Systems metabolic engineering design: Fatty acid production as an emerging case study

Abstract

Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities.

Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering

“…Overexpression of FabZ alone also resulted in a higher fatty acid production, and a combination of fadD knockout, sucC (glycolysis) knockout, and FabZ overexpression gave a strain producing 5.7 g/L C14-C16 fatty acids. 220 Overexpression of FabG leads to a 2–3 fold increase in fatty acid production, 145 whereas overexpression of FabI showed no effect, FabH was semi-lethal, FabF was lethal and FabB in combination with FabA showed modest increases in fatty acid production. Lastly, TEs which are responsible for off-loading the fatty acid from the ACP, have been engineered and overexpressed in many studies, utilizing TEs from various plant, algal or endogenous sources, resulting in shifting the fatty acid profile towards the specificity of the TE (except in algal engineering with foreign TEs and algal TE expression in cyanobacteria).…”

“…Lastly, TEs which are responsible for off-loading the fatty acid from the ACP, have been engineered and overexpressed in many studies, utilizing TEs from various plant, algal or endogenous sources, resulting in shifting the fatty acid profile towards the specificity of the TE (except in algal engineering with foreign TEs and algal TE expression in cyanobacteria). 220 …”

Integrated engineering of β-oxidation reversal and ω-oxidation pathways for the synthesis of medium chain ω-functionalized carboxylic acids

“…The growing demand for the development of technologies capable of producing advanced fuels and chemicals from sustainable feedstocks has resulted in the exploitation and engineering of biological systems enabling the synthesis of longer carbon chain length compounds from 2-and 3-carbon metabolic intermediates (Straathof, 2014;Tee et al, 2014;Wen et al, 2013). While several pathways have been investigated for this purpose, the recently engineered reversal of the β-oxidation cycle provides an attractive platform that can support the synthesis of short-, medium-, and long-chain products at high yields (Clomburg et al, 2012;Dellomonaco et al, 2011;Gulevich et al, 2012;Lian and Zhao, 2014;Zhuang et al, 2014).…”

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

“…Recent efforts in microbial biofuel production hinge upon constructing efficient metabolic pathways to produce a variety of fatty acids (FA)-based fuels (17)(18)(19)(20)(21)(22)(23). To date, most of the work has taken a static perspective to coordinate the expression of enzymes and optimize production titer and yield, including modification of plasmid copy number (24), promoter strength (25,26), and combinations of these strategies (21,27).…”