Abstract

SummarySARS-CoV-2 is the cause of a pandemic with growing global mortality. Using comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS), we identified 309 host proteins that bind the SARS-CoV-2 RNA during active infection. Integration of this data with ChIRP-MS data from three other RNA viruses defined viral specificity of RNA-host protein interactions. Targeted CRISPR screens revealed that the majority of functional RNA-binding proteins protect the host from virus-induced cell death, and comparative CRISPR screens across seven RNA viruses revealed shared and SARS-specific antiviral factors. Finally, by combining the RNA-centric approach and functional CRISPR screens, we demonstrated a physical and functional connection between SARS-CoV-2 and mitochondria, highlighting this organelle as a general platform for antiviral activity. Altogether, these data provide a comprehensive catalog of functional SARS-CoV-2 RNA-host protein interactions, which may inform studies to understand the host-virus interface and nominate host pathways that could be targeted for therapeutic benefit.

Highlights

  • Despite similarities in replication strategies of their compact genomes, positive single-stranded RNA viruses cause a remarkable variety of human diseases

  • ChIRP-MS is advantageous as a discovery tool because it uses formaldehyde as a crosslinking agent to recover entire protein complexes associated with cellular RNAs (Chu and Chang, 2018; Chu et al, 2015)

  • Analysis of enriched ChIRP protein samples showed that mock samples had little protein staining, while we observed an infection- and time-dependent increase in total protein recovered after infection of either cell line with SARS-CoV-2 (Figure 1B)

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Summary

Introduction

Despite similarities in replication strategies of their compact genomes, positive single-stranded RNA (ssRNA) viruses cause a remarkable variety of human diseases. The recent pandemic emergence of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can cause potentially fatal coronavirus disease 2019 (COVID19), illustrates the threat to public health posed by RNA viruses. The process of infecting a host cell is complex, multistep, and often highly virus-specific. RNA viruses deposit large autonomous RNA transcripts into the dense intracellular milieu of the host cells, which eventually generate virally encoded protein products. Together, these RNA and protein species remodel

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