1887

Abstract

Modulation of RNA structure is essential in the life cycle of RNA viruses. Immediate replication upon infection requires RNA unwinding to ensure that RNA templates are not in intra- or intermolecular duplex forms. The calicivirus NS3, one of the highly conserved nonstructural (NS) proteins, has conserved motifs common to helicase superfamily 3 among six genogroups. However, its biological functions are not fully understood. In this study we report the oligomeric state and the nucleotide triphosphatase (NTPase) and RNA chaperone activities of the recombinant full-length NS3 derived from murine norovirus (MNV). The MNV NS3 has an Mg-dependent NTPase activity, and site-directed mutagenesis of the conserved NTPase motifs blocked enzyme activity and viral replication in cells. Further, the NS3 was found via fluorescence resonance energy transfer (FRET)-based assays to destabilize double-stranded RNA in the presence of Mg or Mn in an NTP-independent manner. However, the RNA destabilization activity was not affected by mutagenesis of the conserved motifs of NTPase. These results reveal that the MNV NS3 has an NTPase-independent RNA chaperone-like activity, and that a FRET-based RNA destabilization assay has the potential to identify new antiviral drugs targeting NS3.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001151
2018-09-28
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/jgv/99/11/1482.html?itemId=/content/journal/jgv/10.1099/jgv.0.001151&mimeType=html&fmt=ahah

References

  1. Green KY. Caliciviruses: the noroviruses. In Fields Virology, 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2007 pp. 949–979
    [Google Scholar]
  2. Bok K, Green KY. Norovirus gastroenteritis in immunocompromised patients. N Engl J Med 2012; 367:2126–2132 [View Article][PubMed]
    [Google Scholar]
  3. Jones MK, Watanabe M, Zhu S, Graves CL, Keyes LR et al. Enteric bacteria promote human and mouse norovirus infection of B cells. Science 2014; 346:755–759 [View Article][PubMed]
    [Google Scholar]
  4. Ettayebi K, Crawford SE, Murakami K, Broughman JR, Karandikar U et al. Replication of human noroviruses in stem cell-derived human enteroids. Science 2016; 353:1387–1393 [View Article][PubMed]
    [Google Scholar]
  5. Karst SM, Wobus CE, Lay M, Davidson J, Virgin HW. STAT1-dependent innate immunity to a Norwalk-like virus. Science 2003; 299:1575–1578 [View Article][PubMed]
    [Google Scholar]
  6. Wobus CE, Karst SM, Thackray LB, Chang KO, Sosnovtsev SV et al. Replication of Norovirus in cell culture reveals a tropism for dendritic cells and macrophages. PLoS Biol 2004; 2:e432 [View Article][PubMed]
    [Google Scholar]
  7. Morales M, Bárcena J, Ramírez MA, Boga JA, Parra F et al. Synthesis in vitro of rabbit hemorrhagic disease virus subgenomic RNA by internal initiation on (-)sense genomic RNA: mapping of a subgenomic promoter. J Biol Chem 2004; 279:17013–17018 [View Article][PubMed]
    [Google Scholar]
  8. Bailey D, Kaiser WJ, Hollinshead M, Moffat K, Chaudhry Y et al. Feline calicivirus p32, p39 and p30 proteins localize to the endoplasmic reticulum to initiate replication complex formation. J Gen Virol 2010; 91:739–749 [View Article][PubMed]
    [Google Scholar]
  9. Yunus MA, Lin X, Bailey D, Karakasiliotis I, Chaudhry Y et al. The murine norovirus core subgenomic RNA promoter consists of a stable stem-loop that can direct accurate initiation of RNA synthesis. J Virol 2015; 89:1218–1229 [View Article][PubMed]
    [Google Scholar]
  10. Lin X, Thorne L, Jin Z, Hammad LA, Li S et al. Subgenomic promoter recognition by the norovirus RNA-dependent RNA polymerases. Nucleic Acids Res 2015; 43:446–460 [View Article][PubMed]
    [Google Scholar]
  11. Rajkowitsch L, Schroeder R. Dissecting RNA chaperone activity. RNA 2007; 13:2053–2060 [View Article][PubMed]
    [Google Scholar]
