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Mathematicals models of plant specialized metabolism

Project Goals:..............Development of mathematical models to test and advance our knowledge of how metabolism is regulated in plants
......................Department of Energy - Energy Biosciences Program

Executive Summary

Mathematical models can serve to gain fundamental insights of how flux is distributed between metabolic pathways. Depending on the complexity of the problem and availability of appropriate data, different approaches can be taken. Genome-scale models are based on balancing the reactions of an entire network, where various data sets can be incorporated as constraints for calculations. The scope of kinetic models tends to be more focused and they require detailed information on the biochemical properties of all enzymes. We are integrating mathematic modeling in iterative processes to simulate the biochemistry of a particular biological system of interest and performing experiments to capture pathway regulation at all levels. These approaches have empowered metabolic enigneering and molecular breeding efforts, often with an emphasis on enhancing the accumulation of metabolites in specialized cell types and tissues.

Online Databases

YASMEnv - Toolbox to create and analyze stoichiometric metabolic models (developer: Sean Johnson)

Selected Recent Publications

Lange B.M. (2020) Flux distribution at the interface of central carbon metabolism and terpenoid volatile formation. In Biology of Plant Volatiles, Eran Pichersky, Natalia Dudareva, Eds., CRC Press, Boca Raton, FL, pp. 119-164. Link

Lange B.M., Poirier B.C., Lange I., Schumaker R., Rios-Estepa R. (2020) Organ-specificity of sterol and triterpene accumulation in Arabidopsis thaliana. bioRxiv doi: https://doi.org/10.1101/2020.03.23.004358. Link

Turner G.W., Parrish A.N., Zager J.J., Fischedick J.T., Lange B.M. (2019) Assessment of flux through oleoresin biosynthesis in epithelial cells of loblolly pine resin ducts. J. Exp. Bot. 70, 217-230.

Zager J.J., Lange B.M. (2018) Assessing flux distribution associated with metabolic specialization of glandular trichomes. Trends Plant Sci. 23, 638-647.

Johnson S.R., Lange I., Srividya N., Lange B.M. (2017) Bioenergetics of monoterpenoid essential oil biosynthesis in non-photosynthetic glandular trichomes. Plant Physiol. 175, 681-695.

ange B.M., Rios-Estepa R. (2014) Kinetic modeling of plant metabolism and its predictive power – peppermint essential oil biosynthesis as an example. Methods Mol. Biol. 1083, 287-311.

Lange B.M., Mahmoud S.S., Wildung M.R., Turner G.W., Davis E.M., Lange I., Baker R.C., Boydston R.A., Croteau R.B. (2011) Improving peppermint essential oil yield and composition by metabolic engineering. Proc. Natl. Acad. Sci. USA 108, 16944-16949.

Rios-Estepa R., Lange I., Lee J.M., Lange B.M. (2010) Mathematical modeling-guided evaluation of biochemical, developmental, environmental and genotypic determinants of essential oil composition and yield in peppermint leaves. Plant Physiol. 152, 2105-2119 (COVER STORY).

Rios-Estepa R., Turner G.W., Lee J.M., Croteau R.B., Lange B.M. (2008) A systems biology approach identifies biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint. Proc. Natl. Acad. Sci. USA 105, 2818-2823.