title: Whole-genome metabolic model ofTrichoderma reeseibuilt by comparative reconstruction.
abstract: BACKGROUND
  Trichoderma reeseiis 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 ofT. reeseihas 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 ofT. reeseihas 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 ofT. reeseihas 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 newT. reeseimodel is ready to be used for simulations of protein production processes.
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Sandra
authors.identifier: 0000-0003-3568-787X
authors.initials: S
authors.lastname: Castillo
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Dorothee
authors.initials: D
authors.lastname: Barth
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Mikko
authors.initials: M
authors.lastname: Arvas
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Tiina M
authors.initials: TM
authors.lastname: Pakula
authors.affiliation: Department of Computer Science, University of Helsinki, P.O. 68 (Gustaf Hällströmin katu 2b), 00014 Helsinki, Finland.
authors.forename: Esa
authors.initials: E
authors.lastname: Pitkänen
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Peter
authors.initials: P
authors.lastname: Blomberg
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Tuulikki
authors.initials: T
authors.lastname: Seppanen-Laakso
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Heli
authors.initials: H
authors.lastname: Nygren
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Dhinakaran
authors.initials: D
authors.lastname: Sivasiddarthan
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Merja
authors.initials: M
authors.lastname: Penttilä
authors.affiliation: VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 Espoo, Finland.
authors.forename: Merja
authors.initials: M
authors.lastname: Oja