Skip to main content
SpringerLink
Log in

Flux Balance Analysis as an Alternative Method to Estimate Fluxes Without Labeling

  • Protocol
  • First Online:
Book cover Plant Metabolic Flux Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1090))

Abstract

The analysis of plant metabolic networks essentially contributes to the understanding of the efficiency of plant systems in terms of their biotechnological usage. Metabolic fluxes are determined by biochemical parameters such as metabolite concentrations as well as enzyme properties and activities, which in turn are the result of various regulatory events at various levels between control of transcription and posttranslational regulation of enzyme protein activity. Thus, knowledge about metabolic fluxes on a large scale provides an integrated view on the functional state of a metabolically active cell, organ, or system. In this chapter, we introduce flux balance analysis as a constraint-based method for the prediction of optimal metabolic fluxes in a given metabolic network. Furthermore, we provide a step-by-step protocol for metabolic network reconstruction and constraint-based analysis using the COBRA Toolbox.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Stitt M, Sulpice R, Keurentjes J (2010) Metabolic networks: how to identify key components in the regulation of metabolism and growth. Plant Physiol 152:428–444

    Article  PubMed  CAS  Google Scholar 

  2. Sweetlove LJ, Fell D, Fernie AR (2008) Getting to grips with the plant metabolic network. Biochem J 409:27–41

    Article  PubMed  CAS  Google Scholar 

  3. Kruger NJ, Ratcliffe RG (2012) Pathways and fluxes: exploring the plant metabolic network. J Exp Bot 63:2243–2246

    Article  PubMed  CAS  Google Scholar 

  4. Edwards JS, Ramakrishna R, Schilling CH, Palsson BO (1999) Metabolic Flux Balance Analysis. In: Lee SY, Papoutsakis ET (eds) Metabolic engineering. Marcel Dekker, New York, pp 13–57

    Google Scholar 

  5. Poolman MG, Miguet L, Sweetlove LJ, Fell DA (2009) A genome-scale metabolic model of Arabidopsis and some of its properties. Plant Physiol 151:1570–1581

    Article  PubMed  CAS  Google Scholar 

  6. Williams TC, Poolman MG, Howden AJ et al (2010) A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions. Plant Physiol 154:311–323

    Article  PubMed  CAS  Google Scholar 

  7. de Oliveira Dal'Molin CG, Quek LE, Palfreyman RW et al (2010) AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis. Plant Physiol 152:579–589

    Article  PubMed  Google Scholar 

  8. Radrich K, Tsuruoka Y, Dobson P et al (2010) Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMC Systems Biol 4:114

    Article  Google Scholar 

  9. Kleessen S, Araujo WL, Fernie AR, Nikoloski Z (2012) Model-based confirmation of alternative substrates of mitochondrial electron transport chain. J Biol Chem 287:11122–11131

    Article  PubMed  CAS  Google Scholar 

  10. Grafahrend-Belau E, Schreiber F, Koschutzki D, Junker BH (2009) Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol 149:585–598

    Article  PubMed  CAS  Google Scholar 

  11. Rolletschek H, Melkus G, Grafahrend-Belau E et al (2011) Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm. Plant Cell 23:3041–3054

    Article  PubMed  CAS  Google Scholar 

  12. Grafahrend-Belau E, Junker A, Eschenröder A, Müller J, Schreiber F, Junker BH (2013) Multiscale metabolic modeling: dynamic flux balance analysis on a whole plant scale. Plant Physiol [Epub ahead of print]

    Google Scholar 

  13. Dal'Molin CG, Quek LE, Palfreyman RW et al (2010) C4GEM, a genome-scale metabolic model to study C4 plant metabolism. Plant Physiol 154:1871–1885

    Article  PubMed  Google Scholar 

  14. Saha R, Suthers PF, Maranas CD (2011) Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PLoS One 6:e21784

    Article  PubMed  CAS  Google Scholar 

  15. Schwender J, Hay JO (2012) Predictive modeling of biomass component tradeoffs in Brassica napus developing oilseeds based on in silico manipulation of storage metabolism. Plant Physiol 160:1218–1236

