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BIOMD0000000067 - Fung2005_Metabolic_Oscillator

 

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Reference Publication
Publication ID: 15875027
Fung E, Wong WW, Suen JK, Bulter T, Lee SG, Liao JC.
A synthetic gene-metabolic oscillator.
Nature 2005 May; 435(7038): 118-122
Department of Chemical Engineering, University of California-Los Angeles, Los Angeles, California 90095, USA.  [more]
Model
Original Model: BIOMD0000000067.origin
Submitter: Harish Dharuri
Submission ID: MODEL6624231052
Submission Date: 31 Aug 2006 16:19:30 UTC
Last Modification Date: 16 May 2012 10:20:40 UTC
Creation Date: 28 Aug 2006 08:43:27 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:occursIn Taxonomy Escherichia coli (strain K12)
set #2
bqbiol:isVersionOf Gene Ontology carbon catabolite regulation of transcription
Notes

A Synthetic Gene-Metabolic Oscillator

Reference: Fung et al; Nature (2005) 435:118-122
Name of kinetic law Reaction
Glycolytic flux, V_gly: nil -> AcCoA;
Flux to TCA cycle/ETOH, V_TCA: AcCoA -> TCA/EtOH;
HOAc ex/import,reversible, V_out: HOAc -> HOAc_E
V_Pta: AcCoA + Pi -> AcP + CoA
reversible, V_Ack: AcP + ADP -> OAc + ATP
V_Acs: OAC + ATP -> AcCoA +PPi
Acetic acid-base equillibrium, reversible, V_Ace: OAC + H -> HOAc
Expression of LacI, R_LacI: nil -> LacI
Expression of Acs, R_Acs: nil -> Acs
Expression of Pta, R_Pta: nil -> Pta
LacI degradation, R_dLacI: LacI -> nil
Acs degradation, R_dAcs: Acs -> nil
Pta degradation, R_dPta: Pta -> nil

For this model the differential equation for V_Ace was changed from:
C*(AcP*H-K_eq*OAC) with C = 100 in the supplemental material
to C*(OAc*H-K_eq*HOAc) with C = 100, as in Bulter et. al; PNAS(2004),101,2299-2304 , and a value for K_eq of 5*10^-4 after communication with the authors.

translated to SBML by:
Lukas Endler(luen at tbi.univie.ac.at), Christoph Flamm (xtof at tbi.univie.ac.at)

Biomodels Curation The model reproduces 3a of the paper for glycolytic flux Vgly = 0.5. The authors have agreed that the values on Y-axis are marked wrong and hence there is a discrepancy between model simulation results and the figure. Also, note that the values of concentration and time are in dimensionless units. The model was successfully tested on MathSBML and Jarnac.

Model
Publication ID: 15875027 Submission Date: 31 Aug 2006 16:19:30 UTC Last Modification Date: 16 May 2012 10:20:40 UTC Creation Date: 28 Aug 2006 08:43:27 UTC
Mathematical expressions
Reactions
Glycolytic flux Flux to TCA cycle Intercellular transport of Acetate Phosphate acetyl transferase flux
Acetate kinase Acetyl-CoA synthase flux Acid-base equilibrium LacI synthesis
Acetyl-CoA synthase synthesis Phosphate acetyl transferase synthase LacI degradation Acs degradation
Pta degradation      
Physical entities
Compartments Species
Intracellular Acetyl-CoA Acetyl phosphate Acetate
protonated acetate lac repressor Acetyl-CoA synthase
Phosphate acetyl transferase acetate export  
Global parameters
S0 kTCA k1 KM1
k2 KM2 kAck_f kAck_r
C H Keq k3
alpha0 alpha1 alpha2 alpha3
Kg1 Kg2 Kg3 n
kd      
Reactions (13)
 
 Glycolytic flux  → [Acetyl-CoA];  
 
 Flux to TCA cycle [Acetyl-CoA] → ;  
 
 Intercellular transport of Acetate [protonated acetate] ↔ [acetate export];  
 
 Phosphate acetyl transferase flux [Acetyl-CoA] → [Acetyl phosphate];   {Phosphate acetyl transferase}
 
 Acetate kinase [Acetyl phosphate] ↔ [Acetate];  
 
 Acetyl-CoA synthase flux [Acetate] → [Acetyl-CoA];   {Acetyl-CoA synthase}
 
 Acid-base equilibrium [Acetate] ↔ [protonated acetate];  
 
 LacI synthesis  → [lac repressor];   {Acetyl phosphate}
 
 Acetyl-CoA synthase synthesis  → [Acetyl-CoA synthase];   {Acetyl phosphate}
 
 Phosphate acetyl transferase synthase  → [Phosphate acetyl transferase];   {lac repressor}
 
 LacI degradation [lac repressor] → ;  
 
 Acs degradation [Acetyl-CoA synthase] → ;  
 
 Pta degradation [Phosphate acetyl transferase] → ;  
 
 Intracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 Acetyl-CoA
Compartment: Intracellular
Initial concentration: 0.0
 
 Acetyl phosphate
Compartment: Intracellular
Initial concentration: 0.0
 
 Acetate
Compartment: Intracellular
Initial concentration: 0.0
 
 protonated acetate
Compartment: Intracellular
Initial concentration: 0.0
 
 lac repressor
Compartment: Intracellular
Initial concentration: 0.0
 
 Acetyl-CoA synthase
Compartment: Intracellular
Initial concentration: 0.0
 
 Phosphate acetyl transferase
Compartment: Intracellular
Initial concentration: 0.0
 
 acetate export
Compartment: Intracellular
Initial concentration: 0.0
 
Global Parameters (21)
 
   S0
Value: 0.5
Constant
 
   kTCA
Value: 10.0
Constant
 
   k1
Value: 80.0
Constant
 
   KM1
Value: 0.06
Constant
 
   k2
Value: 0.8
Constant
 
   KM2
Value: 0.1
Constant
 
   kAck_f
Value: 1.0
Constant
 
   kAck_r
Value: 1.0
Constant
 
   C
Value: 100.0
Constant
 
   H
Value: 1.0E-7
Constant
 
   Keq
Value: 5.0E-4
Constant
 
   k3
Value: 0.01
Constant
 
   alpha0
Constant
 
   alpha1
Value: 0.1
Constant
 
   alpha2
Value: 2.0
Constant
 
   alpha3
Value: 2.0
Constant
 
   Kg1
Value: 10.0
Constant
 
   Kg2
Value: 10.0
Constant
 
   Kg3
Value: 0.0010
Constant
 
   n
Value: 2.0
Constant
 
   kd
Value: 0.06
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000067

Curator's comment: (updated: 19 Dec 2006 00:17:59 GMT)

The plot corresponds to Fig 3a for Vgly=0.5. There is a slight discrepancy between the model result and the plot in the publication. The authors have endorsed the result obtained by model simulation as being the right one. Simulation result with Jarnac.

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