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BIOMD0000000245 - Lei2001_Yeast_Aerobic_Metabolism

 

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Reference Publication
Publication ID: 11434967
Lei F, Rotbøll M, Jørgensen SB.
A biochemically structured model for Saccharomyces cerevisiae.
J. Biotechnol. 2001 Jul; 88(3): 205-221
CAPEC, Department of Chemical Engineering, Building 229, Technical University of Denmark, DK-2800 Kgs., Lyngby, Denmark.  [more]
Model
Original Model: BIOMD0000000245.origin
Submitter: Lukas Endler
Submission ID: MODEL1003250000
Submission Date: 25 Mar 2010 01:27:37 UTC
Last Modification Date: 03 Jun 2010 10:40:01 UTC
Creation Date: 25 Mar 2010 02:28:31 UTC
Encoders:  Lukas Endler
set #1
bqbiol:hasVersion KEGG Pathway sce00010
KEGG Pathway sce00020
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
set #2
bqbiol:hasVersion Gene Ontology tricarboxylic acid cycle
Gene Ontology glucose metabolic process
Notes

This the model from the article:
A biochemically structured model for Saccharomyces cerevisiae.
Lei F, Rotbøll M, Jørgensen SB. J Biotechnol. 2001 Jul 12;88(3):205-21. PMID: 11434967 ,DOI: 10.1016/S0168-1656(01)00269-3

Abstract:
A biochemically structured model for the aerobic growth of Saccharomyces cerevisiae on glucose and ethanol is presented. The model focuses on the pyruvate and acetaldehyde branch points where overflow metabolism occurs when the growth changes from oxidative to oxido-reductive. The model is designed to describe the onset of aerobic alcoholic fermentation during steady-state as well as under dynamical conditions, by triggering an increase in the glycolytic flux using a key signalling component which is assumed to be closely related to acetaldehyde. An investigation of the modelled process dynamics in a continuous cultivation revealed multiple steady states in a region of dilution rates around the transition between oxidative and oxido-reductive growth. A bifurcation analysis using the two external variables, the dilution rate, D, and the inlet concentration of glucose, S(f), as parameters, showed that a fold bifurcation occurs close to the critical dilution rate resulting in multiple steady-states. The region of dilution rates within which multiple steady states may occur depends strongly on the substrate feed concentration. Consequently a single steady state may prevail at low feed concentrations, whereas multiple steady states may occur over a relatively wide range of dilution rates at higher feed concentrations.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use .
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 11434967 Submission Date: 25 Mar 2010 01:27:37 UTC Last Modification Date: 03 Jun 2010 10:40:01 UTC Creation Date: 25 Mar 2010 02:28:31 UTC
Mathematical expressions
Reactions
glycolysis TCA (pyruvate) Pyruvate Dehydrogenase Acetald. dehydrogenase
TCA (acetate) ADH BM growth (gluc) BM growth (acetate)
Acdh production active BM degradation Acdh degradation Glucose inflow
Glucose outflow Pyruvate outflow Acetate outflow Acetaldehyde outflow
EtOH outflow active BM outflow BM outflow AcDH BM outflow
Rules
Assignment Rule (variable: BM(active)) Assignment Rule (variable: BM(AcDH)) Rate Rule (variable: X_a) Rate Rule (variable: X_AcDH)
Assignment Rule (variable: qO2) Assignment Rule (variable: qCO2)    
Physical entities
Compartments Species
environment Glucose Pyruvate Acetate
Acetaldehyde EtOH BM
BM(active) BM(AcDH) CO2
Red. Equ. (NADH) Glucose(feed)  
cell      
Global parameters
qO2 qCO2 X_a X_AcDH
k_1h K_1h k_1l K_1l
k_1e K_1e K_1i k_2
K_2 K_2i k_3 K_3
k_4 K_4 k_5 K_5
k_5e K_5e K_5i k_6
K_6 k_6r K_6e k_7
K_7 k_8 k_9 K_9
k_9e K_9e K_9i k_9c
k_10 K_10 k_10e K_10e
k_11 Dilutionrate    
Reactions (20)
 
 glycolysis [Glucose] → 0.978 × [Pyruvate] + 0.178 × [Red. Equ. (NADH)];   {Acetaldehyde} , {BM}
 
