SBML model of yeast central carbon metabolism
Version 1

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The model includes glycolysis, pentosephosphate pathway, purine salvage reactions, purine de novo synthesis, redox balance and biomass growth. The network balances adenylate pool as opened moiety.

SEEK ID: https://fairdomhub.org/models/85?version=1

1 item is associated with this Model:

MOSES SBML model.xml (SBML and XML document - 14.9 KB)

Organism: Saccharomyces cerevisiae

Model type: Metabolic network

Model format: SBML

Execution or visualisation environment: Copasi

Model image: No image specified

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Creators and Submitter

Creator

Maksim Zakhartsev

Submitter

Maksim Zakhartsev

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Views: 6734 Downloads: 0

Created: 16th Oct 2012 at 13:23

Last updated: 16th Oct 2012 at 13:26

Version History

Version 1 (earliest) Created 16th Oct 2012 at 13:23 by Maksim Zakhartsev

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Studies (1)
Assays (1)
Publications (2)

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Maksim Zakhartsev

Projects: MOSES, ExtremoPharm, ZucAt, GenoSysFat, DigiSal, EraCoBiotech 2 nd call proposal preparation, FAIRDOM & LiSyM & de.NBI Data Structuring Training

Institutions: University of Stuttgart, University of Hohenheim, Norwegian University of Life Sciences, Norwegian University of Science and Technology

https://orcid.org/0000-0002-7973-9902

Expertise: Biochemistry, coupling metabolome and environome, rapid sampling experiments, Systems Biology, carbon metabolism, Stoichiometric modelling, Proteomics, Metabolomics, yeast, fungi, Dynamics and Control of Biological Networks

Tools: Biochemistry and protein analysis, Metabolomics, Matlab, Fermentation, Chromatography, Material balance based modeling, stimulus response experiments, continuous cultivation, Enzyme assay, Mass spectrometry (LC-MS/MS), HPLC, GC and LC/MS analysis of metabolites, ODE, Parameter estimation

I've become a SysMO DB PAL for MOSES project in 2007 being a post-doc in lab of Prof. Matthias Reuss at University of Stuttgart. In the MOSES project, our major efforts were in the experimental data acquisition for dynamic model of primary carbon and anaerobic energy metabolism in yeast. The model implements prediction of perturbations of two types: glucose pulse and temperature jump. We implement “stimulus-response” methodology for the unraveling the dynamic structure of the network and to ...

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SysMO

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

The goal pursued by SysMO was 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, SysMO Funders, SilicoTryp, Noisy-Strep

Web page: http://sysmo.net/

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MOSES

MOSES (Micro Organism Systems biology: Energy and Saccharomyces cerevisiae) develops a new Systems Biology approach, which is called 'domino systems biology'. It uses this to unravel the role of cellular free energy ('ATP') in the control and regulation of cell function. MOSES operates though continuous iterations between partner groups through a new systems-biology driven data-management workflow. MOSES also tries to serve as a substrate for three or more other SYSMO programs.

Programme: SysMO

Public web page: http://www.moses.sys-bio.net/

Organisms: Saccharomyces cerevisiae

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Kinetic analysis of metabolic system using transient perturbations

MOSES

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Maksim Zakhartsev

Investigation of dynamics of the central metabolism (glycolysis, PPP, anaplerotic reactions, purines) of yeast Saccharomyces cerevisiae in anaerobic conditions

Submitter: Maksim Zakhartsev

Studies: Metabolic perturbation of the steady state culture by glucose pulse

Assays: Biomass weight during glucose pulse, Cellular size and granularity during glucose pulse, Dynamics of extracellular metabolites during glucose pulse, Dynamics of intracellular metabolites during glucose pulse, Dynamics of macromolecules during glucose pulse, MOSES: dynamic model of glucose pulse

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Created: 2nd Mar 2010 at 21:05, Last updated: 22nd Nov 2011 at 19:12

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Metabolic perturbation of the steady state culture by glucose pulse

MOSES

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Maksim Zakhartsev

The steady state anaerobic culture (D = 0.1 h-1) was pertrubed by sudden increase of the extracellular glucose up to 1 g/L and both extra- and intracellular transient metabolite concentrations were measured

Submitter: Maksim Zakhartsev

Investigation: Kinetic analysis of metabolic system using tran...

