Metaboflux : a method to analyze flux distribution in metabolic networks
Résumé
Trypanosoma brucei is a parasitic protist of vertebrates that causes sleeping sickness in Africa. A part of its energetic metabolism, including the 6 or 7 first glycolytic step, occurs in an organelle called glycosome. A metabolic pathway for the glycosome had been built by exploiting genomic, reverse genetic and metabolomic data [1]. Some known biological constraints, such as the maintenance of the glycosomal ATP/ADP and NADH/NAD+ balances, have not been carefully addressed in the current model. We propose a modelling approach including structural pathway and metabolic flux analysis to help in the understanding of the system's structure and its semi-quantitative behaviour. We model known biological information with a stochastic Petri net (where transitions are given for the reaction and places for metabolites) where delays can be assigned to transitions given a probability distribution. From a given set of probability distribution representing the flux amount of reactions (the input set of parameters), the simulation of the Petri net allows the exploration of the possible behaviours of the system. At the end of a run, if all input metabolites are consumed, we get concentration for intermediate and output metabolites. We integrate expected metabolites concentrations revealed by biological experiments within an objective function, and use simulated annealing and simplex minimization approach for its global optimization. Therefore, simulations are carried out by fitting the set of input parameters until the system reach the best optimization of the objective function. To explore a large set of possible behaviour of the system, several run of simulations combined with the simulated annealing approach are made. A set of solutions is given by different groups of fluxes distributions (that best fit expected metabolites concentrations), and are helpful to make some assumptions and analysis for a given metabolic system. "Metaboflux" was developed to this purpose and applied to T. brucei. Resulting scenarios strongly argue in favour of an unrealistic NADH/NAD+ imbalance and suggest adding to the model new metabolic pathways. A realistic solution may be to integrate the pentose phosphates to the previous model. The resulting new model was tested with Metaboflux and shows relevant fluxes scenarios. References [1] Bringaud F., Rivière L., Coustou V. (2006) Energy metabolism of trypanosomatids : adaptation to available carbon sources. Molecular and biochemical parasitology. 149: 1-9