1887

Abstract

Constant evolution of influenza A viruses (IAVs) leads to the occurrence of new virus strains, which can cause epidemics and occasional pandemics. Here we compared two medically relevant IAVs, namely A/Hamburg/4/09 (H1N1) of the 2009 pandemic and the highly pathogenic avian IAV human isolate A/Thailand/1(KAN-1)/2004 (H5N1), for their ability to trigger intracellular phosphorylation patterns using a highly sensitive peptide-based kinase activity profiling approach. Virus-dependent tyrosine phosphorylations of substrate peptides largely overlap between the two viruses and are also strongly overrepresented in comparison to serine/threonine peptide phosphorylations. Both viruses trigger phosphorylations with distinct kinetics by overlapping and different kinases from which many form highly interconnected networks. As approximately half of the kinases forming a signalling hub have no known function for the IAV life cycle, we interrogated selected members of this group for their ability to interfere with IAV replication. These experiments revealed negative regulation of H1N1 and H5N1 replication by NUAK [novel (nua) kinase] kinases and by redundant ephrin A (EphA) receptor tyrosine kinases.

Funding
This study was supported by the:
  • Deutsche Forschungsgemeinschaft (Award SFB1213/2, project 268555672)
    • Principle Award Recipient: StephanPleschka
  • Deutsche Forschungsgemeinschaft (Award SFB1213/2, project 268555672)
    • Principle Award Recipient: M.Lienhard Schmitz
Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001762
2022-06-30
2024-04-20
Loading full text...

Full text loading...

