SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9

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 nega-tive-sense viral RNA and is required for SARS-CoV-2 RNA synthesis. SND1-depleted cells form smaller repli-cation 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 prim-ing 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.

Automated summary

Regulation of viral RNA biogenesis is crucial for SARS-CoV-2 infection. The host protein SND1 is identified to bind negatively-sense viral RNA and is essential for SARS-CoV-2 RNA synthesis. The viral protein NSP9 is covalently linked to the ends of viral RNA during infection and interacts with SND1 to initiate viral RNA synthesis.