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My Research

PhD working title: “Investigating the molecular and cellular basis for immunity-induced growth inhibition in the roots of Arabidopsis thaliana and crop plants”

Biotic stresses experienced by crops can result in a double blow to crop yield: the direct impact of pathogenic activity on the plant, but also, significantly, the detrimental effect of the plant’s own immunity-induced growth inhibition (Eichmann and Schäfer, 2015). It is increasingly being argued that this growth-immunity antagonism is not simply an inevitable result of sharing finite metabolic resources between multiple physiological processes, but is more likely due to underlying signalling networks being hardwired to suppress growth as a direct response to immunity or defence being triggered (Reitz et al., 2015; Kliebenstein, 2015; Eichmann and Schäfer, 2015). Elucidating in detail the elements involved in these shared signalling pathways and how they may be manipulated to uncouple immunity and growth inhibition is the overarching aim of my project.

Defence responses, including reactive oxygen species burst, mitogen activated protein kinase (MAPK) activation and defence gene expression, can be triggered in laboratory-grown Arabidopsis thaliana roots through the exogenous application of microbe- or pathogen-associated molecular patterns (MAMPs or PAMPs) such as flg22 (a 22 amino acid N-terminal portion of the bacterial flagellin protein (Chinchilla et al. 2007)), or through the exogenous application of endogenous damage-associated molecular patterns (DAMPs), such as Pep1 (Huffaker and Ryan 2007). Such treatment of A. thaliana roots has also been shown to cause significant root growth inhibition (as measured by primary root length). Apparent uncoupling of root growth inhibition and flg22-triggered immunity has previously been achieved by colonising roots with the mutualistic endophytic fungus Piriformospora indica (= Serendipita indica (Weiß et al., 2016)) (Jacobs et al. 2011), thus P. indica presents a promising tool for investigating the molecular basis for this interaction and for identifying possible targets for overcoming it. Multiple lines of evidence support the involvement of hormones in mediating growth-immunity antagonism, and there is also growing interest in the potential involvement of cell cycle regulation.

My project aims to:

1. identify the role of individual hormones in specific aspects of root growth under immunity

2. determine the role of cell cycle regulation in growth under immunity

3. determine how P. indica influences hormonal and/or cell cycle regulation pathways such as to uncouple growth from immunity.

4. investigate the applicability of our A. thaliana findings to crop plants, such as Brassica oleracea.


I will be employing a mixture of 'wet' and 'dry' lab approaches to addressing these objectives. These include:
  • RNAseq and subsequent transcriptomics analyses of root tips in the presence or absense of elicitors of immunity, including in a key cell cycle regulation mutant
  • Bioinformatics to identify possible connections between hormones, the cell cycle and growth under immunity
  • Hormone/cell cycle regulator mutant root growth assays
  • Confocal laser scanning microscopy of root tips expressing hormone markers.


Chinchilla, D., Zipfel, C., Robatzek, S., Kemmerling, B., Nürnberger, T., Jones, J.D.G., Felix, G., and Boller, T. (2007) ‘A Flagellin-Induced Complex of the Receptor FLS2 and BAK1 Initiates Plant Defence.’ Nature 448 (7152), 497–500

Eichmann, R. and Schäfer, P. (2015) ‘Growth versus Immunity—a Redirection of the Cell Cycle?’ Current Opinion in Plant Biology 26, 106–112

Huffaker, A. and Ryan, C. a (2007) ‘Endogenous Peptide Defense Signals in Arabidopsis Differentially Amplify Signaling for the Innate Immune Response.’ Proceedings of the National Academy of Sciences of the United States of America 104 (25), 10732–6

Jacobs, S., Zechmann, B., Molitor, A., Trujillo, M., Petutschnig, E., Lipka, V., Kogel, K.-H., and Schafer, P. (2011) ‘Broad-Spectrum Suppression of Innate Immunity Is Required for Colonization of Arabidopsis Roots by the Fungus Piriformospora Indica’. Plant Physiology 156 (2), 726–740

Kliebenstein, D.J. (2015) ‘False Idolatry of the Mythical Growth versus Immunity Tradeoff in Molecular Systems Plant Pathology’. Physiological and Molecular Plant Pathology 95, 55–59

Reitz, M.U., Gifford, M.L., and Schäfer, P. (2015) ‘Hormone Activities and the Cell Cycle Machinery in Immunity-Triggered Growth Inhibition’. Journal of Experimental Botany 66 (8), 2187–2197

Weiß, M., Waller, F., Zuccaro, A., and Selosse, M.-A. (2016) ‘Sebacinales — One Thousand and One Interactions with Land Plants’. New Phytologist 1–61

Main Supervisor:

Dr Patrick Schäfer

School of Life Sciences
University of Warwick

P dot Schafer at warwick dot ac dot uk


Dr Sascha Ott

Department of Computer Science
University of Warwick

Funded by: