Open AccessYeast optimizes metal utilization based on metabolic network and enzyme kinetics
Author(s) -
Yu Chen,
Feiran Li,
Jiwei Mao,
Jens Nielsen
Publication year - 2021
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.2020154118
Subject(s) - enzyme , metal ions in aqueous solution , yeast , metabolic pathway , metabolism , chemistry , biochemistry , cofactor , saccharomyces cerevisiae , metal , flux (metallurgy) , enzyme kinetics , kinetics , ion , biology , active site , physics , organic chemistry , quantum mechanics
Significance Metal ions are essential to all living cells, as they can serve as cofactors of enzymes to drive catalysis of biochemical reactions. We present a constraint-based model of yeast that relates metabolism with metal ions via enzymes. The model is able to capture responses of metabolism and gene expression upon iron depletion, suggesting that yeast cells allocate iron resource in the way abiding to optimization principles. Interestingly, the model predicts up-regulation of several iron-containing enzymes that coincide with experiments, which raises the possibility that the decrease in activity due to limited iron could be compensated by elevated enzyme abundance. Moreover, the model paves the way for guiding biosynthesis of high-value compounds (e.g.,p -coumaric acid) that relies on iron-containing enzymes.