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Abstract

The emerging pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused social and economic disruption worldwide, infecting over 9.0 million people and killing over 469 000 by 24 June 2020. Unfortunately, no vaccine or antiviral drug that completely eliminates the transmissible disease coronavirus disease 2019 (COVID-19) has been developed to date. Given that coronavirus nonstructural protein 1 (nsp1) is a good target for attenuated vaccines, it is of great significance to explore the detailed characteristics of SARS-CoV-2 nsp1. Here, we first confirmed that SARS-CoV-2 nsp1 had a conserved function similar to that of SARS-CoV nsp1 in inhibiting host-protein synthesis and showed greater inhibition efficiency, as revealed by ribopuromycylation and Renilla luciferase (Rluc) reporter assays. Specifically, bioinformatics and biochemical experiments showed that by interacting with 40S ribosomal subunit, the lysine located at amino acid 164 (K164) was the key residue that enabled SARS-CoV-2 nsp1 to suppress host gene expression. Furthermore, as an inhibitor of host-protein expression, SARS-CoV-2 nsp1 contributed to cell-cycle arrest in G0/G1 phase, which might provide a favourable environment for virus production. Taken together, this research uncovered the detailed mechanism by which SARS-CoV-2 nsp1 K164 inhibited host gene expression, laying the foundation for the development of attenuated vaccines based on nsp1 modification.

Funding
This study was supported by the:
  • The National Key Research and Development Program (Award 2020YFC0845600)
    • Principle Award Recipient: Guiqing Peng
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
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2020-11-05
2024-03-29
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References

  1. Lefkowitz EJ, Dempsey DM, Hendrickson RC, Orton RJ, Siddell SG et al. Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV). Nucleic Acids Res 2018; 46:D708–D717 [View Article] [PubMed]
    [Google Scholar]
  2. Woo PC, Huang Y, Lau SK, Yuen KY. Coronavirus genomics and bioinformatics analysis. Viruses 2010; 2:1804–1820 [View Article] [PubMed]
    [Google Scholar]
  3. Ou X, Liu Y, Lei X, Li P, Mi D et al. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun 2020; 11:1620 [View Article] [PubMed]
    [Google Scholar]
  4. Rabaan AA, Al-Ahmed SH, Haque S, Sah R, Tiwari R et al. SARS-CoV-2, SARS-CoV, and MERS-CoV: a comparative overview. Infez Med 2020; 28:174–184 [PubMed]
    [Google Scholar]
  5. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science 2003; 302:276–278 [View Article] [PubMed]
    [Google Scholar]
  6. Drosten C, Günther S, Preiser W, van der Werf S, Brodt HR et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med 2003; 348:1967–1976 [View Article] [PubMed]
    [Google Scholar]
  7. Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 2012; 367:1814–1820 [View Article] [PubMed]
    [Google Scholar]
  8. Farooq HZ, Davies E, Ahmad S, Machin N, Hesketh L et al. Middle East respiratory syndrome coronavirus (MERS-CoV) - Surveillance and testing in North England from 2012 to 2019. Int J Infect Dis 2020; 93:237–244 [View Article] [PubMed]
    [Google Scholar]
  9. Wang C, Horby PW, Hayden FG, Gao GF. A novel coronavirus outbreak of global health concern. Lancet 2020; 395:470–473 [View Article] [PubMed]
    [Google Scholar]
  10. Zhou P, Yang XL, Wang XG, Hu B, Zhang L et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 2020; 579:270–273 [View Article] [PubMed]
    [Google Scholar]
  11. Yongchen Z, Shen H, Wang X, Shi X, Li Y et al. Different longitudinal patterns of nucleic acid and serology testing results based on disease severity of COVID-19 patients. Emerg Microbes Infect 2020; 9:833–836 [View Article] [PubMed]
    [Google Scholar]
  12. Rivett L, Sridhar S, Sparkes D, Routledge M, Jones NK et al. Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission. elife 2020; 9:e58728 [View Article] [PubMed]
    [Google Scholar]
  13. Hart OE, Halden RU. Computational analysis of SARS-CoV-2/COVID-19 surveillance by wastewater-based epidemiology locally and globally: feasibility, economy, opportunities and challenges. Sci Total Environ 2020; 730:138875 [View Article] [PubMed]
    [Google Scholar]
  14. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 2020; 181:e286281–292 [View Article] [PubMed]
    [Google Scholar]
