Glycerol Synthesis Pathway

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This is a study of the glycerol synthesis pathway, using model predictions and experimental measurements

SEEK ID: https://demo.fairdomhub.org/studies/7

Investigation: Glycerol Synthesis in Saccharomyces cerevisiae

Projects: SysMO DB

Study position:

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Submitter

Katy Wolstencroft

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Views: 5783

Created: 19th Aug 2011 at 09:35

Last updated: 4th Nov 2011 at 10:06

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Assays (3)
Data files (1+1)
Models (1)
Publications (1)

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Katy Wolstencroft

Projects: SulfoSys, SysMO DB

Institutions: University of Amsterdam, School of Computer Science, University of Manchester

Expertise: Biochemistry, Bioinformatics, Data Management

Tools: Data Management, Transcriptomics, Databases, Workflows, Web services, Taverna, Ontologies

I am a Research Fellow at the University of Manchester, working in Bioinformatics and Computer Science. I am also a guest researcher at the Vrije Universiteit.My research interests include scientific workflows, semantic discovery, and applying ontology technologies to biological data

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SysMO

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO is to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB

Web page: http://sysmo.net/

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SysMO DB

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

facilitates and maximises the potential for data exchange between SysMO research groups;
maximises the ‘shelf life’ and ...

Programme: SysMO

Public web page: http://www.sysmo-db.org/

Organisms: Saccharomyces cerevisiae, Lactic Acid Bacteria

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Glycerol Synthesis in Saccharomyces cerevisiae

SysMO DB

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Katy Wolstencroft

Glycerol, a major by-product of ethanol fermentation by Saccharomyces cerevisiae, is of significant importance to the wine, beer, and ethanol production industries. This investigation aims to gain a clearer understanding of and to quantify the extent to which parameters of the pathway affect glycerol flux in S. cerevisiae.

This investigation represents the data and models submitted to JWS online by Cronwright et al (http://jjj.biochem.sun.ac.za/cgi-bin/getMoreInfo.py?modeldir=cronwright) and ...

Submitter: Katy Wolstencroft

Studies: Glycerol Synthesis Pathway

Assays: Extracellular Glycerol, Glycerol Synthesis Model construction, Intracellular Metabolites

Snapshots: No snapshots

Created: 19th Aug 2011 at 09:32, Last updated: 4th Nov 2011 at 10:06

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Glycerol Synthesis Model construction

SysMO DB

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Katy Wolstencroft

A kinetic model of the glycerol synthesis pathway has been constructed. Kinetic parameters were collected from published values. Maximal enzyme activities and intracellular effector concentrations were determined experimentally.

Submitter: Katy Wolstencroft

Biological problem addressed: Metabolism

Investigation: Glycerol Synthesis in Saccharomyces cerevisiae

Study: Glycerol Synthesis Pathway

Organisms: Saccharomyces cerevisiae

Models: Metabolic Control Analysis of Glycerol Synthesi...

SOPs: No SOPs

Data files: Cronwright Parameter Data

Snapshots: No snapshots

Created: 19th Aug 2011 at 09:23, Last updated: 26th Oct 2017 at 09:57

Extracellular Glycerol

SysMO DB

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Katy Wolstencroft

An assay to measure exttracellular glycerol using HPLC

Submitter: Katy Wolstencroft

Assay type: Metabolite Profiling

Technology type: HPLC

Investigation: Glycerol Synthesis in Saccharomyces cerevisiae

Study: Glycerol Synthesis Pathway

Organisms: Saccharomyces cerevisiae

SOPs: No SOPs

Data files: 1 hidden item

Snapshots: No snapshots

Created: 19th Aug 2011 at 10:02, Last updated: 26th Oct 2017 at 09:57

Intracellular Metabolites

SysMO DB

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Katy Wolstencroft

Intracellular metabolite concentrations were determined enzymatically by measuring the oxidation or reduction of NADH or NAD+, respectively, at 340 nm in a Beckman Coulter DU640 spectrophotometer

Submitter: Katy Wolstencroft

Assay type: Intracellular Metabolite Concentration

Technology type: Enzymatic Activity Measurements

Investigation: Glycerol Synthesis in Saccharomyces cerevisiae

Study: Glycerol Synthesis Pathway

Organisms: Saccharomyces cerevisiae

SOPs: No SOPs

Data files: Cronwright Parameter Data

Snapshots: No snapshots

Created: 19th Aug 2011 at 11:28, Last updated: 26th Oct 2017 at 09:57

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Cronwright Parameter Data

SysMO DB

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Jacky Snoep

Intracellular metabolite measurements used for validation of the gycerol synthesis pathway model

Creator: Jacky Snoep

Submitter: Katy Wolstencroft

Investigations: Glycerol Synthesis in Saccharomyces cerevisiae

Studies: Glycerol Synthesis Pathway

Assays: Glycerol Synthesis Model construction, Intracellular Metabolites

Created: 19th Aug 2011 at 11:30, Last updated: 4th Nov 2011 at 09:32

1 hidden item

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Metabolic Control Analysis of Glycerol Synthesis in Saccharomyces cerevisiae

SysMO DB

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Jacky Snoep

MCA of Glycerol Synthesis in Saccharomyces cerevisiae

Creators: Jacky Snoep, Garth R. Cronwright, Johann M. Rohwer, and Bernard A. Prior

Submitter: Katy Wolstencroft

Model type: Ordinary differential equations (ODE)

Model format: SBML

Environment: Not specified

Organism: Saccharomyces cerevisiae

Investigations: Glycerol Synthesis in Saccharomyces cerevisiae

Studies: Glycerol Synthesis Pathway

Assays: Glycerol Synthesis Model construction

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Created: 19th Aug 2011 at 09:09, Last updated: 4th Nov 2011 at 09:10

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Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae

SysMO DB

Abstract (Expand)

Glycerol, a major by-product of ethanol fermentation by Saccharomyces cerevisiae, is of significant importance to the wine, beer, and ethanol production industries. To gain a clearer understanding of … and to quantify the extent to which parameters of the pathway affect glycerol flux in S. cerevisiae, a kinetic model of the glycerol synthesis pathway has been constructed. Kinetic parameters were collected from published values. Maximal enzyme activities and intracellular effector concentrations were determined experimentally. The model was validated by comparing experimental results on the rate of glycerol production to the rate calculated by the model. Values calculated by the model agreed well with those measured in independent experiments. The model also mimics the changes in the rate of glycerol synthesis at different phases of growth. Metabolic control analysis values calculated by the model indicate that the NAD(+)-dependent glycerol 3-phosphate dehydrogenase-catalyzed reaction has a flux control coefficient (C(J)v1) of approximately 0.85 and exercises the majority of the control of flux through the pathway. Response coefficients of parameter metabolites indicate that flux through the pathway is most responsive to dihydroxyacetone phosphate concentration (R(J)DHAP= 0.48 to 0.69), followed by ATP concentration (R(J)ATP = -0.21 to -0.50). Interestingly, the pathway responds weakly to NADH concentration (R(J)NADH = 0.03 to 0.08). The model indicates that the best strategy to increase flux through the pathway is not to increase enzyme activity, substrate concentration, or coenzyme concentration alone but to increase all of these parameters in conjunction with each other.

Authors: Garth R Cronwright, Johann M Rohwer, Bernard A Prior

Date Published: 30th Aug 2002

Publication Type: Not specified

PubMed ID: 12200299

Citation:

Created: 19th Aug 2011 at 09:16, Last updated: 6th Dec 2022 at 11:21