Growth on D-glucose served as reference scenario
SEEK ID: https://fairdomhub.org/assays/404
Projects: SulfoSys - Biotec
Investigation: Amino acid degradation in Sulfolobus solfataricus P2
Biological problem addressed: Genome Scale
Organisms: Sulfolobus solfataricus
Created: 7th Aug 2016 at 19:19
Last updated: 18th Oct 2018 at 11:38
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)
Integrated systems biology approach including transcriptome, metabolome, proteome analyses and modelling to elucidate amino acid degradation in S. solfataricus P2.
Snapshots: No snapshots
To investigate amino acid degradation pathways in Sulfolobus solfataricus transcriptome, proteome and metabolome analyses were performed on cells grown on caseinhydrolysate as carbon source. Cells grown with glucose served as reference condition. Metabolic modelling was used to compare the efficiency of different degradation routes.
Person responsible: Jacqueline Wolf
Snapshots: No snapshots
The distribution of enzymes involved in oxidative Stickland reactions among archaea was estimated using BLAST searches (BLOSUM62) with the protein sequences of acetate-CoA ligase (EC 184.108.40.206, ACS), ketoisovalerate oxidoreductase (EC 220.127.116.11, BC-OR) and indolepyruvate oxdoreductase (EC 18.104.22.168, AR-OR) from Pyrococcus furiosus (Pfu) and Sulfolobus solfataricus (Sso) against all archaea. Positive results are indicated by a '+' (homologue found, e-value 1e-20).
The calculation of amino acid uptake rates for cells of Sulfolobus solfataricus P2 grown on caseinhydrolysate was performed based on the relative consumption of individual amino acids from the growth medium and the previously published absolute concentration of amino acids in the used growth medium.
Protein, RNA and DNA content during the logarithmic growth phase were investigated in this study. The values represent the average of at least three independent experiments. Errors represent the standard deviation between the experiments.
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.
Creator: Helge Stark
Contributor: Helge Stark
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Organism: Sulfolobus solfataricus
Investigations: Amino acid degradation in Sulfolobus solfataric...
Modelling analyses: Metabolic modelling of S. solfataricus during g...