Cited by 27interferon and immune responsesMosquito-borne diseases and controlCytokine Signaling Pathways and Interactions

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Tick‐borne flavivirus NS5 antagonizes interferon signaling by inhibiting the catalytic activity of TYK2

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Abstract

The mechanisms utilized by different flaviviruses to evade antiviral functions of interferons are varied and incompletely understood. Using virological approaches, biochemical assays, and mass spectrometry analyses, we report here that the NS5 protein of tick-borne encephalitis virus (TBEV) and Louping Ill virus (LIV), two related tick-borne flaviviruses, antagonize JAK-STAT signaling through interactions with the tyrosine kinase 2 (TYK2). Co-immunoprecipitation (co-IP) experiments, yeast gap-repair assays, computational protein-protein docking and functional studies identify a stretch of 10 residues of the RNA dependent RNA polymerase domain of tick-borne flavivirus NS5, but not mosquito-borne NS5, that is critical for interactions with the TYK2 kinase domain. Additional co-IP assays performed with several TYK2 orthologs reveal that the interaction is conserved across mammalian species. In vitro kinase assays show that TBEV and LIV NS5 reduce the catalytic activity of TYK2. Our results thus illustrate a novel mechanism by which viruses suppress the interferon response.

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Crossref · 10.15252/embr.202357424

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Research works printed but not linked: 65

