Function and evolution of plant peptides and protein interactions

In this thesis work, we try to understand the function and evolution of small/short plant peptides that are induced under oxidative stress and to further understand the functions of members of two plant transcription factor (TF) families viz. the MADS domain and AT-Hook proteins. An important feature of plant stress response comprises the production of peptides with signaling, antimicrobial and antioxidant activities. Our primary aim was to identify novel translatable sORFs in the model plant A. thaliana as the number of peptides annotated is very few when compared to other eukaryotes. We identified several Transcriptionally Active Regions (TARs) that might encode putative Stress-Induced Peptides (SIPs) and we hypothesize that the SIPs may rely on specific interactions with larger proteins.  Another aim of my PhD research was to study the protein interaction network of the MADS domain TFs in context of the γ triplication event at the origin of core eudicots. MADS-domain TFs are key regulators of reproductive development in plants and understanding the evolution of this class of TFs would help us to understand how modern-day plants evolved. Our study provides clarity through direct observation of ancestral networks. Using network simulations, we evaluated how elementary processes contributed to hierarchical modularity in the MADS domain protein interaction network. Additionally, we tried to understand the gene expression divergence of the AT-Hook TFs as the relation between the AHL protein family members and differences in life cycle between polycarpic and monocarpic plant species is not fully understood.