Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Chemical and Biological Engineering


Chemical Engineering

First Advisor

Zengyi Shao


Due to its robustness, genetic tractability, and industrial relevance, the budding yeast Saccharomyces cerevisiae was selected as study model of the aromatic amino acid biosynthetic pathway. This pathway houses a wide diversity of economically important metabolites ranging from polymer precursors to pain-management drugs, whose productions have been highly sought-after in biotechnological research. However, tight regulations at the transcriptional, translational, and allosteric levels surround the aromatic amino acid pathway, protecting the microbial factories (e.g. S. cerevisiae) from unnecessary energy expenditures. By making use of computational metabolic engineering tools such as Flux Balance Analysis and Metabolic Flux Analysis, together with fast and reliable synthetic biology techniques, the flux into the aromatic amino acid pathway was exploited. Initially, the flux distribution in the central carbon metabolism was studied through 13C-metabolic flux analysis and carbon tracing experiments. Important insights regarding the partition between glycolysis and the pentose phosphate pathway were obtained and correlated with the production of aromatic amino acid derivatives. For the first time, the pentafunctional enzyme, ARO1, composing the core of the shikimic acid pathway was subjected to site-directed mutagenesis to reveal its active domains. This resulted in the development of new variants with disrupted activities specifically designed for increasing production of the two target molecules, namely, muconic acid and shikimic acid. Further analysis with OptForce simulations revealed that overexpressing the ribose-5-phosphate ketol-isomerase gene, RKI1, can enhance carbon funneling into the aromatic amino acid pathway. A multilevel engineering strategy was established to explore novel transcriptional regulators that tightly control the carbon flux into the pathway. Deleting the gene RIC1, involved in efficient protein localization of trans-Golgi network proteins, increased the titers of shikimic acid and muconic acid. These non-intuitive interventions, in combination with the previous genetic platforms, increased the production titers over 3-fold compared to the base strains. The shikimic acid strains produced 1.9 g L-1, while muconic acid and intermediates were accumulated up to 1.6 g L-1, both being the highest reported in S. cerevisiae, in batch fermentations. Future research should focus on devising more dynamic genome engineering strategies that rely on modulating the activity of essential genes while ensuring a good compromise with biomass formation.


Copyright Owner

Jose Miguel Suastegui Pastrana



File Format


File Size

243 pages