The study findings were published on a preprint server and are currently being peer reviewed.
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.
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. 4EHP also forms a translational repressor complex with Grb10-interacting GYF protein 2 (GIGYF2), which represses mRNA translation in CCR4-NOT dependent and independent manners . The GIGYF2/4EHP complex is recruited by a variety of factors including miRNAs [9, 10], the RNA-binding protein Tristetraprolin (TTP) , and the stalled ribosome induced Ribosome-associated Quality Control (RQC) mechanism via ZNF598 or EDF1 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. 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), and binding to the components of the eIF3 complex.
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. 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.
Conversely, host cells also express miRNAs that can interfere with the viral infection by targeting the viral mRNA or silence the antiinflammatory factors. 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. 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.