Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

Abstract

Identifying the factors that determine microbial growth rate under various environmental and genetic conditions is a major challenge of systems biology. While current genome-scale metabolic modeling approaches enable us to successfully predict a variety of metabolic phenotypes, including maximal biomass yield, the prediction of actual growth rate is a long standing goal. This gap stems from strictly relying on data regarding reaction stoichiometry and directionality, without accounting for enzyme kinetic considerations. Here we present a novel metabolic network-based approach, MetabOlic Modeling with ENzyme kineTics (MOMENT), which predicts metabolic flux rate and growth rate by utilizing prior data on enzyme turnover rates and enzyme molecular weights, without requiring measurements of nutrient uptake rates. The method is based on an identified design principle of metabolism in which enzymes catalyzing high flux reactions across different media tend to be more efficient in terms of having higher turnover numbers. Extending upon previous attempts to utilize kinetic data in genome-scale metabolic modeling, our approach takes into account the requirement for specific enzyme concentrations for catalyzing predicted metabolic flux rates, considering isozymes, protein complexes, and multi-functional enzymes. MOMENT is shown to significantly improve the prediction accuracy of various metabolic phenotypes in E. coli, including intracellular flux rates and changes in gene expression levels under different growth rates. Most importantly, MOMENT is shown to predict growth rates of E. coli under a diverse set of media that are correlated with experimental measurements, markedly improving upon existing state-of-the art stoichiometric modeling approaches. These results support the view that a physiological bound on cellular enzyme concentrations is a key factor that determines microbial growth rate.

Metabolic Shift of Escherichia coli under Salt Stress in the Presence of Glycine Betaine

“…To explain the use of overflow pathways when carbon and oxygen sources are abundant in a chemostat, rather than by applying additional constraints on nutrient uptake, it has been proposed that the growth rate may be limited by molecular crowding. This was modeled by adding constraints of the volume occupancy of the enzymes to stoichiometric models (68,69). With this approach, the metabolic fluxes are further constrained by a coefficient proportional to the inverse of the enzymatic catalytic rates, k cat , the turnover number.…”

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

“…2). Although aerobic respiration has higher energy yields than fermentative metabolism, it has been hypothesized that the flux through the respiratory reactions is limited by protein synthesis cost and capacity (38,57,58) (since TCA and the electron transport system require more proteins than glycolysis and acetate secretion) or limitations in membrane space (58) (for electron transport system enzymes). These gene expression and physiological changes may be driven by these key capacity constraints.…”

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

“…We chose to use a kinetically-constrained FBA model because kinetic constraints have been shown to improve the accuracy of metabolic flux and growth rate predictions across experimental conditions (Adadi et al, 2012). The model was originally developed as the metabolic sub-model of a more comprehensive whole-cell model (Karr et al, 2012).…”