Translational shutdown and evasion of the innate immune response by SARS-CoV-2 NSP14 protein

Abstract

The ongoing COVID-19 pandemic has caused an unprecedented global health crisis. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19. Subversion of host protein synthesis is a common strategy that pathogenic viruses use to replicate and propagate in their host. In this study, we show that SARS-CoV-2 is able to shut down host protein synthesis and that SARS-CoV-2 nonstructural protein NSP14 exerts this activity. We show that the translation inhibition activity of NSP14 is conserved in human coronaviruses. NSP14 is required for virus replication through contribution of its exoribonuclease (ExoN) and N7-methyltransferase (N7-MTase) activities. Mutations in the ExoN or N7-MTase active sites of SARS-CoV-2 NSP14 abolish its translation inhibition activity. In addition, we show that the formation of NSP14−NSP10 complex enhances translation inhibition executed by NSP14. Consequently, the translational shutdown by NSP14 abolishes the type I interferon (IFN-I)-dependent induction of interferon-stimulated genes (ISGs). Together, we find that SARS-CoV-2 shuts down host innate immune responses via a translation inhibitor, providing insights into the pathogenesis of SARS-CoV-2.

SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome

“…In our analysis of the promoters of early upregulated genes, we also detected enrichment for binding sites of transcription factors involved in the interferon response. In support of our findings, recent reports showed that Nsp14 reduces the expression of INFb and ISG luciferase reporters (Yuen et al, 2020), as well as the expression of proteins involved in the NFkB pathway (Hsu et al, 2021;Li et al, 2021).…”

“…However, although IMPDH2 protein is conserved (Hedstrom, 2009), the transcription factor activity of IMPDH2 has not been demonstrated in mammalian cells. Furthermore, IMPDH2 can associate with polyribosomes in mammalian cells and modulates the translation of specific mRNAs (Hsu et al, 2021).…”

“…In the context of SARS-CoV-2 infection, a recent study showed that the activation of CXCL8 expression and of NFkB transcriptional reporters induced by Nsp14 expression is mediated by IMPDH2 (Li et al, 2021). Furthermore, another report indicates that Nsp14 blocks the interferon response, which is upstream of the NFkB pathway, by shutting down global translation (Hsu et al, 2021). However, our data indicate that the transcriptional activation of the NFkB pathways occurs very early after transfection and that treatment with an IMPDH inhibitor partially rescues the long-term effects of Nsp14 expression in HEK293T cells.…”

“…The C-terminal region of Nsp14 functions as an S-adenosyl methionine-dependent guanine-N7 methyl transferase that is independent of the ExoN activity (Chen et al, 2009). Recent research suggested that Nsp14 might mediate immune surveillance escape by reducing activity of the interferon pathway and activating the pro-inflammatory response through NFkB transcriptional activity and CXCL8 expression (Yuen et al, 2020;Hsu et al, 2021;Li et al, 2021). However, the biological mechanism behind these events has not fully characterized.…”

“…How the physical interaction between Nsp14 and IMPDH2 impacts the host pathways is not completely understood (Li et al, 2021). Interestingly, a recent study shows that expression of Nsp14 results in global translation inhibition, but it is not clear if this is a direct effect or a downstream consequence of changes that expression of the protein provoke to the cellular environment (Hsu et al, 2021). Indeed, no direct interaction between Nsp14 and ribosomes or a known translational modulator has been reported, suggesting that the potential translational inhibition might be a downstream effect.…”