PhD defence: Architecture and dynamics of hormone-driven gene regulatory networks in plant immunity

Plants defend themselves against pests and pathogens by activating an elaborate gene regulatory network (GRN). Large parts of this GRN are regulated by the defense-related plant hormones jasmonic acid (JA), abscisic acid (ABA) and salicylic acid (SA). The (sub-)GRNs activated by these hormones interact by reinforcing or attenuating each other, thus ensuring an optimized defense response.

In this thesis, I analyzed the architecture and dynamics of the different hormone-driven GRNs and their interactions, focusing mainly on ABA and JA. First, we conducted a time series experiment of plants treated with ABA, and analyzed gene expression. By combining our data with publicly available data we predicted several novel components of the ABA GRN and validated the importance of one of these components with laboratory experiments.

Next, we also executed and analyzed a JA and ABA+JA time series to investigate how the ABA and JA GRNs are integrated. We found many genes that were affected non-additively by the two hormones, indicating substantial crosstalk between the two networks. We predicted several proteins that are involved in crosstalk between the two pathways and found that ABA affects part of the JA GRN by inducing degradation of ORA59, an important regulatory protein of part of the JA GRN. Interestingly, it was already known that SA also suppresses the same part of the JA GRN by inducing degradation of ORA59. In our research we found that SA partly regulates this by the activation of a specific class of proteins known as WRKY transcription factors.