Unveiling the role of PUS7-mediated pseudouridylation in host protein interactions specific for the SARS-CoV-2 RNA genome

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive single-stranded RNA virus, engages in complex interactions with host cell proteins throughout its life cycle. While these interactions enable the host to recognize and inhibit viral replication, they also facilitate essential viral pro-cesses such as transcription, translation, and replication. Many aspects of these virus-host interactions remain poorly understood. Here, we employed the catRAPID algorithm and utilized the RNA-protein interaction detection coupled with mass spectrometry technology to predict and validate the host proteins that specifically bind to the highly structured 50 and 30 terminal regions of the SARS-CoV-2 RNA. Among the interactions identified, we prioritized pseudouridine synthase PUS7, which binds to both ends of the viral RNA. Using nano-pore direct RNA sequencing, we discovered that the viral RNA undergoes extensive post-transcriptional modifications. Modi-fied consensus regions for PUS7 were identified at both termi-nal regions of the SARS-CoV-2 RNA, including one in the viral transcription regulatory sequence leader. Collectively, our find-ings offer insights into host protein interactions with the SARS-CoV-2 UTRs and highlight the likely significance of pseudouridine synthases and other post-transcriptional modi-fications in the viral life cycle. This new knowledge enhances our understanding of virus-host dynamics and could inform the development of targeted therapeutic strategies.

Automated summary

This study predicts and validates the host proteins that specifically bind to the terminal regions of SARS-CoV-2 RNA using the catRAPID algorithm and RNA-protein interaction detection coupled with mass spectrometry technology. It also discovers extensive post-transcriptional modifications in the viral RNA and highlights the significance of pseudouridine synthases in the viral life cycle.