WUFlux: an open-source platform for13C metabolic flux analysis of bacterial metabolism.
BACKGROUND
Flux analyses, including flux balance analysis (FBA) and13C-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 the13C-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 the13C-MFA modeling work, we set out to publish a user-friendly and programming-free platform (WUFlux) for flux calculations in MATLAB®.


RESULTS
We constructed an open-source platform for steady-state13C-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 simplify13C-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.


CONCLUSIONS
Open-source software for13C-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.
Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA. lianheenvi@gmail.com.
Lian
L
He
Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA.
Stephen G
SG
Wu
Department of Computer Science and Engineering, Washington University, St. Louis, MO, 63130, USA.
Muhan
M
Zhang
Department of Computer Science and Engineering, Washington University, St. Louis, MO, 63130, USA.
Yixin
Y
Chen
Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA. yinjie.tang@wustl.edu.
Yinjie J
YJ
Tang
D002247:Carbon Isotopes / Q000032:analysis*; D000458:Cyanobacteria / Q000378:metabolism*; D006801:Humans; D064688:Metabolic Flux Analysis / Q000379:methods*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D008962:Models, Theoretical; D012984:Software
D002247:Carbon Isotopes
13C metabolic flux analysis; Energy metabolism; MATLAB; Software