Using a systems biology approach to elucidate transcriptional networks regulating plant defence

The phytopathogen Botrytis cinerea is responsible for the devastating grey mould disease that affects hundreds of economically important crop species. B. cinerea represents a necrotrophic pathogen that must kill host tissue before if can consume the nutrients, this distinguishes it from other biotrophic pathogens that exist parasitically. Importantly, B. cinerea is capable of infecting the model plant organism Arabidopsis thaliana. Together with the availability of the sequenced B. cinerea genome and the available molecular tools that now allow fungal genome manipulation makes the pathosystem ideal for studying necrotrophic pathogen life style from a systems biology perspective. This thesis focuses on the transcriptional responses of the A. thaliana host to B. cinerea infection. A high resolution transcriptome time series experiment was conducted to compare transcriptional variation between infected and mock infected A. thaliana leaves over 48 hours. This identified 9838 unique host genes differentially expressed over the course of infection. High resolution temporal expression profiles of genes were used to build transcriptional gene regulatory networks using a Variational Bayesian State Space Modeling technique. Approximately 56% of principle network components identified by this method and tested using a reverse genetics approaches showed an effect on defence against B. cinerea. This represents a significant increase in the predictive power (of gene essentiality) when using this method compared to classical forward genetics approaches and simple reverse genetic approaches following on from expression profiling studies. Attempts were made to resolve the local networks surrounding two of these previously uncharacterised principle network components involved in defence against B. cinerea using further transcriptome expression profiling and Yeast-1-Hybrid analysis. Subsequent re-modeling and experimental studies identified a number of high probability targets and several potential regulators of these principle network components. Overall the A. thaliana-B. cinerea interaction presents a experimentally tractable pathosystem for studying necrotrophic plant defence from a systems biology perspective