Abstract
Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a viral peptide discovery approach covering 23 coronavirus strains that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an ΦxFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its ΦxFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction dampened SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.
Highlights
Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors
As transient SLiM-based protein interactions might be lost during purifications of viral proteins for subsequent mass spectrometry analysis, we screened an additional set of 82 peptide-binding domains
Enriched phage pools were analyzed by next-generation sequencing (NGS) to identify viral peptides that bound to the bait
Summary
Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. Numerous large-scale mass spectrometry (MS) based interaction screens[2,3,5], as well as CRISPR based screens[6,7,8,9,10] have been conducted to uncover host factor interactions and dependencies for SARS-CoV-2 allowing repurposing of drugs against human targets[11,12] These methods have been transformative in our understanding of SARS-CoV-2 biology the molecular detail provided by these methods is not always sufficient to readily transform the results into novel antiviral reagents. We describe a novel phage-based viral peptide library to map SLiMs from 23 coronaviruses mediating host factor interactions (Fig. 1a) This approach allows the simultaneous pan-viral identification of SLiM-based interactions with high resolution of the binding sites. We document the power of this approach by identifying novel SARS-CoV-2 specific SLiM mediated host factor interactions and directly translate our screening results into novel mechanistic insights and pinpoint a potential target for antiviral intervention
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