Jacqueline Wolf

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) ...

Present in many industrial effluents and as intermediate of lignin degradation, phenol is a widespread pollutant causing serious environmental problems, due to its toxicity to animals and humans. Removal of phenol from the environment by bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation in hostile environments. We combined metabolomics and transcriptomics together with metabolic modelling to elucidate the organism’s response to growth ...

Integrated systems biology approach including transcriptome, metabolome, proteome analyses and modelling to elucidate amino acid degradation in S. solfataricus P2.

Integrated systems biology approach including transcriptome, metabolome, biochemistry, proteome analyses and modelling to elucidate the catabolic pathway for L-fucose in S. solfataricus P2.

To investigate phenol degradation in Saccharolobus solfataricus transcriptome and metabolome analyses were performed with cells grown on phenol as sole carbon source. Cells grown on D-glucose served as reference. Metabolic modelling was used to compare efficiency of phenol utilization in terms of oxygen demand and energy yield with the reference condition.

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.

Genome scale metabolic model of Sulfolobus solfataricus specific scenario: modelling of L-fucose degradation pathways

Intracellular and extracellular metabolome analysis

Growth on D-glucose served as reference scenario

The file contains the GC-MS raw data as cdf files, a sample list and an excel sheet with the results of metabolome analysis.

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.

Sulfolobus solfataricus P2 was cultivated on 1 % Caseinhydrolysate. Samples of the culture supernatants were taken at regular intervalls and analyzed by GC-MS. To evaluate the stability of amino acids under cultivation conditions an additional non-inoculated control culture was also analyzed.

Intracellular metabolome analysis of S. solfataricus P2 grown on caseinhydrolysate or D-glucose as sole carbon source. Samples were analyzed with GC-MS. CoA derivatives were analyzed with LC-MS.

These files contain the output results from Phenyx searching, providing all necessary information for matching MS data with protein database.

This file contains the results from proteome analysis of Sulfolobus solfataricus grown on Caseinhydrolysate as carbon source (growth on D-glucose served as reference condition).

RNAseq analysis of S. solfataricus grown on either L-fucose or D-glucose

Activity assays in cell free extracts of S. solfataricus grown on either L-fucose or D-glucose and activity assays with recombinant proteins

Comparative GC-MS based metabolomics of S. solfataricus growing on either L-fucose or D-glucose. CoA derivatives were analysed via HPLC-MS

Comparative proteomics of S. solfatricus grown on either L-fucose or D-glucose.

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.