Parsing the Role of NSP1 in SARS-CoV-2 Infection

Overview

Journal bioRxiv

Date 2022 Mar 22

PMID 35313595

Authors

Tal Fisher

Avi Gluck

Krishna Narayanan

Makoto Kuroda

Aharon Nachshon

Jason C Hsu

Peter J Halfmann

Yfat Yahalom-Ronen

Yaara Finkel

Michal Schwartz

Shay Weiss

Chien-Te K Tseng

Tomer Israely

Nir Paran

Yoshihiro Kawaoka

Shinji Makino

Noam Stern-Ginossar

Affiliations

Soon will be listed here.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 19 (COVID-19) pandemic. Despite its urgency, we still do not fully understand the molecular basis of SARS-CoV-2 pathogenesis and its ability to antagonize innate immune responses. SARS-CoV-2 leads to shutoff of cellular protein synthesis and over-expression of nsp1, a central shutoff factor in coronaviruses, inhibits cellular gene translation. However, the diverse molecular mechanisms nsp1 employs as well as its functional importance in infection are still unresolved. By overexpressing various nsp1 mutants and generating a SARS-CoV-2 mutant in which nsp1 does not bind ribosomes, we untangle the effects of nsp1. We uncover that nsp1, through inhibition of translation and induction of mRNA degradation, is the main driver of host shutoff during SARS-CoV-2 infection. Furthermore, we find the propagation of nsp1 mutant virus is inhibited specifically in cells with intact interferon (IFN) response as well as , in infected hamsters, and this attenuation is associated with stronger induction of type I IFN response. This illustrates that nsp1 shutoff activity has an essential role mainly in counteracting the IFN response. Overall, our results reveal the multifaceted approach nsp1 uses to shut off cellular protein synthesis and uncover the central role it plays in SARS-CoV-2 pathogenesis, explicitly through blockage of the IFN response.

References

Ricardo-Lax I, Luna J, Thao T, Le Pen J, Yu Y, Hoffmann H . Replication and single-cycle delivery of SARS-CoV-2 replicons. Science. 2021; 374(6571):1099-1106. PMC: 9007107. DOI: 10.1126/science.abj8430. View

Tseng C, Huang C, Newman P, Wang N, Narayanan K, Watts D . Severe acute respiratory syndrome coronavirus infection of mice transgenic for the human Angiotensin-converting enzyme 2 virus receptor. J Virol. 2006; 81(3):1162-73. PMC: 1797529. DOI: 10.1128/JVI.01702-06. View

Emeny J, Morgan M . Regulation of the interferon system: evidence that Vero cells have a genetic defect in interferon production. J Gen Virol. 1979; 43(1):247-52. DOI: 10.1099/0022-1317-43-1-247. View

Finkel Y, Gluck A, Nachshon A, Winkler R, Fisher T, Rozman B . SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis. Nature. 2021; 594(7862):240-245. DOI: 10.1038/s41586-021-03610-3. View

Carlevaro-Fita J, Liu L, Zhou Y, Zhang S, Chouvardas P, Johnson R . LnCompare: gene set feature analysis for human long non-coding RNAs. Nucleic Acids Res. 2019; 47(W1):W523-W529. PMC: 6602513. DOI: 10.1093/nar/gkz410. View

Hadjadj J, Yatim N, Barnabei L, Corneau A, Boussier J, Smith N . Impaired type I interferon activity and inflammatory responses in severe COVID-19 patients. Science. 2020; 369(6504):718-724. PMC: 7402632. DOI: 10.1126/science.abc6027. View

Jackson J, Markert J, Li L, Carroll S, Cassady K . STAT1 and NF-κB Inhibitors Diminish Basal Interferon-Stimulated Gene Expression and Improve the Productive Infection of Oncolytic HSV in MPNST Cells. Mol Cancer Res. 2016; 14(5):482-92. PMC: 4867290. DOI: 10.1158/1541-7786.MCR-15-0427. View

