| dc.description.abstract | Genome-scale metabolic reconstructions offer a system-level view of metabolic networks with genetic basis and suggest mechanistic determination of cell's physiological homeostatic states. Consequently, they offer the ability to compose strategies to manipulate cell's functional states. This is applicable in many research fields, from metabolic engineering in enhancing the production of existing or novel target metabolites to medical applications in determining susceptibility or immunity towards disease and drug targets.
The focus of this dissertation is the reconstruction, manual curation of genome-scale metabolic models and their application in mechanistic determination of condition specific physiological, homeostatic states of the cell.
A system level view and understanding the underlying mechanistic notion of cell's response to genetic and environmental perturbation, enabled optimization of the metabolic engineering strategies for enhanced heterologous production of polyketide antibiotics. This important research topic contributes to combating the global health crisis brought on by antibiotic resistance. For that purpose first and third generation of genome-scale metabolic models of S. coelicolor were constructed, where the latter integrated time-resolved proteomics data into standard genome scale metabolic stoichiometric presentation with the purpose of giving mechanistic interpretation of both, proteomics and transcriptomics data, sampled in batch fermentation. Mechanistic determination of metabolic switch between primary and secondary metabolism, proposed strain design metabolic strategies for heterologous expression host of S. coelicolor.
As cells have implicit optimality principle build into them when they evolve under selection pressure, distal causality needs to be accounted for in the reconstructions, by integration of biological objective into the stoichiometric framework. The condition specific manner of the biomass objective was addressed by proposing approaches, based on linear optimization and linear interpolation. Proposed strategies were evaluated by demonstrating various phenotypic traits, such as cell's optimal growth rate, respiratory state of the cell and gene essentiality.
Contextualized genome scale metabolic reconstruction with integration of mass constraints and constraints on enzyme availability, enabled mechanistic determination of cell's metabolic response to perturbation on total protein availability (Ptotal), on various levels, such as wild type, single and double mutant. Metabolic response was revealed by epistatic interactions when mass constraints and constraints on enzyme availability as dominant constraints were considered. This response tunes de-coupling/coupling of glycolysis to TCA cycle and oxidative phosphorylation (electron transport chain) as determined from cell's respiratory profile, where the onset of metabolic switch from oxidative fermentative to respiratory state is sensitive to Ptotal. | en_US |
