SulfoSys
Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation
Programme: SysMO
SEEK ID: https://fairdomhub.org/projects/11
Public web page: http://sulfosys.com/
Organisms: Sulfolobus solfataricus
FAIRDOM PALs: Pawel Sierocinski
Related items
Projects: SulfoSys, SulfoSys - Biotec, HOTSOLUTE
Institutions: University Duisburg-Essen, Universität Duisburg-Essen
Head of the group of Molecular Enzyme Technology and Biochemistry (Faculty of Chemistry) at the University of Duisburg-Essen. My research interest is the central carbohydrate metabolism of (hyper)thermophilic Archaea and its regulation, with a special focuss on stress response. The aim is to gain a systems level understanding by the combination of modern highthrouput analyses with classical biochemistry and molecular biology.
Projects: SulfoSys, FAIRDOM user meeting, Service to Milano-Bicocca with respect to their ATP-ROS model (Active NOW), Make Me My Model, Service to University of Lisbon (Portugal) with respect to their CFTR maturation model (Active NOW), Service to LCSB (Luxembourg) with respect to ROS management in Parkinson’s disease and cancer model (Active NOW), Service to URV Tarragona, Spain with respect to their Safety Assessment of Endocrine Disrupting Chemicals model (Active NOW), Service to Universidade Católica Portugues with respect to their Molecular Insight into Autism Spectrum Disorder (ASD) model (Active NOW), Service to Slovenia with respect to their Protease signaling network in neurodegeneration model (Active NOW), Service to University of Duisburg- Essen (Germany): with respect to their The Yin-Yang of Metabolism; Endometatoxicity (YYME) model (Active NOW), Service to Sheffield University (UK): with respect to Mitochondrial perfect adaptation model (Active NOW), Service to Sanquin (Amsterdam): with respect to Modelling of acute and chronic inflammation (Prospective), Service to Munich (Germany): with respect toCharged peptide to charged membrane binding model (Prospective), Training Hunfeld, EraCoBiotech 2 nd call proposal preparation (e.g. Glycon ), ROS detailed model for MSB manucript
Institutions: University of Amsterdam, VU University Amsterdam, Infrastructure Systems Biology Europe
Executive director of ISBE.NL
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
Projects: SulfoSys
Institutions: Wageningen University & Research
Projects: PSYSMO, SulfoSys, SulfoSys - Biotec
Institutions: University of Braunschweig
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
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An investigation in the central carbon metabolism of S. solfataricus with a focus on the unique temperature adaptations and regulation; using a combined modelling and experimental approach.
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The Sulfolobus systems biology (‘‘SulfoSYS’’)-project represented the first (hyper-)thermophilic Systems Biology project, funded within the European trans-national research initiative ‘‘Systems Biology of Microorganisms’’. Within the SulfoSYS-project, focus lies on studying the effect of temperature variation on the central carbohydrate metabolism (CCM) of S. solfataricus that is characterized by the branched Entner–Doudoroff (ED)-like pathway for sugar (glucose, galactose) degradation and the
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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
Carbon loss due to instability of gluconeogenic pathway intermediates (BPG, GAP, DHAP) at high temperature in S. solfataricus
Person responsible: Jacky Snoep
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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
The pilot experiment has been set up in order to develop uniform SOPs for the Sulfosys consortium. It comprises proteomics, transcriptomics, metabolomics as well as enzymatic essays. Cells for all the members of the consortium have been obtained from the same batch fermentations according to fermentation SOP of Sulfosys. The pilot resulted in creating a procedures for all the techniques used in consortium.
Person responsible: Pawel Sierocinski
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
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Changes in metabolite concentrations were either quantified via 31P NMR or enzymatically
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: NMR
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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
Contributor: Theresa Kouril
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Snapshots: No snapshots
Kinetic characterisation of glyceraldehyde 3-phosphate dehydrogenase
Contributor: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Snapshots: No snapshots
Simulation results of TPI experimental data for GAP and DHAP saturation.
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
DownloadSimulation results of temperature degradation of gluconeogenic intermediates
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
Simulation results of experimental data of the reconstituted gluconeogenic system
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.
Creator: Jacky Snoep
Contributor: Jacky Snoep
Simulation results of FBPAase of experimental data for DHAP and GAP saturation
Creator: Jacky Snoep
Contributor: Jacky Snoep
Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
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
Preparation of cell free extracts of the recombinant E. coli strains expressing the gluconeogenic S. solfataricus enzymes.
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
Cloning and heterologous expression of gluconeogenic enzymes from S. solfataricus in E. coli
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
Purification of gluconeogenic enzymes from S. solfataricus in recombinant E.coli extracts
Creators: Jacky Snoep, Theresa Kouril
Contributor: Jacky Snoep
SOPs related with medium composition, fermentation and stocking of S. solfataricus.
Creator: Pawel Sierocinski
Contributor: Pawel Sierocinski
Standard procedure regarding intracellular metabolome analysis using GC-MS.
Creator: Pawel Sierocinski
Contributor: Pawel Sierocinski
Protocol for RNA isolation, cDNA synthesis and labeling and hybridization and cleanup of Sulfolobus solfataricus microarray
Creator: Pawel Sierocinski
Contributor: Pawel Sierocinski
Standard operating procedures regarding iTraq based proteomics.
Creator: Pawel Sierocinski
Contributor: Pawel Sierocinski
Abstract (Expand)
Authors: Sofia Figueiredo, Theresa Kouril, Patrick Haferkamp, Patricia Wieloch, Dietmar Schomburg, Peter Ruoff, Bettina Siebers, Jörg Schaber, Esser D.
Date Published: 12th Jul 2017
Journal: PLoS One
Abstract (Expand)
Authors: Theresa Kouril, Hans Westerhoff, Bettina Siebers, Jacky Snoep, Esser Dominik,Kort Julia
Date Published: 20th Jul 2013
Journal: FEBS J.
Abstract (Expand)
Authors: Melanie Zaparty, Susanne Gertig, Patrick Haferkamp, Theresa Kouril, Andrea Manica, Trong Khoa Pham, Kerstin Schreiber, Pawel Sierocinski, Mathias Von Jan, Patricia Wieloch, Sonja-Verena Albers, Arnold Driessen, Hans-Peter Klenk, Christa Schleper, Dietmar Schomburg, John Van Der Oost, Phil Wright, Bettina Siebers, Esser Dominik,Reimann Julia,Teichmann Daniela,van Wolferen Marleen
Date Published: 31st Aug 2009
Journal: Extremophiles
Abstract (Expand)
Authors: None
Date Published: 4th Dec 2009
Journal: J. Proteome Res.
