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Programmed cell death (PCD) plays critical roles not only when plants are challenged with biotic or abiotic stresses, but also in developmental processes. The molecular mechanism for plant PCD has not been fully identified. A conserved activity, caspase-3-like activity, has been reported in several cases of plant PCD. In this thesis, I present research on the role of cathepsin B, a cysteine protease possessing caspase-3-like activity in Arabidopsis, in PCD. The investigation of the function of cathepsin B in ER stress-induced PCD, using cathepsin B mutant Arabidopsis lines, suggested it positively regulates ER stress-induced PCD. Surprisingly, another protease possessing caspase-3-like activity, PBA1, exhibited a suppression role in ER stress-induced PCD. Several further investigations on the molecular mechanisms in ER stress-induced PCD indicated that lacking cathepsin B reduced misfolded protein accumulation by increasing Unfolded Protein Response (UPR) gene expression. I also analysed which PCD type was mediated by cathepsin B by examining several morphological and biochemical markers, and found that cathepsin B mediated vacuolar PCD in ER stress-induced PCD, while necrotic PCD was induced in the absence of cathepsin B. In order to position cathepsin B in the ER stress-induced PCD pathway, I analysed cathepsin B in mutant lines for several genes. A putative pathway was formed in which Mitogen activated protein kinase 6 (MPK6) positively and Arabidopsis BAX inhibitor-1 (AtBI-1) negatively regulated cathepsin B. In addition to ER stress-induced PCD, I also examined the function of cathepsin B in developmental PCD. Cathepsin B exhibited a positive role in a PCD occurring in cells of seed inner integument layers but not in the PCD during xylem formation. Moreover, a novel PCD was discovered in micropylar endosperm during germination. The micropylar endosperm PCD implicated cathepsin B. Finally, a positive role of cathepsin B in KOD-induced PCD was confirmed, and how cathepsin B could be involved in KOD-induced PCD was analysed via DNA microarray. In summary, cathepsin B had a central role in regulating ER stress-induced PCD and development-induced PCD.

The flower head of the Asteraceae family is its iconic trait, yet little is known about its development. Understanding the fundamentals of the flower head development will help construe the evolution of one of the most successful plant families. In this thesis, we carried out an investigation into the role of auxin in flower head development and patterning in Matricaria inodora and Senecio vulgaris. Auxin is one of the most crucial plant hormones and has been implicated in almost all stages of growth and development. In Matricaria inodora and Senecio vulgaris auxin was found to be involved in flower head development and pattern formation. Manipulation of the endogenous auxin in planta showed homeotic conversions of disc florets to phyllaries or ray florets. Analysis of lateral organ identity genes revealed a concentration dependant response of the identity genes to auxin. The homeotic change of lateral organs in a concentration dependant manner is one of the key traits of a morphogen that had never been documented in planta before. We suggest that auxin acts as a morphogen in the developing flower head to control development and pattern formation. Visualisation of auxin distribution using a Beta-glucuronidase marker gene further confirmed the presence of an auxin gradient in the developing flower head. Auxin appears to have a secondary role in the petal outgrowth and shape in ray florets. In summary, auxin appears to be controlling the development and pattern formation in the flower head through the concentration dependant recruitment of lateral organ identity genes.

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