A Systems Biology Methodology Combining Transcriptome and Interactome Datasets to Assess the Implications of Cytokinin Signaling for Plant Immune Networks

  • Meik Kunz
  • Thomas Dandekar
  • Muhammad NaseemEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1569)


Cytokinins (CKs) play an important role in plant growth and development. Also, several studies highlight the modulatory implications of CKs for plant-pathogen interaction. However, the underlying mechanisms of CK mediating immune networks in plants are still not fully understood. A detailed analysis of high-throughput transcriptome (RNA-Seq and microarrays) datasets under modulated conditions of plant CKs and its mergence with cellular interactome (large-scale protein-protein interaction data) has the potential to unlock the contribution of CKs to plant defense. Here, we specifically describe a detailed systems biology methodology pertinent to the acquisition and analysis of various omics datasets that delineate the role of plant CKs in impacting immune pathways in Arabidopsis.

Key words

Cytokinins Plant immunity Transcriptomes Interactomes Plant hormones 



We thank DFG for funding (FungiNet124/B1).


  1. 1.
    Kunz M, Ahmed N, Dandekar T, Naseem M (2013) Hormone signaling networks open multiple routes for immunity and disease in plants. Biohelikon Immunity and Diseases 1:2Google Scholar
  2. 2.
    Hwang I, Sheen J, Muller B (2012) Cytokinin signaling networks. Annu Rev Plant Biol 63:353–380CrossRefPubMedGoogle Scholar
  3. 3.
    Choi J, Choi D, Lee S, Ryu CM, Hwang I (2011) Cytokinins and plant immunity: old foes or new friends? Trends Plant Sci 16:388–394CrossRefPubMedGoogle Scholar
  4. 4.
    Naseem M, Philippi N, Hussain A, Wangorsch G, Ahmed N, Dandekar T (2012) Integrated systems view on networking by hormones in Arabidopsis immunity reveals multiple crosstalk for cytokinin. Plant Cell 24:1793–1814CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Naseem M, Kunz M, Ahmed N, Dandekar T (2013) Integration of boolean models on hormonal interactions and prospects of cytokinin-auxin crosstalk in plant immunity. Plant Signal Behav 8:e23890CrossRefPubMedGoogle Scholar
  6. 6.
    Argueso CT, Ferreira FJ, Epple P, To JP, Hutchison CE, Schaller GE, Dangl JL, Kieber JJ (2012) Two-component elements mediate interactions between cytokinin and salicylic acid in plant immunity. PLoS Genet 8:e1002448CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Schaller GE, Bishopp A, Kieber JJ (2015) The yin-yang of hormones: cytokinin and auxin interactions in plant development. Plant Cell 27:44–63CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Naseem M, Wolfling M, Dandekar T (2014) Cytokinins for immunity beyond growth, galls and green islands. Trends Plant Sci 19:481–484CrossRefPubMedGoogle Scholar
  9. 9.
    Hinsch J, Vrabka J, Oeser B, Novak O, Galuszka P, Tudzynski P (2015) De novo biosynthesis of cytokinins in the biotrophic fungus Claviceps purpurea. Environ Microbiol 17:2935–2951CrossRefPubMedGoogle Scholar
  10. 10.
    Choi J, Huh SU, Kojima M, Sakakibara H, Paek KH, Hwang I (2010) The cytokinin-activated transcription factor ARR2 promotes plant immunity via TGA3/NPR1-dependent salicylic acid signaling in Arabidopsis. Dev Cell 19:284–295CrossRefPubMedGoogle Scholar
  11. 11.
    Swartzberg D, Kirshner B, Rav-David D, Elad Y, Granot D (2008) Botrytis cinerea induces senescence and is inhibited by autoregulated expression of the IPT gene. Eur J Plant Pathol 120:289–297CrossRefGoogle Scholar
  12. 12.
    Radhika V, Ueda N, Tsuboi Y, Kojima M, Kikuchi J, Kudo T, Sakakibara H (2015) Methylated cytokinins from the phytopathogen Rhodococcus fascians mimic plant hormone activity. Plant Physiol 169:1118–1126CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Siddique S, Radakovic ZS, De La Torre CM, Chronis D, Novak O, Ramireddy E, Holbein J, Matera C, Hütten M, Gutbrod P, Anjam MS, Rozanska E, Habash S, Elashry A, Sobczak M, Kakimoto T, Strnad M, Schmülling T, Mitchum MG, Grundler FM (2015) A parasitic nematode releases cytokinin that controls cell division and orchestrates feeding site formation in host plants. Proc Natl Acad Sci U S A 112:12669–12674CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Naseem M, Dandekar T (2012) The role of auxin-cytokinin antagonism in plant-pathogen interactions. PLoS Pathog 8:e1003026CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics (Oxford, England) 21:3448–3449CrossRefGoogle Scholar
  16. 16.
    Assenov Y, Ramirez F, Schelhorn SE, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics (Oxford, England) 24:282–284CrossRefGoogle Scholar
  17. 17.
    Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T (2012) A travel guide to Cytoscape plugins. Nat Methods 9:1069–1076CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics (Oxford, England) 25:1091–1093CrossRefGoogle Scholar
  20. 20.
    Naseem M, Kunz M, Dandekar T (2014) Probing the unknowns in cytokinin-mediated immune defense in Arabidopsis with systems biology approaches. Bioinformatics Biol Insights 8:35–44Google Scholar
  21. 21.
    Dong J, Horvath S (2007) Understanding network concepts in modules. BMC Syst Biol 1:24CrossRefPubMedPubMedCentralGoogle Scholar

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© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Functional Genomics & Systems Biology Group, Department of Bioinformatics, BiocenterUniversity of WuerzburgWuerzburgGermany
  2. 2.Deptartment of Bioinformatics, Biocenter University of Würzburg Am Hubland Würzburg GermanyJulius-Maximilians-Universität WürzburgWürzburgGermany
  3. 3.Department of Molecular Biology and GeneticsBoğaziçi UniversityBebekTurkey

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