Inhibition of anti-viral stress granule formation by coronavirus endoribonuclease nsp15 ensures efficient virus replication

PLoS Pathog. 2021 Feb 26;17(2):e1008690. doi: 10.1371/journal.ppat.1008690. eCollection 2021 Feb.

Abstract

Cytoplasmic stress granules (SGs) are generally triggered by stress-induced translation arrest for storing mRNAs. Recently, it has been shown that SGs exert anti-viral functions due to their involvement in protein synthesis shut off and recruitment of innate immune signaling intermediates. The largest RNA viruses, coronaviruses, impose great threat to public safety and animal health; however, the significance of SGs in coronavirus infection is largely unknown. Infectious Bronchitis Virus (IBV) is the first identified coronavirus in 1930s and has been prevalent in poultry farm for many years. In this study, we provided evidence that IBV overcomes the host antiviral response by inhibiting SGs formation via the virus-encoded endoribonuclease nsp15. By immunofluorescence analysis, we observed that IBV infection not only did not trigger SGs formation in approximately 80% of the infected cells, but also impaired the formation of SGs triggered by heat shock, sodium arsenite, or NaCl stimuli. We further demonstrated that the intrinsic endoribonuclease activity of nsp15 was responsible for the interference of SGs formation. In fact, nsp15-defective recombinant IBV (rIBV-nsp15-H238A) greatly induced the formation of SGs, along with accumulation of dsRNA and activation of PKR, whereas wild type IBV failed to do so. Consequently, infection with rIBV-nsp15-H238A strongly triggered transcription of IFN-β which in turn greatly affected rIBV-nsp15-H238A replication. Further analysis showed that SGs function as an antiviral hub, as demonstrated by the attenuated IRF3-IFN response and increased production of IBV in SG-defective cells. Additional evidence includes the aggregation of pattern recognition receptors (PRRs) and signaling intermediates to the IBV-induced SGs. Collectively, our data demonstrate that the endoribonuclease nsp15 of IBV interferes with the formation of antiviral hub SGs by regulating the accumulation of viral dsRNA and by antagonizing the activation of PKR, eventually ensuring productive virus replication. We further demonstrated that nsp15s from PEDV, TGEV, SARS-CoV, and SARS-CoV-2 harbor the conserved function to interfere with the formation of chemically-induced SGs. Thus, we speculate that coronaviruses employ similar nsp15-mediated mechanisms to antagonize the host anti-viral SGs formation to ensure efficient virus replication.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19 / metabolism
  • COVID-19 / virology*
  • Cell Line
  • Coronavirus / immunology
  • Cytoplasmic Granules / immunology
  • Cytoplasmic Granules / metabolism*
  • Cytoplasmic Granules / virology
  • Endoribonucleases / immunology*
  • Endoribonucleases / metabolism*
  • Humans
  • Interferon-beta / immunology
  • Interferon-beta / metabolism
  • SARS-CoV-2 / metabolism
  • SARS-CoV-2 / physiology*
  • Signal Transduction
  • Viral Nonstructural Proteins / immunology*
  • Viral Nonstructural Proteins / metabolism*
  • Virus Replication / physiology

Substances

  • Viral Nonstructural Proteins
  • Interferon-beta
  • Endoribonucleases
  • nidoviral uridylate-specific endoribonuclease

Grants and funding

This work was supported by the grant from the National Natural Science Foundation of China (No. 31772724) awarded to Y.L., the National Key Research and Development Program (No. 2017YFD0500802) awarded to Y.L., Elite Youth Program of Chinese Academy of Agricultural Sciences awarded to Y.L., the Central Public-interest Scientific Institution Basal Research Fund (2019JB03) awarded to Y.L., and National Natural Science Foundation of China (No. 31530074) awarded to C.D. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.