  12. Zúñiga S, Sola I, Cruz JL, Enjuanes L. Role of RNA chaperones in virus replication. Virus Res 2009; 139:253–266 [View Article][PubMed]
    [Google Scholar]
  13. Musier-Forsyth K. RNA remodeling by chaperones and helicases. RNA Biol 2010; 7:632–633 [View Article][PubMed]
    [Google Scholar]
  14. Liu F, Putnam A, Jankowsky E. ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding. Proc Natl Acad Sci USA 2008; 105:20209–20214 [View Article][PubMed]
    [Google Scholar]
  15. Kadaré G, Haenni AL. Virus-encoded RNA helicases. J Virol 1997; 71:2583–2590[PubMed]
    [Google Scholar]
  16. Jankowsky E. RNA helicases at work: binding and rearranging. Trends Biochem Sci 2011; 36:19–29 [View Article][PubMed]
    [Google Scholar]
  17. Rein A, Henderson LE, Levin JG. Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: significance for viral replication. Trends Biochem Sci 1998; 23:297–301 [View Article][PubMed]
    [Google Scholar]
  18. Cheng Z, Yang J, Xia H, Qiu Y, Wang Z et al. The nonstructural protein 2C of a Picorna-like virus displays nucleic acid helix destabilizing activity that can be functionally separated from its ATPase activity. J Virol 2013; 87:5205–5218 [View Article][PubMed]
    [Google Scholar]
  19. Xia H, Wang P, Wang GC, Yang J, Sun X et al. Human enterovirus nonstructural protein 2CATpase functions as both an RNA helicase and ATP-independent RNA chaperone. PLoS Pathog 2015; 11:e1005067 [View Article][PubMed]
    [Google Scholar]
  20. Frick DN. The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target. Curr Issues Mol Biol 2007; 9:1–20[PubMed]
    [Google Scholar]
  21. Karpe YA, Aher PP, Lole KS. NTPase and 5'-RNA triphosphatase activities of Chikungunya virus nsP2 protein. PLoS One 2011; 6:e22336 [View Article][PubMed]
    [Google Scholar]
  22. Lee NR, Kwon HM, Park K, Oh S, Jeong YJ et al. Cooperative translocation enhances the unwinding of duplex DNA by SARS coronavirus helicase nsP13. Nucleic Acids Res 2010; 38:7626–7636 [View Article][PubMed]
    [Google Scholar]
  23. Wang Q, Han Y, Qiu Y, Zhang S, Tang F et al. Identification and characterization of RNA duplex unwinding and ATPase activities of an alphatetravirus superfamily 1 helicase. Virology 2012; 433:440–448 [View Article][PubMed]
    [Google Scholar]
  24. Marín MS, Casais R, Alonso JM, Parra F. ATP binding and ATPase activities associated with recombinant rabbit hemorrhagic disease virus 2C-like polypeptide. J Virol 2000; 74:10846–10851 [View Article][PubMed]
    [Google Scholar]
  25. Pfister T, Wimmer E. Polypeptide p41 of a Norwalk-like virus is a nucleic acid-independent nucleoside triphosphatase. J Virol 2001; 75:1611–1619 [View Article][PubMed]
    [Google Scholar]
  26. Li TF, Hosmillo M, Schwanke H, Shu T, Wang Z et al. Human norovirus NS3 has RNA helicase and chaperoning activities. J Virol 2018; 92:e01606-17 [View Article][PubMed]
    [Google Scholar]
  27. Cotton BT, Hyde JL, Sarvestani ST, Sosnovtsev SV, Green KY et al. The norovirus NS3 protein is a dynamic lipid- and microtubule-associated protein involved in viral RNA replication. J Virol 2017; 91:e02138-16 [View Article][PubMed]
    [Google Scholar]
  28. Adams P, Kandiah E, Effantin G, Steven AC, Ehrenfeld E. Poliovirus 2C protein forms homo-oligomeric structures required for ATPase activity. J Biol Chem 2009; 284:22012–22021 [View Article][PubMed]
    [Google Scholar]
  29. Levin MK, Patel SS. The helicase from hepatitis C virus is active as an oligomer. J Biol Chem 1999; 274:31839–31846 [View Article][PubMed]
    [Google Scholar]
  30. Jankowsky A, Guenther UP, Jankowsky E. The RNA helicase database. Nucleic Acids Res 2011; 39:D338–D341 [View Article][PubMed]
    [Google Scholar]
  31. Thorne L, Bailey D, Goodfellow I. High-resolution functional profiling of the norovirus genome. J Virol 2012; 86:11441–11456 [View Article][PubMed]
    [Google Scholar]
