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  An automated workflow that generates atom mappings for large scale metabolic models and its application to Arabidopsis thaliana

Huß, S., Judd, R. S., Koper, K., Maeda, H. A., & Nikoloski, Z. (2022). An automated workflow that generates atom mappings for large scale metabolic models and its application to Arabidopsis thaliana. The Plant Journal, 111(5), 1486-1500. doi:10.1111/tpj.15903.

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Genre: Journal Article
Alternative Title : The Plant Journal

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 Creators:
Huß, S.1, Author           
Judd, Rika Siedah2, Author
Koper, Kaan2, Author
Maeda, Hiroshi A.2, Author
Nikoloski, Z.1, Author           
Affiliations:
1Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753310              
2external, ou_persistent22              

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Free keywords: atom mapping, genome-scale metabolic model, isotopic labeling, metabolic flux analysis
 Abstract: SUMMARY Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA) that relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches, such as Reaction Decoder Toolkit (RDT), can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating 15N-isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future 15N-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been assembled and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.

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Language(s): eng - English
 Dates: 2022-07-122022-09
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1111/tpj.15903
 Degree: -

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Title: The Plant Journal
  Other : Plant J.
Source Genre: Journal
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Publ. Info: Oxford : Blackwell Science
Pages: - Volume / Issue: 111 (5) Sequence Number: - Start / End Page: 1486 - 1500 Identifier: ISSN: 0960-7412
CoNE: https://pure.mpg.de/cone/journals/resource/954925579095_1