Abstract
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.
Highlights
IntroductionChemical engineering draws from a wide range of disciplines such as physics, chemistry, computer science, mathematics, operations research, and the life sciences
Significant strides have been made in recent years to construct and investigate detailed models of cellular processes [5–8]
Synthetic biology offers the promise of replacing traditional, high carbon footprint processes fed by unsustainable feedstocks with tunable microbial reactors
Summary
Chemical engineering draws from a wide range of disciplines such as physics, chemistry, computer science, mathematics, operations research, and the life sciences. A quadruple rise in production was achieved by refining the original mold species, developing an effective growth medium, and changing the fermentation process from rudimentary surface culture to submersion in tanks [1]. These early efforts were the vanguards of current mechanistic descriptions of biological processes. The elucidation, and subsequent prediction of the behavior of metabolic systems is one of the major challenges of the postgenomic era [2–4]. To this end, significant strides have been made in recent years to construct and investigate detailed models of cellular processes [5–8]. Microbial fermentation is a popular production mode for many biofuels and biochemicals as it generally (1) relies on a sustainable feedstock (i.e., usually sugars), (2) involves a reduced environmental footprint, (3) is scalable, and (4) bypasses the need for complex separations
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