SARS-CoV-NSP2 Protein Enhances microRNA-Mediated Translational Repression With Serious Long Term Health Implications

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A new study by researchers from Queen’s University Belfast, Belfast, UK has discovered that the SARS-CoV-2 encoded non-structural protein 2 (NSP2) enhances microRNA-mediated translational repression.

The study findings were published on a preprint server and are currently being peer reviewed.
https://www.biorxiv.org/content/10.1101/2023.01.01.522328v1

microRNAs (miRNA) are small, ~22 nucleotides long, non-coding RNAs that modulate the stability and translation efficiency of their target mRNAs. This is mediated by miRNA-Induced Silencing Complex (miRISC), an assembly of a miRNA, Argonaute (AGO), and other proteins, in which miRNA guides the complex to the target mRNA by sequence complementarity[1].

This leads to translational repression followed by deadenylation and decapping of the mRNA, resulting in the exposure of the mRNA to exonuclease-mediated degradation[1–4]. The CCR4-NOT complex plays a key role in coordinating the intricate mechanism of regulation of mRNA translation and decay induced by miRNAs.

While miRNA-mediated deadenylation is achieved by the activity of the components of the catalytic subunits of the CCR4-NOT complex (CNOT6/6L and CNOT7/8)[5, 6], translational repression and decapping are engendered through recruitment of several CCR4-NOT binding proteins.

We previously showed that recruitment of the mRNA cap-binding eIF4E-homologue protein (4EHP), by CCR4–NOT is critical for the miRNA-mediated translational repression of target mRNAs[7]. 4EHP also forms a translational repressor complex with Grb10-interacting GYF protein 2 (GIGYF2)[8], which represses mRNA translation in CCR4-NOT dependent and independent manners [9]. The GIGYF2/4EHP complex is recruited by a variety of factors including miRNAs [9, 10], the RNA-binding protein Tristetraprolin (TTP) [11], and the stalled ribosome induced Ribosome-associated Quality Control (RQC) mechanism via ZNF598 or EDF1[12] to repress translation.

Viruses use a variety of mechanisms to modulate host gene expression. A common strategy adopted by viruses involves the general shut down of the host mRNAs translation, which allows redirecting the host’s ribosomes toward the viral mRNAs to express the viral proteins[13]. These mechanisms include blocking the cap-dependent translation initiation via sequestering or cleavage of the eukaryotic Initiation factor 4G (eIF4G)[14, 15], binding to and inducing the inhibition or degradation of the poly(A)-binding protein (PABP)[16], and binding to the components of the eIF3 complex[17].

Many RNA viruses bypass the need for capdependent translation initiation by utilising an internal ribosome entry site (IRES) in the viral mRNA’s 5’ UTRs to enable translation in a “cap-independent” manner[13]. In addition to shutdown of general cap-dependent translation, viruses also employ “targeted” impairment of the host cell’s homeostasis and proinflammatory responses by changing the expression of miRNAs that target specific host mRNAs[18, 19]. Furthermore, certain viruses express their own miRNAs that target cellular mRNAs[20].

Conversely, host cells also express miRNAs that can interfere with the viral infection by targeting the viral mRNA or silence the antiinflammatory factors[21]. Therefore, the precise regulation of the miRNA-mediated silencing mechanisms is important for the viral infection as well as the host antiviral immune response.

We recently reported that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encoded non-structural protein 2 (NSP2) functions as a repressor of cellular mRNA translation via direct binding and stabilisation of the GIGYF2/4EHP complex[22]. However, it is not known whether and how NSP2 affects miRNA-mediated silencing, which also utilises the GIGYF2/4EHP complex for translational repression of target mRNAs.

Here we provide evidence of a pervasive effect of NSP2 on miRNA-mediated silencing. We show that besides GIGYF2, NSP2 also interacts with the components of miRISC complex and enhances the translational repression of their target mRNAs.

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