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Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis
Author(s) -
Jouhten Paula,
Wiebe Marilyn,
Penttilä Merja
Publication year - 2012
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/j.1742-4658.2012.08649.x
Subject(s) - flux balance analysis , saccharomyces cerevisiae , anabolism , context (archaeology) , flux (metallurgy) , metabolic flux analysis , metabolism , biology , metabolic network , yeast , biochemistry , chemistry , paleontology , organic chemistry
Dynamic flux balance analysis was utilized to simulate the metabolic behaviour of initially fully respirative and respirofermentative steady‐state cultures of Saccharomyces cerevisiae during sudden oxygen depletion. The hybrid model for the dynamic flux balance analysis included a stoichiometric genome‐scale metabolic model as a static part and dynamic equations for the uptake of glucose and the cessation of respirative metabolism. The yeast consensus genome‐scale metabolic model [Herrgård MJ et al. (2008) Nat Biotechnol 26 , 1155–1160; Dobson PD et al. (2010) BMC Syst Biol 4 , 145] was refined with respect to oxygen‐dependent energy metabolism and further modified to reflect S. cerevisiae anabolism in the absence of oxygen. Dynamic flux balance analysis captured well the essential features of the dynamic metabolic behaviour of S. cerevisiae during adaptation to anaerobiosis. Modelling and simulation enabled the identification of short time‐scale flux distribution dynamics under the transition to anaerobic metabolism, during which the specific growth rate was reduced, as well as longer time‐scale process dynamics when the specific growth rate recovered. Expression of the metabolic genes was set into the context of the identified dynamics. Metabolic gene expression responses associated with the specific growth rate and with the cessation of respirative metabolism were distinguished.