Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis

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    Abstract

    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 Biotechnol26, 1155-1160; Dobson PD et al. (2010) BMC Syst Biol4, 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.

    Original languageEnglish
    Pages (from-to)3338-3354
    JournalFEBS Journal
    Volume279
    Issue number18
    DOIs
    Publication statusPublished - 1 Sep 2012
    MoE publication typeA1 Journal article-refereed

    Keywords

    • dynamic flux balance analysis
    • metabolism
    • modelling
    • oxygen
    • Saccharomyces cerevisiae

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