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

ABSTRACT: 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.

SUBMITTER: Schwender J

PROVIDER: S-EPMC4246676 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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

Schwender Jörg J König Christina C Klapperstück Matthias M Heinzel Nicolas N Munz Eberhard E Hebbelmann Inga I Hay Jordan O JO Denolf Peter P De Bodt Stefanie S Redestig Henning H Caestecker Evelyne E Jakob Peter M PM Borisjuk Ljudmilla L Rolletschek Hardy H

Frontiers in plant science 20141128

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 ...[more]

PMID: 25506350

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Dataset Information

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

Publications

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

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