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Study of metabolic network of Cupriavidus necator DSM 545 growing on glycerol by applying elementary flux modes and yield space analysis

  • Markan Lopar
  • Ivna Vrana Špoljarić
  • Nikolina Cepanec
  • Martin KollerEmail author
  • Gerhart Braunegg
  • Predrag Horvat
Biocatalysis

Abstract

A metabolic network consisting of 48 reactions was established to describe intracellular processes during growth and poly-3-hydroxybutyrate (PHB) production for Cupriavidus necator DSM 545. Glycerol acted as the sole carbon source during exponential, steady-state cultivation conditions. Elementary flux modes were obtained by the program Metatool and analyzed by using yield space analysis. Four sets of elementary modes were obtained, depending on whether the pair NAD/NADH or FAD/FADH2 contributes to the reaction of glycerol-3-phosphate dehydrogenase (GLY-3-P DH), and whether 6-phosphogluconate dehydrogenase (6-PG DH) is present or not. Established metabolic network and the related system of equations provide multiple solutions for the simultaneous synthesis of PHB and biomass; this number of solutions can be further increased if NAD/NADH or FAD/FADH2 were assumed to contribute in the reaction of GLY-3-P DH. As a major outcome, it was demonstrated that experimentally determined yields for biomass and PHB with respect to glycerol fit well to the values obtained in silico when the Entner–Doudoroff pathway (ED) dominates over the glycolytic pathway; this is also the case if the Embden–Meyerhof–Parnas pathway dominates over the ED.

Keywords

Cupriavidus necator Elementary flux modes Glycerol PHB Yield space analysis 

Notes

Acknowledgments

This work was financially supported by the Collaborative EU-FP7 project ANIMPOL (“Biotechnological conversion of carbon containing wastes for eco-efficient production of high added value products”; Grant agreement No.: 245084). We are thankful to Dr. Matthias Raberg and Prof. Alexander Steinbüchel (UNI Münster), Dr. Anja Pöhlein and Prof. Rolf Daniel (UNI Göttingen) for useful information provided.

Conflict of interest

All authors have agreed to submit the manuscript to the Journal of Industrial Microbiology and Biotechnology. The authors declare no conflict of interest.

Supplementary material

10295_2014_1439_MOESM1_ESM.doc (52 kb)
Online resource 1: ESM 1.doc (Metabolic reactions, list of chemical reactions for established metabolic network). (DOC 51 kb)
10295_2014_1439_MOESM2_ESM.doc (154 kb)
Online resource 2: ESM 2.doc (List of mass balance equations for established metabolic network). (DOC 153 kb)
10295_2014_1439_MOESM3_ESM.xls (47 kb)
Online resource 3: ESM 3.xls (Matrix A_NAD, matrix with stoichiometric coefficients of internal metabolites in case when NAD and NADH are reactants in reaction of GLY-3-P DH). (XLS 47 kb)
10295_2014_1439_MOESM4_ESM.xls (45 kb)
Online resource 4: ESM 4.xls (Matrix A_FAD, matrix with stoichiometric coefficients of internal metabolites in case when FAD and FADH are reactants in reaction of GLY-3-P DH). (XLS 45 kb)
10295_2014_1439_MOESM5_ESM.xls (32 kb)
Online resource 5: ESM 5.xls” (Matrix B, matrix with stoichiometric coefficients of external species). (XLS 32 kb)

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Copyright information

© Society for Industrial Microbiology and Biotechnology 2014

Authors and Affiliations

  • Markan Lopar
    • 1
  • Ivna Vrana Špoljarić
    • 1
  • Nikolina Cepanec
    • 1
  • Martin Koller
    • 2
    • 3
    • 4
    Email author
  • Gerhart Braunegg
    • 3
  • Predrag Horvat
    • 1
  1. 1.Department of Biochemical Engineering, Faculty of Food Technology and BiotechnologyUniversity of ZagrebZagrebCroatia
  2. 2.Institute of Biotechnology and Biochemical EngineeringGraz University of TechnologyGrazAustria
  3. 3.ARENA, Arbeitsgemeinschaft für Ressourcenschonende and Nachhaltige TechnologienGraz University of TechnologyGrazAustria
  4. 4.Institute of ChemistryUniversity of GrazGrazAustria

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