SARS-CoV-2 nsp16 is regulated by host E3 ubiquitin ligases, UBR5 and MARCHF7

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), remains a global public health threat with major economic implications. The non-structural protein 16 (nsp16) of SARS-CoV-2, in complex with nsp10, catalyses the final step of viral mRNA capping via its 2’-O-methylase activity, enabling the virus to evade host immunity and protect viral mRNA from degradation. However, host factors regulating nsp16 have not been thoroughly explored. Although various E3 ubiquitin ligases are known to interact with SARS-CoV-2 proteins, their specific roles in targeting nsp16 for degradation remain unclear. In this study, we demonstrate that nsp16 is ubiquitinated and degraded by host E3 ubiquitin ligases UBR5 and MARCHF7, acting through the ubiquitin-proteasome system (UPS). UBR5 and MARCHF7 induce nsp16 degradation via K48- and K27-linked ubiquitination, respectively, in independent processes that inhibit SARS-CoV-2 replication both in vitro and in vivo. Furthermore, UBR5 and MARCHF7 exhibited broad-spectrum antiviral activity by degrading nsp16 variants from different SARS-CoV-2 strains. Our findings uncover novel mechanisms by which the UPS antagonises SARS-CoV-2 replication and provide promising targets for therapeutic intervention against COVID-19.