 TCA (pyruvate) [Pyruvate] → 1.499 × [CO2] + 0.908 × [Red. Equ. (NADH)];   {BM} , {Glucose}
 
 Pyruvate Dehydrogenase [Pyruvate] → 0.5 × [Acetaldehyde] + 0.33 × [CO2];   {BM}
 
 Acetald. dehydrogenase [Acetaldehyde] → 1.363 × [Acetate] + 0.363 × [Red. Equ. (NADH)];   {BM} , {EtOH}
 
 TCA (acetate) [Acetate] → 1.446 × [CO2] + 1.066 × [Red. Equ. (NADH)];   {BM} , {Glucose}
 
 ADH [Acetaldehyde] + 0.363 × [Red. Equ. (NADH)] ↔ 1.045 × [EtOH];   {BM}
 
 BM growth (gluc) [Glucose] → 0.732 × [BM] + 0.127 × [CO2] + 0.063 × [Red. Equ. (NADH)];   {BM}
 
 BM growth (acetate) [Acetate] → 0.619 × [BM] + 0.325 × [CO2] + 0.214 × [Red. Equ. (NADH)];   {BM} , {Glucose}
 
 Acdh production [BM(active)] → [BM(AcDH)];   {BM} , {Glucose} , {EtOH}
 
 active BM degradation [BM(active)] → ;   {BM} , {Glucose} , {EtOH}
 
 Acdh degradation [BM(AcDH)] → ;   {BM}
 
 Glucose inflow [Glucose(feed)] → [Glucose];  
 
 Glucose outflow [Glucose] → ;  
 
 Pyruvate outflow [Pyruvate] → ;  
 
 Acetate outflow [Acetate] → ;  
 
 Acetaldehyde outflow [Acetaldehyde] → ;  
 
 EtOH outflow [EtOH] → ;  
 
 active BM outflow [BM(active)] → ;  
 
 BM outflow [BM] → ;  
 
 AcDH BM outflow [BM(AcDH)] → ;  
 
Rules (6)
 
 Assignment Rule (name: a) BM(active) = x*X_a
 
 Assignment Rule (name: AcDH) BM(AcDH) = x*X_AcDH
 
 Rate Rule (name: X_a) d [ X_a] / d t= ((0.732*r7+0.619*r8)*(1-X_a)-r9-r10)/(x*env)
 
 Rate Rule (name: X_AcDH) d [ X_AcDH] / d t= (r9-r11-(0.732*r7+0.619*r8)*X_AcDH)/(x*env)
 
 Assignment Rule (name: qO2) qO2 = 1000/32*(0.178*r1+0.908*r2+0.363*r4+1.066*r5-0.363*r6+0.063*r7+0.214*r8)/(x*env)
 
 Assignment Rule (name: qCO2) qCO2 = 1000/44.01*(1.499*r2+0.5*r3+1.466*r5+0.127*r7+0.325*r8)/(x*env)
 
 environment Spatial dimensions: 3.0  Compartment size: 1.0
 
 Glucose
Compartment: environment
Initial concentration: 15.0
 
 Pyruvate
Compartment: environment
Initial concentration: 0.0
 
 Acetate
Compartment: environment
Initial concentration: 0.0
 
 Acetaldehyde
Compartment: environment
Initial concentration: 0.0
 
 EtOH
Compartment: environment
Initial concentration: 0.0
 
 BM
Compartment: environment
Initial concentration: 0.0020
 
  BM(active)
Compartment: environment
Initial concentration: 0.0
 
  BM(AcDH)
Compartment: environment
Initial concentration: 0.0
 
 CO2
Compartment: environment
Initial concentration: 0.0
 
 Red. Equ. (NADH)
Compartment: environment
Initial concentration: 0.0
 
 Glucose(feed)
Compartment: environment
Initial concentration: 15.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
Global Parameters (42)
 
   qO2  
 
   qCO2  
 
   X_a
Value: 0.1   (Units: dimensionless)
 
