Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection.

BioRxiv : the Preprint Server for Biology
Ryan A FlynnAnsuman T Satpathy

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a pandemic with growing global mortality. There is an urgent need to understand the molecular pathways required for host infection and anti-viral immunity. 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 viral ChIRP-MS data from three other positive-sense RNA viruses defined pan-viral and SARS-CoV-2-specific host interactions. Functional interrogation of these factors with a genome-wide CRISPR screen revealed that the vast majority of viral RNA-binding proteins protect the host from virus-induced cell death, and we identified known and novel anti-viral proteins that regulate SARS-CoV-2 pathogenicity. Finally, our RNA-centric approach demonstrated a physical connection between SARS-CoV-2 RNA and host mitochondria, which we validated with functional and electron microscopy data, providing new insights into a more general virus-specific protein logic for mitochondrial interactions. Altogether, these data provide a comprehensive catalogue of SARS-CoV-2 RNA-host protein interactions, which may inform...Continue Reading

Citations

Dec 29, 2020·Biochemical Society Transactions·Ilaria Manfredonia, Danny Incarnato
Feb 9, 2021·Molecular Biology and Evolution·Andrea Di GioacchinoSimona Cocco
Jun 11, 2021·Nature Protocols·Hsueh-Ping ChuJeannie T Lee

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Methods Mentioned

BETA
ChIRP
pulldown
RNA-seq
Antisense Purification
GTPase
chemical modification
Electron microscopy

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