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BIOMD0000000610 - Petelenz-kurdzeil2013 - Osmo adaptation gpd1D

 

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Reference Publication
Publication ID: 23762021
Petelenz-Kurdziel E, Kuehn C, Nordlander B, Klein D, Hong KK, Jacobson T, Dahl P, Schaber J, Nielsen J, Hohmann S, Klipp E.
Quantitative analysis of glycerol accumulation, glycolysis and growth under hyper osmotic stress.
PLoS Comput. Biol. 2013; 9(6): e1003084
Department of Chemistry and Molecular Biology/Microbiology, University of Gothenburg, Göteborg, Sweden.  [more]
Model
Original Model: BIOMD0000000610.origin
Submitter: Clemens Kühn
Submission ID: MODEL1204190004
Submission Date: 19 Apr 2012 15:04:39 UTC
Last Modification Date: 21 Mar 2017 16:13:58 UTC
Creation Date: 20 Apr 2016 12:45:03 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Clemens Kühn
   Ryan Gutenkunst
   Joji Teves
   Jun-young Kim
   Kotaro Fujimaki
   Virginia Valori
set #1
bqmodel:isDerivedFrom PubMed 18793130
PubMed 20563574
PubMed 16025103
PubMed 10951190
set #2
bqbiol:isVersionOf Gene Ontology cellular response to osmotic stress
set #3
bqbiol:hasTaxon Taxonomy Saccharomyces cerevisiae
Notes
Petelenz-kurdzeil2013 - Osmo adaptation gpd1D

This model is described in the article:

Petelenz-Kurdziel E, Kuehn C, Nordlander B, Klein D, Hong KK, Jacobson T, Dahl P, Schaber J, Nielsen J, Hohmann S, Klipp E.
PLoS Comput. Biol. 2013; 9(6): e1003084

Abstract:

We provide an integrated dynamic view on a eukaryotic osmolyte system, linking signaling with regulation of gene expression, metabolic control and growth. Adaptation to osmotic changes enables cells to adjust cellular activity and turgor pressure to an altered environment. The yeast Saccharomyces cerevisiae adapts to hyperosmotic stress by activating the HOG signaling cascade, which controls glycerol accumulation. The Hog1 kinase stimulates transcription of genes encoding enzymes required for glycerol production (Gpd1, Gpp2) and glycerol import (Stl1) and activates a regulatory enzyme in glycolysis (Pfk26/27). In addition, glycerol outflow is prevented by closure of the Fps1 glycerol facilitator. In order to better understand the contributions to glycerol accumulation of these different mechanisms and how redox and energy metabolism as well as biomass production are maintained under such conditions we collected an extensive dataset. Over a period of 180 min after hyperosmotic shock we monitored in wild type and different mutant cells the concentrations of key metabolites and proteins relevant for osmoadaptation. The dataset was used to parameterize an ODE model that reproduces the generated data very well. A detailed computational analysis using time-dependent response coefficients showed that Pfk26/27 contributes to rerouting glycolytic flux towards lower glycolysis. The transient growth arrest following hyperosmotic shock further adds to redirecting almost all glycolytic flux from biomass towards glycerol production. Osmoadaptation is robust to loss of individual adaptation pathways because of the existence and upregulation of alternative routes of glycerol accumulation. For instance, the Stl1 glycerol importer contributes to glycerol accumulation in a mutant with diminished glycerol production capacity. In addition, our observations suggest a role for trehalose accumulation in osmoadaptation and that Hog1 probably directly contributes to the regulation of the Fps1 glycerol facilitator. Taken together, we elucidated how different metabolic adaptation mechanisms cooperate and provide hypotheses for further experimental studies.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: 23762021 Submission Date: 19 Apr 2012 15:04:39 UTC Last Modification Date: 21 Mar 2017 16:13:58 UTC Creation Date: 20 Apr 2016 12:45:03 UTC
Mathematical expressions
Reactions
v1 v10 v10Batch v11
v11Batch v12 v12Batch v13a
v13aBatch v13b v13bBatch v14
v15f v15r v16f v16r
v17f v17r v18f v18r
v19f v19r v1Batch v2
v20f v20r v21f v21r
v22 v23f v23r v3
v4 v5 v6 v6b
v7 v8 v9 vVacetate_i
vVcin vVethanol_i vVF16DP vVG6P
vVgluci vVGpd1 vVgpd1mRNA vVHog1
vVos vVPfk2627a vVPfk2627i vVpyruvate
vVStl1 vVstl1mRNA vVtrehalose vVtrioseP
vVglyci vVHog1PP    
Rules
Assignment Rule (variable: Vm) Assignment Rule (variable: CellSurface) Assignment Rule (variable: v11speed) Assignment Rule (variable: v13aspeed)
Assignment Rule (variable: v12speed) Assignment Rule (variable: v10speed) Assignment Rule (variable: input) Assignment Rule (variable: Turgor)
Assignment Rule (variable: OsmoE) Assignment Rule (variable: volchangespeed) Assignment Rule (variable: relVM) Assignment Rule (variable: OD)
Assignment Rule (variable: cellnum) Assignment Rule (variable: v1speed) Assignment Rule (variable: v13bspeed) Assignment Rule (variable: kv16r_1VARIABLE)
Assignment Rule (variable: glycerol_measured) Assignment Rule (variable: Hog1PP_measured) Assignment Rule (variable: Gpd1_measured) Assignment Rule (variable: gpd1mRNA_measured)
Assignment Rule (variable: glucose_measured) Assignment Rule (variable: pyruvate_measured) Assignment Rule (variable: acetate_measured) Assignment Rule (variable: ethanol_measured)
Assignment Rule (variable: trehalose_measured) Assignment Rule (variable: F16DP_measured) Assignment Rule (variable: stl1mRNA_measured) Assignment Rule (variable: trioseP_measured)
Physical entities
Compartments Species
intra glycerol_i cin glucose_i
G6P trehalose F16DP
F26DP trioseP Gpd1
pyruvate acetate_i ethanol_i
Hog1 Hog1PP Pfk2627a
Pfk2627i AOG gpd1mRNA
stl1mRNA Stl1 AOGi
Fps1r biomass cellvol
     
