A SARS-CoV-2 – host proximity interactome

Abstract

Viral replication is dependent on interactions between viral polypeptides and host proteins. Identifying virus-host protein interactions can thus uncover unique opportunities for interfering with the virus life cycle via novel drug compounds or drug repurposing. Importantly, many viral-host protein interactions take place at intracellular membranes and poorly soluble organelles, which are difficult to profile using classical biochemical purification approaches. Applying proximity-dependent biotinylation (BioID) with the fast-acting miniTurbo enzyme to 27 SARS-CoV-2 proteins in a lung adenocarcinoma cell line (A549), we detected 7810 proximity interactions (7382 of which are new for SARS-CoV-2) with 2242 host proteins (results available at covid19interactome.org). These results complement and dramatically expand upon recent affinity purification-based studies identifying stable host-virus protein complexes, and offer an unparalleled view of membrane-associated processes critical for viral production. Host cell organellar markers were also subjected to BioID in parallel, allowing us to propose modes of action for several viral proteins in the context of host proteome remodelling. In summary, our dataset identifies numerous high confidence proximity partners for SARS-CoV-2 viral proteins, and describes potential mechanisms for their effects on specific host cell functions.

The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions

“…This interaction, coupled with the fact that BRD2 is known to regulate the transcription of over 1,400 genes, 32 suggests that it may be worth exploring BRD2 as a potential host cell target to mitigate COVID-19 symptoms. 30 Known inhibitors of many other host cell factors that interact with viral proteins 30,31,33 or host cell signaling networks altered by viral infection 34 represent candidates for repurposed therapeutics against SARS-CoV-2.…”

SARS-CoV-2 infection remodels the host protein thermal stability landscape

“…Importantly, both UGDH and PAAF1 are required for SARS-CoV-2 infection 25 , and nsp6 was previously found to physically interact with UGDH, and the viral membrane glycoprotein M with UGDH and PAAF1 in BioID experiments 20 (Figure 4b). These data suggest that thermal destabilisation of UGDH and PAAF1 during SARS-CoV-2 infection capture functionally relevant changes in their biophysical state that impact SARS-CoV-2 proliferation.…”

“…To do this, we compared this list of proteins to previously acquired proteome-wide datasets describing SARS-CoV-2-host PPIs and phosphosite regulation upon infection 2,3 . We found an overlap of 30 proteins that had altered abundance or thermal stability and were previously shown to physically interact with viral baits in a nity puri cation mass spectrometry (AP-MS) experiments 3 ( Figure S3a), and 204 proteins in BioID experiments 20 ( Figure S3b). Additionally, 107 of the proteins with altered abundance or thermal stability also exhibited altered phosphorylation states during SARS-CoV-2 infection ( Figure S3c) 2 .…”

Mapping the SARS-CoV-2–Host Protein–Protein Interactome by Affinity Purification Mass Spectrometry and Proximity-Dependent Biotin Labeling: A Rational and Straightforward Route to Discover Host-Directed Anti-SARS-CoV-2 Therapeutics

“…Maps of PPIs between SARS-CoV-2 proteins and human proteins have been very recently identified (determined/uncovered) by both AP-MS [ 17 , 18 , 19 , 20 , 21 ] and BioID approaches [ 22 , 23 , 24 ]. The intriguing and fascinating SARS-CoV-2 landscapes emerging from these studies offer an extraordinary springboard for the systematic exploration of the virus–host interface in the search of host proteins already targeted by existing drugs.…”

“…In the studies here reviewed, the viral proteins are “affinity tagged” in order to identify their binding partners present in the specific host cellular system. To specifically construct SARS-CoV-2 PPI maps in several reports AP-MS was used [ 17 , 18 , 19 , 20 , 21 ], while in other studies the authors [ 22 , 23 , 24 ] used the different technology BioID in combination with MS [ 37 ]. The main steps of workflows describing these two approaches are illustrated in Figure 1 .…”