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A Systems Biology approach to disclose auxin synthesis in plants

Final Report Summary - SYSBIOAUX (A Systems Biology approach to disclose auxin synthesis in plants)

Plants utilize a very sophisticated network of phytohormones to control their growth and development. This regulatory network of interacting plant hormones is also paramount to integrate endogenous and exogenous stimuli and trigger adequate developmental responses, such as adapted growth velocities, tropisms, or initiation of chemical defense measures. In this framework, the substance class of auxins with its numerous precursors and derivatives plays an essential role. Auxins, and here especially the indole-3-acetic acid (IAA) as the most commonly occurring auxin in nature, are crucially involved in virtually every step of plant growth and development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental cues.
It is assumed that the main pathway for auxin formation in plants leads via the indole-3-pyruvic acid (IPyA)-pathway, involving a small family of tryptophan transaminases (TAA1, TARs) (Tao et al., 2008; Stepanova et al., 2008) and a bigger family of flavin containing monooxygenases, referred to as YUCCA enzymes (Mashiguchi et al., 2011; Won et al., 2011; Stepanova et al., 2011). Up to date, however, it cannot be completely excluded that a small number of alternative biosynthetic pathways also contribute to auxin biosynthesis in plants. Besides one Trp-independent pathway, at least two further Trp-dependent pathways for auxin biosynthesis have been proposed, each of them designated for an intermediate that is a hallmark of the pathway. These are the indole-3-acetaldoxime (IAOx)-pathway and the indole-3-acetamide (IAM)-pathway.
The major objective of the SysBioAux project was to provide detailed insight into the occurrence and regulation of these possible routes for the production of IAA in the model plant Arabidopsis thaliana, and how they are interconnected with each other, in particular in terms of stress responses to external stimuli. In this respect, we based our experiments on a Systems Biology approach, including genomics, transcriptomics and metabolomics studies. Based on the results obtained in these experiments, we gained deeper insight into regulatory circuits through which transcript accumulation of a variety of IAA-biosynthesis related genes is controlled. Secondly, we conducted a number of transcriptomics and metabolomics studies, using both gain-of-function and loss-of-function mutants of auxin biosynthesis-related genes. It was possible to generate some novel higher-order mutants, which were also analyzed along with the already available mutants. On this broad basis of results, a model of the interconnection of the different auxin-biosynthetic pathways in Arabidopsis thaliana has been established. In addition, it was possible to carve out novel connections between auxin homeostasis and plant stress responses over the runtime of the project.