Comparison of Sulfolobus solfataricus P2 grown on caseinhydrolysate and D-glucose
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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.
SEEK ID: https://fairdomhub.org/studies/169
Amino acid degradation in Sulfolobus solfataricus P2
Projects: SulfoSys - Biotec
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Experimentalists: Andreas Albersmeier, Trong Khoa Pham, Jacqueline Wolf Modelling: Helge Stark
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Creators and SubmitterCreators
Jacqueline Wolf- Helge Stark
Dietmar Schomburg
Trong Khoa Pham
Phil Wright
Bettina Siebers
Theresa Kouril- Stefan Albaum
Additional credit
Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)
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Created: 7th Aug 2016 at 16:10
Last updated: 18th Oct 2018 at 09:38
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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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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) ...
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Public web page: http://www.sulfosys.com/
Integrated systems biology approach including transcriptome, metabolome, proteome analyses and modelling to elucidate amino acid degradation in S. solfataricus P2.
Submitter: Jacqueline Wolf
Studies: Comparison of Sulfolobus solfataricus P2 grown on caseinhydrolysate and ...
Assays: Metabolic modelling of S. solfataricus during growth on casaminoacids, Metabolome analysis: Casaminoacids versus D-Glc, Proteome analysis: Casaminoacids versus D-Glc, RNA sequencing: Casaminoacids vs D-glc
Submitter: Jacqueline Wolf
Assay type: RNA-seq Profiling
Technology type: Rna-seq
Investigation: Amino acid degradation in Sulfolobus solfataric...
Submitter: Jacqueline Wolf
Assay type: Proteomics
Technology type: Tandem Mass Spectrometry
Investigation: Amino acid degradation in Sulfolobus solfataric...
Intracellular and extracellular metabolome analysis
Submitter: Jacqueline Wolf
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Amino acid degradation in Sulfolobus solfataric...
Growth on D-glucose served as reference scenario
Submitter: Jacqueline Wolf
Biological problem addressed: Genome Scale
Investigation: Amino acid degradation in Sulfolobus solfataric...
Reference genome of Sulfolobus solfataricus P2 used for mapping of RNA-seq results. Based on NCBI genome of Sulfolobus solfataricus.
Creators: Stefan Albaum, Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)
Submitter: Stefan Albaum
RNA-Seq raw data: Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose.
Creators: Stefan Albaum, Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)
Submitter: Stefan Albaum
RNA-Seq mapping results (part1): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).
Creators: Stefan Albaum, Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)
Submitter: Stefan Albaum
RNA-Seq mapping results (part2): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).
Creators: Stefan Albaum, Andreas Albersmeier (CeBiTec, University of Bielefeld), Jörn Kalinowski (CeBiTec, University of Bielefeld)
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Supplementary file required by main Zip archive file for file extraction.
Creators: Helge Stark, Trong Khoa Pham, Phil Wright
Submitter: Helge Stark
Cells of S. solfataricus were grown on either caseinhydrolysate or D-glucose (reference) as sole carbon source.
Creator: Helge Stark
Submitter: Helge Stark
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 6.2.1.13, ACS), ketoisovalerate oxidoreductase (EC 1.2.7.7, BC-OR) and indolepyruvate oxdoreductase (EC 1.2.7.8, 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) and negative results by a '-' (no ...
Creator: Helge Stark
Submitter: Helge Stark
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.
Creator: Helge Stark
Submitter: Helge Stark
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.
Creators: Helge Stark, Jacqueline Wolf
Submitter: Helge Stark
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.
Creators: Jacqueline Wolf, Dietmar Schomburg, Meina Neumann-Schaal, Julia Hofmann
Submitter: Jacqueline Wolf
Creator: Helge Stark
Submitter: Helge Stark
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.
Creators: Jacqueline Wolf, Dietmar Schomburg
Submitter: Jacqueline Wolf
These files contain the output results from Phenyx searching, providing all necessary information for matching MS data with protein database.
Creators: Jacqueline Wolf, Trong Khoa Pham, Phil Wright
Submitter: Jacqueline Wolf
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).
Creators: Jacqueline Wolf, Trong Khoa Pham, Phil Wright
Submitter: Jacqueline Wolf
Raw MS data files of the comparison of Sulfolobus solfataricus grown on either caseinhydrolysate or D-glucose. The numbers represents the fractions collected from the HPLC run (e.g. 22 indicates that this sample was collected from 21 min to 22 min). For MS analysis every two fractions were combined, indicated by double numbers (e.g. 80-81: combined fractions 80 and 81). Furhter all combined fractions were run twice on the MS. Zip archive. Requires the supplementary .z01, .z02 and .z03 files for ...
Creators: Helge Stark, Trong Khoa Pham, Phil Wright
Submitter: Helge Stark
Supplementary file required by main Zip archive file for file extraction.
Creators: Helge Stark, Trong Khoa Pham, Phil Wright
Submitter: Helge Stark
Supplementary file required by main Zip archive file for file extraction.
Creators: Helge Stark, Trong Khoa Pham, Phil Wright
Submitter: Helge Stark
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
Submitter: Helge Stark
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: Helge Stark, Jacqueline Wolf, Andreas Albersmeier, Trong K. Pham, Julia D. Hofmann, Bettina Siebers, Jörn Kalinowski, Phillip C. Wright, Meina Neumann-Schaal, Dietmar Schomburg
Date Published: 29th May 2017
Publication Type: Not specified
