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  Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism

Pries, C., Razaghi-Moghadam, Z., Kopka, J., & Nikoloski, Z. (2021). Integration of relative metabolomics and transcriptomics time-course data in a metabolic model pinpoints effects of ribosome biogenesis defects on Arabidopsis thaliana metabolism. Scientific Reports, 11(1): 4787. Retrieved from https://doi.org/10.1038/s41598-021-84114-y.

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Pries, Christopher1, Author
Razaghi-Moghadam, Z.2, Author              
Kopka, J.3, Author              
Nikoloski, Z.2, Author              
Affiliations:
1external, ou_persistent22              
2Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753310              
3Applied Metabolome Analysis, Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753338              

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 Abstract: Ribosome biogenesis is tightly associated to plant metabolism due to the usage of ribosomes in the synthesis of proteins necessary to drive metabolic pathways. Given the central role of ribosome biogenesis in cell physiology, it is important to characterize the impact of different components involved in this process on plant metabolism. Double mutants of the Arabidopsis thaliana cytosolic 60S maturation factors REIL1 and REIL2 do not resume growth after shift to moderate 10 $$^{\circ }\hbox {C}$$chilling conditions. To gain mechanistic insights into the metabolic effects of this ribosome biogenesis defect on metabolism, we developed TC-iReMet2, a constraint-based modelling approach that integrates relative metabolomics and transcriptomics time-course data to predict differential fluxes on a genome-scale level. We employed TC-iReMet2 with metabolomics and transcriptomics data from the Arabidopsis Columbia 0 wild type and the reil1-1 reil2-1 double mutant before and after cold shift. We identified reactions and pathways that are highly altered in a mutant relative to the wild type. These pathways include the Calvin–Benson cycle, photorespiration, gluconeogenesis, and glycolysis. Our findings also indicated differential NAD(P)/NAD(P)H ratios after cold shift. TC-iReMet2 allows for mechanistic hypothesis generation and interpretation of system biology experiments related to metabolic fluxes on a genome-scale level.

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 Dates: 2021
 Publication Status: Published in print
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 Identifiers: URI: https://doi.org/10.1038/s41598-021-84114-y
Other: Pries2021
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Title: Scientific Reports
Source Genre: Journal
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Pages: - Volume / Issue: 11 (1) Sequence Number: 4787 Start / End Page: - Identifier: ISBN: 2045-2322