extra glycerol_e glucose_e acetate_e
ethanol_e trehalose_e  
Global parameters
cellvol_init kv19f_1 kv19r_1 kv17f_1
kv17f_3 kv17f_6 parameter_97 vV_1
vV_2 vV_R vV_T t_stress
kv1_1 kv1_2 initcellnum kv2_1
kv2_2 kv3_1 kv3_2 kv3_3
kv3_4 kv4_1 kv4_2 kv4_3
kv4_4 kv4_5 kv5_1 kv5_2
kv5_3 kv5_4 kv6_1 kv6_2
kv6_3 kv6b_1 kv6b_2 kv6b_3
kv6b_4 kv6b_5 kv7_1 kv7_2
kv8_1 kv8_2 kv9_1 kv9_2
kv16f_1 kv16f_2 kv16f_3 kv16r_1
kv15f_1 kv15f_2 kv15r_1 kv15r_2
kv17f_2 kv17f_4 kv17f_5 kv17r_1
kv18f_1 kv18r_1 kv20f_1 kv20f_2
kv20f_3 kv20f_x kv20r_1 kv21f_1
kv21r_1 kv23f_1 kv23f_2 kv23f_3
kv23r_1 kv22_1 kv22_2 kv22_3
kv14_1 kv14_2 kv14_3 kv14_4
kv14_5 kv10_1 kv10_2 kv11_1
kv11_2 kv12_1 kv12_2 kv13a_1
kv13b_1 kv13b_2 kx1 kx2
kv22_4_Hog1A v kv22_Hog1D_t kv22_Hog1D_fT
kv22_Hog1D_d v15f_v v15r_v v19r_v
Vm CellSurface v13aspeed v12speed
v11speed v10speed Turgor OsmoE
input volchangespeed relVM OD
cellnum v1speed v13bspeed kv16r_1VARIABLE
glycerol_measured Hog1PP_measured Gpd1_measured gpd1mRNA_measured
glucose_measured pyruvate_measured acetate_measured ethanol_measured
trehalose_measured F16DP_measured quantity trioseP_measured
stl1mRNA_measured kv6b_x    
Reactions (58)
 
 v1 [glucose_e] → [glucose_i];  
 
 v10 [trehalose] ↔ [trehalose_e];  
 
 v10Batch  ↔ [trehalose_e];  
 
 v11 [acetate_i] ↔ [acetate_e];  
 
 v11Batch  ↔ [acetate_e];  
 
 v12 [ethanol_i] ↔ [ethanol_e];  
 
 v12Batch  ↔ [ethanol_e];  
 
 v13a [glycerol_i] ↔ [glycerol_e];   {Fps1r}
 
 v13aBatch  ↔ [glycerol_e];  
 
