The universal role of Nsp1: Common mechanisms of translational shutdown by coronaviruses

By Dr. Priyom Bose, Ph.D.Reviewed by Benedette Cuffari, M.Sc.Jun 5 2023

The non-structural protein 1 (Nsp1) produced by coronaviruses appears to inhibit host protein synthesis in infected cells. Previous studies have shown that the C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 binds to the small ribosomal subunit and inhibits translation. However, it remains unknown whether this is a mechanism that is broadly used by coronaviruses.

In a recent study published on the bioRxiv* preprint server, researchers investigate Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV using biophysical, structural, and biochemical assays.

Study: Universal features of Nsp1-mediated translational shutdown by coronaviruses. Image Credit: Jerome-Cronenberger / Shutterstock.com

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Background

Infection with members of the Betacoronavirus (β-CoV) genus causes serious respiratory diseases in humans. A capped 5' untranslated region (5'UTR) marks the start of the approximately 30 kilobase (kb) β-CoV genome, which contains several protein-encoding open reading frames (ORFs) and ends with a polyadenylated 3'UTR.

Many Nsps collectively aid in viral infection through unclear mechanisms. Thus, understanding these mechanisms better could accelerate the development of new therapeutics.

The SARS-CoV-2 Nsp1 CTD binds to the entry region of the messenger ribonucleic acid (mRNA) channel on the 40S subunit, where it sterically clashes with mRNA and inhibits translation. It remains unclear whether Nsp1 proteins from other β-CoVs share this mechanistic action.

About the study

In the current study, Nsp1 proteins from three representative β-CoVs were selected. These included the SARS-CoV-2 subgenus Sarbecovirus, MERS-CoV subgenus Merbecovirus, and Bat-Hp-CoV. Bat-Hp-CoV, which is the only member of the Hibecovirus subgenus, was selected as it binds the human ribosome.

A key aim of this study is to obtain biochemical and structural evidence demonstrating that Nsp1 from all selected β-CoVs mutes the translation of host mRNAs by binding to the mRNA channel of the 40S ribosomal subunit. To this end, paired structural and single-molecule analyses were used to show that the N-terminal domain (NTD) of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit.

Key findings

The binding of the Nsp1 CTD to the mRNA channel of the 40S subunit was shown to be the conserved mechanism. Furthermore, the evasion of Nsp1-mediated translation inhibition by mRNAs was also documented. Furthermore, the binding of the elusive NTD of Nsp1 to the decoding center of the 40S subunit was visualized using the Bat-Hp-CoV protein as a model system.

Although only the NTD for Bat-Hp-CoV Nsp1 was visualized, the biochemical data suggest that the Nsps from all selected β-CoVs elicit mechanistic effects on translation and binding mode. In vitro translation experiments showed that both the NTD and CTD significantly contribute to translation inhibition across all tested viral systems. Furthermore, the regions of Nsp1 responsible for ribosome interactions appear to be crucial for the selective translation of viral mRNAs.

The evaluation of the relative occupancies of Nsp1 domains on the 40S subunit revealed that Nsp1 forms a bi-partite interaction with the 40S subunit. The CTD of Nsp1 appears to bind with the 40S mRNA entry channel with high affinity. These findings are consistent with a previous model in which the CTD domain anchors the protein on the 40S subunit, and the Nsp1 NTD quickly samples the 40S decoding center.

The Nsp1 NTDs and viral mRNAs first co-evolved and evaded translation inhibition by matching the Nsp1 proteins from the three viruses to their corresponding viral mRNAs.

The next stage was the loss of the translation evasion function, which was caused by mutation of either the critical nucleotides in stem-loop one of the viral 5'UTR or conserved residues of Nsp1 NTD. Thus, the inhibitory potential of Nsp1 is likely reduced if viral mRNAs compete with the 40S subunit to interact with the Nsp1 NTD and block its accommodation into the decoding center.

Conclusions

A fundamental limitation of this study is that an interaction between the viral mRNA and ribosome-bound Nsp1 NTD has yet to be observed directly. Nevertheless, the framework provided here rationalizes a significant amount of scientific literature on the role of Nsp1.

These findings also provide the foundation for additional investigation into how coronaviruses, using viral protein synthesis, balance suppression of the host immune response. Future research is needed to expand upon these findings to ultimately develop effective anti-viral therapeutics targeting Nsp1 activity across Betacoronaviruses.

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.