  15. Zhou G, Zhao Q. Perspectives on therapeutic neutralizing antibodies against the novel coronavirus SARS-CoV-2. Int J Biol Sci 2020; 16:1718–1723 [View Article] [PubMed]
    [Google Scholar]
  16. Gao Q, Bao L, Mao H, Wang L, Xu K et al. Development of an inactivated vaccine candidate for SARS-CoV-2. Science 2020; 369:77–81 [View Article] [PubMed]
    [Google Scholar]
  17. Lan J, Ge J, Yu J, Shan S, Zhou H et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 2020; 581:215–220 [View Article] [PubMed]
    [Google Scholar]
  18. Shang J, Ye G, Shi K, Wan Y, Luo C et al. Structural basis of receptor recognition by SARS-CoV-2. Nature 2020; 581:221–224 [View Article]
    [Google Scholar]
  19. Zheng M, Song L. Novel antibody epitopes dominate the antigenicity of spike glycoprotein in SARS-CoV-2 compared to SARS-CoV. Cell Mol Immunol 2020; 17:536–538 [View Article] [PubMed]
    [Google Scholar]
  20. Shen Z, Wang G, Yang Y, Shi J, Fang L et al. A conserved region of nonstructural protein 1 from alphacoronaviruses inhibits host gene expression and is critical for viral virulence. J Biol Chem 2019; 294:13606–13618 [View Article] [PubMed]
    [Google Scholar]
  21. Züst R, Cervantes-Barragán L, Kuri T, Blakqori G, Weber F et al. Coronavirus non-structural protein 1 is a major pathogenicity factor: implications for the rational design of coronavirus vaccines. PLoS Pathog 2007; 3:e109 [View Article] [PubMed]
    [Google Scholar]
  22. Wathelet MG, Orr M, Frieman MB, Baric RS. Severe acute respiratory syndrome coronavirus evades antiviral signaling: role of nsp1 and rational design of an attenuated strain. J Virol 2007; 81:11620–11633 [View Article] [PubMed]
    [Google Scholar]
  23. Narayanan K, Huang C, Lokugamage K, Kamitani W, Ikegami T et al. Severe acute respiratory syndrome coronavirus NSP1 suppresses host gene expression, including that of type I interferon, in infected cells. J Virol 2008; 82:4471–4479 [View Article] [PubMed]
    [Google Scholar]
  24. Kamitani W, Huang C, Narayanan K, Lokugamage KG, Makino S. A two-pronged strategy to suppress host protein synthesis by SARS coronavirus NSP1 protein. Nat Struct Mol Biol 2009; 16:1134–1140 [View Article] [PubMed]
    [Google Scholar]
  25. Tanaka T, Kamitani W, DeDiego ML, Enjuanes L, Matsuura Y. Severe acute respiratory syndrome coronavirus NSP1 facilitates efficient propagation in cells through a specific translational shutoff of host mRNA. J Virol 2012; 86:11128–11137 [View Article] [PubMed]
    [Google Scholar]
  26. Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T et al. Structural basis for translational shutdown and immune evasion by the NSP1 protein of SARS-CoV-2. Science 2020; 369:1249–1255 [View Article] [PubMed]
    [Google Scholar]
  27. Lau SK, Chan JF. Coronaviruses: emerging and re-emerging pathogens in humans and animals. Virol J 2015; 12:209 [View Article] [PubMed]
    [Google Scholar]
  28. Vergara-Alert J, Vidal E, Bensaid A, Segalés J. Searching for animal models and potential target species for emerging pathogens: experience gained from middle East respiratory syndrome (MERS) coronavirus. One Health 2017; 3:34–40 [View Article] [PubMed]
    [Google Scholar]
  29. Wong S, Lau S, Woo P, Yuen KY. Bats as a continuing source of emerging infections in humans. Rev Med Virol 2007; 17:67–91 [View Article] [PubMed]
    [Google Scholar]
  30. Wang D, Hu B, Hu C, Zhu F, Liu X et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. JAMA 2020; 323:1061 [View Article] [PubMed]
    [Google Scholar]
  31. de Wit E, van Doremalen N, Falzarano D, Munster VJ. SARS and MERS: recent insights into emerging coronaviruses. Nat Rev Microbiol 2016; 14:523–534 [View Article] [PubMed]
    [Google Scholar]
  32. Kawana A. SARS, MERS and coronavirus infections. Nihon Rinsho 2016; 74:1967–1972 [PubMed]
    [Google Scholar]
  33. Chen L, Zhong L. Genomics functional analysis and drug screening of SARS-CoV-2. Genes Dis 2020 [View Article] [PubMed]
    [Google Scholar]
  34. Bzówka M, Mitusińska K, Raczyńska A, Samol A, Tuszyński JA et al. Structural and evolutionary analysis indicate that the SARS-CoV-2 Mpro is a challenging target for small-molecule inhibitor design. Int J Mol Sci 2020; 21:3099 [View Article] [PubMed]
    [Google Scholar]
  35. Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B et al. A sequence homology and bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2. Cell Host Microbe 2020; 27:e672671–680 [View Article] [PubMed]
    [Google Scholar]
