Integration and analysis of metabolic fluxes using genome-scale stoichiometric models

Abstract

Metabolic fluxes are an ultimate phenotype of the cell because they arise as a result of interplays among various cellular components under specific genetic and environmental condition. A unique characteristic of metabolic fluxes is that they drastically change upon genetic and/or environmental perturbations in an unpredictable manner. In this regard, systematic integration and analysis of metabolic fluxes would enhance our understanding of them. In this thesis, we elucidate causal relationships among metabolic fluxes from various conditions so as to produce an integral network, which shows influencing patterns among them in response to specific perturbations. To do so, we firstly need to determine metabolic fluxes. Now, several experimental and mathematical methods have been developed to elucidate them: metabolic flux analysis, flux balance analysis, minimization of metabolic adjustment, and regulation on/off adjustment, the last three of which are also called constraint-based flux analysis. These methods are briefly reviewed in Chapter 1. Also, we can build a metabolic stoichiometric model of an organism through the concept of metabolic flux analysis, but it needs to be comprehensive enough to accurately predict cellular physiology at systems level. Therefore, we reconstruct the genome-scale stoichiometric model of the target organism, which exploits biological information from metabolic databases, experiments, genome annotation data, and literature. Metabolic databases provide an initial backbone for the model, and other information sources provide supplemental information to remove any ambiguities existing in the model. This reconstruction procedure is discussed in Chapter 2 in detail with examples of Mannheimia succiniciproducens MBEL55E and Vibrio vulnificus CMCP6. Finally, we develop a framework that sequentially employs constraint-based flux analysis, Bayesian network analysis, and mutual information to integrate and analyze metabolic fluxes, and apply...