Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

Abstract

The worldwide SARS-CoV-2 outbreak poses a serious challenge to human societies and economies. SARS-CoV-2 proteins orchestrate complex pathogenic mechanisms that underlie COVID-19 disease. Thus, understanding how viral polypeptides rewire host protein networks enables better-founded therapeutic research. In complement to existing proteomic studies, in this study we define the first proximal interaction network of SARS-CoV-2 proteins, at the whole proteome level in human cells. Applying a proximity-dependent biotinylation (BioID)-based approach greatly expanded the current knowledge by detecting interactions within poorly soluble compartments, transient, and/or of weak affinity in living cells. Our BioID study was complemented by a stringent filtering and uncovered 2,128 unique cellular targets (1,717 not previously associated with SARS-CoV-1 or 2 proteins) connected to the N- and C-ter BioID-tagged 28 SARS-CoV-2 proteins by a total of 5,415 (5,236 new) proximal interactions. In order to facilitate data exploitation, an innovative interactive 3D web interface was developed to allow customized analysis and exploration of the landscape of interactions (accessible at http://www.sars-cov-2-interactome.org/). Interestingly, 342 membrane proteins including interferon and interleukin pathways factors, were associated with specific viral proteins. We uncovered ORF7a and ORF7b protein proximal partners that could be related to anosmia and ageusia symptoms. Moreover, comparing proximal interactomes in basal and infection-mimicking conditions (poly(I:C) treatment) allowed us to detect novel links with major antiviral response pathway components, such as ORF9b with MAVS and ISG20; N with PKR and TARB2; NSP2 with RIG-I and STAT1; NSP16 with PARP9-DTX3L. Altogether, our study provides an unprecedented comprehensive resource for understanding how SARS-CoV-2 proteins orchestrate host proteome remodeling and innate immune response evasion, which can inform development of targeted therapeutic strategies.

Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets with therapeutic potential

“…3F, G). Adding confidence to these observations, approximately half of these hits were also identified in a recent SARS-CoV-2 proximity labelling study (ATP5F1B, GOLGA3, NUP107, PNN, SRC and WNK)(7), and GOLGA3 was additionally identified in an interactome study as an nsp13 interaction partner (6).…”

“…NUP107 is a member of the nuclear pore complex, with nucleo-cytoplasmic transport a frequent target for viral disregulation (32). GOLGA3 is thought to play a role in localisation of the Golgi and Golgi-nuclear interactions, and was identified in two recent studies of SARS-CoV-2 interactions (6, 7). PNN is a transcriptional activator, forming part of the exon junction complex, with roles in splicing and nonsense-mediated decay.…”

“…An understanding of any modifications to these antigens observed during natural infection, such as glycosylation, phosphorylation and proteolytic cleavage, is critical to enable the rational design and validation of vaccine antigens and the selection of appropriate systems for their production. Mass spectrometry-based proteomic approaches have already led to rapid advances in our understanding of SARS-CoV-2, with notable examples including the rapid release of the cellular interactome (6) and proximity interactome (7) for a majority of SARS-CoV-2 proteins, as well as proteomic (3, 5), phosphoproteomic (4, 8) and ubiquitomic analyses (9) Larger scale-initiatives have been launched focusing on community efforts to profile the immune response to infection, and provide in-depth characterization of viral antigens (20). Mass spectrometry has particular advantages for investigation of proteolytic cleavage as analysis can be conducted in an unbiased manner, and identify not only the substrate, but the precise site of proteolytic cleavage (21).…”

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.…”

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.…”