    Article  PubMed  CAS  Google Scholar 

  16. Boyle NR, Morgan JA (2009) Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii. BMC Syst Biol 3:4

    Article  PubMed  Google Scholar 

  17. Cogne G, Rugen M, Bockmayr A et al (2011) A model-based method for investigating bioenergetic processes in autotrophically growing eukaryotic microalgae: application to the green algae Chlamydomonas reinhardtii. Biotechnol Prog 27:631–640

    Article  PubMed  CAS  Google Scholar 

  18. Dal‘Molin CG, Quek LE, Palfreyman RW, Nielsen LK (2011) AlgaGEM—a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome. BMC Genomics 12(Suppl 4):S5

    Article  PubMed  Google Scholar 

  19. Knoop H, Zilliges Y, Lockau W, Steuer R (2010) The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. Plant Physiol 154:410–422

    Article  PubMed  CAS  Google Scholar 

  20. Montagud A, Navarro E, Fernandez de Cordoba P, Urchueguia JF, Patil KR (2010) Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC Syst Biol 4:156

    Article  PubMed  Google Scholar 

  21. Becker SA, Feist AM, Mo ML et al (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox. Nat Protoc 2:727–738

    Article  PubMed  CAS  Google Scholar 

  22. Schellenberger J, Que R, Fleming RM et al (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat protoc 6:1290–1307

    Article  PubMed  CAS  Google Scholar 

  23. Thiele I, Palsson BO (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5:93–121

    Article  PubMed  CAS  Google Scholar 

  24. Edwards JS, Ramakrishna R, Palsson BO (2002) Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng 77:27–36

    Article  PubMed  CAS  Google Scholar 

  25. Amthor JS (2010) From sunlight to phytomass: on the potential efficiency of converting solar radiation to phyto-energy. New Phytol 188:939–959

    Article  PubMed  CAS  Google Scholar 

  26. Amthor JS (2000) The McCree±de Wit±Penning de Vries±Thornley respiration paradigms: 30 years later. Ann Bot 86:1–20

    Article  CAS  Google Scholar 

  27. Klamt S, Stelling J, Ginkel M, Gilles ED (2003) FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 19:261–269

    Article  PubMed  CAS  Google Scholar 

  28. Grafahrend-Belau E, Klukas C, Junker BH, Schreiber F (2009) FBA-SimVis: interactive visualization of constraint-based metabolic models. Bioinformatics 25:2755–2757

    Article  PubMed  CAS  Google Scholar 

  29. Wright J, Wagner A (2008) The systems biology research tool: evolvable open-source software. BMC Syst Biol 2:55

    Article  PubMed  Google Scholar 

  30. Urbanczik R (2006) SNA—a toolbox for the stoichiometric analysis of metabolic networks. BMC Bioinformatics 7:129

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Leibniz-Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK), Gatersleben, Germany

    Eva Grafahrend-Belau, Astrid Junker & Falk Schreiber

  2. Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany

    Falk Schreiber

  3. Clayton School of Information Technology, Monash University, Clayton, VIC, Australia

    Falk Schreiber

  4. Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

    Björn H. Junker

Authors
  1. Eva Grafahrend-Belau
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Astrid Junker
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Falk Schreiber
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Björn H. Junker
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. INRA Bordeaux Université Bordeaux Segalen, Villenave d'Ornon, France

    Martine Dieuaide-Noubhani

  2. Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA

    Ana Paula Alonso

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer Science+Business Media, New York

About this protocol

Cite this protocol

Grafahrend-Belau, E., Junker, A., Schreiber, F., Junker, B.H. (2014). Flux Balance Analysis as an Alternative Method to Estimate Fluxes Without Labeling. In: Dieuaide-Noubhani, M., Alonso, A. (eds) Plant Metabolic Flux Analysis. Methods in Molecular Biology, vol 1090. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-688-7_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-688-7_17

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-687-0

  • Online ISBN: 978-1-62703-688-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation