An investigation in the CCM of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.
SEEK ID: https://demo.fairdomhub.org/investigations/6
Projects: SulfoSys
Investigation position:
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Created: 29th Jan 2013 at 14:09
Last updated: 28th May 2015 at 08:50
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- Publications (1)
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO is to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB
Web page: http://sysmo.net/
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
Public web page: http://sulfosys.com/
Organisms: Sulfolobus solfataricus
Submitter: Jacky Snoep
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Assays: Model reconstituted system, Reconstituted system reference state
Snapshots: No snapshots
Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus
Submitter: Jacky Snoep
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Assays: Experimental assays of the temperature dependent degradation of GAP and ..., FBPA/ase, FBPAase model, GAPDH, GAPDH modeling, Gluconeogenic model, Modelling temperature dependent degradation of GAP and DHAP, PGK, PGK modeling, TPI, TPI modeling
Snapshots: No snapshots
By varying the input or output flux via PGK and FBPAase manipulation respectively the pathway efficiency can be optimised.
Submitter: Jacky Snoep
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Assays: Modelling pathway optimisation, PGK and FBPAase titrations
Snapshots: No snapshots
Kinetic characterisation of Phosphoglycerokinase
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
SOPs: Expression of S. solfataricus enzymes in E. col..., Preparation of cell free extract of recombinant..., Protein purification from E. coli extracts.
Data files: Model simulation and experimental data for ADP,..., PGK kinetics 3PG, PGK kinetics ADP, PGK kinetics ATP, PGK kinetics BPG
Snapshots: No snapshots
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
SOPs: Expression of S. solfataricus enzymes in E. col..., Preparation of cell free extract of recombinant..., Protein purification from E. coli extracts.
Data files: GAPDH kinetics 3PG, GAPDH kinetics GAP, GAPDH kinetics NADP, GAPDH kinetics NADPH, GAPDH kinetics Pi
Snapshots: No snapshots
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
SOPs: Expression of S. solfataricus enzymes in E. col..., Preparation of cell free extract of recombinant..., Protein purification from E. coli extracts.
Data files: Model simulation and exp data for TIM kinetics,..., TPI kinetics DHAP, TPI kinetics GAP, TPI kinetics PEP inhibition GAP, TPI kinetics PEP inhibition of DHAP
Snapshots: No snapshots
Kinetic characterization of the FBPA/ase with respect to GAP en DHAP saturation.
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Initial Rate Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: Sulfolobus solfataricus : P2 (wild-type / wild-type)
SOPs: Expression of S. solfataricus enzymes in E. col..., Preparation of cell free extract of recombinant..., Protein purification from E. coli extracts.
Data files: FBPA/ase kinetics DHAP, FBPA/ase kinetics GAP, Model simulation and experimental data for DHAP...
Snapshots: No snapshots
GAP and DHAP concentrations were measured over time at 70C.
Submitter: Jacky Snoep
Assay type: Experimental Assay Type
Technology type: Progressive Curve Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model gluconeogenesis
Organisms: No organisms
SOPs: No SOPs
Data files: T degradation DHAP, T degradation GAP
Snapshots: No snapshots
Combined plot fo the model simulations and the experimental data for the PGK and FBPAase titrations.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Pathway optimisation
Assays: Modelling pathway optimisation, PGK and FBPAase titrations
Model simulation showing the effect of varying PGK or FBPAase concentration on the efficiency for 3PG to F6P conversion.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Pathway optimisation
Assays: Modelling pathway optimisation
Saturation of PGK with 3PG
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: PGK, PGK modeling
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: PGK, PGK modeling
Kinetic characterisation of Phosphoglycerokinase. Measures enzyme reaction rate with increasing concentration of ATP
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: PGK, PGK modeling
An exponential decay model was fitted to the experimental data set of GAP degradation at 70C. The model is uploaded as an SBML file. A data file showing the model fit to the experimental data set is included. The rate constant for GAP degradation at 70C was estimated to be 0.056 1/min, equivalent to a half life time of 12.4 min.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
An exponential decay model was fitted to the experimental data set of DHAP degradation at 70C. The model is uploaded as an SBML file. A data file showing the model fit to the experimental data set is included. The rate constant for DHAP degradation at 70C was estimated to be 0.0225 1/min, equivalent to a half life time of 30.8 min.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: JWS Online
Organism: Not specified
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Mathematical model for FBPAase kinetics
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: FBPAase model
Mathematical model for GAPDH kinetics, saturation for GAP, BPG, NADP, NADPH, Pi.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: GAPDH modeling
Mathematical model for TIM kinetics, GAP and DHAP saturation and PEP inhibition.
Creator: Jacky Snoep
Submitter: Jacky Snoep
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Assays: TPI modeling
Cloning and heterologous expression of gluconeogenic enzymes in E. coli
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Preparation of cell free extracts of the recombinant E. coli strains expressing the respective S. solfataricus enzymes.
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
The recombinant enzymes were purified from the cell free extracts of E. coli expressing the respective enzymes.
Creators: None
Submitter: Jacky Snoep
Investigations: Central Carbon Metabolism of Sulfolobus solfata...
Studies: Model gluconeogenesis
Abstract (Expand)
Authors: T. Kouril, D. Esser, J. Kort, H. V. Westerhoff, B. Siebers, J. L. Snoep
Date Published: 22nd Aug 2013
Publication Type: Not specified
PubMed ID: 23865479
Citation: FEBS J. 2013 Sep;280(18):4666-80. doi: 10.1111/febs.12438. Epub 2013 Aug 22.