'Domino' systems biology and the 'A' of ATP

Malkhey Verma, Maksim Zakhartsev, Matthias Reuss, Hans V. Westerhoff

    Research output: Contribution to journalArticlepeer-review

    Abstract

    We develop a strategic 'domino' approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in Adenosine triphosphate (ATP) upon glucose addition, (ii) the lack of increase in Adenosine diphosphate (ADP) when ATP is hydrolyzed, and (iii) the rapid disappearance of the 'A' (adenine) moiety of ATP. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of Adenosine monophosphate (AMP) explains. Cycling of the 'A' moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the 'A' component of ATP. Crown Copyright © 2012 Published by Elsevier B.V. All rights reserved.
    Original languageEnglish
    Pages (from-to)19-29
    Number of pages10
    JournalBiochimica et Biophysica Acta. Bioenergetics
    Volume1827
    Issue number1
    DOIs
    Publication statusPublished - Jan 2013

    Keywords

    • Adenine nucleotide
    • Domino process
    • Domino systems biology
    • Glycolysis
    • IMP salvage
    • Saccharomyces cerevisiae

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