An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

Abstract

Background: Metabolic fluxes provide invaluable insight on the integrated response of a cell to environmental stimuli or genetic modifications. Current computational methods for estimating the metabolic fluxes from 13 C isotopomer measurement data rely either on manual derivation of analytic equations constraining the fluxes or on the numerical solution of a highly nonlinear system of isotopomer balance equations. In the first approach, analytic equations have to be tediously derived for each organism, substrate or labelling pattern, while in the second approach, the global nature of an optimum solution is difficult to prove and comprehensive measurements of external fluxes to augment the 13 C isotopomer data are typically needed.

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis

“…This phase is automated by the 13C-FLUX export in ReMatch, removing this hindrance from the 13 C metabolic flux analysis modelling workflow. ReMatch will also support the file format of the upcoming version of 13C-FLUX [25], as well FluxDirect [16], an upcoming software for 13 C metabolic flux analysis developed in the same research group as ReMatch.…”

“…Also the stoichiometric matrix of the model, directly exported from ReMatch, was used in the data generation. More importantly, the constructed model was applied to analysis of isotopomer measurement data with FluxDirect [16]. The constructed model was further used as a starting point in construction of metabolic models of B. subtilis and E. coli by first taking a copy of the model of S. cerevisiae and then modifying it.…”

“…We constructed the model to estimate metabolic fluxes based on isotopomer measurement data from metabolites and biomass amino acids and to generate artificial 13 C isotopomer data for testing the framework for 13 C metabolic flux analysis under development, FluxDirect [16]. Therefore each reaction of the model had to be associated with a carbon map and the model had to contain the necessary reactions for amino acid synthesis.…”

“…Adding carbon mappings manually to basic stoichiometric models is an extremely error prone task as even small models of central carbon metabolism contain hundreds, even thousands of carbon mappings. On the other hand, recent advancements in the computational analysis techniques [24,16,25] and in the techniques for conducting isotopomer measurements [26,27] would facilitate the use of more detailed models in 13 C metabolic flux analysis. These detailed models are not readily available, but have to be constructed before 13 C metabolic flux analysis can take place.…”

“…As two metabolic pathways that converge to a common metabolite may manipulate the carbon chains of metabolites differently, the relative abundances of the different 13 C labelling patterns may differ in the molecules produced by different pathways. Thus, by measuring the abundances of different 13 C labelling patterns from the metabolites, information about the metabolic fluxes can be inferred [14,15,16]. For the quantitative estimations of metabolic fluxes from 13 C labelling measurements, basic stoichiometric models of metabolism have to be augmented with mappings that describe how carbon atoms are transferred from substrates to products in each reaction (see Figure 2).…”