  1. Ashour J, Laurent‐Rolle M, Shi P‐Y, García‐Sastre A (2009) NS5 of dengue virus mediates STAT2 binding and degradation. J Virol 83: 5408–5418 · DOI
  2. Best SM (2017) The many faces of the flavivirus NS5 protein in antagonism of type I interferon signaling. J Virol 91: e01970‐16
  3. Best SM, Morris KL, Shannon JG, Robertson SJ, Mitzel DN, Park GS, Boer E, Wolfinbarger JB, Bloom ME (2005) Inhibition of interferon‐stimulated JAK‐STAT signaling by a tick‐borne flavivirus and identification of NS5 as an interferon antagonist. J Virol 79: 12828–12839 · DOI
  4. Burfoot MS, Rogers NC, Watling D, Smith JM, Pons S, Paonessaw G, Pellegrini S, White MF, Kerr IM (1997) Janus kinase‐dependent activation of insulin receptor substrate 1 in response to interleukin‐4, oncostatin M, and the interferons. J Biol Chem 272: 24183–24190 · DOI
  5. Carletti T, Zakaria MK, Faoro V, Reale L, Kazungu Y, Licastro D, Marcello A (2019) Viral priming of cell intrinsic innate antiviral signaling by the unfolded protein response. Nat Commun 10: 3889 · DOI
  6. Chazal M, Beauclair G, Gracias S, Najburg V, Simon‐Loriere E, Tangy F, Komarova AV, Jouvenet N (2018) RIG‐I recognizes the 5′ region of dengue and zika virus genomes. Cell Rep 24: 320–328 · DOI
  7. Dowling JW, Forero A (2022) Beyond good and evil: molecular mechanisms of type I and III IFN functions. J Immunol 208: 247–256 · DOI
  8. Gauzzi MC, Velazquez L, McKendry R, Mogensen KE, Fellous M, Pellegrini S (1996) Interferon‐α‐dependent activation of Tyk2 requires phosphorylation of positive regulatory tyrosines by another kinase. J Biol Chem 271: 20494–20500 · DOI
  9. Gehrke R, Ecker M, Aberle SW, Allison SL, Heinz FX, Mandl CW (2003) Incorporation of tick‐borne encephalitis virus replicons into virus‐like particles by a packaging cell line. J Virol 77: 8924–8933 · DOI
  10. Geiger TR, Martin JM (2006) The Epstein‐Barr virus‐encoded LMP‐1 oncoprotein negatively affects Tyk2 phosphorylation and interferon signaling in human B cells. J Virol 80: 11638–11650 · DOI
  11. Gilbert L (2016) Louping ill virus in the UK: a review of the hosts, transmission and ecological consequences of control. Exp Appl Acarol 68: 363–374 · DOI
  12. Grandvaux N, Servant MJ, tenOever B, Sen GC, Balachandran S, Barber GN, Lin R, Hiscott J (2002) Transcriptional profiling of interferon regulatory factor 3 target genes: direct involvement in the regulation of interferon‐stimulated genes. J Virol 76: 5532–5539 · DOI
  13. Grant A, Ponia SS, Tripathi S, Balasubramaniam V, Miorin L, Sourisseau M, Schwarz MC, Sanchez‐Seco MP, Evans MJ, Best SM et al (2016) Zika virus targets human STAT2 to inhibit type I interferon signaling. Cell Host Microbe 19: 882–890 · DOI
  14. Hai VV, Almeras L, Socolovschi C, Raoult D, Parola P, Pagès F (2014) Monitoring human tick‐borne disease risk and tick bite exposure in Europe: available tools and promising future methods. Ticks Tick Borne Dis 5: 607–619 · DOI
  15. Hu X, Li J, Fu M, Zhao X, Wang W (2021) The JAK/STAT signaling pathway: from bench to clinic. Signal Transduct Target Ther 6: 1–33
  16. Jeffries CL, Mansfield KL, Phipps LP, Wakeley PR, Mearns R, Schock A, Bell S, Breed AC, Fooks AR, Johnson N (2014) Louping ill virus: an endemic tick‐borne disease of Great Britain. J Gen Virol 95: 1005–1014 · DOI
  17. Ji W, Luo G (2020) Zika virus NS5 nuclear accumulation is protective of protein degradation and is required for viral RNA replication. Virology 541: 124–135 · DOI
  18. Kemenesi G, Bányai K (2018) Tick‐borne flaviviruses, with a focus on powassan virus. Clin Microbiol Rev 32: e00106‐17 · DOI
  19. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774–797 · DOI
  20. Laurent‐Rolle M, Morrison J, Rajsbaum R, Macleod JM, Pisanelli G, Pham A, Ayllon J, Miorin L, Martinez‐Romero C, tenOever BR et al (2014) The interferon signaling antagonist function of yellow fever virus NS5 protein is activated by type I interferon. Cell Host Microbe 16: 314–327 · DOI
  21. Lawson D, Arensburger P, Atkinson P, Besansky NJ, Bruggner RV, Butler R, Campbell KS, Christophides GK, Christley S, Dialynas E et al (2009) VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res 37: D583–D587 · DOI
  22. Le Breton M, Meyniel‐Schicklin L, Deloire A, Coutard B, Canard B, de Lamballerie X, Andre P, Rabourdin‐Combe C, Lotteau V, Davoust N (2011) Flavivirus NS3 and NS5 proteins interaction network: a high‐throughput yeast two‐hybrid screen. BMC Microbiol 11: 234 · DOI
  23. Lemasson M, Caignard G, Unterfinger Y, Attoui H, Bell‐Sakyi L, Hirchaud E, Moutailler S, Johnson N, Vitour D, Richardson J et al (2021) Exploration of binary protein–protein interactions between tick‐borne flaviviruses and Ixodes ricinus. Parasit Vectors 14: 144 · DOI
  24. Li S, Labrecque S, Gauzzi MC, Cuddihy AR, Wong AH, Pellegrini S, Matlashewski GJ, Koromilas AE (1999) The human papilloma virus (HPV)‐18 E6 oncoprotein physically associates with Tyk2 and impairs Jak‐STAT activation by interferon‐α. Oncogene 18: 5727–5737 · DOI
  25. Li M, Johnson JR, Truong B, Kim G, Weinbren N, Dittmar M, Shah PS, Von Dollen J, Newton BW, Jang GM et al (2019) Identification of antiviral roles for the exon–junction complex and nonsense‐mediated decay in flaviviral infection. Nat Microbiol 4: 985–995 · DOI
  26. Lin R‐J, Liao C‐L, Lin E, Lin Y‐L (2004) Blocking of the alpha interferon‐induced Jak‐Stat signaling pathway by Japanese encephalitis virus infection. J Virol 78: 9285–9294 · DOI
  27. Lin R‐J, Chang B‐L, Yu H‐P, Liao C‐L, Lin Y‐L (2006) Blocking of interferon‐induced Jak‐Stat signaling by Japanese encephalitis virus NS5 through a protein tyrosine phosphatase‐mediated mechanism. J Virol 80: 5908–5918 · DOI
  28. Liu L, Dai J, Zhao YO, Narasimhan S, Yang Y, Zhang L, Fikrig E (2012) Ixodes scapularis JAK‐STAT pathway regulates tick antimicrobial peptides, thereby controlling the agent of human granulocytic anaplasmosis. J Infect Dis 206: 1233–1241 · DOI
  29. López‐Denman AJ, Tuipulotu DE, Ross JB, Trenerry AM, White PA, Mackenzie JM (2021) Nuclear localisation of West Nile virus NS5 protein modulates host gene expression. Virology 559: 131–144 · DOI
  30. Lubick KJ, Robertson SJ, McNally KL, Freedman BA, Rasmussen AL, Taylor RT, Walts AD, Tsuruda S, Sakai M, Ishizuka M et al (2015) Flavivirus antagonism of type I interferon signaling reveals prolidase as a regulator of IFNAR1 surface expression. Cell Host Microbe 18: 61–74 · DOI
  31. Marze NA, Roy Burman SS, Sheffler W, Gray JJ (2018) Efficient flexible backbone protein‐protein docking for challenging targets. Bioinformatics 34: 3461–3469 · DOI · Paper page
