Abstract
BackgroundFlux analyses, including flux balance analysis (FBA) and 13C-metabolic flux analysis (13C-MFA), offer direct insights into cell metabolism, and have been widely used to characterize model and non-model microbial species. Nonetheless, constructing the 13C-MFA model and performing flux calculation are demanding for new learners, because they require knowledge of metabolic networks, carbon transitions, and computer programming. To facilitate and standardize the 13C-MFA modeling work, we set out to publish a user-friendly and programming-free platform (WUFlux) for flux calculations in MATLAB®.ResultsWe constructed an open-source platform for steady-state 13C-MFA. Using GUIDE (graphical user interface design environment) in MATLAB, we built a user interface that allows users to modify models based on their own experimental conditions. WUFlux is capable of directly correcting mass spectrum data of TBDMS (N-tert-butyldimethylsilyl-N-methyltrifluoroacetamide)-derivatized proteinogenic amino acids by removing background noise. To simplify 13C-MFA of different prokaryotic species, the software provides several metabolic network templates, including those for chemoheterotrophic bacteria and mixotrophic cyanobacteria. Users can modify the network and constraints, and then analyze the microbial carbon and energy metabolisms of various carbon substrates (e.g., glucose, pyruvate/lactate, acetate, xylose, and glycerol). WUFlux also offers several ways of visualizing the flux results with respect to the constructed network. To validate our model’s applicability, we have compared and discussed the flux results obtained from WUFlux and other MFA software. We have also illustrated how model constraints of cofactor and ATP balances influence fluxome results.ConclusionOpen-source software for 13C-MFA, WUFlux, with a user-friendly interface and easy-to-modify templates, is now available at http://www.13cmfa.org/or (http://tang.eece.wustl.edu/ToolDevelopment.htm). We will continue documenting curated models of non-model microbial species and improving WUFlux performance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1314-0) contains supplementary material, which is available to authorized users.
Highlights
Flux analyses, including flux balance analysis (FBA) and 13C-metabolic flux analysis (13C-MFA), offer direct insights into cell metabolism, and have been widely used to characterize model and non-model microbial species
Once 13C has reached a steady state distribution throughout the metabolic network, the labeling patterns of proteinogenic amino acids or free metabolites can be used by a 13C-MFA model to decipher the intracellular flux distributions. 13C-MFA
Construction of the 13C-MFA model and flux calculation are demanding for new learners, because they require knowledge of metabolic networks and carbon transitions through the pathways, and computer programming skills (Fig. 1)
Summary
We constructed an open-source platform for steady-state 13C-MFA. Using GUIDE (graphical user interface design environment) in MATLAB, we built a user interface that allows users to modify models based on their own experimental conditions. To simplify 13C-MFA of different prokaryotic species, the software provides several metabolic network templates, including those for chemoheterotrophic bacteria and mixotrophic cyanobacteria. Users can modify the network and constraints, and analyze the microbial carbon and energy metabolisms of various carbon substrates (e.g., glucose, pyruvate/lactate, acetate, xylose, and glycerol). WUFlux offers several ways of visualizing the flux results with respect to the constructed network. To validate our model’s applicability, we have compared and discussed the flux results obtained from WUFlux and other MFA software. We have illustrated how model constraints of cofactor and ATP balances influence fluxome results
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