Branch point control at malonyl-CoA node: A computational framework to uncover the design principles of an ideal genetic-metabolic switch

• Published in: Metabolic engineering communications Vol. 10; p. e00127
• Main Author: Xu, Peng
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2020; Elsevier
• Subjects: artificial intelligence; Autonomous oscillation; binding capacity; Biophysical models; Controller architecture; differential equation; enzymes; Escherichia coli; fatty acids; gene expression; malonyl coenzyme A; Metabolic engineering; Metabolic switches; protein degradation; repressor proteins; Special issue on The Natural Product Issue edited by Greg Stephanopoulos, Anthony Sinskey and Kang Zhou; Synthetic biology; transactivators; Metabolic switches; Metabolic engineering; Synthetic biology; Autonomous oscillation; Biophysical models; Controller architecture
• ISSN: 2214-0301; 2214-0301
• DOI: 10.1016/j.mec.2020.e00127

Living organism is an intelligent system coded by hierarchically-organized information to perform precisely-controlled biological functions. Biophysical models are important tools to uncover the design rules underlying complex genetic-metabolic circuit interactions. Based on a previously engineered synthetic malonyl-CoA switch (Xu et al., PNAS, 2014), we have formulated nine differential equations to unravel the design principles underlying an ideal metabolic switch to improve fatty acids production in E. coli. By interrogating the physiologically accessible parameter space, we have determined the optimal controller architecture to configure both the metabolic source pathway and metabolic sink pathway. We determined that low protein degradation rate, medium strength of metabolic inhibitory constant, high metabolic source pathway induction rate, strong binding affinity of the transcriptional activator toward the metabolic source pathway, weak binding affinity of the transcriptional repressor toward the metabolic sink pathway, and a strong cooperative interaction of transcriptional repressor toward metabolic sink pathway benefit the accumulation of the target molecule (fatty acids). The target molecule (fatty acid) production is increased from 50% to 10-folds upon application of the autonomous metabolic switch. With strong metabolic inhibitory constant, the system displays multiple steady states. Stable oscillation of metabolic intermediate is the driving force to allow the system deviate from its equilibrium state and permits bidirectional ON-OFF gene expression control, which autonomously compensates enzyme level for both the metabolic source and metabolic sink pathways. The computational framework may facilitate us to design and engineer predictable genetic-metabolic switches, quest for the optimal controller architecture of the metabolic source/sink pathways, as well as leverage autonomous oscillation as a powerful tool to engineer cell function. •Metabolic engineer can engineer both the chemistry and control modules in the cell.•9 differential equations used to define a previously engineered malonyl-CoA switch.•Optimal control architecture of metabolic source and sink pathways were determined.•Models were used to unravel the design principles underlying an ideal metabolic switch.•Stable oscillation of metabolic intermediates permits alternating ON-OFF genetic control.