Summary Regulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection. To characterize host RNA-binding proteins (RBPs) involved in this process, we biochemically identified proteins bound to genomic and subgenomic SARS-CoV-2 RNAs. We find that the host protein SND1 binds the 5′ end of negative-sense viral RNA and is required for SARS-CoV-2 RNA synthesis. SND1-depleted cells form smaller replication organelles and display diminished virus growth kinetics. We discover that NSP9, a viral RBP and direct SND1 interaction partner, is covalently linked to the 5′ ends of positive- and negative-sense RNAs produced during infection. These linkages occur at replication-transcription initiation sites, consistent with NSP9 priming viral RNA synthesis. Mechanistically, SND1 remodels NSP9 occupancy and alters the covalent linkage of NSP9 to initiating nucleotides in viral RNA. Our findings implicate NSP9 in the initiation of SARS-CoV-2 RNA synthesis and unravel an unsuspected role of a cellular protein in orchestrating viral RNA production. Graphical abstract Highlights • SND1 is required for nascent SARS-CoV-2 RNA synthesis early during infection • SND1 directly interacts with NSP9 and both proteins bind negative-sense viral RNA • NSP9 is covalently linked to viral RNA at initiation sites, indicating protein priming • SND1 modulates the covalent linkage of NSP9 to positive- and negative-sense viral RNA Mapping of subgenome-resolved SARS-CoV-2 RNA-protein interactions reveals that the host protein SND1 binds negative-sense SARS-CoV-2 RNA and promotes viral RNA synthesis by recruiting NSP9, which likely serves as a protein primer for RNA production.
【저자키워드】 SARS-CoV-2, proteomics, host factors, Systems biology, RNA virus, RNA Biology, RNA interactome, RNA binding proteins, omics technologies, virus host interactions,