Abstract
Plant immunity is a highly dynamic process and requires dynamic modeling to capture the events of complexity mediated by the interaction between plant host and the attacking pathogen. The events of recognition are invoked by pathogen-based epitopes, while the subversion of host defenses are orchestrated by pathogen-originated effector molecules. The pathogen constitutes an immune signaling network inside the host cells. We model plant immune dynamics by using JIMENA-package, which is a java-based genetic regulatory network (GRN) simulation framework. It can efficiently compute network behavior and system states mediated by pathogenic perturbations. Here, we describe a step-by-step protocol to introduce the application of JIMENA-package to quantify immune dynamics in plant–pathogen interaction networks.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Glazebrook J (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43:205–227
Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SCM (2012) Hormonal modulation of plant immunity. Annu Rev Cell Dev Biol 28:489–521
Jones JDG, Dangl JL (2006) The plant immune system. Nature 444:323–329
Xin X-F, He SY (2013) Pseudomonas syringae pv. tomato DC3000: a model pathogen for probing disease susceptibility and hormone signaling in plants. Annu Rev Phytopathol 51:473–498
Monaghan J, Zipfel C (2012) Plant pattern recognition receptor complexes at the plasma membrane. Curr Opin Plant Biol 15:349–357
Zipfel C, Kunze G, Chinchilla D, Caniard A, Jones JDG, Boller T, Felix G (2006) Perception of the bacterial PAMP EF-Tu by the receptor EFR restricts agrobacterium-mediated transformation. Cell 125:749–760
Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nürnberger T, Jones JDG, Felix G, Boller T (2007) A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature 448:497–500
Asai T, Tena G, Plotnikova J, Willmann MR, Chiu W-L, Gomez-Gomez L, Boller T, Ausubel FM, Sheen J (2002) MAP kinase signalling cascade in Arabidopsis innate immunity. Nature 415:977–983
Sarris PF et al (2015) A plant immune receptor detects pathogen effectors that target WRKY transcription factors. Cell 161:1089–1100
Göhre V, Robatzek S (2008) Breaking the barriers: microbial effector molecules subvert plant immunity. Annu Rev Phytopathol 46:189–215
Cui H, Tsuda K, Parker JE (2014) Effector-triggered immunity: from pathogen perception to robust defense. Annu Rev Plant Biol 66:1–25
Dong X, Jiang Z, Peng YL, Zhang Z (2015) Revealing shared and distinct gene network organization in Arabidopsis immune responses by integrative analysis. Plant Physiol 167(3):1186–1203
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 24:1793–1814
Karl S, Dandekar T (2015) Jimena: efficient computing and system state identification for genetic regulatory networks. BMC Bioinformatics 14:306. https://doi.org/10.1186/1471-2105-14-306
Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L (2007) Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics 8(1):462
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30
Kanehisa M, Sato Y, Furumichi M, Morishima K, Tanabe M (2019) New approach for understanding genome variations in KEGG. Nucleic Acids Res 47:D590–D595
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, Jensen LJ, Mering CV (2019) STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 47(D1):D607–D613. https://doi.org/10.1093/nar/gky1131
Schläpfer P, Zhang P, Wang C, Kim T, Banf M, Chae L et al (2017) Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants. Plant Physiol 173(4):2041–2059
Kaltdorf M, Dandekar T, Naseem M (2017) Reconstruction of an immune dynamic model to simulate the contrasting role of auxin and cytokinin in plant immunity. In: Hurny A, Benková E (eds) Auxins and cytokinins in plant biology. Humana Press, New York, NY, pp 83–92
Acknowledgments
We thank the Land Bavaria (contribution to DFG Project number 324392634/TR221 to T.D.) for funding and are thankful for a grant from the Research Incentive Fund (R19073) and a CLUSTER grant (R20141) by Zayed University to M.N.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Osmanoglu, Ö., Shams, S., Dandekar, T., Naseem, M. (2021). Modeling Immune Dynamics in Plants Using JIMENA-Package. In: MUKHTAR, S. (eds) Modeling Transcriptional Regulation. Methods in Molecular Biology, vol 2328. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1534-8_11
Download citation
DOI: https://doi.org/10.1007/978-1-0716-1534-8_11
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-1533-1
Online ISBN: 978-1-0716-1534-8
eBook Packages: Springer Protocols