L-fucose degradation in Sulfolobus solfataricus P2
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Integrated systems biology approach including transcriptome, metabolome, biochemistry, proteome analyses and modelling to elucidate the catabolic pathway for L-fucose in S. solfataricus P2.
SEEK ID: https://fairdomhub.org/investigations/57
Projects: SulfoSys - Biotec
Investigation position:
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Creators and SubmitterCreators
Theresa Kouril
Jacqueline Wolf
Dietmar Schomburg- Helge Stark
Phil Wright
Trong Khoa Pham- Stefan Albaum
Sonja-Verena Albers
Bettina Siebers
Katharina Kruse
Additional credit
Andreas Albersmeier, Jörn Kalinowski
Submitter
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Created: 25th Aug 2014 at 12:07
Last updated: 20th Oct 2016 at 06:23
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Head of the group of Molecular Enzyme Technology and Biochemistry (Faculty of Chemistry) at the University of Duisburg-Essen. My research interest is on archaeal physiology with a special focuss on the central carbohydrate metabolism of (hyper)thermophilic Archaea and its regulation. The aim is to gain a systems level understanding by the combination of modern highthrouput analyses with classical biochemistry and molecular biology. Archaea possess many novel enzymes and pathways and our aim is ...
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e:Bio - Innovations Competition Systems Biology
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Web page: http://www.fona.de/en/14276
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) ...
Programme: e:Bio
Public web page: http://www.sulfosys.com/
Submitter: Theresa Kouril
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Assays: Cell free extract activity measurements: L-fuc/d-glc, Metabolic model of Sulfolobus solfataricus, Proteome analysis: d-fuc / l-glu, RNA sequencing:l-fuc/d-glu, intracellular metabolome analysis: l-fucose vs d-glucose
Submitter: Theresa Kouril
Assay type: RNA-seq Profiling
Technology type: Next generation sequencing
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Submitter: Theresa Kouril
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Submitter: Theresa Kouril
Assay type: Proteomics
Technology type: Tandem Mass Spectrometry
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Submitter: Jacqueline Wolf
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
Genome scale metabolic model of Sulfolobus solfataricus specific scenario: modelling of L-fucose degradation pathways
Submitter: Jacqueline Wolf
Biological problem addressed: Metabolic Network
Investigation: L-fucose degradation in Sulfolobus solfataricus P2
RNAseq analysis of S. solfataricus grown on either L-fucose or D-glucose
Creators: Jacqueline Wolf, Theresa Kouril, Andreas Albersmeier, Jörn Kalinowski
Submitter: Jacqueline Wolf
Activity assays in cell free extracts of S. solfataricus grown on either L-fucose or D-glucose and activity assays with recombinant proteins
Creators: Jacqueline Wolf, Katharina Kruse, Bettina Siebers, Theresa Kouril
Submitter: Jacqueline Wolf
Comparative GC-MS based metabolomics of S. solfataricus growing on either L-fucose or D-glucose. CoA derivatives were analysed via HPLC-MS
Creators: Jacqueline Wolf, Dietmar Schomburg
Submitter: Jacqueline Wolf
Comparative proteomics of S. solfatricus grown on either L-fucose or D-glucose.
Creators: Jacqueline Wolf, Trong Khoa Pham, Phil Wright
Submitter: Jacqueline Wolf
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.
Creators: Jacqueline Wolf, Helge Stark, Dietmar Schomburg
Submitter: Jacqueline Wolf
Model type: Metabolic network
Model format: SBML
Environment: Not specified
Creators: Theresa Kouril, Andreas Albersmeier, CeBiTech, University Bielefeld, Germany; Jörn Kalinowski, CeBiTech, University Bielefeld;
Submitter: Theresa Kouril
Protein extraction, iTRAQ labeling, peptides separation, mass spectrometry and data analysis
Creators: Theresa Kouril, Phil Wright, Trong Khoa Pham
Submitter: Theresa Kouril
Abstract (Expand)
Authors: J. Wolf, H. Stark, K. Fafenrot, A. Albersmeier, T. K. Pham, K. B. Muller, B. Meyer, L. Hoffmann, L. Shen, S. P. Albaum, T. Kouril, K. Schmidt-Hohagen, M. Neumann-Schaal, C. Brasen, J. Kalinowski, P. C. Wright, S. V. Albers, D. Schomburg, B. Siebers
Date Published: 10th Sep 2016
Publication Type: Not specified
