Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli

Abstract

BackgroundA kinetic model provides insights into the dynamic response of biological systems and predicts how their complex metabolic and gene regulatory networks generate particular functions. Of many biological systems, Escherichia coli metabolic pathways have been modeled extensively at the enzymatic and genetic levels, but existing models cannot accurately reproduce experimental behaviors in a batch culture, due to the inadequate estimation of a specific cell growth rate and a large number of unmeasured parameters.ResultsIn this study, we developed a detailed kinetic model for the central carbon metabolism of E. coli in a batch culture, which includes the glycolytic pathway, tricarboxylic acid cycle, pentose phosphate pathway, Entner-Doudoroff pathway, anaplerotic pathway, glyoxylate shunt, oxidative phosphorylation, phosphotransferase system (Pts), non-Pts and metabolic gene regulations by four protein transcription factors: cAMP receptor, catabolite repressor/activator, pyruvate dehydrogenase complex repressor and isocitrate lyase regulator. The kinetic parameters were estimated by a constrained optimization method on a supercomputer. The model estimated a specific growth rate based on reaction kinetics and accurately reproduced the dynamics of wild-type E. coli and multiple genetic mutants in a batch culture.ConclusionsThis model overcame the intrinsic limitations of existing kinetic models in a batch culture, predicted the effects of multilayer regulations (allosteric effectors and gene expression) on central carbon metabolism and proposed rationally designed fast-growing cells based on understandings of molecular processes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-016-0511-x) contains supplementary material, which is available to authorized users.

Modeling and simulation of the redox regulation of the metabolism in Escherichia coli at different oxygen concentrations

“…Kinetic models of these pathways have been developed to investigate carbon uptake and metabolism under aerobic conditions [13–15, 17, 20]. Here, we constructed a kinetic model applicable under micro-aerobic (and anaerobic) conditions as well.…”

“…A detailed kinetic model of central carbon metabolism in E. coli that incorporates a constrained optimization method for parameter estimation on a supercomputer was recently developed [20]. As compared with other kinetic models, this model enabled more accurate prediction of the dynamics of wild-type (WT) cells and multiple-gene-knockout mutants in batch culture.…”

Overproduction of L‐tryptophan via simultaneous feed of glucose and anthranilic acid from recombinant Escherichia coli W3110: Kinetic modeling and process scale‐up

“…For instance, different E. coli mutants have been developed to improve the conversion efficiency from glucose to L‐tryptophan (Chan, Tsai, Chen, & Mou, ; Ikeda, ; Wang et al, ; Zhao et al, ), and metabolic reaction pathways for bacterial L‐tryptophan synthesis have been identified in detail (Jahan, Maeda, Matsuoka, Sugimoto, & Kurata, ; Luo et al, ; Nishio et al, ). In addition, recent studies observed that acetate is excreted by E. coli during aerobic fermentation when the carbon flux into cells exceeds the capacity of the carbon central metabolic pathway (Dodge & Gerstner, ), which inhibits both cell growth and L‐tryptophan biosynthesis (Cheng et al, ).…”

“…What is more, to facilitate process design and optimization, it is essential to construct accurate kinetic models capable of simulating biomass growth, glucose uptake, and L‐tryptophan production in different scales of systems. However, in spite of the intensive modeling studies focused on the metabolic reaction network level (Jahan et al, ; Luo et al, ; Nishio et al, ), few attention has been paid to address this issue.…”

“…However, in spite of the intensive modeling studies focused on the metabolic reaction network level (Jahan et al, 2016;Luo et al, 2013;Nishio et al, 2013), few attention has been paid to address this issue. Therefore, to resolve the above challenges, in this research three glucose feeding strategies, namely DO feedback control, DO-stat control, and anthranilic acid feeding integrated DO-stat control, were employed to enhance glucose utilization efficiency and L-tryptophan production.…”