Experimental and mathematical approaches to modeling plant metabolic networks

Ríos‐Estepa, Rigoberto; Lange, B. Markus

doi:10.1016/j.phytochem.2007.04.021

Cited by 86 publications

(48 citation statements)

References 141 publications

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“…However, data on the utility of these stochastic approaches for plant metabolism are sparse (Rios-Estepa and Lange, 2007), and we felt that it was important to find an approximation that was supported directly by experimental data. Fortunately, data on dynamic changes of gene expression and protein levels in peppermint glandular trichomes under various controlled experimental conditions were available to us.…”

Section: Can Enzyme Concentrations In Peppermint Glandularmentioning

confidence: 99%

“…When experimental designs supporting metabolic and isotopic steady state are employed, isotope labeling data can be utilized for the development of quantitative flux maps of metabolic pathways (for review, see Libourel and Shachar-Hill, 2008). For dynamic systems, kinetic modeling is regarded as the generally most suitable method (McNeil et al, 2000;Poolman et al, 2004;Bruggeman and Westerhoff, 2006;Rios-Estepa and Lange, 2007;Mendes et al, 2009). Building on the rich body of published data on the enzymology and physiology of the peppermint monoterpene pathway (for review, see Croteau et al, 2005), we recently developed a first generation kinetic model to simulate the dynamics of peppermint monoterpene composition (Rios-Estepa et al, 2008).…”

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confidence: 99%

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Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves

et al. 2010

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We have previously reported the use of a combination of computational simulations and targeted experiments to build a first generation mathematical model of peppermint (Mentha 3 piperita) essential oil biosynthesis. Here, we report on the expansion of this approach to identify the key factors controlling monoterpenoid essential oil biosynthesis under adverse environmental conditions. We also investigated determinants of essential oil biosynthesis in transgenic peppermint lines with modulated essential oil profiles. A computational perturbation analysis, which was implemented to identify the variables that exert prominent control over the outputs of the model, indicated that the essential oil composition should be highly dependent on certain biosynthetic enzyme concentrations [(+)-pulegone reductase and (+)-menthofuran synthase], whereas oil yield should be particularly sensitive to the density and/or distribution of leaf glandular trichomes, the specialized anatomical structures responsible for the synthesis and storage of essential oils. A microscopic evaluation of leaf surfaces demonstrated that the final mature size of glandular trichomes was the same across all experiments. However, as predicted by the perturbation analysis, differences in the size distribution and the total number of glandular trichomes strongly correlated with differences in monoterpenoid essential oil yield. Building on various experimental data sets, appropriate mathematical functions were selected to approximate the dynamics of glandular trichome distribution/density and enzyme concentrations in our kinetic model. Based on a x 2 statistical analysis, simulated and measured essential oil profiles were in very good agreement, indicating that modeling is a valuable tool for guiding metabolic engineering efforts aimed at improving essential oil quality and quantity.

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Section: Can Enzyme Concentrations In Peppermint Glandularmentioning

confidence: 99%

mentioning

confidence: 99%

Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves

et al. 2010

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“…The dynamics of metabolic networks has traditionally been investigated by methods rooted in ordinary differential equations, which require a large amount of information for simulating the temporal changes of metabolite concentrations/levels and reaction fluxes (21,22). To this end, the phenomenological parameters of specific enzyme kinetics (e.g.…”

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Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain

Kleeßen

Araújo

Fernie

et al. 2012

Journal of Biological Chemistry

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Background: There are alternative substrates to the mitochondrial respiration. Results: Data-driven model-based analysis renders predictions of alternative substrates to the mitochondrial respiration. Conclusion: Metabolomics data in conjunction with flux-based models can discriminate among hypotheses based on enzymology alone. Significance: This analysis provides a basic framework for in silico studies of alternative pathways in metabolism.

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“…Furthermore, the steady state of is assumed. These two assumptions are commonly taken for granted in the literature (Heinrich et al 1996;Klamt et al 2003;Rios-Estepa et al 2007). Therefore, Eq.…”

Section: Time Evolution Of the Intracellular Species Concentrationsmentioning

confidence: 99%

Structured Model of VERO Cells Metabolism in a Fixed-Bed Bioreactor

Gelbgras¹,

Wylock²,

Drugmand³

et al. 2011

Chemical Product and Process Modeling

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In this work, a structured mathematical model of the VERvet Origin (VERO) cell metabolism in a fixed-bed bioreactor is developed. Mass balance equations for the extra-and intracellular species are written considering the main pathways of the animal cell metabolism. From the model equations, an undetermined set of equations relating the consumption or production velocities of the extracellular species and the velocities of the metabolic reactions can be developed. The monitoring of a reference cell culture enables to transform this undetermined set of equations in a determined one. The resolution of this determined set of equations enables to analyze and characterize the cell metabolism. From the model and the cell metabolism characterization, a monitoring tool is developed to simulate the time evolution of the species concentrations when the time evolution of the cell concentration is known. This simulation tool is used to simulate five experimental cell cultures. The comparison of the experimentally determined and computed time evolutions of the species concentrations enables to validate the developed monitoring tool. The validated monitoring tool can be used to optimize the operating conditions of the culture, as the medium feeding rate, the range of the species concentrations.

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Experimental and mathematical approaches to modeling plant metabolic networks

Cited by 86 publications

References 141 publications

Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves

Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves

Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain

Structured Model of VERO Cells Metabolism in a Fixed-Bed Bioreactor

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