The E3 ligase TRIM22 restricts SARS-CoV-2 replication by promoting proteasomal degradation of NSP8

Abstract

Replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome is mediated by a complex of non-structural proteins (NSPs), of which NSP7 and NSP8 serve as subunits and play a key role in promoting the activity of RNA-dependent RNA polymerase (RdRp) of NSP12. However, the stability of subunits of the RdRp complex has rarely been reported. Here, we found that NSP8 was degraded by the proteasome in host cells, and identified tripartite motif containing 22 (TRIM22) as its E3 ligase. The interferon (IFN) signaling pathway was activated upon viral invasion into host cells, and TRIM22 expression increased. TRIM22 interacted with NSP8 and ubiquitinated it at Lys97 via K48-type ubiquitination. TRIM22 overexpression significantly reduced viral RNA and protein levels. Knockdown of TRIM22 enhanced viral replication. This study provides a new explanation for treating patients suffering from SARS-CoV-2 with IFNs and new possibilities for drug development targeting the interaction between NSP8 and TRIM22. IMPORTANCE Non-structural proteins (NSPs) play a crucial role in the replication of severe acute respiratory syndrome coronavirus 2, facilitating virus amplification and propagation. In this study, we conducted a comprehensive investigation into the stability of all subunits comprising the RNA-dependent RNA polymerase complex. Notably, our results reveal for the first time that NSP8 is a relatively unstable protein, which is found to be readily recognized and degraded by the proteasome. This degradation process is mediated by the host E3 ligase tripartite motif containing 22 (TRIM22), which is also a member of the interferon stimulated gene (ISG) family. Our study elucidates a novel mechanism of antiviral effect of TRIM22, which utilizes its own E3 ubiquitin ligase activity to hinder viral replication by inducing ubiquitination and subsequent degradation of NSP8. These findings provide new ideas for the development of novel therapeutic strategies. In addition, the conserved property of NSP8 raises the possibility of developing broad antiviral drugs targeting the TRIM22-NSP8 interaction.

Exploring TRIM proteins’ role in antiviral defense against influenza A virus and respiratory coronaviruses

“…Another well-characterized antiviral TRIM protein is the E3 ubiquitin ligase TRIM22. TRIM22 restricted IAV and SARS-CoV-2 replication through ubiquitin-proteasome degrading NP and NSP8, respectively ( Di Pietro et al., 2013 ; Fan et al., 2024 ). Rather, TRIM22 suppressed RSV replication by targeting JAK-STAT1/2 signaling ( Wang et al., 2021a ).…”

“…The results showed that NSP8 was a relatively unstable protein, which could be readily recognized by the E3 ubiquitin ligase TRIM22. TRIM22 was induced upon SARS-CoV-2 infection and mediated Lys48-linked ubiquitination and proteasomal degradation of NSP8 at Lys97 ( Fan et al., 2024 ). TRIM56 has been demonstrated to inhibit various virus replications, such as influenza virus, human coronavirus (HCoV) OC43, yellow fever virus (YFV), and dengue virus serotype 2 (DENV2) ( Liu et al., 2014 ; Liu et al., 2016 ).…”

“…TRIM22 has been reported to restrict numerous viruses by distinct mechanisms, including blocking the release of HIV Gag-only particles and the RNA synthesis of hepatitis B virus, inhibiting respiratory syncytial virus (RSV) replication by targeting JAK-STAT1/2 signaling, and interrupting herpes simplex virus 1 by epigenetic silencing of viral immediate-early genes ( Barr et al., 2008 ; Gao et al., 2009 ; Reddi et al., 2021 ; Wang et al., 2021a ). TRIM22 also suppresses the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by ubiquitin-proteasome degrading NSP8 ( Fan et al., 2024 ). It can interact with influenza A virus (IAV) and porcine reproductive and respiratory syndrome virus nucleoprotein for degradation ( Di Pietro et al., 2013 ; Jing et al., 2019 ).…”

A Cullin 5-based complex serves as an essential modulator of ORF9b stability in SARS-CoV-2 replication

“…Some E3 ligases have been identified as anti-coronavirus host factors by inducing viral protein degradation. 26 – 29 Notably, the Cullin–RING (really interesting new gene) ligases (CRLs) form the largest E3 family, which is evolutionarily conserved and plays crucial roles in many biological processes, including virus infection. 30 – 33 In humans, the Cullin family comprises eight members: CUL1 (Cullin 1), CUL2, CUL3, CUL4A, CUL4B, CUL5, CUL7, and CUL9.…”