Deymier, S. | bioRxiv Science

bioRxiv2024

The SARS-CoV-2 nucleocapsid protein inhibits the cellular Nonsense-Mediated mRNA Decay (NMD) pathway preventing the full enzymatic activation of UPF1.

The Nonsense-mediated mRNA decay (NMD) pathway triggers the degradation of defective mRNAs and governs the expression of mRNAs with specific characteristics. Current understanding indicates that NMD is often significantly suppressed during viral infections to protect the viral genome. In numerous viruses, this inhibition is achieved through direct or indirect interference with the RNA helicase UPF1, thereby promoting viral replication and enhancing pathogenesis. In this study, we employed biochemical, biophysical assays, and cellular investigations to explore the interplay between UPF1 and the Nucleocapsid (Np) protein of SARS-CoV-2. We evaluated their direct interaction and its impact on inhibiting cellular NMD. Furthermore, we characterized how this interaction affects UPF1s enzymatic function. Our findings demonstrate that Np inhibits the unwinding activity of UPF1 by physically obstructing its access to structured nucleic acid substrates. Additionally, we showed that Np binds directly to UPF2, disrupting the formation of the UPF1/UPF2 complex essential for NMD progression. Intriguingly, our research also uncovered a surprising pro-viral role of UPF1 and an antiviral function of UPF2. These results unveil a novel, multi-faceted mechanism by which SARS-CoV-2 evades the hosts defenses and manipulates cellular components. This underscores the potential therapeutic strategy of targeting Np-UPF1/UPF2 interactions to treat COVID-19.

biochemistry↗

bioRxiv2023

Stable Structures or poly(A)-binding protein loading protect cellular and viral RNAs against ISG20-mediated decay

ISG20 is an interferon-induced 3-to-5 RNA exonuclease that acts as a broad antiviral factor. At present, the features that expose RNA to ISG20 remain unclear, although recent studies have pointed to the modulatory role of epitranscriptomic modifications in the susceptibility of target RNAs to ISG20. These findings raise the question as to how cellular RNAs, on which these modifications are abundant, cope with ISG20. To obtain an unbiased perspective on this topic, we used RNAseq and biochemical assays to identify elements that regulate the behavior of RNAs against ISG20. The results we have obtained indicate that poly(A)-binding protein (PABP1) loading on the RNA 3 tail provides a primal protection against ISG20, easily explaining the overall protection of cellular mRNAs observed by RNAseq. The second element we uncovered is provided by terminal stem-loop RNA structures, that have been associated to ISG20 protection before, but that we re-examine here systematically to define the stabilities that tilt the balance between resistance and susceptibility to ISG20. Given that these elements are present on cellular mRNAs, but can be co-opted by viruses as well, these results shed new light on the complex interplay that regulates the susceptibility of different classes of viruses against ISG20.

microbiology↗