 v13b [glycerol_e] → [glycerol_i];   {Stl1}
 
 v13bBatch [glycerol_e] → ;  
 
 v14 [G6P] → [biomass];   {cellvol}
 
 v15f [G6P] → [F26DP];   {Pfk2627a}
 
 v15r [F26DP] → [G6P];  
 
 v16f [Hog1] → [Hog1PP];  
 
 v16r [Hog1PP] → [Hog1];  
 
 v17f  → [gpd1mRNA];   {Hog1PP} , {AOG}
 
 v17r [gpd1mRNA] → ;  
 
 v18f  → [Gpd1];   {gpd1mRNA}
 
 v18r [Gpd1] → ;  
 
 v19f [Pfk2627i] → [Pfk2627a];   {Hog1PP}
 
 v19r [Pfk2627a] → [Pfk2627i];  
 
 v1Batch [glucose_e] → ;  
 
 v2 [glucose_i] → [G6P];  
 
 v20f  → [stl1mRNA];   {Hog1PP}
 
 v20r [stl1mRNA] → ;  
 
 v21f  → [Stl1];   {stl1mRNA}
 
 v21r [Stl1] → ;  
 
 v22  → [Fps1r];   {Hog1PP}
 
 v23f [AOGi] → [AOG];  
 
 v23r [AOG] → [AOGi];  
 
 v3 2.0 × [G6P] ↔ [trehalose];  
 
 v4 [G6P] → [F16DP];   {F26DP}
 
 v5 [F16DP] ↔ 2.0 × [trioseP];  
 
 v6 [trioseP] → [glycerol_i];   {Gpd1}
 
 v6b [trioseP] → [glycerol_i];  
 
 v7 [trioseP] → [pyruvate];  
 
 v8 [pyruvate] → [acetate_i];  
 
 v9 [pyruvate] → [ethanol_i];  
 
 vVacetate_i [acetate_i] ↔ ;   {cellvol}
 
 vVcin [cin] ↔ ;   {cellvol}
 
 vVethanol_i [ethanol_i] ↔ ;   {cellvol}
 
 vVF16DP [F16DP] ↔ ;   {cellvol}
 
 vVG6P [G6P] ↔ ;   {cellvol}
 
 vVgluci [glucose_i] ↔ ;   {cellvol}
 
 vVGpd1 [Gpd1] ↔ ;   {cellvol}
 
 vVgpd1mRNA [gpd1mRNA] ↔ ;   {cellvol}
 
 vVHog1 [Hog1] ↔ ;   {cellvol}
 
 vVos  ↔ [cellvol];   {glycerol_e} , {glycerol_i} , {cin}
 
 vVPfk2627a [Pfk2627a] ↔ ;   {cellvol}
 
 vVPfk2627i [Pfk2627i] ↔ ;   {cellvol}
 
 vVpyruvate [pyruvate] ↔ ;   {cellvol}
 
 vVStl1 [Stl1] ↔ ;   {cellvol}
 
 vVstl1mRNA [stl1mRNA] ↔ ;   {cellvol}
 
 vVtrehalose [trehalose] ↔ ;   {cellvol}
 
 vVtrioseP [trioseP] ↔ ;   {cellvol}
 
 vVglyci [glycerol_i] ↔ ;   {cellvol}
 
 vVHog1PP [Hog1PP] ↔ ;   {cellvol}
 
Rules (28)
 
 Assignment Rule (name: Vm) Vm = cellvol+0.00024
 
 Assignment Rule (name: CellSurface) CellSurface = (36*pi)^(1/3)*Vm^(2/3)
 
 Assignment Rule (name: v11speed) v11speed = kv11_1*CellSurface*(acetate_i-kv11_2*acetate_e)
 
 Assignment Rule (name: v13aspeed) v13aspeed = Fps1r*kv13a_1*CellSurface*(glycerol_i-glycerol_e)
 
 Assignment Rule (name: v12speed) v12speed = kv12_1*CellSurface*(ethanol_i-kv12_2*ethanol_e)
 
 Assignment Rule (name: v10speed) v10speed = kv10_1*CellSurface*(trehalose-kv10_2*trehalose_e)
 
 Assignment Rule (name: input) input = piecewise(0, time < t_stress, piecewise((time-t_stress)/5, time < (t_stress+5), 1))
 