  36. Goujon C, Moncorgé O, Bauby H, Doyle T, Ward CC et al. Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection. Nature 2013; 502:559–562 [View Article] [PubMed]
    [Google Scholar]
  37. Ye X, Pan T, Wang D, Fang L, Ma J et al. Foot-and-Mouth Disease Virus Counteracts on Internal Ribosome Entry Site Suppression by G3BP1 and Inhibits G3BP1-Mediated Stress Granule Assembly via Post-Translational Mechanisms. Front Immunol 2018; 9:1142 [View Article] [PubMed]
    [Google Scholar]
  38. Castelló A, Quintas A, Sánchez EG, Sabina P, Nogal M et al. Regulation of host translational machinery by African swine fever virus. PLoS Pathog 2009; 5:e1000562 [View Article] [PubMed]
    [Google Scholar]
  39. Chuluunbaatar U, Roller R, Feldman ME, Brown S, Shokat KM et al. Constitutive mTORC1 activation by a herpesvirus Akt surrogate stimulates mRNA translation and viral replication. Genes Dev 2010; 24:2627–2639 [View Article] [PubMed]
    [Google Scholar]
  40. George A, Panda S, Kudmulwar D, Chhatbar SP, Nayak SC et al. Hepatitis C virus NS5A binds to the mRNA cap-binding eukaryotic translation initiation 4F (eIF4F) complex and up-regulates host translation initiation machinery through eIF4E-binding protein 1 inactivation. J Biol Chem 2012; 287:5042–5058 [View Article] [PubMed]
    [Google Scholar]
  41. Chaimayo C, Dunagan M, Hayashi T, Santoso N, Takimoto T. Specificity and functional interplay between influenza virus PA-X and NS1 shutoff activity. PLoS Pathog 2018; 14:e1007465 [View Article] [PubMed]
    [Google Scholar]
  42. Dauber B, Poon D, Dos Santos T, Duguay BA, Mehta N et al. The herpes simplex virus virion host shutoff protein enhances translation of viral true late mRNAs independently of suppressing protein kinase R and stress granule formation. J Virol 2016; 90:6049–6057 [View Article] [PubMed]
    [Google Scholar]
  43. Aumayr M, Schrempf A, Üzülmez Öykü, Olek KM, Skern T. Interaction of 2A proteinase of human rhinovirus genetic group A with eIF4E is required for eIF4G cleavage during infection. Virology 2017; 511:123–134 [View Article] [PubMed]
    [Google Scholar]
  44. Brocard M, Iadevaia V, Klein P, Hall B, Lewis G et al. Norovirus infection results in eIF2α independent host translation shut-off and remodels the G3BP1 interactome evading stress granule formation. PLoS Pathog 2020; 16:e1008250 [View Article] [PubMed]
    [Google Scholar]
  45. Narayanan K, Ramirez SI, Lokugamage KG, Makino S. Coronavirus nonstructural protein 1: common and distinct functions in the regulation of host and viral gene expression. Virus Res 2015; 202:89–100 [View Article] [PubMed]
    [Google Scholar]
  46. Tohya Y, Narayanan K, Kamitani W, Huang C, Lokugamage K et al. Suppression of host gene expression by NSP1 proteins of group 2 bat coronaviruses. J Virol 2009; 83:5282–5288 [View Article] [PubMed]
    [Google Scholar]
  47. Nakagawa K, Narayanan K, Wada M, Popov VL, Cajimat M et al. The endonucleolytic RNA cleavage function of NSP1 of middle East respiratory syndrome coronavirus promotes the production of infectious virus particles in specific human cell lines. J Virol 2018; 92: [View Article] [PubMed]
    [Google Scholar]
  48. Zhang Q, Ma J, Yoo D. Inhibition of NF-κB activity by the porcine epidemic diarrhea virus nonstructural protein 1 for innate immune evasion. Virology 2017; 510:111–126 [View Article] [PubMed]
    [Google Scholar]
  49. Zhang Q, Shi K, Yoo D. Suppression of type I interferon production by porcine epidemic diarrhea virus and degradation of CREB-binding protein by NSP1. Virology 2016; 489:252–268 [View Article] [PubMed]
    [Google Scholar]
  50. Lei L, Ying S, Baojun L, Yi Y, Xiang H et al. Attenuation of mouse hepatitis virus by deletion of the LLRKxGxKG region of NSP1. PLoS One 2013; 8:e61166 [View Article] [PubMed]
    [Google Scholar]
  51. Davies C, Brown CM, Westphal D, Ward JM, Ward VK. Murine norovirus replication induces G0/G1 cell cycle arrest in asynchronously growing cells. J Virol 2015; 89:6057–6066 [View Article] [PubMed]
    [Google Scholar]
  52. Wang Z, Wang Y, Wang S, Meng X, Song F et al. Coxsackievirus A6 induces cell cycle arrest in G0/G1 phase for viral production. Front Cell Infect Microbiol 2018; 8:279 [View Article] [PubMed]
    [Google Scholar]
  53. Wang ZY, Zhong T, Wang Y, Song FM, Yu XF et al. Human enterovirus 68 interferes with the host cell cycle to facilitate viral production. Front Cell Infect Microbiol 2017; 7:29 [View Article] [PubMed]
    [Google Scholar]
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