Engineering microbial chemical factories using metabolic models

Living organisms in analogy with chemical factories use simple molecules such as sugars to produce a variety of compounds which are necessary for sustaining life and some of which are also commercially valuable. The metabolisms of simple (such as bacteria) and higher organisms (such as plants) alike can be exploited to convert low value inputs into high value outputs. Unlike conventional chemical factories, microbial production chassis are not necessarily tuned for a single product overproduction. Despite the same end goal, metabolic and industrial engineers rely on different techniques for achieving productivity goals. Metabolic engineers cannot affect reaction rates by manipulating pressure and temperature, instead they have at their disposal a range of enzymes and transcriptional and translational processes to optimize accordingly. In this review, we first highlight how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed in systems and control engineering. Specifically, how algorithmic concepts derived in operations research can help explain the structure and organization of metabolic networks. Finally, we consider the future directions and challenges faced by the field of metabolic network modeling and the possible contributions of concepts drawn from the classical fields of chemical and control engineering. The aim of the review is to offer a current perspective of metabolic engineering and all that it entails without requiring specialized knowledge of bioinformatics or systems biology.