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Transcript abundance on its own cannot be used to infer fluxes in central metabolism

An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accu...

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Autores principales: Schwender, Jörg, König, Christina, Klapperstück, Matthias, Heinzel, Nicolas, Munz, Eberhard, Hebbelmann, Inga, Hay, Jordan O., Denolf, Peter, De Bodt, Stefanie, Redestig, Henning, Caestecker, Evelyne, Jakob, Peter M., Borisjuk, Ljudmilla, Rolletschek, Hardy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246676/
https://www.ncbi.nlm.nih.gov/pubmed/25506350
http://dx.doi.org/10.3389/fpls.2014.00668
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author Schwender, Jörg
König, Christina
Klapperstück, Matthias
Heinzel, Nicolas
Munz, Eberhard
Hebbelmann, Inga
Hay, Jordan O.
Denolf, Peter
De Bodt, Stefanie
Redestig, Henning
Caestecker, Evelyne
Jakob, Peter M.
Borisjuk, Ljudmilla
Rolletschek, Hardy
author_facet Schwender, Jörg
König, Christina
Klapperstück, Matthias
Heinzel, Nicolas
Munz, Eberhard
Hebbelmann, Inga
Hay, Jordan O.
Denolf, Peter
De Bodt, Stefanie
Redestig, Henning
Caestecker, Evelyne
Jakob, Peter M.
Borisjuk, Ljudmilla
Rolletschek, Hardy
author_sort Schwender, Jörg
collection PubMed
description An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident flux information was eventually used for comparative analysis of flux vs. transcript (metabolite). Metabolite profiling succeeded in identifying 79 intermediates within the central metabolism, some of which differed quantitatively between the two accessions and displayed a significant shift corresponding to flux. An RNA-Seq based transcriptome analysis revealed a large number of genes which were differentially transcribed in the two accessions, including some enzymes/proteins active in major metabolic pathways. With a few exceptions, differential activity in the major pathways (glycolysis, TCA cycle, amino acid, and fatty acid synthesis) was not reflected in contrasting abundances of the relevant transcripts. The conclusion was that transcript abundance on its own cannot be used to infer metabolic activity/fluxes in central plant metabolism. This limitation needs to be borne in mind in evaluating transcriptome data and designing metabolic engineering experiments.
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spelling pubmed-42466762014-12-12 Transcript abundance on its own cannot be used to infer fluxes in central metabolism Schwender, Jörg König, Christina Klapperstück, Matthias Heinzel, Nicolas Munz, Eberhard Hebbelmann, Inga Hay, Jordan O. Denolf, Peter De Bodt, Stefanie Redestig, Henning Caestecker, Evelyne Jakob, Peter M. Borisjuk, Ljudmilla Rolletschek, Hardy Front Plant Sci Plant Science An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident flux information was eventually used for comparative analysis of flux vs. transcript (metabolite). Metabolite profiling succeeded in identifying 79 intermediates within the central metabolism, some of which differed quantitatively between the two accessions and displayed a significant shift corresponding to flux. An RNA-Seq based transcriptome analysis revealed a large number of genes which were differentially transcribed in the two accessions, including some enzymes/proteins active in major metabolic pathways. With a few exceptions, differential activity in the major pathways (glycolysis, TCA cycle, amino acid, and fatty acid synthesis) was not reflected in contrasting abundances of the relevant transcripts. The conclusion was that transcript abundance on its own cannot be used to infer metabolic activity/fluxes in central plant metabolism. This limitation needs to be borne in mind in evaluating transcriptome data and designing metabolic engineering experiments. Frontiers Media S.A. 2014-11-28 /pmc/articles/PMC4246676/ /pubmed/25506350 http://dx.doi.org/10.3389/fpls.2014.00668 Text en Copyright © 2014 Schwender, König, Klapperstück, Heinzel, Munz, Hebbelmann, Hay, Denolf, De Bodt, Redestig, Caestecker, Jakob, Borisjuk and Rolletschek. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Schwender, Jörg
König, Christina
Klapperstück, Matthias
Heinzel, Nicolas
Munz, Eberhard
Hebbelmann, Inga
Hay, Jordan O.
Denolf, Peter
De Bodt, Stefanie
Redestig, Henning
Caestecker, Evelyne
Jakob, Peter M.
Borisjuk, Ljudmilla
Rolletschek, Hardy
Transcript abundance on its own cannot be used to infer fluxes in central metabolism
title Transcript abundance on its own cannot be used to infer fluxes in central metabolism
title_full Transcript abundance on its own cannot be used to infer fluxes in central metabolism
title_fullStr Transcript abundance on its own cannot be used to infer fluxes in central metabolism
title_full_unstemmed Transcript abundance on its own cannot be used to infer fluxes in central metabolism
title_short Transcript abundance on its own cannot be used to infer fluxes in central metabolism
title_sort transcript abundance on its own cannot be used to infer fluxes in central metabolism
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4246676/
https://www.ncbi.nlm.nih.gov/pubmed/25506350
http://dx.doi.org/10.3389/fpls.2014.00668
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