A BioID-derived proximity interactome for SARS-CoV-2 proteins

Abstract

The novel coronavirus SARS-CoV-2 is responsible for the ongoing COVID-19 pandemic and has caused a major health and economic burden worldwide. Understanding how SARS-CoV-2 viral proteins behave in host cells can reveal underlying mechanisms of pathogenesis and assist in development of antiviral therapies. Here we use BioID to map the SARS-CoV-2 virus-host interactome using human lung cancer derived A549 cells expressing individual SARS-CoV-2 viral proteins. Functional enrichment analyses revealed previously reported and unreported cellular pathways that are in association with SARS-CoV-2 proteins. We have also established a website to host the proteomic data to allow for public access and continued analysis of host-viral protein associations and whole-cell proteomes of cells expressing the viral-BioID fusion proteins. Collectively, these studies provide a valuable resource to potentially uncover novel SARS-CoV-2 biology and inform development of antivirals.

ER-export and ARFRP1/AP-1-dependent delivery of SARS-CoV-2 Envelope to lysosomes controls late stages of viral replication

“…Notably, we recovered many new PDZ-domain containing proteins that were biotinylated in a manner requiring E's extreme C-terminus, many of which have been subsequently validated, including PALS1 23 and TJP1 50 and which likely contribute to epithelial barrier function. Our interactomes differ from those reported by affinity purification 1 , but do not suffer from high-level overexpression or placement of affinity or BioID tags that would disrupt the normal localisation of E 1,[51][52][53] . Secondly, we present a trans-complementation assay allowing depletion and rescue of sub-genomic RNAs encoding SARS-CoV-2 structural proteins, allowing us to take reverse genetic approaches without needing to create genetically modified recombinant SARS-CoV-2 viruses.…”

Multiomics approach reveals the ubiquitination-specific processes hijacked by SARS-CoV-2

“…The SARS-CoV-2-host interactome was constructed in several studies through affinity-purification-mass spectrometry (AP-MS) or proximity-dependent biotinylation (BioID). [36][37][38][39][40] We integrated the interaction data from these studies to construct a relatively complete set of SARS-CoV-2-host interactome (Supplementary Table 4). Interestingly, we found that the ubiquitination of many host proteins that interact with SARS-CoV-2 was also changed after viral infection (Supplementary Fig.…”

“…Interestingly, SARS-CoV-2 genome does not encode E3 ubiquitin ligases, indicating that the ubiquitination of viral proteins was catalyzed by host E3 ligases. Based on the interactome data, [36][37][38][39][40] we found twenty-five viral proteins, which interacted with host E3 ligases (e.g., ORF8 with FBXL12, NSP8 with HERC5, ORF8 with LGALS3BP) and sixteen viral proteins, which interacted with DUB (e.g., NSP2 with USP47, NSP10 with USP11) (Fig. 4g, h).…”

“…The high-confidence host-SARS-CoV-2 protein interaction networks were curated from five published works [37][38][39][40][41] (Supplementary Table 4). The interactions with fold-change no more than 2 were excluded as background.…”

Trans-synaptic dwelling of SARS-CoV-2 particles perturbs neural synapse organization and function

“…3B-C ). Interestingly, the protein FLRT3, the main receptor of LPHN3 ( 33 ), was recently identified to be closely associated to the viral protein Spike in a BioID proximity labeling assay (PLA) ( 34 ). However, we were not able to highlight interactions between FLRT3 and Spike in primary neurons by co-immunoprecipitation, while ACE-2 successfully pulled-down ( Suppl Fig.…”