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Dietmar Schomburg

About Dietmar Schomburg:
No description specified

SEEK ID: https://fairdomhub.org/people/66

Location:  Germany

Expertise: Microbiology, Biochemistry, Bioinformatics, Data Management, Systems Biology, Bacterial metabolism | Metabolic engineering

Tools: Not specified

ORCID: Not specified

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SulfoSys - Biotec

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/

PSYSMO

Systems analysis of process-induced stresses: towards a quantum increase in process performance of Pseudomonas putida as the cell factory of choice for white biotechnology.

The specific goal of this project is to exploit the full biotechnological efficacy of Pseudomonas putida KT2440 by developing new optimization strategies that increase its performance through a systems biology understanding of key metabolic and regulatory parameters that control callular responses to key stresses generated
...

Programme: SysMO

Public web page: http://www.psysmo.org/

SulfoSys

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

Programme: SysMO

Public web page: http://sulfosys.com/

University of Braunschweig

Country:  Germany

City: Not specified

Web page: Not specified

Phenol degradation in Saccharolobus solfataricus P2
SulfoSys - Biotec

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
...

Snapshots: No snapshots

Amino acid degradation in Sulfolobus solfataricus P2
SulfoSys - Biotec

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

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L-fucose degradation in Sulfolobus solfataricus P2
SulfoSys - Biotec

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

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Comparison of S. solfataricus P2 grown on phenol vs D-glucose
SulfoSys - Biotec

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.

Person responsible: Jacqueline Wolf

Snapshots: No snapshots

Comparison of Sulfolobus solfataricus P2 grown on caseinhydrolysate and D-glucose
SulfoSys - Biotec

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

Comparison of S. solfataricus grown on l-fucose and d-glucose
SulfoSys - Biotec
No description specified

Person responsible: Theresa Kouril

Snapshots: No snapshots

Metabolome analysis: phenol vs D-glucose
SulfoSys - Biotec
No description specified

Submitter: Jacqueline Wolf

Assay type: Experimental Assay Type

Technology type: Gas Chromatography

Snapshots: No snapshots

Metabolome analysis: Casaminoacids versus D-Glc
SulfoSys - Biotec

Intracellular and extracellular metabolome analysis

Submitter: Jacqueline Wolf

Assay type: Metabolite Profiling

Technology type: Gas Chromatography Mass Spectrometry

Snapshots: No snapshots

Metabolic modelling of S. solfataricus during growth on casaminoacids
SulfoSys - Biotec

Growth on D-glucose served as reference scenario

Submitter: Jacqueline Wolf

Biological problem addressed: Genome Scale

Snapshots: No snapshots

intracellular metabolome analysis: l-fucose vs d-glucose
SulfoSys - Biotec
No description specified

Submitter: Theresa Kouril

Assay type: Metabolite Profiling

Technology type: Gas Chromatography Mass Spectrometry

Snapshots: No snapshots

Metabolic model of Sulfolobus solfataricus
SulfoSys - Biotec

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

Submitter: Jacqueline Wolf

Biological problem addressed: Metabolic Network

Snapshots: No snapshots

Amino acid depletion profile of S. solfataricus during growth on 1 % casaminoacids
SulfoSys - Biotec

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

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Metabolomics Casaminoacids vs Glc
SulfoSys - Biotec

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

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Metabolomics L-fuc vs D-glc
SulfoSys - Biotec

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

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Metabolic model of Sulfolobus solfataricus
SulfoSys - Biotec

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

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Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus.
SulfoSys, SulfoSys - Biotec

Abstract (Expand)