 Assignment Rule (name: Turgor) Turgor = piecewise((-2.9)*(1-(0.00025-(Vm-0.00025))/(0.00025-0.00025*0.9)), Vm > (0.00025*0.9+0.00025), 0)
 
 Assignment Rule (name: OsmoE) OsmoE = 0.355586+parameter_97*input
 
 Assignment Rule (name: volchangespeed) volchangespeed = vV_1*CellSurface*(Turgor-vV_2*vV_R*vV_T*((glycerol_e+OsmoE)-(glycerol_i+cin)))
 
 Assignment Rule (name: relVM) relVM = Vm/0.00048
 
 Assignment Rule (name: OD) OD = 2.94557E-9*time^2+6.49182E-5*time+0.595608
 
 Assignment Rule (name: cellnum) cellnum = ((-6548240)*OD^2+30565100*OD)-4727510
 
 Assignment Rule (name: v1speed) v1speed = kv1_1*glucose_e/(kv1_2+glucose_e)
 
 Assignment Rule (name: v13bspeed) v13bspeed = glycerol_e*kv13b_1*Stl1/(kv13b_2+glycerol_e)
 
 Assignment Rule (name: kv16r_1VARIABLE) kv16r_1VARIABLE = piecewise(0.444296, time < 4800, 0.444296*(time/4800)^3)
 
 Assignment Rule (name: glycerol_measured) glycerol_measured = glycerol_i*cellvol/cellvol_init
 
 Assignment Rule (name: Hog1PP_measured) Hog1PP_measured = Hog1PP*cellvol/cellvol_init
 
 Assignment Rule (name: Gpd1_measured) Gpd1_measured = Gpd1*cellvol/cellvol_init
 
 Assignment Rule (name: gpd1mRNA_measured) gpd1mRNA_measured = gpd1mRNA*cellvol/cellvol_init
 
 Assignment Rule (name: glucose_measured) glucose_measured = glucose_i*cellvol/cellvol_init
 
 Assignment Rule (name: pyruvate_measured) pyruvate_measured = pyruvate*cellvol/cellvol_init
 
 Assignment Rule (name: acetate_measured) acetate_measured = acetate_i*cellvol/cellvol_init
 
 Assignment Rule (name: ethanol_measured) ethanol_measured = ethanol_i*cellvol/cellvol_init
 
 Assignment Rule (name: trehalose_measured) trehalose_measured = trehalose*cellvol/cellvol_init
 
 Assignment Rule (name: F16DP_measured) F16DP_measured = F16DP*cellvol/cellvol_init
 
 Assignment Rule (name: stl1mRNA_measured) stl1mRNA_measured = stl1mRNA*cellvol/cellvol_init
 
 Assignment Rule (name: trioseP_measured) trioseP_measured = trioseP*cellvol/cellvol_init
 
Functions (51)
 
 Function for v17f lambda(0)
 
 function_4_v22 lambda(Fps1r, Hog1PP, Turgor, kv22_1, kv22_2, kv22_3, kv22_1*(-Turgor)/(kv22_3+(-Turgor))*1.5*(1-Hog1PP/(Hog1PP+kv22_2))-kv22_1*Fps1r)
 
 Function for v6 lambda(0)
 
 function_4_v14_1 lambda(G6P, OsmoE, cellvol, kv14_1, kv14_2, kv14_3, kv14_4, kv14_5, kv14_1*cellvol^kv14_3/(cellvol^kv14_3+kv14_2)*(1-OsmoE/(OsmoE+kv14_4))*G6P/kv14_5/(1+G6P/kv14_5))
 
 function_4_v10Batch_1 lambda(cellnum, initcellnum, v10speed, v10speed*cellnum/initcellnum-v10speed)
 
 function_4_vVG6P_1 lambda(G6P, cellvol, volchangespeed, G6P*volchangespeed/cellvol)
 
 function_4_vVgluci_1 lambda(cellvol, glucose_i, volchangespeed, glucose_i*volchangespeed/cellvol)
 
 function_4_vVStl1_1 lambda(Stl1, cellvol, volchangespeed, Stl1*volchangespeed/cellvol)
 
 function_4_v4_1 lambda(F26DP, G6P, kv4_1, kv4_2, kv4_3, kv4_4, kv4_5, (kv4_2*(1-F26DP^kv4_5/(F26DP+kv4_3)^kv4_5)+kv4_1*F26DP^kv4_5/(F26DP+kv4_3)^kv4_5)*(G6P/kv4_4)^2/(1+(G6P/kv4_4)^2))
 