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Created: 2nd Mar 2010 at 22:01, Last updated: 22nd Nov 2011 at 19:12

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MOSES: dynamic model of glucose pulse

MOSES

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Maksim Zakhartsev

The dynamic model describes response of yeast metabolic network on metabolic perturbation (i.e. glucose-pulse). One compartmental ODE-based model of yeast anaerobic metabolism includes: glycolysis, pentose phosphate reactions, purine de novo synthesis pathway, purine salvage reactions, redox reactions and biomass growth. The model describes metabolic perturbation of steady state growing cells in chemostat.

Submitter: Maksim Zakhartsev

Biological problem addressed: Metabolic Network

Investigation: Kinetic analysis of metabolic system using tran...

Study: Metabolic perturbation of the steady state cult...

Organisms: Saccharomyces cerevisiae : CEN.PK113-7D haploid (wild-type / wild-type)

Models: SBML model of yeast central carbon metabolism

SOPs: No SOPs

Data files: Dynamics of extracellular metabolites during gl..., Dynamics of intracellular metabolites during gl..., Measured steady state concentrations of extrace..., Measured steady state concentrations of intrace..., Measured steady state metabolic fluxes, Off-gas monitoring during glucose pulse

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Created: 4th Mar 2011 at 10:13, Last updated: 8th Nov 2017 at 14:21

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Fast sampling for quantitative microbial metabolomics: new aspects on cold methanol quenching: metabolite co-precipitation

MOSES

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Maksim Zakhartsev

Matthias Reuss

Abstract (Expand)

The intra- and extracellular concentrations of 16 metabolites were measured in chemostat (D = 0.1 h−1) anaerobic cultures of the yeast Saccharomyces cerevisiae CEN.PK-113-7D growing on minimal medium. … Two independent sampling workflows were employed: (i) conventional cold methanol quenching and (ii) a differential approach. Metabolites were quantified in different sample fractions (total, extracellular, quenching supernatant, methanol/water extract and pellet) in order to derive their mass balance. The differential method in combination with absolute metabolite quantification by gas-chromatography with isotope dilution mass spectrometry (GC–IDMS) was used as a benchmark to assess quality of the cold methanol quenching procedure. Quantitative comparison of metabolite concentrations in all fractions collected by different quenching techniques indicates asystematic loss of the total mass of various metabolites in course of the cold methanol quenching. Pellet resulting from the cold methanol quenching besides biomass contains considerable amounts of precipitated inorganic salts from the fermentation media. Quantitative analysis has revealed significant co-precipitation of polar extracellular metabolites together with these salts. This phenomenon is especially significant for metabolites with large extracellular mass-fraction. We report that the co-precipitation is a hitherto neglected phenomenon and concluded that its degree strongly linked to culturing conditions (i.e. media composition) and chemical properties of the particular metabolite. Thus, intracellular metabolite levels measured from samples collected by cold methanol quenching might be uncertain and variably biased due to corruption by described phenomena.

Authors: Maksim Zakhartsev, Oliver Vielhauer, Thomas Horn, Xuelian Yang, Matthias Reuss

Date Published: 1st Apr 2015

Publication Type: Not specified

DOI: 10.1007/s11306-014-0700-8

Citation: Metabolomics 11(2) : 286

Created: 1st Nov 2015 at 17:50, Last updated: 8th Dec 2022 at 17:26

‘Domino’ systems biology and the ‘A’ of ATP

MOSES

Abstract (Expand)

We develop a strategic ‘domino’ approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to … explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in ATP upon glucose addition, (ii) the lack of increase in ADP when ATP is hydrolyzed, and (iii) the rapid disappearance of the ‘A’ (adenine) moiety of ATP. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of AMP explains. Cycling of the ‘A’ moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the ‘A’ component of ATP.

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Date Published: 1st Sep 2012

Publication Type: Not specified

DOI: 10.1016/j.bbabio.2012.09.014

Citation:

Created: 16th Oct 2012 at 08:40, Last updated: 8th Dec 2022 at 17:26

SBML model of yeast central carbon metabolism Version 1

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Version History

Version 1 (earliest) Created 16th Oct 2012 at 13:23 by Maksim Zakhartsev

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SBML model of yeast central carbon metabolism
Version 1