Sulfolobus solfataricus is a thermoacidophilic Archaeon that thrives in terrestrial hot springs (solfatares) with optimal growth at 80 degrees C and pH 2-4. It catabolizes specific carbon sources, such … as D-glucose, to pyruvate via the modified Entner-Doudoroff (ED) pathway. This pathway has two parallel branches, the semi-phosphorylative and the non-phosphorylative. However, the strategy of S.solfataricus to endure in such an extreme environment in terms of robustness and adaptation is not yet completely understood. Here, we present the first dynamic mathematical model of the ED pathway parameterized with quantitative experimental data. These data consist of enzyme activities of the branched pathway at 70 degrees C and 80 degrees C and of metabolomics data at the same temperatures for the wild type and for a metabolic engineered knockout of the semi-phosphorylative branch. We use the validated model to address two questions: 1. Is this system more robust to perturbations at its optimal growth temperature? 2. Is the ED robust to deletion and perturbations? We employed a systems biology approach to answer these questions and to gain further knowledge on the emergent properties of this biological system. Specifically, we applied deterministic and stochastic approaches to study the sensitivity and robustness of the system, respectively. The mathematical model we present here, shows that: 1. Steady state metabolite concentrations of the ED pathway are consistently more robust to stochastic internal perturbations at 80 degrees C than at 70 degrees C; 2. These metabolite concentrations are highly robust when faced with the knockout of either branch. Connected with this observation, these two branches show different properties at the level of metabolite production and flux control. These new results reveal how enzyme kinetics and metabolomics synergizes with mathematical modelling to unveil new systemic properties of the ED pathway in S.solfataricus in terms of its adaptation and robustness.

Authors: A. S. Figueiredo, T. Kouril, D. Esser, P. Haferkamp, P. Wieloch, D. Schomburg, P. Ruoff, B. Siebers, J. Schaber

Date Published: 12th Jul 2017

Publication Type: Not specified

Oxidative Stickland reactions in an obligate aerobic organism - amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus
SulfoSys - Biotec

Abstract (Expand)

The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adaptation to extreme environments and renowned for its ability to degrade a broad variety of substrates. It … has been well characterised concerning the utilisation of numerous carbohydrates as carbon source. However, its amino acid metabolism, especially the degradation of single amino acids, is not as well understood. In this work, we performed metabolic modelling as well as metabolome, transcriptome and proteome analysis on cells grown on caseinhydrolysate as carbon source in order to draw a comprehensive picture of amino acid metabolism in S. solfataricus P2. We found that 10 out of 16 detectable amino acids are imported from the growth medium. Overall, uptake of glutamate, methionine, leucine, phenylalanine and isoleucine was the highest of all observed amino acids. Our simulations predict an incomplete degradation of leucine and tyrosine to organic acids, and in accordance with this, we detected the export of branched-chain and aromatic organic acids as well as amino acids, ammonium and trehalose into the culture supernatants. The branched-chain amino acids as well as phenylalanine and tyrosine are degraded to organic acids via oxidative Stickland reactions. Such reactions are known for prokaryotes capable of anaerobic growth, but so far have never been observed in an obligate aerobe. Also, 3-methyl-2-butenoate and 2-methyl-2-butenoate are for the first time found as products of modified Stickland reactions for the degradation of branched-chain amino acids. This work presents the first detailed description of branched-chain and aromatic amino acid catabolism in S. solfataricus.

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

A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose
SulfoSys - Biotec

Abstract (Expand)

Archaea are characterised by a complex metabolism with many unique enzymes that differ from their bacterial and eukaryotic counterparts. The thermoacidophilic archaeon Sulfolobus solfataricus is known … for its metabolic versatility and is able to utilize a great variety of different carbon sources. However, the underlying degradation pathways and their regulation are often unknown. In this work, we analyse growth on different carbon sources using an integrated systems biology approach. The comparison of growth on L-fucose and D-glucose allows first insights into the genome-wide changes in response to the two carbon sources and revealed a new pathway for L-fucose degradation in S. solfataricus. During growth on L-fucose we observed major changes in the central carbon metabolic network, as well as an increased activity of the glyoxylate bypass and the 3-hydroxypropionate/4-hydroxybutyrate cycle. Within the newly discovered pathway for L-fucose degradation the following key reactions were identified: (i) L-fucose oxidation to L-fuconate via a dehydrogenase, (ii) dehydration to 2-keto-3-deoxy-L-fuconate via dehydratase, (iii) 2-keto-3-deoxy-L-fuconate cleavage to pyruvate and L-lactaldehyde via aldolase and (iv) L-lactaldehyde conversion to L-lactate via aldehyde dehydrogenase. This pathway as well as L-fucose transport shows interesting overlaps to the D-arabinose pathway, representing another example for pathway promiscuity in Sulfolobus species. This article is protected by copyright. All rights reserved.