 function_4_vVpyruvate_1 lambda(cellvol, pyruvate, volchangespeed, pyruvate*volchangespeed/cellvol)
 
 function_4_vVPfk2627a_1 lambda(Pfk2627a, cellvol, volchangespeed, Pfk2627a*volchangespeed/cellvol)
 
 function_4_vVstl1mRNA_1 lambda(cellvol, stl1mRNA, volchangespeed, stl1mRNA*volchangespeed/cellvol)
 
 function_4_v1Batch_1 lambda(cellnum, initcellnum, v1speed, v1speed*cellnum/initcellnum-v1speed)
 
 function_4_vVcin_1 lambda(cellvol, cin, volchangespeed, cin*volchangespeed/cellvol)
 
 function_4_vVos_1 lambda(CellSurface, OsmoE, Turgor, cin, glycerol_e, glycerol_i, vV_1, vV_2, vV_R, vV_T, vV_1*CellSurface*(Turgor-vV_2*vV_R*vV_T*((glycerol_e+OsmoE)-(glycerol_i+cin))))
 
 function_4_vVethanol_i_1 lambda(cellvol, ethanol_i, volchangespeed, ethanol_i*volchangespeed/cellvol)
 
 function_4_vVF16DP_1 lambda(F16DP, cellvol, volchangespeed, F16DP*volchangespeed/cellvol)
 
 function_4_vVtrioseP_1 lambda(cellvol, trioseP, volchangespeed, trioseP*volchangespeed/cellvol)
 
 function_4_vVPfk2627i_1 lambda(Pfk2627i, cellvol, volchangespeed, Pfk2627i*volchangespeed/cellvol)
 
 function_4_v13a_1 lambda(CellSurface, Fps1r, glycerol_e, glycerol_i, kDiff, kv13a_1, kv13a_1*CellSurface*Fps1r*(glycerol_i-kDiff*glycerol_e))
 
 function_4_v13b_1 lambda(Stl1, glycerol_e, kv13b_1, kv13b_2, glycerol_e*kv13b_1*Stl1/(kv13b_2+glycerol_e))
 
 function_4_v18f_1 lambda(gpd1mRNA, kv18f_1, kv18f_1*gpd1mRNA)
 
 function_4_v11_1 lambda(CellSurface, acetate_e, acetate_i, kv11_1, kv11_2, kv11_1*CellSurface*(acetate_i-kv11_2*acetate_e))
 
 function_4_v20f_1 lambda(Hog1PP, kv20f_1, kv20f_2, kv20f_3, kv20f_x, kv20f_1*Hog1PP^kv20f_x/(Hog1PP^kv20f_x+kv20f_2)+kv20f_3)
 
 function_4_v16f_1 lambda(Hog1, OsmoE, Vm, kv16f_1, kv16f_2, kv16f_3, Hog1*kv16f_1*OsmoE*(kv16f_2/Vm)^kv16f_3)
 
 function_4_v21f_1 lambda(kv21f_1, stl1mRNA, kv21f_1*stl1mRNA)
 
 function_4_v23f_1 lambda(AOGi, Vm, kv23f_1, kv23f_2, kv23f_3, AOGi*kv23f_1*(kv23f_2/Vm)^kv23f_3)
 
 function_4_v3_1 lambda(G6P, kv3_1, kv3_2, kv3_3, kv3_4, trehalose, (kv3_1*G6P/kv3_2-kv3_3*trehalose/kv3_4)/(1+G6P/kv3_2+trehalose/kv3_4))
 
 function_4_v13aBatch_1 lambda(cellnum, initcellnum, v13aspeed, v13aspeed*cellnum/initcellnum-v13aspeed)
 
 function_4_v13bBatch_1 lambda(cellnum, initcellnum, v13bspeed, v13bspeed*cellnum/initcellnum-v13bspeed)
 
 function_4_v12_1 lambda(CellSurface, ethanol_e, ethanol_i, kv12_1, kv12_2, kv12_1*CellSurface*(ethanol_i-kv12_2*ethanol_e))
 
 function_4_v5_1 lambda(F16DP, kv5_1, kv5_2, kv5_3, kv5_4, trioseP, kv5_1*F16DP/kv5_2/(1+F16DP/kv5_2)-kv5_3*trioseP/kv5_4/(1+trioseP/kv5_4))
 
 function_4_vVGpd1_1 lambda(Gpd1, cellvol, volchangespeed, Gpd1*volchangespeed/cellvol)
 
