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Abstract
Microbes, such as Escherichia coli (E. coli), are promising organisms that have attracted vast research interest for understanding and modifying living systems. Various tools and strategies have been therefore established not only shedding light on rules of nature, but also leading to synthesis of valuable biochemicals in microbes that have profound impact on our society. Metabolic engineering thus have emerged based on the interdisciplinary development of molecular biology, cellular biology, protein science, microbiology and engineering principles. Metabolic engineering is an enabling approach and methodology that studies and modifies cellular metabolism towards desired products, by incorporating biology and engineering. Among all the metabolic pathways, aromatic metabolism is of particular interest that involves in the synthesis of aromatic amino acid as pharmaceutical precursors, as well as lignin degradation towards the sustainable utilization of the largely under-tapped biomass. Therefore, my dissertation studies are centered to expand and enhance the aromatic biosynthesis roadmap, by designing synthetic metabolic pathways and applying novel genetic tools. Specifically, my first project sought to improve the plasmid stability while eliminating the use of antibiotics by creating a synthetic symbiosis. The stably maintained plasmid harboring the synthetic pathway of salicylic acid held phenotype for over 80 generations. My second project sought to develop a quantifiable antisense-RNA based regulation tool for inhibiting cellular function. The multiplexed and multileveled repression of fabD and ydiI resulted in increased titer of 4-hydroxycoumarin production. Along the aromatic metabolic pathway, a transcriptional factor was also studied as a synthetic biosensor for ligand responses and applicability in dynamic regulation of bioproduction of tryptophan and its derivative 5-hydroxytryptophan. Throughout protein engineering and operator mutation, biosensor variants were characterized with various dynamics and ligand preferences. In additional to biosynthesis through anabolic pathways of aromatic compounds, utilization of lignin-degraded aromatics towards valuable compounds was studied. By establishing a synthetic catechol meta-cleaving route connecting central metabolism, E. coli was enabled to convert aromatics to citramalate, as well as 1,3-butanediol via a newly designed pathway. Within the context of aromatic molecules metabolism, the presented work tried to answer two of the central questions in metabolic engineering: How can we develop and improve tools to facilitate metabolic engineering practices? How can we expand and improve the metabolic pathways for bioproduction?