Open Access Research

A systems biology approach to analyse leaf carbohydrate metabolism in Arabidopsis thaliana

Sebastian Henkel1, Thomas Nägele2*, Imke Hörmiller2, Thomas Sauter3, Oliver Sawodny1, Michael Ederer1 and Arnd G Heyer2

Author Affiliations

1 Institut für Systemdynamik, Universität Stuttgart, D-70550 Stuttgart, Germany

2 Biologisches Institut, Abteilung Pflanzenbiotechnologie, Universität Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany

3 Life Science Research Unit, Université du Luxembourg, L-1511 Luxembourg, Germany

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EURASIP Journal on Bioinformatics and Systems Biology 2011, 2011:2  doi:10.1186/1687-4153-2011-2

Published: 17 June 2011

Abstract

Plant carbohydrate metabolism comprises numerous metabolite interconversions, some of which form cycles of metabolite degradation and re-synthesis and are thus referred to as futile cycles. In this study, we present a systems biology approach to analyse any possible regulatory principle that operates such futile cycles based on experimental data for sucrose (Scr) cycling in photosynthetically active leaves of the model plant Arabidopsis thaliana. Kinetic parameters of enzymatic steps in Scr cycling were identified by fitting model simulations to experimental data. A statistical analysis of the kinetic parameters and calculated flux rates allowed for estimation of the variability and supported the predictability of the model. A principal component analysis of the parameter results revealed the identifiability of the model parameters. We investigated the stability properties of Scr cycling and found that feedback inhibition of enzymes catalysing metabolite interconversions at different steps of the cycle have differential influence on stability. Applying this observation to futile cycling of Scr in leaf cells points to the enzyme hexokinase as an important regulator, while the step of Scr degradation by invertases appears subordinate.

Keywords:
Systems biology; carbohydrate metabolism; Arabidopsis thaliana; kinetic modelling; stability analysis; sucrose cycling