References

  1. Krammer F, Smith GJD, Fouchier RAM, Peiris M, Kedzierska K et al. Influenza. Nat Rev Dis Primers 2018; 4:3 [View Article] [PubMed]
    [Google Scholar]
  2. Mostafa A, Abdelwhab EM, Mettenleiter TC, Pleschka S. Zoonotic potential of influenza A viruses: a comprehensive overview. Viruses 2018; 10:E497 [View Article] [PubMed]
    [Google Scholar]
  3. Ghebrehewet S, MacPherson P, Ho A. Influenza. BMJ 2016; 355:i6258 [View Article] [PubMed]
    [Google Scholar]
  4. Mummert A, Weiss H, Long L-P, Amigó JM, Wan X-F. A perspective on multiple waves of influenza pandemics. PLoS One 2013; 8:e60343 [View Article] [PubMed]
    [Google Scholar]
  5. Morens DM, Taubenberger JK. Pandemic influenza: certain uncertainties. Rev Med Virol 2011; 21:262–284 [View Article] [PubMed]
    [Google Scholar]
  6. Matsuoka Y, Matsumae H, Katoh M, Eisfeld AJ, Neumann G et al. A comprehensive map of the influenza A virus replication cycle. BMC Syst Biol 2013; 7:97 [View Article] [PubMed]
    [Google Scholar]
  7. Watanabe T, Watanabe S, Kawaoka Y. Cellular networks involved in the influenza virus life cycle. Cell Host Microbe 2010; 7:427–439 [View Article] [PubMed]
    [Google Scholar]
  8. Edinger TO, Pohl MO, Stertz S. Entry of influenza A virus: host factors and antiviral targets. J Gen Virol 2014; 95:263–277 [View Article] [PubMed]
    [Google Scholar]
  9. Kash JC, Goodman AG, Korth MJ, Katze MG. Hijacking of the host-cell response and translational control during influenza virus infection. Virus Res 2006; 119:111–120 [View Article] [PubMed]
    [Google Scholar]
  10. Kash JC, Tumpey TM, Proll SC, Carter V, Perwitasari O et al. Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus. Nature 2006; 443:578–581 [View Article] [PubMed]
    [Google Scholar]
  11. Schmitz ML, Kracht M, Saul VV. The intricate interplay between RNA viruses and NF-κB. Biochim Biophys Acta 2014; 1843:2754–2764 [View Article] [PubMed]
    [Google Scholar]
  12. Ahmed F, Kleffmann T, Husain M. Acetylation, methylation and allysine modification profile of viral and host proteins during influenza A virus infection. Viruses 2021; 13:1415 [View Article] [PubMed]
    [Google Scholar]
  13. Schmidt N, Domingues P, Golebiowski F, Patzina C, Tatham MH et al. An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity. Proc Natl Acad Sci U S A 2019; 116:17399–17408 [View Article] [PubMed]
    [Google Scholar]
  14. Weber A, Dam S, Saul VV, Kuznetsova I, Müller C et al. Phosphoproteome analysis of cells infected with adapted and nonadapted influenza A virus reveals novel pro- and antiviral signaling networks. J Virol 2019; 93:13 [View Article] [PubMed]
    [Google Scholar]
  15. Sharma K, D’Souza RCJ, Tyanova S, Schaab C, Wiśniewski JR et al. Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep 2014; 8:1583–1594 [View Article] [PubMed]
    [Google Scholar]
  16. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. The protein kinase complement of the human genome. Science 2002; 298:1912–1934 [View Article] [PubMed]
    [Google Scholar]
  17. Lochhead PA, Sibbet G, Morrice N, Cleghon V. Activation-loop autophosphorylation is mediated by a novel transitional intermediate form of DYRKs. Cell 2005; 121:925–936 [View Article] [PubMed]
    [Google Scholar]
  18. Saul VV, de la Vega L, Milanovic M, Krüger M, Braun T et al. HIPK2 kinase activity depends on cis-autophosphorylation of its activation loop. J Mol Cell Biol 2013; 5:27–38 [View Article] [PubMed]
    [Google Scholar]
  19. Söderholm S, Kainov DE, Öhman T, Denisova OV, Schepens B et al. Phosphoproteomics to characterize host response during influenza A virus infection of human macrophages. Mol Cell Proteomics 2016; 15:3203–3219 [View Article] [PubMed]
    [Google Scholar]
  20. Yángüez E, Hunziker A, Dobay MP, Yildiz S, Schading S et al. Phosphoproteomic-based kinase profiling early in influenza virus infection identifies GRK2 as antiviral drug target. Nat Commun 2018; 9:3679 [View Article] [PubMed]
    [Google Scholar]
  21. Ferguson FM, Gray NS. Kinase inhibitors: the road ahead. Nat Rev Drug Discov 2018; 17:353–377 [View Article] [PubMed]
    [Google Scholar]
  22. Laure M, Hamza H, Koch-Heier J, Quernheim M, Müller C et al. Antiviral efficacy against influenza virus and pharmacokinetic analysis of a novel MEK-inhibitor, ATR-002, in cell culture and in the mouse model. Antiviral Res 2020; 178:104806 [View Article] [PubMed]
    [Google Scholar]
  23. Zarrin AA, Bao K, Lupardus P, Vucic D. Kinase inhibition in autoimmunity and inflammation. Nat Rev Drug Discov 2021; 20:39–63 [View Article] [PubMed]
    [Google Scholar]
  24. Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM et al. Too many roads not taken. Nature 2011; 470:163–165 [View Article] [PubMed]
    [Google Scholar]
  25. Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V et al. A global protein kinase and phosphatase interaction network in yeast. Science 2010; 328:1043–1046 [View Article] [PubMed]
    [Google Scholar]
  26. Varjosalo M, Keskitalo S, Van Drogen A, Nurkkala H, Vichalkovski A et al. The protein interaction landscape of the human CMGC kinase group. Cell Rep 2013; 3:1306–1320 [View Article] [PubMed]
    [Google Scholar]
  27. Schnitzler SU, Schnitzler P. An update on swine-origin influenza virus A/H1N1: A review. Virus Genes 2009; 39:279–292 [View Article] [PubMed]
    [Google Scholar]
  28. Wong JY, Kelly H, Cheung C-MM, Shiu EY, Wu P et al. Hospitalization Fatality Risk of Influenza A(H1N1)pdm09: A Systematic Review and Meta-Analysis. Am J Epidemiol 2015; 182:294–301 [View Article] [PubMed]
