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Pathway optimisation

Pathway optimisation

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

SEEK ID: https://demo.fairdomhub.org/studies/11

Investigation: Central Carbon Metabolism of Sulfolobus solfataricus

Projects: SulfoSys

Person responsible: Jacky Snoep

Experimentalists: Theresa Kouril

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Creators and Submitter

Creators

Not specified

Submitter

Jacky Snoep

Activity

Views: 6965

Created: 3rd Feb 2013 at 09:53

Last updated: 28th May 2015 at 08:50

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People (1)
Projects (1)
Investigations (1)
Assays (2)
Data files (4)
Models (1)
Publications (1)

Jacky Snoep

Projects: SysMO-LAB, PSYSMO, MOSES, SulfoSys, SysMO DB

Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, University of Stellenbosch

SulfoSys

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

Central Carbon Metabolism of Sulfolobus solfataricus

SulfoSys

All contributors

Jacky Snoep

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.

Snapshots: Snapshot 1

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

Assays: Experimental assays of the temperature dependent degradation of GAP and ..., FBPA/ase, FBPAase model, GAPDH, GAPDH modeling, Gluconeogenic model, Model reconstituted system, Modelling pathway optimisation, Modelling temperature dependent degradation of GAP and DHAP, PGK, PGK and FBPAase titrations, PGK modeling, Reconstituted system reference state, TPI, TPI modeling

Scales: Not specified

Created: 29th Jan 2013 at 14:09, Last updated: 28th May 2015 at 08:50

Modelling pathway optimisation

SulfoSys

All contributors

Jacky Snoep

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

Submitter: Jacky Snoep

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

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

Created: 3rd Feb 2013 at 09:56, Last updated: 26th Oct 2017 at 09:57

PGK and FBPAase titrations

SulfoSys

All contributors

Jacky Snoep

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

Submitter: 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

Created: 3rd Feb 2013 at 10:18, Last updated: 26th Oct 2017 at 09:57

Model simulation and experimental data for PGK and FBPAase titrations

SulfoSys

All contributors

Jacky Snoep

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

Scales: Not specified

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Created: 3rd Feb 2013 at 10:13, Last updated: 26th Oct 2017 at 09:57

Pathway efficiency for 3PG to F6P conversion as function of PGK or FBPAase concentration

SulfoSys

All contributors

Jacky Snoep

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

Scales: Not specified

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Created: 3rd Feb 2013 at 10:24, Last updated: 26th Oct 2017 at 09:57

PGK titration of reconstituted system

SulfoSys

All contributors

Jacky Snoep

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

Creator: Jacky Snoep

Submitter: Jacky Snoep

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Pathway optimisation

Assays: Modelling pathway optimisation, PGK and FBPAase titrations

Scales: Not specified

Download

Created: 3rd Feb 2013 at 10:03, Last updated: 28th May 2015 at 08:50

FBPAase titration of reconstituted system

SulfoSys

All contributors

Jacky Snoep

Increasing the amount of FBPAase in the reconstituted system and measuring the 3PG and F6P fluxes.

Creator: Jacky Snoep

Submitter: Jacky Snoep

Investigations: Central Carbon Metabolism of Sulfolobus solfata...

Studies: Pathway optimisation

Assays: Modelling pathway optimisation, PGK and FBPAase titrations

Scales: Not specified

Download

Created: 3rd Feb 2013 at 10:05, Last updated: 28th May 2015 at 08:50

Mathematical model for the combined four enzyme system

SulfoSys

All contributors

Jacky Snoep

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

Creator: Jacky Snoep

Submitter: 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

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Created: 6th Feb 2013 at 10:07, Last updated: 28th May 2015 at 08:50

Intermediate instability at high temperature leads to low pathway efficiency for an in vitro reconstituted system of gluconeogenesis in Sulfolobus solfataricus

SulfoSys

All contributors

Jacky Snoep

Abstract (Expand)

Four enzymes of the gluconeogenic pathway in Sulfolobus solfataricus were purified and kinetically characterized. The enzymes were reconstituted in vitro to quantify the contribution of temperature … instability of the pathway intermediates to carbon loss from the system. The reconstituted system, consisting of phosphoglycerate kinase, glyceraldehyde 3-phosphate dehydrogenase, triose phosphate isomerase and the fructose 1,6-bisphosphate aldolase/phosphatase, maintained a constant consumption rate of 3-phosphoglycerate and production of fructose 6-phosphate over a 1-h period. Cofactors ATP and NADPH were regenerated via pyruvate kinase and glucose dehydrogenase. A mathematical model was constructed on the basis of the kinetics of the purified enzymes and the measured half-life times of the pathway intermediates. The model quantitatively predicted the system fluxes and metabolite concentrations. Relative enzyme concentrations were chosen such that half the carbon in the system was lost due to degradation of the thermolabile intermediates dihydroxyacetone phosphate, glyceraldehyde 3-phosphate and 1,3-bisphosphoglycerate, indicating that intermediate instability at high temperature can significantly affect pathway efficiency.

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.

Scales: Not specified

Created: 9th Jun 2015 at 12:00