Interactome Analysis of the Nucleocapsid Protein of SARS-CoV-2 Virus

Figure 1. Identification of potential cellular proteins that interact with SARS-CoV-2 N protein by transient transfection and affinity purification from HEK293T and Calu-3 cells. (A) Detection of 2x Strep-tagged N protein in lysates and immunoprecipitates by western blotting with anti-Strep antibodies. (B) Protein complexes immunoprecipitated using Strep beads separated by SDS-PAGE and subjected to silver staining.

Figure 2. SARS-CoV-2 N-human protein–protein interaction network. An interaction network (Cytoscape) between host factors and N proteins was generated. Interactomes in two cell lines were integrated (yellow nodes = interactors in HEK293T cells, orange nodes = interactors in Calu-3 cells, pink nodes = common interactors in both cell types). Curated host–host protein interactions from the CORUM and STRING databases are displayed as coloured subnetworks. Select human protein–protein complexes that are represented by at least three nodes are labelled.

Figure 3. Functional analysis of the SARS-CoV-2 N interactome. (A) Bubble visualisation of enriched protein domains among SARS-CoV-2 N interactome members (FDR < 0.05). The colour of the dots represents the false discovery rate (FDR) value for each enriched domain term, and the size represents the percentage of proteins enriched. (B) Bar graph of the top 20 enriched functional (GO and KEGG) terms across the SARS-CoV-2 N interactome, coloured by −log10 (p-value).

Figure 4. Overlapping information between the N protein interactome and other SARS-CoV-2-induced proteomes and transcriptomes. (A). Venn diagram showing the overlapping N protein interactions between our study and data obtained from the BioGRID [25] database. (B). Heatmap showing the variation in 43 genes overlapping between the N protein interactome of our study and previous SARS-CoV-2 induced transcriptome datasets [31]. (C). Point bar graph showing the expression of overlapped proteins between the N protein interactions and SARS-CoV-2 induced RNA-binding proteome [30]. FC, fold change.