    [Google Scholar]
  29. Tiensin T, Chaitaweesub P, Songserm T, Chaisingh A, Hoonsuwan W et al. Highly pathogenic avian influenza H5N1, Thailand, 2004. Emerg Infect Dis 2005; 11:1664–1672 [View Article] [PubMed]
    [Google Scholar]
  30. Haas J, Bloesel D, Bacher S, Kracht M, Schmitz ML. Chromatin targeting of HIPK2 leads to acetylation-dependent chromatin decondensation. Front Cell Dev Biol 2020; 8:852 [View Article] [PubMed]
    [Google Scholar]
  31. Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2019; 47:D607–D613 [View Article] [PubMed]
    [Google Scholar]
  32. Ding X, Lu J, Yu R, Wang X, Wang T et al. Preliminary proteomic analysis of A549 cells infected with avian influenza virus H7N9 and influenza A virus H1N1. PLoS One 2016; 11:e0156017 [View Article] [PubMed]
    [Google Scholar]
  33. Kheirollahi V, Wasnick RM, Biasin V, Vazquez-Armendariz AI, Chu X et al. Metformin induces lipogenic differentiation in myofibroblasts to reverse lung fibrosis. Nat Commun 2019; 10:2987 [View Article] [PubMed]
    [Google Scholar]
  34. Schwill M, Tamaskovic R, Gajadhar AS, Kast F, White FM et al. Systemic analysis of tyrosine kinase signaling reveals a common adaptive response program in a HER2-positive breast cancer. Sci Signal 2019; 12:565 [View Article] [PubMed]
    [Google Scholar]
  35. Pleschka S, Wolff T, Ehrhardt C, Hobom G, Planz O et al. Influenza virus propagation is impaired by inhibition of the Raf/MEK/ERK signalling cascade. Nat Cell Biol 2001; 3:301–305 [View Article] [PubMed]
    [Google Scholar]
  36. Sharma A, Batra J, Stuchlik O, Reed MS, Pohl J et al. Influenza A virus nucleoprotein activates the JNK stress-signaling pathway for viral replication by sequestering host filamin A protein. Front Microbiol 2020; 11:581867 [View Article] [PubMed]
    [Google Scholar]
  37. Hunter T. The genesis of tyrosine phosphorylation. Cold Spring Harb Perspect Biol 2014; 6:a020644 [View Article] [PubMed]
    [Google Scholar]
  38. Darling TK, Lamb TJ. Emerging roles for Eph receptors and ephrin ligands in immunity. Front Immunol 2019; 10:1473 [View Article] [PubMed]
    [Google Scholar]
  39. Colinge J, César-Razquin A, Huber K, Breitwieser FP, Májek P et al. Building and exploring an integrated human kinase network: global organization and medical entry points. J Proteomics 2014; 107:113–127 [View Article] [PubMed]
    [Google Scholar]
  40. Invergo BM, Petursson B, Akhtar N, Bradley D, Giudice G et al. Prediction of signed protein kinase regulatory circuits. Cell Syst 2020; 10:384–396 [View Article] [PubMed]
    [Google Scholar]
  41. Hardman G, Perkins S, Brownridge PJ, Clarke CJ, Byrne DP et al. Strong anion exchange-mediated phosphoproteomics reveals extensive human non-canonical phosphorylation. EMBO J 2019; 38:21 [View Article] [PubMed]
    [Google Scholar]
  42. Chang Z, Wang Y, Zhou X, Long JE. STAT3 roles in viral infection: antiviral or proviral?. Future Virol 2018; 13:557–574 [View Article] [PubMed]
    [Google Scholar]
  43. Trilling M, Le VTK, Rashidi-Alavijeh J, Katschinski B, Scheller J et al. “Activated” STAT proteins: a paradoxical consequence of inhibited JAK-STAT signaling in cytomegalovirus-infected cells. J Immunol 2014; 192:447–458 [View Article] [PubMed]
    [Google Scholar]
  44. Choy EH. Clinical significance of Janus Kinase inhibitor selectivity. Rheumatology (Oxford) 2019; 58:1122 [View Article] [PubMed]
    [Google Scholar]
  45. Garcia D, Shaw RJ. AMPK: mechanisms of cellular energy sensing and restoration of metabolic balance. Mol Cell 2017; 66:789–800 [View Article] [PubMed]
    [Google Scholar]
  46. Escalona E, Muñoz M, Pincheira R, Elorza ÁA, Castro AF. Cytosolic NUAK1 enhances ATP production by maintaining proper glycolysis and mitochondrial function in cancer cells. Front Oncol 2020; 10:1123 [View Article] [PubMed]
    [Google Scholar]
  47. Inazuka F, Sugiyama N, Tomita M, Abe T, Shioi G et al. Muscle-specific knock-out of NUAK family SNF1-like kinase 1 (NUAK1) prevents high fat diet-induced glucose intolerance. J Biol Chem 2012; 287:16379–16389 [View Article] [PubMed]
    [Google Scholar]
  48. Ehrhardt C, Wolff T, Pleschka S, Planz O, Beermann W et al. Influenza A virus NS1 protein activates the PI3K/Akt pathway to mediate antiapoptotic signaling responses. J Virol 2007; 81:3058–3067 [View Article] [PubMed]
    [Google Scholar]
  49. Miao H, Wang B. EphA receptor signaling--complexity and emerging themes. Semin Cell Dev Biol 2012; 23:16–25 [View Article] [PubMed]
    [Google Scholar]
  50. Bonaparte MI, Dimitrov AS, Bossart KN, Crameri G, Mungall BA et al. Ephrin-B2 ligand is a functional receptor for Hendra virus and Nipah virus. Proc Natl Acad Sci U S A 2005; 102:10652–10657 [View Article] [PubMed]
    [Google Scholar]
  51. Lai K-O, Chen Y, Po H-M, Lok K-C, Gong K et al. Identification of the Jak/Stat proteins as novel downstream targets of EphA4 signaling in muscle: implications in the regulation of acetylcholinesterase expression. J Biol Chem 2004; 279:13383–13392 [View Article] [PubMed]
    [Google Scholar]
  52. de Boer ECW, van Gils JM, van Gils MJ. Ephrin-Eph signaling usage by a variety of viruses. Pharmacol Res 2020; 159:105038 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001762
Loading
/content/journal/jgv/10.1099/jgv.0.001762
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Supplementary material 3

EXCEL

Supplementary material 4

EXCEL
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