  32. Mesev EV, LeDesma RA, Ploss A (2019) Decoding type I and III interferon signalling during viral infection. Nat Microbiol 4: 914–924 · DOI · Paper page
  33. Michelitsch A, Wernike K, Klaus C, Dobler G, Beer M (2019) Exploring the reservoir hosts of tick‐borne encephalitis virus. Viruses 11: 669 · DOI
  34. Morrison J, Laurent‐Rolle M, Maestre AM, Rajsbaum R, Pisanelli G, Simon V, Mulder LCF, Fernandez‐Sesma A, García‐Sastre A (2013) Dengue virus co‐opts UBR4 to degrade STAT2 and antagonize type I interferon signaling. PLoS Pathog 9: e1003265 · DOI
  35. Ng IHW, Chan KW‐K, Tan MJA, Gwee CP, Smith KM, Jeffress SJ, Saw W‐G, Swarbrick CMD, Watanabe S, Jans DA et al (2019) Zika virus NS5 forms supramolecular nuclear bodies that sequester importin‐α and modulate the host immune and pro‐inflammatory response in neuronal cells. ACS Infect Dis 5: 932–948 · DOI
  36. Park GS, Morris KL, Hallett RG, Bloom ME, Best SM (2007) Identification of residues critical for the interferon antagonist function of Langat virus NS5 reveals a role for the RNA‐dependent RNA polymerase domain. J Virol 81: 6936–6946 · DOI
  37. Petit MJ, Kenaston MW, Pham OH, Nagainis AA, Fishburn AT, Shah PS (2021) Nuclear dengue virus NS5 antagonizes expression of PAF1‐dependent immune response genes. PLoS Pathog 17: e1010100 · DOI
  38. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE (2021) UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci 30: 70–82 · DOI
  39. Pierson TC, Diamond MS (2020) The continued threat of emerging flaviviruses. Nat Microbiol 5: 796–812 · DOI
  40. Ragimbeau J, Dondi E, Alcover A, Eid P, Uzé G, Pellegrini S (2003) The tyrosine kinase Tyk2 controls IFNAR1 cell surface expression. EMBO J 22: 537–547 · DOI
  41. Rusinova I, Forster S, Yu S, Kannan A, Masse M, Cumming H, Chapman R, Hertzog PJ (2013) Interferome v2.0: an updated database of annotated interferon‐regulated genes. Nucleic Acids Res 41: D1040–D1046 · DOI · Paper page
  42. Ruzek D, Avšič Županc T, Borde J, Chrdle A, Eyer L, Karganova G, Kholodilov I, Knap N, Kozlovskaya L, Matveev A et al (2019) Tick‐borne encephalitis in Europe and Russia: review of pathogenesis, clinical features, therapy, and vaccines. Antiviral Res 164: 23–51 · DOI
  43. Schindelin J, Arganda‐Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B et al (2012) Fiji: an open‐source platform for biological‐image analysis. Nature Methods 9: 676–682 · DOI · Paper page
  44. Schoggins JW (2018) Recent advances in antiviral interferon‐stimulated gene biology. F1000Res 7: 309 · DOI
  45. Schoggins JW (2019) Interferon‐stimulated genes: what do they all do? Annu Rev Virol 6: 567–584 · DOI · Paper page
  46. Semenza JC, Suk JE (2018) Vector‐borne diseases and climate change: a European perspective. FEMS Microbiol Lett 365: fnx244 · DOI · Paper page
  47. Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L et al (2018) Comparative flavivirus‐host protein interaction mapping reveals mechanisms of dengue and Zika virus pathogenesis. Cell 175: 1931–1945 · DOI
  48. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498–2504 · DOI · Paper page
  49. Sourisseau M, Unterfinger Y, Lemasson M, Caignard G, Piumi F, Grot A, Moutailler S, Vitour D, Coulpier M, Lacour SA et al (2022) Integrated protein‐protein interaction and RNA interference screens reveal novel restriction and dependency factors for a tick‐borne flavivirus in its human host. bioRxivhttps://doi.org/10.1101/2022.11.03.514869 [PREPRINT] · DOI
  50. Streicher F, Jouvenet N (2019) Stimulation of innate immunity by host and viral RNAs. Trends Immunol 40: 1134–1148 · DOI
  51. Strobl B, Stoiber D, Sexl V, Mueller M (2011) Tyrosine kinase 2 (TYK2) in cytokine signalling and host immunity. Front Biosci 16: 3214–3232 · DOI
  52. Taylor RT, Lubick KJ, Robertson SJ, Broughton JP, Bloom ME, Bresnahan WA, Best SM (2011) TRIM79α, an interferon‐stimulated gene product, restricts tick‐borne encephalitis virus replication by degrading the viral RNA polymerase. Cell Host Microbe 10: 185–196 · DOI
  53. Teo G, Liu G, Zhang J, Nesvizhskii AI, Gingras A‐C, Choi H (2014) SAINTexpress: improvements and additional features in significance analysis of INTeractome software. J Proteomics 100: 37–43 · DOI
  54. Thurmond S, Wang B, Song J, Hai R (2018) Suppression of type I interferon signaling by flavivirus NS5. Viruses 10: E712 · DOI
  55. van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ (2016) The HADDOCK2.2 web server: user‐friendly integrative modeling of biomolecular complexes. J Mol Biol 428: 720–725 · DOI · Paper page
  56. Velazquez L, Mogensen KE, Barbieri G, Fellous M, Uzé G, Pellegrini S (1995) Distinct domains of the protein tyrosine kinase tyk2 required for binding of interferon‐alpha/beta and for signal transduction. J Biol Chem 270: 3327–3334 · DOI
  57. Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan N (2015) Scoring large scale affinity purification mass spectrometry datasets with MIST. Curr Protoc Bioinformatics 49: 8.19.1–8.19.16 · DOI
  58. Walhout AJM, Vidal M (2001) High‐throughput yeast two‐hybrid assays for large‐scale protein interaction mapping. Methods 24: 297–306 · DOI
  59. Wallweber HJA, Tam C, Franke Y, Starovasnik MA, Lupardus PJ (2014) Structural basis of recognition of interferon‐α receptor by tyrosine kinase 2. Nat Struct Mol Biol 21: 443–448 · DOI
  60. Werme K, Wigerius M, Johansson M (2008) Tick‐borne encephalitis virus NS5 associates with membrane protein scribble and impairs interferon‐stimulated JAK‐STAT signalling. Cell Microbiol 10: 696–712 · DOI
  61. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A et al (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67: 235–242 · DOI · Paper page
  62. Wispelaere M, Khou C, Frenkiel MP, Desprès P, Pardigon N (2015) A single amino acid substitution in the M protein attenuates Japanese encephalitis virus in mammalian hosts. J Virol. 90: 2676–2689 · DOI
  63. Yamaoka K, Saharinen P, Pesu M, Holt VE, Silvennoinen O, O'Shea JJ (2004) The Janus kinases (Jaks). Genome Biol 5: 253 · DOI
  64. Yang J, Jing X, Yi W, Li X‐D, Yao C, Zhang B, Zheng Z, Wang H, Gong P (2021) Crystal structure of a tick‐borne flavivirus RNA‐dependent RNA polymerase suggests a host adaptation hotspot in RNA viruses. Nucleic Acids Res 49: 1567–1580 · DOI
  65. Zhao Z, Tao M, Han W, Fan Z, Imran M, Cao S, Ye J (2021) Nuclear localization of Zika virus NS5 contributes to suppression of type I interferon production and response. J Gen Virol 102: 001376 · DOI

