Phosphoglycerate kinase acts as a futile cycle at high temperature
The gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate was compared at 30 C and at 70 C. At 30 C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 C, 1,3- bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. At both temperatures it was possible to convert 3-phosphoglycerate to glyceraldehyde 3-phosphate (although the latter was degraded at 70C) using phosphoglycerate kinase and glyceraldehyde 3-phosphate dehydrogenase.
SEEK ID: https://fairdomhub.org/investigations/156
Projects: SulfoSys, SulfoSys - Biotec
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Created: 27th Sep 2017 at 14:36
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https://orcid.org/0000-0003-2633-0537
Projects: SulfoSys, SulfoSys - Biotec
Institutions: University Duisburg-Essen
Projects: PSYSMO, MOSES, SysMO DB, SysMO-LAB, SulfoSys, SulfoSys - Biotec, Whole body modelling of glucose metabolism in malaria patients, FAIRDOM, Molecular Systems Biology, COMBINE Multicellular Modelling, HOTSOLUTE, Steroid biosynthesis, Yeast glycolytic oscillations
Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch, School of Computer Science, University of Manchester, Stellenbosch University
Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts ‘extremozymes’ for utilization in White Biotechnology.
Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012)
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Programme: e:Bio
Public web page: http://www.sulfosys.com/
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
PGK-GAPDH reactions were studied in vitro at 30 and 70 using yeast or Sso enzymes
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4b/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig4c/simulate
Person responsible: Theresa Kouril
Snapshots: No snapshots
PGK reaction at 30 C. Yeast PGK was incubated at 30 C, in the presence or absence of the ATP recycling system, and the conversion of 3 PG to BPG was followed.
SED-ML simulations
Fig. 1A: https://jjj.bio.vu.nl/models/experiments/kouril2017_fig1a/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
PGK reaction at 70C. Sulfolobus solfataricus PGK was incubated at 70C in presence and absence of an ATP recycling system.
Changes in metabolite concentrations was followed via 31P NMR or enzymatic analyses.
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3b/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3c/simulate
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig3d/simulate
Person responsible: Theresa Kouril
Snapshots: No snapshots
BPG produced with yeast PGK was incubated at 70 C,upon which BPG rapidly dephosphorylates to 3PG.
SED-ML:
https://jjj.bio.vu.nl/models/experiments/kouril2017_fig2b/simulate
Person responsible: Jacky Snoep
Snapshots: No snapshots
Experimental data for the yeast PGK incubations at 30C, with and without recycling of ATP.
Contributor: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: NMR
Snapshots: No snapshots
BPG degradation at 70C
Contributor: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Snapshots: No snapshots
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
A model for the PGK reaction of yeast in presence or absence of the ATP recycling reactions
BPG stability analysis
PGK 70C model
PGK - GAPDH models
incubations with yeast enzymes at 30C
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
metabolite quantification via enzymatic analysis
Creators: Theresa Kouril, Jacky Snoep
Contributor: Theresa Kouril
PGK-GAPDH model Sulfolobus kouril8
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH model yeast kouril7
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
PGK-GAPDH models yeast and Sulfolobus Fig. 4 in manuscript
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
PGK 70C model, Fig 3 in manuscript
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
PGK 70C SBML
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
BPG stability notebook
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
PGK yeast Fig1a
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Mathematica
PGK yeast with/without recycling
Creator: Jacky Snoep
Contributor: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
