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Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction

Castillo, Sandra, Barth, Dorothee, Arvas, Mikko, Pakula, Tiina M., Pitkänen, Esa, Blomberg, Peter, Seppanen-Laakso, Tuulikki, Nygren, Heli, Sivasiddarthan, Dhinakaran, Penttilä, Merja, Oja, Merja
Biotechnology for biofuels 2016 v.9 no.1 pp. 252
Trichoderma reesei, algorithms, biomass production, biotechnology, databases, enzymes, equations, exports, industry, metabolism, model validation, models, prediction
BACKGROUND: Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism’s metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis. RESULTS: A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model. CONCLUSIONS: The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes.