Flux balance analysis of Escherichia coli metabolism.

Abstract

The present thesis represents an effort in the emerging area of metabolic engineering. While the physical principles governing the unit operations of bioprocessing are quite well known, the design of the cellular component is poorly understood. Here we place microbial metabolism in an engineering context. We have determined a flux balance metabolic model for the bacterium Escherichia coli that includes the catabolic and biosynthetic reactions. Growth of the bacterium is defined in the model as a demand for metabolites based on published composition analyses. The flux balance model is able to determine metabolic pathway utilization in the bacterium for specific objectives such as biochemical production or cell growth. We propose the principle of stoichiometric optimality, the hypothesis that metabolism functions to achieve an optimal pathway utilization to enhance growth and multiplication of the bacterial cell. Predictions from the model for E. coli growth and by-product secretion under various oxygen supply rates are found to provide an elegant interpretation for the observed physiology of E. coli metabolism. We have applied the flux balance model to growth and product formation from clonal populations in a bioreactor. The effect of oxygen supply in the model is investigated for its ability to enhance the productivity and economics of a bioprocess. We also undertake an experimental confirmation of the model's validity. We show how the flux balance model may be applied to bioprocesses to predict time profiles of cell growth, and nutrient and by-product concentration. Taken together these results provide a quantitative mathematical framework to describe and understand microbial metabolism. The engineering principles developed here should prove of use to bioprocess design and development.