   X_AcDH
Value: 0.0075   (Units: dimensionless)
 
   k_1h
Value: 0.584   (Units: gram per liter per hour)
Constant
 
   K_1h
Value: 0.0116   (Units: gram per liter)
Constant
 
   k_1l
Value: 1.43   (Units: gram per liter per hour)
Constant
 
   K_1l
Value: 0.94   (Units: gram per liter)
Constant
 
   k_1e
Value: 47.1   (Units: gram per liter per hour)
Constant
 
   K_1e
Value: 0.12   (Units: gram per liter)
Constant
 
   K_1i
Value: 14.2   (Units: liter per gram)
Constant
 
   k_2
Value: 0.501   (Units: gram per liter per hour)
Constant
 
   K_2
Value: 2.0E-5   (Units: gram per liter)
Constant
 
   K_2i
Value: 0.101   (Units: liter per gram)
Constant
 
   k_3
Value: 5.81   (Units: gram per liter per hour)
Constant
 
   K_3
Value: 5.0E-7   (Units: gram per liter)
Constant
 
   k_4
Value: 4.8   (Units: gram per liter per hour)
Constant
 
   K_4
Value: 2.64E-4   (Units: gram per liter)
Constant
 
   k_5
Value: 0.0104   (Units: gram per liter per hour)
Constant
 
   K_5
Value: 0.0102   (Units: gram per liter)
Constant
 
   k_5e
Value: 0.775   (Units: gram per liter per hour)
Constant
 
   K_5e
Value: 0.1   (Units: gram per liter)
Constant
 
   K_5i
Value: 440.0   (Units: liter per gram)
Constant
 
   k_6
Value: 2.82   (Units: gram per liter per hour)
Constant
 
   K_6
Value: 0.034   (Units: gram per liter)
Constant
 
   k_6r
Value: 0.0125   (Units: dimensionless)
Constant
 
   K_6e
Value: 0.057   (Units: gram per liter)
Constant
 
   k_7
Value: 1.203   (Units: gram per liter per hour)
Constant
 
   K_7
Value: 0.0101   (Units: gram per liter)
Constant
 
   k_8
Value: 0.589   (Units: gram per liter per hour)
Constant
 
   k_9
Value: 0.0080   (Units: gram per liter per hour)
Constant
 
   K_9
Value: 1.0E-6   (Units: gram per liter)
Constant
 
   k_9e
Value: 0.0751   (Units: gram per liter per hour)
Constant
 
   K_9e
Value: 13.0   (Units: gram per liter)
Constant
 
   K_9i
Value: 25.0   (Units: liter per gram)
Constant
 
   k_9c
Value: 0.00399   (Units: gram per liter per hour)
Constant
 
   k_10
Value: 0.392   (Units: gram per liter per hour)
Constant
 
   K_10
Value: 0.0023   (Units: gram per liter)
Constant
 
   k_10e
Value: 0.00339   (Units: gram per liter per hour)
Constant
 
   K_10e
Value: 0.0018   (Units: gram per liter)
Constant
 
   k_11
Value: 0.02   (Units: gram per liter per hour)
Constant
 
   Dilutionrate
Value: 0.1   (Units: per hour)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000245

Curator's comment: (updated: 25 Mar 2010 02:28:01 GMT)

Reproduction of some results from fig 3 and 4 of the article. Steady state calculations over the indicated range of D, the dilution rate, with a Glucose concentration in the feeding solution (S_f) of 15 g/l with were performed using the parameter scan task of Copasi (v4.5 build 31).

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