title: iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models.
abstract: Understanding the rerouting of metabolic reaction fluxes upon perturbations has the potential to link changes in molecular state of a cellular system to alteration of growth. Yet, differential flux profiling on a genome-scale level remains one of the biggest challenges in systems biology. This is particularly relevant in plants, for which fluxes in autotrophic growth necessitate time-consuming instationary labeling experiments and costly computations, feasible for small-scale networks.
  
  
  
  Here we present a computationally and experimentally facile approach, termed iReMet-Flux, which integrates relative metabolomics data in a metabolic model to predict differential fluxes at a genome-scale level. Our approach and its variants complement the flux estimation methods based on radioactive tracer labeling. We employ iReMet-Flux with publically available metabolic profiles to predict reactions and pathways with altered fluxes in photo-autotrophically grown Arabidopsis and four photorespiratory mutants undergoing high-to-low CO2 acclimation. We also provide predictions about reactions and pathways which are most strongly regulated in the investigated experiments. The robustness and variability analyses, tailored to the formulation of iReMet-Flux, demonstrate that the findings provide biologically relevant information that is validated with external measurements of net CO2 exchange and biomass production. Therefore, iReMet-Flux paves the wave for mechanistic dissection of the interplay between pathways of primary and secondary metabolisms at a genome-scale.
  
  
  
  The source code is available from the authors upon request.
  
  
  
  nikoloski@mpimp-golm.mpg.de
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Systems Biology and Mathematical Modeling Group.
authors: Max
authors: M
authors: Sajitz-Hermstein
authors: Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel.
authors: Nadine
authors: N
authors: Töpfer
authors: Targenomix GmbH, Am Mühlenberg 11, Potsdam 14476, Germany.
authors: Sabrina
authors: S
authors: Kleessen
authors: Central Metabolism Group, Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam 14476, Germany.
authors: Alisdair R
authors: AR
authors: Fernie
authors: Systems Biology and Mathematical Modeling Group.
authors: Zoran
authors: Z
authors: Nikoloski
mesh_terms: D005544:Forecasting; D016678:Genome; D053858:Metabolic Networks and Pathways; D055432:Metabolomics; D008954:Models, Biological; D049490:Systems Biology