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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

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**Views:** 1818

**Created**: 29th Jan 2013 at 15:09

**Last updated**: 28th May 2015 at 10:50

## Related items

- People (1)
- Projects (1)
- Studies (3)
- Assays (15+1)
- Data files (28+1)
- Models (6+1)
- SOPs (3)
- Publications (1)

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

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

**Scales:**
Not specified

Mathematical model of a subset of reactions comprising the three most temperature sensitive intermediates of the gluconeogenic pathway in S. solfataricus

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

**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

**Scales:**
Not specified

By varying the input or output flux via PGK and FBPAase manipulation respectively the pathway efficiency can be optimised.

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

**Scales:**
Not specified

Kinetic characterisation of Phosphoglycerokinase

**Contributor**: Jacky Snoep

**Assay type**: Experimental Assay Type

**Technology type**: Initial Rate Experiment

**Snapshots: **No snapshots

**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

**Scales:**
Not specified

**Contributor**: Jacky Snoep

**Assay type**: Experimental Assay Type

**Technology type**: Initial Rate Experiment

**Snapshots: **No snapshots

**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

**Scales:**
Not specified

**Contributor**: Jacky Snoep

**Assay type**: Experimental Assay Type

**Technology type**: Initial Rate Experiment

**Snapshots: **No snapshots

**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

**Scales:**
Not specified

Kinetic characterization of the FBPA/ase with respect to GAP en DHAP saturation.

**Contributor**: Jacky Snoep

**Assay type**: Experimental Assay Type

**Technology type**: Initial Rate Experiment

**Snapshots: **No snapshots

**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...

**Scales:**
Not specified

GAP and DHAP concentrations were measured over time at 70C.

**Contributor**: Jacky Snoep

**Assay type**: Experimental Assay Type

**Technology type**: Progressive Curve Experiment

**Snapshots: **No snapshots

**Investigation:** Central Carbon Metabolism of Sulfolobus solfata...

**Study:** Model gluconeogenesis

**Organisms**: No organisms

**SOPs:** No SOPs

**Data files:** T degradation DHAP, T degradation GAP

**Scales:**
Not specified

Combined plot fo the model simulations and the experimental data for the PGK and FBPAase titrations.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Pathway optimisation

**Assays:** Modelling pathway optimisation, PGK and FBPAase titrations

**Scales:**
Not specified

Model simulation showing the effect of varying PGK or FBPAase concentration on the efficiency for 3PG to F6P conversion.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Pathway optimisation

**Assays:** Modelling pathway optimisation

**Scales:**
Not specified

Experimental data for the reconstituted system are plotted together with the model prediction

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Carbon loss at high T

**Assays:** Model reconstituted system, Reconstituted system reference state

**Scales:**
Not specified

Saturation of PGK with 3PG

**Creators: **None

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Model gluconeogenesis

**Assays:** PGK, PGK modeling

**Scales:**
Not specified

**Creators: **None

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Model gluconeogenesis

**Assays:** PGK, PGK modeling

**Scales:**
Not specified

The PGK, GAPDH, TPI and FBPAase were modelled together using the individual rate equations. Closed system.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

**Model type**: Ordinary differential equations (ODE)

**Model format**: SBML

**Environment**: JWS Online

**Organism**: Sulfolobus solfataricus

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Carbon loss at high T, Model gluconeogenesis, Pathway optimisation

**Modelling analyses:** Gluconeogenic model, Model reconstituted system, Modelling pathway optimisation

**Scales:**
Not specified

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

**Contributor**: 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

**Modelling analyses:** Modelling temperature dependent degradation of ...

**Scales:**
Not specified

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

**Contributor**: 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

**Modelling analyses:** Modelling temperature dependent degradation of ...

**Scales:**
Not specified

Mathematical model for FBPAase kinetics

**Creator: **Jacky Snoep

**Contributor**: 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

**Modelling analyses:** FBPAase model

**Scales:**
Not specified

Mathematical model for GAPDH kinetics, saturation for GAP, BPG, NADP, NADPH, Pi.

**Creator: **Jacky Snoep

**Contributor**: 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

**Modelling analyses:** GAPDH modeling

**Scales:**
Not specified

Cloning and heterologous expression of gluconeogenic enzymes in E. coli

**Creators: **None

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Model gluconeogenesis

**Scales:**
Not specified

Preparation of cell free extracts of the recombinant E. coli strains expressing the respective S. solfataricus enzymes.

**Creators: **None

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Model gluconeogenesis

**Scales:**
Not specified

The recombinant enzymes were purified from the cell free extracts of E. coli expressing the respective enzymes.

**Creators: **None

**Contributor**: Jacky Snoep

**Investigations:** Central Carbon Metabolism of Sulfolobus solfata...

**Studies:** Model gluconeogenesis

**Scales:**
Not specified

**Abstract** (Expand)

**Authors: **Jacky Snoep, Kouril T.,Esser D.,Kort J.,Westerhoff H. V.,Siebers B.

**Date Published**: 22nd Aug 2013

**Journal**: FEBS J

**PubMed ID**: 23865479

**Citation**: FEBS J. 2013 Sep;280(18):4666-80. doi: 10.1111/febs.12438. Epub 2013 Aug 22.

**Scales:**
Not specified