 function_4_vVtrehalose_1 lambda(cellvol, trehalose, volchangespeed, trehalose*volchangespeed/cellvol)
 
 function_4_vVgpd1mRNA_1 lambda(cellvol, gpd1mRNA, volchangespeed, gpd1mRNA*volchangespeed/cellvol)
 
 function_4_v10_1 lambda(CellSurface, kv10_1, kv10_2, trehalose, trehalose_e, kv10_1*CellSurface*(trehalose-kv10_2*trehalose_e))
 
 function_4_v12Batch_1 lambda(cellnum, initcellnum, v12speed, v12speed*cellnum/initcellnum-v12speed)
 
 function_4_v11Batch_1 lambda(cellnum, initcellnum, v11speed, v11speed*cellnum/initcellnum-v11speed)
 
 function_4_vVHog1_1 lambda(Hog1, cellvol, volchangespeed, Hog1*volchangespeed/cellvol)
 
 function_4_vVacetate_i_1 lambda(acetate_i, cellvol, volchangespeed, acetate_i*volchangespeed/cellvol)
 
 Henri-Michaelis-Menten (irreversible)_1 lambda(glucose_e, kv1_1, kv1_2, kv1_1*glucose_e/(kv1_2+glucose_e))
 
 function_4_v6b_1_1 lambda(kv6b_4, kv6b_5, kv6b_x, trioseP, kv6b_x*kv6b_4*trioseP^2/kv6b_5/(1+trioseP^2/kv6b_5))
 
 function_4_vVStl1_1_1 lambda(cellvol, glycerol_i, volchangespeed, glycerol_i*volchangespeed/cellvol)
 
 function_4_vVtrioseP_1_1 lambda(Hog1PP, cellvol, volchangespeed, Hog1PP*volchangespeed/cellvol)
 
 function_4_v19f_1 lambda(Hog1PP, Pfk2627i, kv19f_1, kv19f_1*Hog1PP*Pfk2627i)
 
 function_4_v15f_1 lambda(G6P, Pfk2627a, kv15f_1, kv15f_2, G6P*kv15f_1*Pfk2627a/(kv15f_2+G6P))
 
 Henri-Michaelis-Menten (irreversible)_2 lambda(F26DP, kv15r_1, kv15r_2, kv15r_1*F26DP/(kv15r_2+F26DP))
 
 Henri-Michaelis-Menten (irreversible)_3 lambda(glucose_i, kv2_1, kv2_2, kv2_1*glucose_i/(kv2_2+glucose_i))
 
 Henri-Michaelis-Menten (irreversible)_4 lambda(kv7_1, kv7_2, trioseP, kv7_1*trioseP/(kv7_2+trioseP))
 
 Henri-Michaelis-Menten (irreversible)_5 lambda(kv8_1, kv8_2, pyruvate, kv8_1*pyruvate/(kv8_2+pyruvate))
 
 Henri-Michaelis-Menten (irreversible)_6 lambda(kv9_1, kv9_2, pyruvate, kv9_1*pyruvate/(kv9_2+pyruvate))
 
