Identification of flux trade-offs in metabolic networks
- Trade-offs are inherent to biochemical networks governing diverse cellular functions, from gene expression to metabolism. Yet, trade-offs between fluxes of biochemical reactions in a metabolic network have not been formally studied. Here, we introduce the concept of absolute flux trade-offs and devise a constraint-based approach, termed FluTO, to identify and enumerate flux trade-offs in a given genome-scale metabolic network. By employing the metabolic networks of Escherichia coli and Saccharomyces cerevisiae, we demonstrate that the flux trade-offs are specific to carbon sources provided but that reactions involved in the cofactor and prosthetic group biosynthesis are present in trade-offs across all carbon sources supporting growth. We also show that absolute flux trade-offs depend on the biomass reaction used to model the growth of Arabidopsis thaliana under different carbon and nitrogen conditions. The identified flux trade-offs reflect the tight coupling between nitrogen, carbon, and sulphur metabolisms in leaves of C-3 plants.Trade-offs are inherent to biochemical networks governing diverse cellular functions, from gene expression to metabolism. Yet, trade-offs between fluxes of biochemical reactions in a metabolic network have not been formally studied. Here, we introduce the concept of absolute flux trade-offs and devise a constraint-based approach, termed FluTO, to identify and enumerate flux trade-offs in a given genome-scale metabolic network. By employing the metabolic networks of Escherichia coli and Saccharomyces cerevisiae, we demonstrate that the flux trade-offs are specific to carbon sources provided but that reactions involved in the cofactor and prosthetic group biosynthesis are present in trade-offs across all carbon sources supporting growth. We also show that absolute flux trade-offs depend on the biomass reaction used to model the growth of Arabidopsis thaliana under different carbon and nitrogen conditions. The identified flux trade-offs reflect the tight coupling between nitrogen, carbon, and sulphur metabolisms in leaves of C-3 plants. Altogether, FluTO provides the means to explore the space of alternative metabolic routes reflecting the constraints imposed by inherent flux trade-offs in large-scale metabolic networks.…
Author details: | Seirana HashemiORCiD, Zahra Razaghi-MoghadamORCiD, Zoran NikoloskiORCiDGND |
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DOI: | https://doi.org/10.1038/s41598-021-03224-9 |
ISSN: | 2045-2322 |
Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/34893666 |
Title of parent work (English): | Scientific reports |
Publisher: | Macmillan Publishers Limited, part of Springer Nature |
Place of publishing: | London |
Publication type: | Article |
Language: | English |
Date of first publication: | 2021/12/10 |
Publication year: | 2021 |
Release date: | 2023/07/06 |
Volume: | 11 |
Issue: | 1 |
Article number: | 23776 |
Number of pages: | 10 |
Funding institution: | DFGGerman Research Foundation (DFG)European Commission [NI 1472/4-2] |
Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
DDC classification: | 5 Naturwissenschaften und Mathematik / 50 Naturwissenschaften / 500 Naturwissenschaften und Mathematik |
6 Technik, Medizin, angewandte Wissenschaften / 60 Technik / 600 Technik, Technologie | |
Peer review: | Referiert |
Publishing method: | Open Access / Gold Open-Access |
DOAJ gelistet | |
License (German): | CC-BY - Namensnennung 4.0 International |