ArticleBMC systems biology2011
Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells.
Article in BMC systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Evaluating transcriptomic integration for cyanobacterial constraint-based metabolic modelling.Frontiers in bioinformatics · 2026Article
- Constraint-Based Modeling Highlights Cell Energy, Redox Status and α-Ketoglutarate Availability as Metabolic Drivers for Anthocyanin Accumulation in Grape Cells Under Nitrogen Limitation.Frontiers in plant science · 2018Article
- Respiration climacteric in tomato fruits elucidated by constraint-based modelling.The New phytologist · 2017Article
- E-Flux2 and SPOT: Validated Methods for Inferring Intracellular Metabolic Flux Distributions from Transcriptomic Data.PloS one · 2016Article
- Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit.The Plant journal : for cell and molecular biology · 2015Article
- Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.The Plant cell · 2014Review
- Methods for integration of transcriptomic data in genome-scale metabolic models.Computational and structural biotechnology journal · 2014Review
- Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs.BMC systems biology · 2014Article
- Identification of metabolic engineering targets through analysis of optimal and sub-optimal routes.PloS one · 2013Article
- Functional genomics tools applied to plant metabolism: a survey on plant respiration, its connections and the annotation of complex gene functions.Frontiers in plant science · 2012Article
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Abstract
background(13)C metabolic flux analysis is one of the pertinent ways to compare two or more physiological states. From a more theoretical standpoint, the structural properties of metabolic networks can be analysed to explore feasible metabolic behaviours and to define the boundaries of steady state flux distributions. Elementary flux mode analysis is one of the most efficient methods for performing this analysis. In this context, recent approaches have tended to compare experimental flux measurements with topological network analysis.
resultsMetabolic networks describing the main pathways of central carbon metabolism were set up for a bacteria species (Corynebacterium glutamicum) and a plant species (Brassica napus) for which experimental flux maps were available. The structural properties of each network were then studied using the concept of elementary flux modes. To do this, coefficients of flux efficiency were calculated for each reaction within the networks by using selected sets of elementary flux modes. Then the relative differences - reflecting the change of substrate i.e. a sugar source for C. glutamicum and a nitrogen source for B. napus - of both flux efficiency and flux measured experimentally were compared. For both organisms, there is a clear relationship between these parameters, thus indicating that the network structure described by the elementary flux modes had captured a significant part of the metabolic activity in both biological systems. In B. napus, the extension of the elementary flux mode analysis to an enlarged metabolic network still resulted in a clear relationship between the change in the coefficients and that of the measured fluxes. Nevertheless, the limitations of the method to fit some particular fluxes are discussed.
conclusionThis consistency between EFM analysis and experimental flux measurements, validated on two metabolic systems allows us to conclude that elementary flux mode analysis could be a useful tool to complement (13)C metabolic flux analysis, by allowing the prediction of changes in internal fluxes before carbon labelling experiments.
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