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Theory Biosci. 2016 Jun;135(1-2):73-87. doi: 10.1007/s12064-016-0225-y. Epub 2016 Apr 5.

Approximating the stabilization of cellular metabolism by compartmentalization.

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Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.


Biochemical regulation in compartmentalized metabolic networks is highly complex and non-intuitive. This is particularly true for cells of higher plants showing one of the most compartmentalized cellular structures across all kingdoms of life. The interpretation and testable hypothesis generation from experimental data on such complex systems is a challenging step in biological research and biotechnological applications. While it is known that subcellular compartments provide defined reaction spaces within a cell allowing for the tight coordination of complex biochemical reaction sequences, its role in the coordination of metabolic signals during metabolic reprogramming due to environmental fluctuations is less clear. In the present study, we numerically analysed the effects of environmental fluctuations in a subcellular metabolic network with regard to the stability of an experimentally observed steady state in the genetic model plant Arabidopsis thaliana. Applying a method for kinetic parameter normalization, several millions of probable enzyme kinetic parameter constellations were simulated and evaluated with regard to the stability information of the metabolic homeostasis. Information about the stability of the metabolic steady state was derived from real parts of eigenvalues of Jacobian matrices. Our results provide evidence for a differential stabilizing contribution of different subcellular compartments. We could identify stabilizing and destabilizing network components which we could classify according to their subcellular localization. The findings prove that a highly dynamic interplay between intracellular compartments is preliminary for an efficient stabilization of a metabolic homeostasis after environmental perturbation. Further, our results provide evidence that feedback-inhibition originating from the cytosol and plastid seem to stabilize the sucrose homeostasis more efficiently than vacuolar control. In summary, our results indicate stabilizing and destabilizing network components in context of their subcellular organization.


Compartmentalization; Eigenvalue; Jacobian matrix; Stability; Subcellular network; Systems biology

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