  32. Lee JH, Park BS, Han KR, Biering SB, Kim SJ et al. Insight into the interaction between RNA polymerase and vpg for murine norovirus replication. Front Microbiol 2018; 9:1466 [View Article][PubMed]
    [Google Scholar]
  33. Orchard RC, Wilen CB, Doench JG, Baldridge MT, McCune BT et al. Discovery of a proteinaceous cellular receptor for a norovirus. Science 2016; 353:933–936 [View Article][PubMed]
    [Google Scholar]
  34. Fuller-Pace FV. RNA helicases: modulators of RNA structure. Trends Cell Biol 1994; 4:271–274 [View Article][PubMed]
    [Google Scholar]
  35. Cho MW, Richards OC, Dmitrieva TM, Agol V, Ehrenfeld E. RNA duplex unwinding activity of poliovirus RNA-dependent RNA polymerase 3Dpol. J Virol 1993; 67:3010–3018[PubMed]
    [Google Scholar]
  36. Destefano JJ, Titilope O. Poliovirus protein 3AB displays nucleic acid chaperone and helix-destabilizing activities. J Virol 2006; 80:1662–1671 [View Article][PubMed]
    [Google Scholar]
  37. Gangaramani DR, Eden EL, Shah M, Destefano JJ. The twenty-nine amino acid C-terminal cytoplasmic domain of poliovirus 3AB is critical for nucleic acid chaperone activity. RNA Biol 2010; 7:820–829 [View Article][PubMed]
    [Google Scholar]
  38. Green KY, Mory A, Fogg MH, Weisberg A, Belliot G et al. Isolation of enzymatically active replication complexes from feline calicivirus-infected cells. J Virol 2002; 76:8582–8595 [View Article][PubMed]
    [Google Scholar]
  39. Hyde JL, Gillespie LK, Mackenzie JM. Mouse norovirus 1 utilizes the cytoskeleton network to establish localization of the replication complex proximal to the microtubule organizing center. J Virol 2012; 86:4110–4122 [View Article][PubMed]
    [Google Scholar]
  40. Rodríguez PL, Carrasco L. Poliovirus protein 2C has ATPase and GTPase activities. J Biol Chem 1993; 268:8105–8110[PubMed]
    [Google Scholar]
  41. Yen JB, Wei LH, Chen LW, Chen LY, Hung CH et al. Subcellular localization and functional characterization of GII.4 norovirus-encoded NTPase. J Virol 2018; 92:e01824-17 [View Article][PubMed]
    [Google Scholar]
  42. Tompa P, Csermely P. The role of structural disorder in the function of RNA and protein chaperones. FASEB J 2004; 18:1169–1175 [View Article][PubMed]
    [Google Scholar]
  43. Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins 2009; 77:89–99 [View Article][PubMed]
    [Google Scholar]
  44. Doerflinger SY, Cortese M, Romero-Brey I, Menne Z, Tubiana T et al. Membrane alterations induced by nonstructural proteins of human norovirus. PLoS Pathog 2017; 13:e1006705 [View Article][PubMed]
    [Google Scholar]
  45. Simmonds P, Karakasiliotis I, Bailey D, Chaudhry Y, Evans DJ et al. Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses. Nucleic Acids Res 2008; 36:2530–2546 [View Article][PubMed]
    [Google Scholar]
  46. Alhatlani B, Vashist S, Goodfellow I. Functions of the 5' and 3' ends of calicivirus genomes. Virus Res 2015; 206:134–143 [View Article][PubMed]
    [Google Scholar]
  47. Li Z, Nagy PD. Diverse roles of host RNA binding proteins in RNA virus replication. RNA Biol 2011; 8:305–315 [View Article][PubMed]
    [Google Scholar]
  48. Ovchinnikov S, Park H, Kim DE, Dimaio F, Baker D. Protein structure prediction using Rosetta in CASP12. Proteins 2018; 86:113–121 [View Article][PubMed]
    [Google Scholar]
  49. Sameshima T, Iizuka R, Ueno T, Funatsu T. Denatured proteins facilitate the formation of the football-shaped GroEL-(GroES)2 complex. Biochem J 2010; 427:247–254 [View Article][PubMed]
    [Google Scholar]
  50. Biering SB, Choi J, Halstrom RA, Brown HM, Beatty WL et al. Viral replication complexes are targeted by lc3-guided interferon-inducible GTPases. Cell Host Microbe 2017; 22:74.e7–85.e7 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001151
Loading
/content/journal/jgv/10.1099/jgv.0.001151
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error