Elementary flux modes, flux balance analysis and their application to plant metabolism

Katrin Lotz, Anja Hartmann, Eva Grafahrend-Belau, Falk Schreiber, Björn H. Junker

Research output: Chapter in Book/Report/Conference proceedingChapter (Book)Researchpeer-review

5 Citations (Scopus)

Abstract

In recent years the number of sequenced and annotated plant genomes has increased significantly, and novel approaches are required to retrieve valuable information from these data sets. The field of systems biology has accelerated the simulation and prediction of phenotypes derived from specific genotypic modifications under defined growth conditions. The biochemical potential of a cell from a specific plant tissue (e.g., seed endosperm) can be derived from its genome in the form of a mathematical model by the method of metabolic network reconstruction. This model can be further analyzed by studying its network properties, analyzing feasible pathway routes through the network, or simulating possible flux distributions of the network. Here, we describe two approaches for identification of all feasible routes through the network (elementary mode analysis) and for simulation of flux distribution in the network based on plant physiological uptake and excretion rates (flux balance analysis). © 2014 Springer Science+Business Media, New York.

Original languageEnglish
Title of host publicationPlant Metabolism
Subtitle of host publicationMethods and Protocols
EditorsGanesh Sriram
Place of PublicationNew York NY
PublisherHumana Press
Chapter14
Pages231 - 252
Number of pages22
Edition1st
ISBN (Electronic)9781627036610
ISBN (Print)9781627036603
DOIs
Publication statusPublished - 2014
Externally publishedYes

Publication series

NameMethods in Molecular Biology
PublisherSpringer
Volume1083
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • Constraint-based modeling
  • Elementary flux modes
  • Flux balance analysis
  • Metabolic flux analysis
  • Metabolic modeling
  • Metabolic reconstruction
  • Primary plant metabolism

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