Sulfolobus solfataricus

Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Within the e:Bio - Innovationswettbewerb Systembiologie (Federal Ministry of Education and Research (BMBF)), the SulfoSYSBIOTECH consortium (10 partners), aim to unravel the complexity and regulation of the carbon metabolic network of the thermoacidophilic archaeon Sulfolobus solfataricus (optimal growth at 80°C and pH 3) in order to provide new catalysts ‘extremozymes’ for utilization in White Biotechnology.

Based on the available S. solfataricus genome scale metabolic model (Ulas et al., 2012) ...

The pilot experiment was conducted in order to create SOPs and to gain insight in transcriptome of cells grown at 70 and 80C

Samples obtained form the central fermentation facility of Sulfosys have been compared using iTRAQ (isobaric tag for relative and absolute quantification). A pilot experiment resulted in creation of SOP and initial data on cells grown at 70 and 80C

In order to get uniform data from all geographically separated partners in a consortium, central fermentation facility has been set-up. Based on empirical data, standard procedures for growing S. solfataricus cells have been developed.

Based on initial cell material, series of SOPs connected with assays of enzymes involved in Central Carbon Metabolism of S. solfataricus have been developed.

Pilot experiment concerning metabolome of S. solfataricus was conducted in order to acquire SOPs regarding the technique and gain insight on differences in metabolite concentrations at 70 and 80C

Kinetic characterisation of phosphoglycerate kinase

Mathematical model for PGK kinetics, saturation with ADP, ATP, 3PG and BPG.

Kinetic characterisation of glyceraldehyde 3-phosphate dehydrogenase

In vitro reconstitution of the PGK, GAPHD, TPI and FBPAase enzymes from S. solfataricus

Model prediction of the conversion of 3PG to fructose-6-phosphate and the gluconeogenic pathway intermediates. https://jjj.bio.vu.nl/models/experiments/kouril3_experiment-user/simulate

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

Kinetic characterisation of triose phosphate isomerase

Mathematical model for TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP

Kinetic characterisation of fructose 1,6-bisphosphate aldolase phosphatase

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

Temperature degradation of BPG, GAP and DHAP

Modelling the degradation of BPG, GAP and DHAP at high temperature

Experimental data for the conversion of 3PG to F6P and the gluconeogenic pathway intermediates

PGK model for S. solfataricus

PGK-GAPDH model Sulfolobus kouril8

PGK 70C SBML

Metabolic model of Sulfolobus solfataricus P2 in the SBML (sbml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or caseinhydrolysate as sole carbon source.

Metabolic model of Sulfolobus solfataricus P2 in the SBML (xml) and metano (txt, sce, fba) format. Scenarios are specific for growth on D-glucose or L-fucose as sole carbon source. Different theoretical routes of L-fucose degradation were modeled (E. coli-like, Xanthomonas-like and lactaldehyde-forming). Highest overall agreement between the model and experimental data was observed for the lactaldehyde-forming route.

Model of reconstituted gluconeogenesis system in S. solfataricus based on the individual kinetic models for PGK, GAPDH, TPI, FBPAase.

Exponential decay model of gluconeogenic intermediates

Mathematical model for TPI kinetics, GAP and DHAP saturation, and inhibition with 3PG and PEP.

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

Mathematical model for FBPAase kinetics, saturation with DHAP and GAP

Mathematical model for PGK kinetics, ADP, ATP, 3PG and BPG saturation.

The model describes the Entner-Doudoroff pathway in Sulfolobus solfataricus under temperature variation. The package contains source code written in FORTRAN as well as binaries for Mac OSX, Linux, and Windows. If compiling from source code, a FORTRAN compiler is required. On-line versions of the model are also available at: http://bioinfo.ux.uis.no/sulfosys http://jjj.biochem.sun.ac.za/sysmo/projects/Sulfo-Sys/index.html