies viral protein interactions with the canonical NF-κB pathway.
a: Schematic overview of the geometric weighted pathway interaction score (GWPIS) for quantifying the interactions between viral proteins and immune-related pathways in infected host cells. Step 1: Data collection of the sequences of SARS-CoV-2 proteins and host proteins in the immune pathways shown in Fig 1d. Step 2: V-H protein interaction score: The D-SCRIPT protein language model was used to compute the interaction scores between SARS-CoV-2 proteins and host proteins in immune-related pathways. Step 3: Pathway-level interaction scores were calculated by integrating the pairwise interaction scores from Step 2 and the gene weights obtained from the PROGENy gene-pathway weight matrix. Created in BioRender. Yang, Q. (2026) https://BioRender.com/41xkykd. b: Interactions between SARS-CoV-2 proteins and the canonical NF-κB pathway, as calculated by GWPIS. Each circle represents a SARS-CoV-2 protein, and the color intensity and thickness of the lines reflect the interaction scores. Green, structural proteins (S, E, M, and N); blue, ORF proteins; red/pink, nonstructural proteins. c: Western blot analysis showing the regulation of key proteins in the canonical NF-κB pathway in HEK293T cells expressing SARS-CoV-2 Nsps or GFP as a control (Ctrl). The phosphorylated and total protein levels of p65 and IκBα were probed with the corresponding antibodies, and the relative intensity signals were quantified using ImageJ. d: Bar chart showing the ratios of phosphorylated and total protein levels in (c). The red dashed line represents the ratio in the GFP-expressing control cells (black). e: Activities of the promoter containing NF-κB response elements (κB sites) were measured by a dual luciferase assay. HEK293T cells were transfected with a plasmid expressing a Renilla luciferase reporter driven by a promoter containing 2 κB sites and a control Firefly luciferase 24 hr before transfection of Nsp1 or control GFP-expressing plasmids. The cells were collected 24 h later for the dual luciferase assay. Each dot represents a replicate, and the mean and SEM are shown. P values, Mann-Whitney test. f: Relative mRNA levels of IL-8, IP-10 and TNF-α in HEK293T cells transfected with plasmids expressing cMYC-tagged Nsp1 or the GFP control (Ctrl). GAPDH was used as an internal control. Each dot represents a replicate, and the mean and SEM are shown. P values, Mann-Whitney test. The results in e-f are representative of two independent experiments.