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

The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: highlights from a multi-level omics approach
PSYSMO

Abstract (Expand)

BACKGROUND: Pseudomonas putida KT2442 is a natural producer of polyhydroxyalkanoates (PHAs), which can substitute petroleum-based non-renewable plastics and form the basis for the production of tailor-made … biopolymers. However, despite the substantial body of work on PHA production by P. putida strains, it is not yet clear how the bacterium re-arranges its whole metabolism when it senses the limitation of nitrogen and the excess of fatty acids as carbon source, to result in a large accumulation of PHAs within the cell. In the present study we investigated the metabolic response of KT2442 using a systems biology approach to highlight the differences between single- and multiple-nutrient-limited growth in chemostat cultures. RESULTS: We found that 26, 62, and 81% of the cell dry weight consist of PHA under conditions of carbon, dual, and nitrogen limitation, respectively. Under nitrogen limitation a specific PHA production rate of 0.43 (g.(g.h)-1) was obtained. The residual biomass was not constant for dual- and strict nitrogen-limiting growth, showing a different feature in comparison to other P. putida strains. Dual limitation resulted in patterns of gene expression, protein level, and metabolite concentrations that substantially differ from those observed under exclusive carbon or nitrogen limitation. The most pronounced differences were found in the energy metabolism, fatty acid metabolism, as well as stress proteins and enzymes belonging to the transport system. CONCLUSION: This is the first study where the interrelationship between nutrient limitations and PHA synthesis has been investigated under well-controlled conditions using a system level approach. The knowledge generated will be of great assistance for the development of bioprocesses and further metabolic engineering work in this versatile organism to both enhance and diversify the industrial production of PHAs.

Authors: , I. F. Escapa, C. Jager, J. Puchalka, , , ,

Date Published: 20th Mar 2012

Publication Type: Not specified

"Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus
SulfoSys

Abstract (Expand)

Within the archaea, the thermoacidophilic crenarchaeote Sulfolobus solfataricus has become an important model organism for physiology and biochemistry, comparative and functional genomics, as well as, … more recently also for systems biology approaches. Within the Sulfolobus Systems Biology ("SulfoSYS")-project the effect of changing growth temperatures on a metabolic network is investigated at the systems level by integrating genomic, transcriptomic, proteomic, metabolomic and enzymatic information for production of a silicon cell-model. The network under investigation is the central carbohydrate metabolism. The generation of high-quality quantitative data, which is critical for the investigation of biological systems and the successful integration of the different datasets, derived for example from high-throughput approaches (e.g., transcriptome or proteome analyses), requires the application and compliance of uniform standard protocols, e.g., for growth and handling of the organism as well as the "-omics" approaches. Here, we report on the establishment and implementation of standard operating procedures for the different wet-lab and in silico techniques that are applied within the SulfoSYS-project and that we believe can be useful for future projects on Sulfolobus or (hyper)thermophiles in general. Beside established techniques, it includes new methodologies like strain surveillance, the improved identification of membrane proteins and the application of crenarchaeal metabolomics.

Authors: , Dominik Esser, , , , , , Julia Reimann, , , Daniela Teichmann, Marleen van Wolferen, , , , , , , , , ,

Date Published: 31st Aug 2009

Publication Type: Not specified

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