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Authors: Thoms et al.

Link to paper: https://doi.org/10.1101/2020.05.18.102467.

Pre-Print: bioRxiv preprint

Tags: Immunology/Immunity, Biochemistry, Molecular Biology, Structural Biology

Research Highlights 

1. SARS-CoV-2 Nsp1 binds to and inhibits canonical host translation, analogous to SARS-CoV Nsp1.

2. SARS-CoV-2 Nsp1-mediated translational repression counteracts the host innate immune response by suppressing the expression of both type I interferons and interferon stimulated genes induced by RIG-I signalling.

3. SARS-CoV-2 Nsp1 binds to distinct populations of 80S ribosomes, interacts with the 40S ribosomal subunit via the C-terminal KH motif and blocks the mRNA entry tunnel.

Summary 

Using cryoEM, the study reveals the structure of SARS-CoV-2 Nsp1 recombinant protein in association with human 40S or 80S ribosomes and identified important amino acid residues mediating this interaction. The authors propose that Nsp1 directly binds to the 40S ribosomal subunit and obstructs mRNA entry, and hence inhibits translation. The Nsp1-40S interaction and the consequential translational suppression are further supported by in vitro binding assays, translation assays and cell culture transfection work. Lastly, the study shows a significant reduction in the production of type I interferons and interferon stimulated genes, resulting from translational suppression and leading to host immune suppression.

Impact for SARS-CoV2/COVID19 research efforts

Understand the virology and/or cell biology of SARS-CoV2/COVID19

Study Type

· In vitro study

Strengths and limitations of the paper

Novelty: First to show detailed structural data revealing the interactions between SARS-CoV-2 Nsp1 and host ribosome, which leads to novel characterisation of the inhibitory mechanism of Nsp1. Also the first to observe that Nsp1 can bind to ribosomes at different stages, hence may interfere with ribosomal functions in distinct ways.

Standing in the field:

The confirmed translational inhibition activity of SARS-CoV-2 Nsp1 agrees with previous work on Nsp1 proteins from other coronavirus. The revealed ribosomal binding mechanism also supports previous bioinformatic and structural work on other coronavirus Nsp1 proteins.

Appropriate statistics:

Three replicates are used in all quantitative work. Statistics are performed appropriately when being applied. Some biochemical tests lack of evidence of repeats.

Viral model used:

SARS-CoV (gene segment)

SARS-CoV-2 (gene segment)

Translatability: Very early stage of translational work. Structural data provides a good starting point for inhibitory drug design.

Main limitations:

· Ribosomal binding and translational suppression are not done in the context of infection. Degree of translational suppression and interferon response stimulation may vary during infection by SARS-CoV-2.

· The analysis of the interferon response is limited to HEK293T cells and few parameters/reporters.

· It remains open how viral protein production may be affected by Nsp1.

· Single-site mutation of the more conserved K164 residue is not studied to determine whether ribosomal binding requires both K164 and H165 or only K164.

· Did not resolve the full structure of Nsp1 binding to ribosomes. Could not infer any other steric hindrance effect on translational inactivation.

· It is not mentioned in the structural data whether the presence of Nsp1 or incoming mRNA allows formation of mutually exclusive ribosome populations, which would have been a good support for the proposed mechanism that Nsp1 blocks mRNA entry channel.