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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:** 3012

**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

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

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

**Person responsible**: Jacky Snoep

**Snapshots: **No snapshots

**Scales:**
Not specified

Experimental analysis of pathway fluxes with varying PGK and FBPAase concentrations in the incubation assay.

**Contributor**: Jacky Snoep

**Assay type**: Extracellular Metabolite Concentration

**Technology type**: Progressive Curve Experiment

**Snapshots: **No snapshots

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

**Study:** Pathway optimisation

**Organisms**: Sulfolobus solfataricus : P2 (wild-type / wild-type)

**SOPs:** No SOPs

**Data files:** FBPAase titration of reconstituted system, Model simulation and experimental data for PGK ..., PGK titration of reconstituted system

**Scales:**
Not specified

Varying the relative amounts of PGK and FBPAase and analyse the 3PG uptake and F6P production rates.

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

**Study:** Pathway optimisation

**Organisms**: Sulfolobus solfataricus : P2 (wild-type / wild-type)

**Models:** Mathematical model for the combined four enzyme...

**SOPs:** No SOPs

**Data files:** FBPAase titration of reconstituted system, Model simulation and experimental data for PGK ..., PGK titration of reconstituted system, Pathway efficiency for 3PG to F6P conversion as...

**Scales:**
Not specified

Mathematical model for the reconstituted system with PGK, GAPDH, TPI and FBPAase.

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

**Study:** Carbon loss at high T

**Organisms**: Sulfolobus solfataricus : P2 (wild-type / wild-type)

**Models:** Mathematical model for the combined four enzyme...

**SOPs:** No SOPs

**Data files:** Metabolite concentrations during reconstituted ..., Model simulation and Exp data for reconstituted...

**Scales:**
Not specified

The four purified enzymes were incubated in assay buffer and consumption of 3PG and production of F6P were measured in time, together with GAP and DHAP concentrations.

**Contributor**: Jacky Snoep

**Assay type**: Experimental Assay Type

**Technology type**: Progressive Curve Experiment

**Snapshots: **No snapshots

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

**Study:** Carbon loss at high T

**Organisms**: Sulfolobus solfataricus : P2 (wild-type / wild-type)

**SOPs:** No SOPs

**Data files:** Metabolite concentrations during reconstituted ..., Model simulation and Exp data for reconstituted...

**Scales:**
Not specified

Mathematical model for the analysis of carbon loss of BPG, GAP and DHAP in reconstituted system of S. solfataricus at 70C.

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

**Study:** Model gluconeogenesis

**Organisms**: Sulfolobus solfataricus : P2 (wild-type / wild-type)

**Models:** Mathematical model for the combined four enzyme...

**SOPs:** No SOPs

**Data files:** Metabolite concentrations during reconstituted ...

**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

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

Increasing the amount of PGK in the incubation assay and measuring the 3PG and F6P fluxes.

**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

A time simulation of the mathematical model is shown together with the experimental data to which the model was fitted.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

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

**Studies:** Model gluconeogenesis

**Scales:**
Not specified

A time simulation of the mathematical model is shown together with the experimental data to which the model was fitted.

**Creator: **Jacky Snoep

**Contributor**: Jacky Snoep

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

**Studies:** Model gluconeogenesis

**Scales:**
Not specified

Mathematical model for TIM kinetics, GAP and DHAP saturation and PEP inhibition.

**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:** TPI modeling

**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

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

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

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

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

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

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

**Abstract** (Expand)

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

**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