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Heise R, Fernie AR, Stitt M, et al. Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana. Front Plant Sci. 2015;6:386doi: 10.3389/fpls.2015.00386.
Heise, R., Fernie, A. R., Stitt, M., & Nikoloski, Z. (2015). Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana. Frontiers in plant science, 6386. https://doi.org/10.3389/fpls.2015.00386
Heise, Robert, et al. "Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana." Frontiers in plant science vol. 6 (2015): 386. doi: https://doi.org/10.3389/fpls.2015.00386
Heise R, Fernie AR, Stitt M, Nikoloski Z. Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana. Front Plant Sci. 2015 Jun 02;6:386. doi: 10.3389/fpls.2015.00386. eCollection 2015. PMID: 26082786; PMCID: PMC4451360.
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Front Plant Sci. 2015 Jun 02;6:386. doi: 10.3389/fpls.2015.00386. eCollection 2015.

Pool size measurements facilitate the determination of fluxes at branching points in non-stationary metabolic flux analysis: the case of Arabidopsis thaliana.

Frontiers in plant science

Robert Heise, Alisdair R Fernie, Mark Stitt, Zoran Nikoloski

Affiliations

  1. Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology Potsdam, Germany.
  2. Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology Potsdam, Germany.
  3. System Regulation Group, Max Planck Institute of Molecular Plant Physiology Potsdam, Germany.

PMID: 26082786 PMCID: PMC4451360 DOI: 10.3389/fpls.2015.00386

Abstract

Pool size measurements are important for the estimation of absolute intracellular fluxes in particular scenarios based on data from heavy carbon isotope experiments. Recently, steady-state fluxes estimates were obtained for central carbon metabolism in an intact illuminated rosette of Arabidopsis thaliana grown photoautotrophically (Szecowka et al., 2013; Heise et al., 2014). Fluxes were estimated therein by integrating mass-spectrometric data of the dynamics of the unlabeled metabolic fraction, data on metabolic pool sizes, partitioning of metabolic pools between cellular compartments and estimates of photosynthetically inactive pools, with a simplified model of plant central carbon metabolism. However, the fluxes were determined by treating the pool sizes as fixed parameters. Here we investigated whether and, if so, to what extent the treatment of pool sizes as parameters to be optimized in three scenarios may affect the flux estimates. The results are discussed in terms of benchmark values for canonical pathways and reactions, including starch and sucrose synthesis as well as the ribulose-1,5-bisphosphate carboxylation and oxygenation reactions. In addition, we discuss pathways emerging from a divergent branch point for which pool sizes are required for flux estimation, irrespective of the computational approach used for the simulation of the observable labeling pattern. Therefore, our findings indicate the necessity for development of techniques for accurate pool size measurements to improve the quality of flux estimates from non-stationary flux estimates in intact plant cells in the absence of alternative flux measurements.

Keywords: Arabidopsis thaliana; carbon metabolism; flux profiling; isotopic labeling; isotopically non-stationary; metabolic flux analysis; metabolite pool sizes; photoautotrophic growth

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