Proteome analysis: d-fuc / l-glu

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SEEK ID: https://fairdomhub.org/assays/275

Class: Experimental Assay

Submitter: Theresa Kouril

Projects: SulfoSys - Biotec

Investigation: L-fucose degradation in Sulfolobus solfataricus P2

Study: Comparison of S. solfataricus grown on l-fucose and d-glucose

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Assay type: Proteomics

Technology type: Tandem Mass Spectrometry

Organisms: Sulfolobus solfataricus (batch)

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Creators and Submitter

Creators

Theresa Kouril
Phil Wright
Trong Khoa Pham

Submitter

Theresa Kouril

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Views: 3752

Created: 5th Feb 2015 at 13:42

Last updated: 8th Nov 2017 at 15:21

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People (3)
Programmes (1)
Projects (1)
Investigations (1)
Studies (1)
Data files (1)
SOPs (1)
Publications (1)

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Theresa Kouril

Projects: SulfoSys, SulfoSys - Biotec, Glucose metabolism in cancer cell lines

Institutions: University Duisburg-Essen, Stellenbosch University

Expertise: Biochemistry, carbon metabolism, Carbohydrate Metabolism of Archaea, functional protein expression, Glycolysis, Microbiology, Molecular Biology, Systems Biology

Tools: Biochemistry, Molecular Biology, Enzyme assays

Trong Khoa Pham

Projects: SulfoSys, SulfoSys - Biotec

Institutions: University of Sheffield

Expertise: Proteomics, Saccharomyces cerevisiae, Sulfolobus solfataricus

Tools: shotgun proteomics, iTRAQ for quantitative proteomics

Phil Wright

Projects: SulfoSys, SulfoSys - Biotec

Institutions: University of Sheffield

Expertise: Bioinformatics, Proteomics, bioreactor models, biochemical

Tools: Biochemistry and protein analysis, Protein chemical methods (protein overproduction, Proteomics (2D-PAGE), Computational Systems Biology, Proteomics (Glycoproteins), shotgun proteomics

I am the foundation Professor of Systems Biology and Engineering within the Department of Chemical and Process Engineering (CPE), at The University of Sheffield. My research philosophy is centred on a mechanistic systems biology approach to solve biochemical reaction engineered processes. I wish to pursue issues involved in the effective utilisation of biological resources. The approach is specifically targeted at the conjunction of chemical engineering (metabolic engineering and synthetic biology), ...

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e:Bio

e:Bio - Innovations Competition Systems Biology

Projects: SulfoSys - Biotec, SBEpo - Systems Biology of Erythropoietin

Web page: http://www.fona.de/en/14276

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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/

Organisms: Sulfolobus solfataricus

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L-fucose degradation in Sulfolobus solfataricus P2

SulfoSys - Biotec

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Theresa Kouril

Jacqueline Wolf

Dietmar Schomburg

Helge Stark

Phil Wright

Trong Khoa Pham

Stefan Albaum

Sonja-Verena Albers

Bettina Siebers

Katharina Kruse

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

Submitter: Theresa Kouril

Studies: Comparison of S. solfataricus grown on l-fucose and d-glucose

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

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Created: 25th Aug 2014 at 14:07, Last updated: 20th Oct 2016 at 08:23

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Comparison of S. solfataricus grown on l-fucose and d-glucose

SulfoSys - Biotec

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Theresa Kouril

Stefan Albaum

Sonja-Verena Albers

Katharina Kruse

Trong Khoa Pham

Dietmar Schomburg

Bettina Siebers

Helge Stark

Jacqueline Wolf

Phil Wright

No description specified

Submitter: Theresa Kouril

Investigation: L-fucose degradation in Sulfolobus solfataricus P2

Snapshots: No snapshots

Created: 25th Aug 2014 at 14:28, Last updated: 20th Oct 2016 at 09:31

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Proteomics L-fuc vs D-glc

SulfoSys - Biotec

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Jacqueline Wolf

Trong Khoa Pham

Phil Wright

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

Creators: Jacqueline Wolf, Trong Khoa Pham, Phil Wright

Submitter: Jacqueline Wolf

Relationship type: Not specified

Investigations: L-fucose degradation in Sulfolobus solfataricus P2

Studies: Comparison of S. solfataricus grown on l-fucose...

Assays: Proteome analysis: d-fuc / l-glu

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Created: 1st Aug 2016 at 11:28, Last updated: 20th Oct 2016 at 08:23

Views: 4616, Downloads: 172

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SULFOSYSbiotech_Proteome analysis

SulfoSys - Biotec

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Theresa Kouril

Phil Wright

Trong Khoa Pham

Protein extraction, iTRAQ labeling, peptides separation, mass spectrometry and data analysis

Creators: Theresa Kouril, Phil Wright, Trong Khoa Pham

Submitter: Theresa Kouril

Investigations: Amino acid degradation in Sulfolobus solfataric..., L-fucose degradation in Sulfolobus solfataricus P2

Studies: Comparison of S. solfataricus grown on l-fucose..., Comparison of Sulfolobus solfataricus P2 grown ...

Assays: Proteome analysis: Casaminoacids versus D-Glc, Proteome analysis: d-fuc / l-glu

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Created: 5th Feb 2015 at 13:45, Last updated: 20th Oct 2016 at 08:23

Views: 3921, Downloads: 152

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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

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Jacqueline Wolf

Helge Stark

Andreas Albersmeier

Trong Khoa Pham

Stefan Albaum

Theresa Kouril

Phil Wright

Sonja-Verena Albers

Dietmar Schomburg

Bettina Siebers

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

PubMed ID: 27611014

Citation: Mol Microbiol. 2016 Sep 9. doi: 10.1111/mmi.13498.

Created: 19th Oct 2016 at 10:29, Last updated: 8th Dec 2022 at 18:26

Views: 5101, Downloads: 0