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, the cellular impact of expressing SARS-CoV-2 viral proteins was studied by global proteomic analysis, and proximity biotinylation (BioID) was used to map the SARS-CoV-2 virus–host interactome in human lung cancer-derived cells. Functional enrichment analyses revealed previously reported and unreported cellular pathways that are associated with SARS-CoV-2 proteins. We have 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. Furthermore, we identified 66 high-confidence interactions by comparing this study with previous reports, providing a strong foundation for future follow-up studies. Finally, we cross-referenced candidate interactors with the CLUE drug library to identify potential therapeutics for drug-repurposing efforts. Collectively, these studies provide a valuable resource to uncover novel SARS-CoV-2 biology and inform development of antivirals.

Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines

“…Many recent studies have incorporated TurboID and split-TurboID 20 to characterize interactomes and secretomes via fusion with proteins, organelles, and inter-cellular contacts. 14,16,21,57,[60][61][62][63][64] While one application of TurboID-based proteomics is to identify protein-protein interactors of proteins of interest or within specific subcellular compartments, another application of TurboID is to broadly label the cellular proteome of a specific cell type, so that cell typespecific proteomics can be resolved from a complex mixture of proteins derived from multiple cell types. The viability of the latter application was recently tested in vivo using genetic Cre/lox strategies to resolve neuronal and astrocyte proteomes in the native state of these cells in mouse brain, a method referred to as cell type-specific in vivo biotinylation of proteins (CIBOP).…”

Chemical and Biological Strategies for Profiling Protein‐Protein Interactions in Living Cells

“…Importantly, these enzymes can be easily expressed with POI within live cells and several animal models, [82] which may allow to accurately profile the interacting proteins in native states. Recently, they have been used to map the SARS‐CoV‐2 virus‐host interactome in human cells to reveal underlying mechanisms of pathogenesis [83,84] …”

Identification of Human Host Substrates of the SARS-CoV-2 Mpro and PLpro Using Subtiligase N-Terminomics

“…In addition to proteolytic processing of viral polyproteins, viral proteases can cleave host substrates to modulate immune evasion and host gene expression shutoff. , Although the interactomes of SARS-CoV-2 viral proteins have been well studied, − it is more challenging to characterize the entire range of substrates of viral proteases using conventional immunoprecipitation methods since proteolysis can lead to substrate release and the subsequent degradation of protein fragments. Even with a catalytically dead protease mutant, the protease–substrate interactions can be transient and difficult to detect.…”