Metadata

Authors
Gracias, S., Chazal, M., Decombe, A., Unterfinger, Y., Sogues, A., Pruvost, L., Robert, V., Lacour, S. A., Lemasson, M., Sourisseau, M., Li, Z., Richardson, J., Pellegrini, S., Decroly, E., Caval, V., & Jouvenet, N.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • École Nationale Vétérinaire d'Alfort (FR)
  • VIB-VUB Center for Structural Biology (BE)
  • Inserm (FR)
Corresponding author
  • Caval, Vincent
  • Jouvenet, Nolwenn
Venue
The EMBO Reports
Published
2023-10-20
Volume
24
Issue
12
Pages
e57424-e57424
ISSN
  • 1469-221X (ISSN-L)
  • 1469-3178
OpenAlex
W4387798834
Cited by
27
References
1
Citations by year
2026: 12 · 2025: 5 · 2024: 7 · 2023: 3
FWCI
2.96
Type
journal article
Language
en
Open access
Locations
  • EMBO Reports (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, other-oa)
Funders
Agence Nationale de la Recherche (ANR‐19‐CE35‐0015, ANR‐20‐CE11‐0024)
Topics
  • Life Sciences › Immunology and Microbiology › Immunology › interferon and immune responses
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Mosquito-borne diseases and control
  • Life Sciences › Immunology and Microbiology › Immunology › Cytokine Signaling Pathways and Interactions
Keywords
tick-borne flaviviruses, tick-borne encephalitis virus, louping ill virus, NS5 protein, RNA-dependent RNA polymerase, TYK2, interferon signaling, JAK/STAT signaling, interferon antagonism, kinase inhibition, protein-protein interaction, antiviral evasion
MeSH terms
Animals, Encephalitis Viruses, Tick-Borne, Humans, Interferons, Mammals, Ticks, Viral Nonstructural Proteins, TYK2 Kinase

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