Sa Ribero M, Jouvenet N, Dreux M, Nisole S . Interplay between SARS-CoV-2 and the type I interferon response. PLoS Pathog. 2020; 16(7):e1008737. PMC: 7390284. DOI: 10.1371/journal.ppat.1008737. View

Mantlo E, Bukreyeva N, Maruyama J, Paessler S, Huang C . Antiviral activities of type I interferons to SARS-CoV-2 infection. Antiviral Res. 2020; 179:104811. PMC: 7188648. DOI: 10.1016/j.antiviral.2020.104811. View

10.

Jimenez-Guardeno J, Regla-Nava J, Nieto-Torres J, DeDiego M, Castano-Rodriguez C, Fernandez-Delgado R . Identification of the Mechanisms Causing Reversion to Virulence in an Attenuated SARS-CoV for the Design of a Genetically Stable Vaccine. PLoS Pathog. 2015; 11(10):e1005215. PMC: 4626112. DOI: 10.1371/journal.ppat.1005215. View

11.

Zhu N, Zhang D, Wang W, Li X, Yang B, Song J . A Novel Coronavirus from Patients with Pneumonia in China, 2019. N Engl J Med. 2020; 382(8):727-733. PMC: 7092803. DOI: 10.1056/NEJMoa2001017. View

12.

Herzog V, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard T . Thiol-linked alkylation of RNA to assess expression dynamics. Nat Methods. 2017; 14(12):1198-1204. PMC: 5712218. DOI: 10.1038/nmeth.4435. View

13.

Yoshikawa N, Yoshikawa T, Hill T, Huang C, Watts D, Makino S . Differential virological and immunological outcome of severe acute respiratory syndrome coronavirus infection in susceptible and resistant transgenic mice expressing human angiotensin-converting enzyme 2. J Virol. 2009; 83(11):5451-65. PMC: 2681954. DOI: 10.1128/JVI.02272-08. View

14.

Zhang K, Miorin L, Makio T, Dehghan I, Gao S, Xie Y . Nsp1 protein of SARS-CoV-2 disrupts the mRNA export machinery to inhibit host gene expression. Sci Adv. 2021; 7(6). PMC: 7864571. DOI: 10.1126/sciadv.abe7386. View

15.

Kim D, Lee J, Yang J, Kim J, Kim V, Chang H . The Architecture of SARS-CoV-2 Transcriptome. Cell. 2020; 181(4):914-921.e10. PMC: 7179501. DOI: 10.1016/j.cell.2020.04.011. View

16.

Abernathy E, Glaunsinger B . Emerging roles for RNA degradation in viral replication and antiviral defense. Virology. 2015; 479-480:600-8. PMC: 4424162. DOI: 10.1016/j.virol.2015.02.007. View

17.

Love M, Huber W, Anders S . Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014; 15(12):550. PMC: 4302049. DOI: 10.1186/s13059-014-0550-8. View

18.

Wolff G, Limpens R, Zevenhoven-Dobbe J, Laugks U, Zheng S, de Jong A . A molecular pore spans the double membrane of the coronavirus replication organelle. Science. 2020; 369(6509):1395-1398. PMC: 7665310. DOI: 10.1126/science.abd3629. View

19.

Katsura H, Sontake V, Tata A, Kobayashi Y, Edwards C, Heaton B . Human Lung Stem Cell-Based Alveolospheres Provide Insights into SARS-CoV-2-Mediated Interferon Responses and Pneumocyte Dysfunction. Cell Stem Cell. 2020; 27(6):890-904.e8. PMC: 7577733. DOI: 10.1016/j.stem.2020.10.005. View

20.

Tidu A, Janvier A, Schaeffer L, Sosnowski P, Kuhn L, Hammann P . The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation. RNA. 2020; . PMC: 7901841. DOI: 10.1261/rna.078121.120. View