 intra Spatial dimensions: 3.0  Compartment size: 2.5E-4
 
 glycerol_i
Compartment: intra
Initial concentration: 0.112096
 
 cin
Compartment: intra
Initial concentration: 0.651922
 
 glucose_i
Compartment: intra
Initial concentration: 2.77983
 
 G6P
Compartment: intra
Initial concentration: 1.37587
 
 trehalose
Compartment: intra
Initial concentration: 0.00309562
 
 F16DP
Compartment: intra
Initial concentration: 0.328796
 
 F26DP
Compartment: intra
Initial concentration: 1.50228E-4
 
 trioseP
Compartment: intra
Initial concentration: 0.635777
 
 Gpd1
Compartment: intra
Initial concentration: 0.0
 
 pyruvate
Compartment: intra
Initial concentration: 0.0113917
 
 acetate_i
Compartment: intra
Initial concentration: 0.949708
 
 ethanol_i
Compartment: intra
Initial concentration: 9.65129
 
 Hog1
Compartment: intra
Initial concentration: 0.420913
 
 Hog1PP
Compartment: intra
Initial concentration: 0.0178316
 
 Pfk2627a
Compartment: intra
Initial concentration: 0.108018
 
 Pfk2627i
Compartment: intra
Initial concentration: 0.485157999999999
 
 AOG
Compartment: intra
Initial concentration: 8.50262E-4
 
 gpd1mRNA
Compartment: intra
Initial concentration: 0.0
 
 stl1mRNA
Compartment: intra
Initial concentration: 0.00418600999999999
 
 Stl1
Compartment: intra
Initial concentration: 1.25486E-4
 
 AOGi
Compartment: intra
Initial concentration: 0.0168496
 
 Fps1r
Compartment: intra
Initial concentration: 2.43688
 
   biomass
Compartment: intra
Initial concentration: 4.23631000000001
 
   cellvol
Compartment: intra
Initial concentration: 2.40000000000001E-4
 
 extra Spatial dimensions: 3.0  Compartment size: 0.5
 
 glycerol_e
Compartment: extra
Initial concentration: 0.00144282
 
 glucose_e
Compartment: extra
Initial concentration: 0.106197
 
 acetate_e
Compartment: extra
Initial concentration: 0.0032412
 
 ethanol_e
Compartment: extra
Initial concentration: 0.0293241
 
 trehalose_e
Compartment: extra
Initial concentration: 1.63972E-4
 
Global Parameters (126)
 
