Zournas, Apostolos. INST-FLUX an open source tool for Isotopically Non-Stationary Metabolic Flux Analysis (INST-MFA). Retrieved from https://doi.org/doi:10.7282/t3-qqw7-6m49
DescriptionInference of in vivo metabolic uxes is one of the most powerful tools available for metabolic engineering. Within the last three decades, Metabolic flux analysis has been developed and improved, and currently it is one of the most accurate methods to infer metabolic uxes. In 13C-MFA, the labeling of intracellular metabolites is measured, and the uxes that can best _t these measurements are calculated [10]. 13C-MFA has been used to calculate uxes with measurements from systems that have achieved isotopic steady state. However, some systems (e.g. photosynthetic metabolism) cannot be described using isotopically stationary measurements. Isotopically Non-Stationary MFA (INST-MFA), is a variation of MFA that calculates intracellular uxes from the labeling trajectories of intracellular metabolites, measured in a metabolic steady state, but isotopically non-stationary phase [7]. Themost e_cient method to date to solve the _tting is the Elementary Metabolite Unit (EMU) Framework [2]. There are several software packages applying INST-MFA using the EMU framework. These software packages include METRAN [1], INCA [20], and OpenMebius [8]. Out of the three, OpenMebius is the only open-source software and it has various limitations. The greatest limitation is that it requires input of the pool sizes of all the metabolites in the network, instead of calculating them. This means that Open-Mebius cannot be used for experiments on large or even medium-sized networks, since it is experimentally challenging with current techniques to accurately measure pool sizes for many metabolites (e.g. all the components of central metabolism) simultaneously. This limits availability of this technique by increasing the experimental effort needed to implement it, instead of fully utilizing its potential. Additionally, one of the strengths of INST-MFA is that it can be applied to autotrophic metabolism. Open-Mebius, however, does not allow the CO2 labeling state to be set as an input to the software. It handles the labeling state of CO2 as an independent variable, for which labeling changes in time depending on a set of parameters which are randomly assigned and optimized for. This does not allow the used to directly input the CO2 labeling state, unless two CO2 variables are introduced into the metabolic network. This issue arises especially in photoautotrophic metabolism, where CO2 is the substrate of the network and the labeling of intracellular pool of CO2 might not depend on the flux of any network reactions. Here we present INST-FLUX a novel, open-source software tool, operating in MATLAB for INST-MFA. INST-FLUX can robustly handle both autotrophic and heterotrophic metabolic networks with relatively low requirements for experimental data acquisition.