Metabolic Flux Balance Analysis: MATLAB COBRA Toolbox Brandon Palomo

Flux Balance Analysis Phenotype Optimization Discussion Flux balance analysis (FBA) is used to The optimization of a phenotype using FBA can be determined using the Constraint To determine how substrate uptake rates calculate the flow of metabolites through a Based Reconstruction and Analysis (COBRA) Toolbox in MATLAB. Representing influence the phenotype of the , glucose to study genome-scale biomass production as the objective function Z allows for the prediction of the and oxygen uptake reaction rates were metabolic network reconstructions. In maximum growth rate by calculating the maximum flux allowed through the biomass varied simultaneously with respect to the Silico modeling of the metabolic network reaction. The objective function is calculated as 푍 = 풄푇 ∙ 풗 where c is a vector of biomass production rate. The results reveal can predict the growth rate of an weights. As an example, arginine biosynthesis was coupled to biomass production in the line of optimality that determines the and the production rate of a bio-valuable a genome-scale model of E. coli k-12 W3110 from the Biochemical Genetic and optimal phenotype for bio-production of product. The results can be analyzed to Genomic BiGG Database. is used to calculated flux distribution. arginine without limitation on substrate study the phenotype under varying cellular availability as shown in the Figure 2. In and environmental conditions. Arginine Biosynthesis Flux Phase Plane Analysis Figure 1, the biomass production rate was determined from FBA to be 1.4078 hr-1, Green => frwd rxn which means the E. coli cells are predicted Blue => rev rxn Line of Optimality to double every 29.54 minutes. Constraint Based Analysis ARGSL = 0.4164

-1 FBA is mathematically represented as a Z = 1.4078 hr Future Directions numerical matrix S of stoichiometric coefficients for all reactions involved in To improve the yield of arginine, the flux the model. The stoichiometries impose thorough precursor reactions will be mass balance constraints on the system at improved by evaluation of gene knockout steady state. The flux through all the designs and robustness analysis. Additional reactions in the model are represented by reactions may be added into the network to vector v and the concentrations of the simulate synthetic metabolic networks and metabolizes are represented by vector x. flux variability analysis will be explored to 푑풙 final alternative optimal solutions. 푺 ∙ 풗 = = ퟎ 푑푡 References Additional constraints on the system Arginine Biosynthesis Conditions include defining upper and lower bounds Orth, J.D., Thiele, I. & Palsson, B.O. What for the allowable fluxes of every reaction. The biosynthesis of arginine in an in silico model of E. coli k-12 W3110 was is flux balance analysis? Nat. Biotech. 28, To optimize a phenotype, the constraints determined under aerobic conditions using an uptake exchange reaction of 245–248 (2010) must be studied with an objective 18.5 mmol/gDW/hr for glucose and 20 mmol/gDW/hr for oxygen (biologically function (e.g. biomass production). realistic uptake rates).