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The Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics.(Research Article)

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 u... Full description

Journal Title: PLoS ONE July 26, 2013, Vol.8(7), p.e68960
Main Author: Groenenboom, Marian
Other Authors: Gomez - Roldan, Victoria , Stigter, Hans , Astola, Laura , Van Daelen, Raymond , Beekwilder, Jules , Bovy, Arnaud , Hall, Robert , Molenaar, Jaap
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0068960
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recordid: gale_hrca477990995
title: The Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics.(Research Article)
format: Article
creator:
  • Groenenboom, Marian
  • Gomez - Roldan, Victoria
  • Stigter, Hans
  • Astola, Laura
  • Van Daelen, Raymond
  • Beekwilder, Jules
  • Bovy, Arnaud
  • Hall, Robert
  • Molenaar, Jaap
subjects:
  • Isoflavones -- Analysis
  • Enzymes -- Analysis
  • Plant Metabolites -- Analysis
ispartof: PLoS ONE, July 26, 2013, Vol.8(7), p.e68960
description: 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.
language: English
source:
identifier: ISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0068960
fulltext: fulltext
issn:
  • 1932-6203
  • 19326203
url: Link


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titleThe Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics.(Research Article)
creatorGroenenboom, Marian ; Gomez - Roldan, Victoria ; Stigter, Hans ; Astola, Laura ; Van Daelen, Raymond ; Beekwilder, Jules ; Bovy, Arnaud ; Hall, Robert ; Molenaar, Jaap
ispartofPLoS ONE, July 26, 2013, Vol.8(7), p.e68960
identifierISSN: 1932-6203 ; DOI: 10.1371/journal.pone.0068960
subjectIsoflavones -- Analysis ; Enzymes -- Analysis ; Plant Metabolites -- Analysis
descriptionFlavonoids 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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titleThe Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics.(Research Article)
descriptionFlavonoids 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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titleThe Flavonoid Pathway in Tomato Seedlings: Transcript Abundance and the Modeling of Metabolite Dynamics.(Research Article)
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abstractFlavonoids 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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doi10.1371/journal.pone.0068960
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date2013-07-26