Atlas of interactions between SARS-CoV-2 macromolecules and host proteins

Abstract

The proteins and RNAs of viruses extensively interact with host proteins after infection. We collected and reanalyzed all available datasets of protein-protein and RNA-protein interactions related to SARS-CoV-2. We investigated the reproducibility of those interactions and made strict filters to identify highly confident interactions. We systematically analyzed the interaction network and identified preferred subcellular localizations of viral proteins, some of which such as ORF8 in ER and ORF7A/B in ER membrane were validated using dual fluorescence imaging. Moreover, we showed that viral proteins frequently interact with host machinery related to protein processing in ER and vesicle-associated processes. Integrating the protein- and RNA-interactomes, we found that SARS-CoV-2 RNA and its N protein closely interacted with stress granules including 40 core factors, of which we specifically validated G3BP1, IGF2BP1, and MOV10 using RIP and Co-IP assays. Combining CRISPR screening results, we further identified 86 antiviral and 62 proviral factors and associated drugs. Using network diffusion, we found additional 44 interacting proteins including two proviral factors previously validated. Furthermore, we showed that this atlas could be applied to identify the complications associated with COVID-19. All data are available in the AIMaP database (https://mvip.whu.edu.cn/aimap/) for users to easily explore the interaction map.

Keywords: Drug repurposing; Protein localization; Protein-interactome; RNA-Interactome; SARS-CoV-2.

Graphical abstract

Fig. 1

Overview of the approaches for systematically analyzing viral protein and RNA interactomes. (A) Schematic of strategies for exploring protein-protein interaction and RNA-protein interaction between SARS-CoV-2 and host. (B) Matrix-like plot showing the viral protein baits information in each study of AP-MS and PL-MS. The datasets with processed results were labeled with red circles on the right.

Fig. 2

Summary ofSARS-CoV-2protein-host protein interactions. (A) The number of viral protein-host protein interactions from different studies. (B–C) Pie charts showing the proportion of virus protein-host protein interactions from different studies, which were identified by AP-MS (B) and PL-MS (C) experimental strategy, respectively. (D) The network of virus protein-host protein interactions identified by AP-MS (AP-interactome). Hexagon yellow nodes represent viral proteins. Circular blue nodes represent host proteins. Edges indicate virus-host protein interactions. Edge thickness represents the credibility level of interactions.

Fig. 3

Comparison between viral proteinAP-interactomeand PL-interactome. (A) The number of interacting proteins of each viral protein identified in AP-interactome, PL-interactome, or both. (B–C) Localization analysis of viral proteins based on host proteins in AP-interactome (B) and PL-interactome (C). Previously validated proteins localizing in the membrane are marked in blue dotted boxes and proteins validated in this study are labeled with red dotted boxes. (D) Western blotting of expressed mCherry-tagged viral proteins (left) and eGFP-tagged marker proteins (right). (E-H) Representative fluorescence images showing co-localization between ORF7A (E)/ORF7B (F)/ORF8 (G)/ORF10 (H) (red) and LBR/SEC61B (green). The plots on the right showed the fluorescence intensity along the region of interest (ROI).

Fig. 4

A compendium of high-confident protein-protein interactions between SARS-CoV-2 and host. Hexagon yellow nodes represent viral proteins. Circular grey nodes represent host proteins. Edges indicate virus-host protein interactions that supported by AP-MS (blue) or PL-MS (pink). Protein complexes (and cellular component) according to GO-term analysis and proteins sharing the identical domain are enclosed within rounded quadrilateral. Edge thickness represents the strength of interactions.

Fig. 5

Overview ofSARS-CoV-2RNA-host protein interactions. (A) The number of viral RNA-host protein interactions from different studies. (B) Pie chart showing the proportion of viral RNA-host protein interactions from different studies. (C) A compendium of SARS-CoV-2 RNA-interactome. Central nodes represent SARS-CoV-2 RNAs. Ellipses represent host proteins. Edges represent viral RNA-protein interactions (pink) and protein-protein interactions (blue). Edge thickness indicates the affinity of interactions. Protein complexes (and cellular components) according to GO-term analysis are enclosed within sectors. (D) The dynamics of SARS-CoV-2 RNA-interactomes at different time points after viral infection. (E) Venn plot showing the overlap among the viral protein N-interactome, SG&PB proteome, and SARS-CoV-2 RNA-interactome. (F) The enrichment ratio of SG proteins (G3BP1, IGF2BP1, and MOV10)-bound NSP12 and N RNAs in SARS-CoV-2 infected cells using RNA immunoprecipitation followed by qRT-PCR. The relative RNA levels were normalized with ACTB RNA and the enrichment ratios were normalized with IgG samples. (G) Co-immunoprecipitation between viral N protein and the SG marker proteins (G3BP1, IGF2BP1, and MOV10) in SARS-CoV-2 infected cells. (H) A competitive model of SARS-CoV-2 RNA and N protein for the assembly of stress granule.

Fig. 6

Functional characteristics ofSARS-CoV-2interactomes. (A) Density map showing the distribution of mean CRISPR screening enrichment scores of host proteins after SARS-CoV-2 infection. Background 1 represents proteins that were identified but removed as background interactions. Background 2 (non-interactome) represents all other human genes that were not in the background and the SARS-CoV-2 interactome. Dashed lines indicated estimated 95% confidence interval values of the mean enrichment scores. (B) Heatmap plot showing the CRISPR screening enrichment scores of host proteins after SARS-CoV-2 infection. The numbers of provial and antiviral proteins are marked. (C) Network of predicted proviral protein-drug interactions. Circular nodes represent viral proteins (blue), viral RNA (yellow), host proteins (grey), and drugs in DGIdb (red). Edges indicate viral protein/RNA-host protein interactions (blue) and host protein-drug interactions (green). (D) Two subnetworks identified by the network diffusion approach. Circular nodes represent seed nodes (yellow) and candidate nodes (red). The size of nodes indicates the network diffusion score. (E) Disease enrichment analysis of the host proteins in SARS-CoV-2 protein AP-interactome (red), PL-interactome (green), and RNA-interactome (blue).