   cellvol_init
Value: 2.40000000000001E-4
Constant
 
   kv19f_1
Value: 0.299127
Constant
 
   kv19r_1
Value: 0.0605655
Constant
 
   kv17f_1
Value: 4.11446E-4
Constant
 
   kv17f_3
Value: 0.421394
Constant
 
   kv17f_6
Value: 7.85767E-9
Constant
 
   parameter_97
Value: 0.8
Constant
 
   vV_1
Value: 3.56294E-5
Constant
 
   vV_2
Value: 0.00116532
Constant
 
   vV_R
Value: 8.314
Constant
 
   vV_T
Value: 298.5
Constant
 
   t_stress
Value: 3600.0
Constant
 
   kv1_1
Value: 5.05249E-6
Constant
 
   kv1_2
Value: 0.899814
Constant
 
   initcellnum
Value: 6954722.464
Constant
 
   kv2_1
Value: 0.00303855
Constant
 
   kv2_2
Value: 0.40864
Constant
 
   kv3_1
Value: 6.17387E-6
Constant
 
   kv3_2
Value: 0.81114
Constant
 
   kv3_3
Value: 7.37808E-4
Constant
 
   kv3_4
Value: 0.166996
Constant
 
   kv4_1
Value: 0.0628885
Constant
 
   kv4_2
Value: 0.00230714
Constant
 
   kv4_3
Value: 0.00171631
Constant
 
   kv4_4
Value: 2.67143
Constant
 
   kv4_5
Value: 0.583865
Constant
 
   kv5_1
Value: 0.00383315
Constant
 
   kv5_2
Value: 1.74463
Constant
 
   kv5_3
Value: 0.00656128
Constant
 
   kv5_4
Value: 1.13994
Constant
 
   kv6_1
Value: 0.0118992
Constant
 
   kv6_2
Value: 0.230864
Constant
 
   kv6_3
Value: 1.76504
Constant
 
   kv6b_1
Value: 0.859104
Constant
 
   kv6b_2
Value: 0.0307535
Constant
 
   kv6b_3
Value: 1.20045
Constant
 
   kv6b_4
Value: 4.61918E-5
Constant
 
   kv6b_5
Value: 0.292627
Constant
 
   kv7_1
Value: 0.00983997
Constant
 
   kv7_2
Value: 0.317879
Constant
 
   kv8_1
Value: 0.0135676
Constant
 
   kv8_2
Value: 1.50827
Constant
 
   kv9_1
Value: 0.214937
Constant
 
   kv9_2
Value: 0.923665
Constant
 
   kv16f_1
Value: 0.156118
Constant
 
   kv16f_2
Value: 4.52424E-4
Constant
 
   kv16f_3
Value: 14.9448
Constant
 
   kv16r_1
Value: 0.588072
Constant
 
   kv15f_1
Value: 4.99507E-5
Constant
 
   kv15f_2
Value: 6.95877
Constant
 
   kv15r_1
Value: 1.84829E-7
Constant
 
   kv15r_2
Value: 3.3187E-5
Constant
 
   kv17f_2
Value: 0.547886
Constant
 
   kv17f_4
Value: 6.86959E-10
Constant
 
   kv17f_5
Value: 18.9989
Constant
 
   kv17r_1
Value: 0.00151498
Constant
 
   kv18f_1
Value: 0.00646553
Constant
 
   kv18r_1
Value: 1.32549E-4
Constant
 
   kv20f_1
Value: 9.81887E-5
Constant
 
   kv20f_2
Value: 0.0167845
Constant
 
   kv20f_3
Value: 4.05843E-6
Constant
 
   kv20f_x
Value: 1.55858
Constant
 
   kv20r_1
Value: 7.05933E-4
Constant
 
   kv21f_1
Value: 0.00121673
Constant
 
   kv21r_1
Value: 2.14247E-4
Constant
 
   kv23f_1
Value: 8.80535E-6
Constant
 
   kv23f_2
Value: 5.1235E-4
Constant
 
   kv23f_3
Value: 6.95727
Constant
 
   kv23r_1
Value: 2.09875E-4
Constant
 
   kv22_1
Value: 8.0075
Constant
 
   kv22_2
Value: 0.0215179
Constant
 
   kv22_3
Value: 0.0554729
Constant
 
   kv14_1
Value: 0.808051
Constant
 
   kv14_2
Value: 6.05922E-6
Constant
 
   kv14_3
Value: 2.05157
Constant
 
   kv14_4
Value: 0.420621
Constant
 
   kv14_5
Value: 1.23049
Constant
 
   kv10_1
Value: 1.83291E-7
Constant
 
   kv10_2
Value: 4.26512
Constant
 
   kv11_1
Value: 3.2863E-6
Constant
 
   kv11_2
Value: 1.17279
Constant
 
   kv12_1
Value: 1.00927E-5
Constant
 
   kv12_2
Value: 0.148586
Constant
 
   kv13a_1
Value: 6.28899E-6
Constant
 
   kv13b_1
Value: 1.27001E-7
Constant
 
   kv13b_2
Value: 3.69196E-7
Constant
 
   kx1
Value: 1.97771
Constant
 
   kx2
Value: 5.37171
Constant
 
   kv22_4_Hog1A
Value: 1.25187
Constant
 
   v
Value: 1.0
Constant
 
   kv22_Hog1D_t
Value: 5536.0
Constant
 
   kv22_Hog1D_fT
Value: 0.0256901
Constant
 
   kv22_Hog1D_d
Value: 2.94357E-4
Constant
 
   v15f_v
Value: 1.0
Constant
 
   v15r_v
Value: 1.0
Constant
 
   v19r_v
Value: 1.0
Constant
 
   Vm
Value: 4.80000000000001E-4
 
   CellSurface
Value: 0.0296468313433281
 
   v13aspeed
Value: 5.0275596254809E-8
 
   v12speed
Value: 2.88652220351019E-6
 
   v11speed
Value: 9.21581643247704E-8
 
   v10speed
Value: 1.30212691282784E-11
 
   Turgor
Value: -0.580000000000118
 
   OsmoE
Value: 0.355586
 
   input  
 
   volchangespeed
Value: 6.30627442832138E-7
 
   relVM
Value: 1.0
 
   OD
Value: 0.595608
 
   cellnum
Value: 1.11543272115466E7
 
   v1speed
Value: 5.33353293880484E-7
 
   v13bspeed
Value: 1.59327705289657E-11
 
   kv16r_1VARIABLE
Value: 0.444296
 
   glycerol_measured
Value: 0.112096
 
   Hog1PP_measured
Value: 0.0178316
 
   Gpd1_measured  
 
   gpd1mRNA_measured  
 
   glucose_measured
Value: 2.77983
 
   pyruvate_measured
Value: 0.0113917
 
   acetate_measured
Value: 0.949708
 
   ethanol_measured
Value: 9.65129
 
   trehalose_measured
Value: 0.00309562
 
   F16DP_measured
Value: 0.328796
 
   quantity
Constant
 
   trioseP_measured
Value: 0.635777
 
   stl1mRNA_measured
Value: 0.00418600999999999
 
   kv6b_x
Value: 28.5
Constant
 
v13a (1)
 
   kDiff
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000610

Curator's comment: (updated: 20 Apr 2016 13:53:10 BST)

Figure S12E has been reproduced here using Copasi 4.16 (Build 104).

Note: The initially submitted SBML file did not work for reproduction. Clemens Kühn, one of the authors, identified that the rate law for reaction v16r should be proportional to kv16r_1VARIABLE, instead of kv16r. Note that there is an error in Text S1 from the publication, which does not record the usage of kv16r_1VARIABLE.

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