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

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.

Poly(hydroxyalkanoate) Production by Cupriavidus necator from Fatty Waste Can Be Enhanced by phaZ1 Inactivation

“…The production of different kinds of PHAs by C. necator using several inexpensive feedstock, including glycerol, has been recently reported 18,19,20,21,22 , indicating that some strains of this bacterial species could be used for the conversion of fatty residues into PHA. As an alternative, the use of costly commercial enzymes or genetic modification of microorganisms exhibiting high PHA product yields would be required 23 .…”

Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies

“…Implementing the tools EFMs, YSA, and a high structured metabolic modelling, Lopar and associated colleagues have analyzed the five-step cascadic continuous chemostat production of PHB by C. necator DSM 545 on glucose , as well as glycerol metabolism pathways in fed-batch cultures of the same organism (Lopar et al 2014). These works constitute extensions of previously developed formal kinetic and low structured models Š poljarić et al 2013a, b).…”

Mathematical Modelling as a Tool for Optimized PHA Production

“…Lopar and associated colleagues analyzed the five-step continuous production of PHB on glucose 115 as well as glycerol metabolism pathways by C. necator DSM 545 116 , respectively. Elementary flux modes, yield space analysis and a high-structured metabolic model were used as tools.…”

“…For analyzing metabolic pathways of C. necator DSM 545 when growing on glycerol, a model with a metabolic network consisting of 48 reactions was established in order to describe intracellular processes and PHB production 116 . Special attention was devoted to the branching points in sugar metabolism pathways, direction of reversible reactions, fluxes in gluconeogenesis route, and to the possible coenzymes (NAD or FAD) involved in the glycerol-3-P-dehydrogenase (GLY-3-P DH) reaction.…”