Exploring mechanisms leading to robust biochemical systems

Abstract

Cell robustness and complexity have been recognized as unique features of biological systems. This is attributable to the existence of multiple (or redundant) metabolic pathways and the concomitant multiple flux distributions, with each pathway leading to a single phenotype. Moreover, the multiple pathways may result in a variety of products or byproducts under different environmental conditions, e.g., substrate concentration, PH, and temperature. Appropriately controlling environmental or genetic conditions renders it possible to maximize the rate of substrate conversion and the production of a desired product or products by circumventing the occurrence of the secondary reactions yielding undesirable intermediates and byproducts. As such, we would enable us to devise or design biochemical manufacturing processes with enhanced energy efficiency and robustness; the resultant processes would be capable of increasing the rates of production, thereby lowering their costs. Proposed herein is an effective approach for exploring metabolic pathways, which algorithmically synthesizes all the candidate pathways by a rigorous graph-theoretic method based on P-graphs (process graphs).