Identification of active pathways of Chlorella protothecoides by elementary mode analysis integrated with fluxomic data

Microalgae are bio-factories for CO₂ fixation, biofuel production, and high-value added product biosynthesis and wastewater treatment. Deep understandings of the intracellular pathways, metabolic regulations and physiological responses of microalgae are critical for process optimization and strain modification. In this study, a metabolic network in small scale was reconstructed for the green microalgae, Chlorella protothecoides. The reliability of this metabolic network model was confirmed by metabolic phenotype prediction. The pathway length distribution of all the elementary modes was calculated. These elementary modes were divided into 5 groups based on their macroreactions of elementary modes. The group with a short pathway length was that of lactate production. The group with a long pathway length included biomass formation. In addition, the active pathways were identified by decomposition of the determined metabolic fluxes under three conditions from references onto elementary modes with six objective functions, maximum biomass formation, minimum norm, maximum entropy production principle, maximum activity of the shortest pathway length by linear programming, maximum activity of the shortest pathway length by quadratic programming and maximum activity of the longest pathway length by linear programming. The identified active pathways were consistent with the physiological states of microalgae. These results were helpful for exploring metabolic regulatory mechanism in microalgae.