Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 441770
Title The Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics
Author(s) Groenenboom, M.; Gomez-Roldan, V.; Stigter, J.D.; Astola, L.; Daelen, R. van; Beekwilder, M.J.; Bovy, A.G.; Hall, R.D.; Molenaar, J.
Source PLoS One 8 (2013)7. - ISSN 1932-6203 - 11 p.
Department(s) Biometris (WU MAT)
PRI BIOS Applied Metabolic Systems
Publication type Refereed Article in a scientific journal
Publication year 2013
Keyword(s) gene-expression - arabidopsis seedlings - systems biology - fruit - biosynthesis - accumulation - evolution - enzymes - plants
Abstract Flavonoids are secondary metabolites present in all terrestrial plants. The flavonoid pathway has been extensively studied, and many of the involved genes and metabolites have been described in the literature. Despite this extensive knowledge, the functioning of the pathway in vivo is still poorly understood. Here, we study the flavonoid pathway using both experiments and mathematical models. We measured flavonoid metabolite dynamics in two tissues, hypocotyls and cotyledons, during tomato seedling development. Interestingly, the same backbone of interactions leads to very different accumulation patterns in the different tissues. Initially, we developed a mathematical model with constant enzyme concentrations that described the metabolic networks separately in both tissues. This model was unable to fit the measured flavonoid dynamics in the hypocotyls, even if we allowed unrealistic parameter values. This suggested us to investigate the effect of transcript abundance on flavonoid accumulation. We found that the expression of candidate flavonoid genes varies considerably with time. Variation in transcript abundance results in enzymatic variation, which could have a large effect on metabolite accumulation. Candidate transcript abundance was included in the mathematical model as representative for enzyme concentration. We fitted the resulting model to the flavonoid dynamics in the cotyledons, and tested it by applying it to the data from hypocotyls. When transcript abundance is included, we are indeed able to explain flavonoid dynamics in both tissues. Importantly, this is possible under the biologically relevant restriction that the enzymatic properties estimated by the model are conserved between the tissues.
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