A worldwide need to liberate ourselves from unsustainable petrochemicals has led to numerous metabolic engineering projects, mostly carried out in microbial hosts. Using systems biology for predicting and altering the metabolism of microorganisms towards production of a desired metabolite, these projects have increased revenues on fermentative production of several biochemicals. The use of systems biology is,
however, not limited to microorganisms. Recent advances in biotechnology methods have provided a wealth of data within functional genomics, metabolomics, transcriptomics, proteomics and fluxomics for a considerable number of organisms. Unfortunately, transferring the wealth of data to valuable information for metabolic engineering purposes is a non-obvious task. This PhD thesis describes a palate of tools used in generation of cell factories for production of specialized plant metabolites, namely the plant defense compounds camalexin and glucosinolates. The thesis shows methodologies for elucidation of biosynthesis pathways and describes how to transfer obtained knowledge of metabolic pathways to other organisms through establishment of a synthetic biology platform. Through pathway engineering novel biosynthetic genes are uncovered and a hypothesis on reasons for incompatibilities observed upon transfer of pathways from plants to microorganisms is developed. The work shows how applied science can feed back to understanding of basic biological principles.