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BIOMD0000000244 - Kotte2010_Ecoli_Metabolic_Adaption

 

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Reference Publication
Publication ID: 20212527
Kotte O, Zaugg JB, Heinemann M.
Bacterial adaptation through distributed sensing of metabolic fluxes.
Mol. Syst. Biol. 2010; 6: 355
Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.  [more]
Model
Original Model: http://www.nature.com/msb/...
Submitter: Lukas Endler
Submission ID: MODEL1003100000
Submission Date: 10 Mar 2010 00:30:53 UTC
Last Modification Date: 04 Apr 2014 15:39:09 UTC
Creation Date: 14 Mar 2010 23:34:51 UTC
Encoders:  Lukas Endler
set #1
bqbiol:occursIn Taxonomy Escherichia coli
bqbiol:isVersionOf Gene Ontology regulation of glucose metabolic process
Gene Ontology regulation of acetate catabolic process
bqbiol:hasVersion Gene Ontology phosphoenolpyruvate-protein phosphotransferase activity
Gene Ontology acetate metabolic process
Gene Ontology glycolytic process
Gene Ontology glyoxylate cycle
Gene Ontology gluconeogenesis
Notes

This is the model described in: Bacterial adaptation through distributed sensing of metabolic fluxes
Oliver Kotte, Judith B Zaugg and Matthias Heinemann;Mol Sys Biol2010;6:355. doi:10.1038/msb.2010.10;
Abstract:
The recognition of carbon sources and the regulatory adjustments to recognized changes are of particular importance for bacterial survival in fluctuating environments. Despite a thorough knowledge base of Escherichia coli's central metabolism and its regulation, fundamental aspects of the employed sensing and regulatory adjustment mechanisms remain unclear. In this paper, using a differential equation model that couples enzymatic and transcriptional regulation of E. coli's central metabolism, we show that the interplay of known interactions explains in molecular-level detail the system-wide adjustments of metabolic operation between glycolytic and gluconeogenic carbon sources. We show that these adaptations are enabled by an indirect recognition of carbon sources through a mechanism we termed distributed sensing of intracellular metabolic fluxes. This mechanism uses two general motifs to establish flux-signaling metabolites, whose bindings to transcription factors form flux sensors. As these sensors are embedded in global feedback loop architectures, closed-loop self-regulation can emerge within metabolism itself and therefore, metabolic operation may adapt itself autonomously (not requiring upstream sensing and signaling) to fluctuating carbon sources.

In its current form this SBML model is parametrized for the glucose to acetate transition and to simulate the extended diauxic shift as shown in figure 3 and scenario 6 of the attached matlab file. In this scenario the cells first are grown from an OD600 (BM) of 0.03 with a starting glucose concentration of 0.5 g/l for 8.15 h (29340 sec). Then a medium containing 5 g/l acetate is inoculated with these cells to an OD600 of 0.03 and grown for another 19.7 hours (70920 sec). Finally the cells are shifted to a medium containing both glucose and acetate at a concentration of 3 g/l with a starting OD600 of 0.0005.
The shifts where implemented using events triggering at the times determined by the parameters shift1 and shift2 (in hours). To simulate other scenarios the initial conditions need to be changed as described in the supplemental materials (supplement 1)
The original SBML model and the MATLAB file used for the calculations can be down loaded as supplementary materials of the publication from the MSB website. (supplement 2).

The units of the external metabolites are in [g/l], those of the biomass in optical density,OD600, taken as dimensionless, and [micromole/(gramm dry weight)] for all intracellular metabolites. As the latter cannot be implemented in SBML, it was chosen to be micromole only and the units of the parameters are left mostly undefined.

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: 20212527 Submission Date: 10 Mar 2010 00:30:53 UTC Last Modification Date: 04 Apr 2014 15:39:09 UTC Creation Date: 14 Mar 2010 23:34:51 UTC
Mathematical expressions
Reactions
bm_ACoA bm_AKG bm_G6P bm_OAA
bm_PEP bm_PG3 bm_PYR pts_r1
pts_r4 e_AceK_Ki e_AceK_Ph tf_Cra
tf_Crp tf_PdhR e_AceA e_AceB
e_Acoa2act e_Acs e_Akg2mal e_CAMPdegr
e_Cya e_Emp e_Eno e_Fdp
e_GltA e_Icd e_Mdh e_Me
e_PckA e_Pdh e_PfkA e_Ppc
e_PpsA e_PykF g_aceA g_aceB
g_aceK g_acoa2act g_acs g_akg2mal
g_cAMPdegr g_cra g_crp g_cya
g_emp g_eno g_fdp g_gltA
g_icd g_iclr g_mdh g_me
g_pckA g_pdh g_pdhr g_pfkA
g_ppc g_ppsA g_pykF g_EIIA
g_EIICB d_AceA d_AceB d_AceK
d_Acoa2act d_Acs d_Akg2mal d_CAMPdegr
d_Cra d_CraFBP d_Crp d_CrpcAMP
d_Cya d_Emp d_Eno d_Fdp
d_GltA d_Icd d_Icd_P d_IclR
d_Mdh d_Me d_PckA d_Pdh
d_PdhR d_PdhRPYR d_PfkA d_Ppc
d_PpsA d_PykF d_EIIA d_EIIA_P
d_EIICB d_ACoA d_AKG d_cAMP
d_FBP d_G6P d_GLX d_ICT
d_MAL d_OAA d_PEP d_PG3
d_PYR env_growth env_GLCup env_ACTup
env_ACTex      
Rules
Assignment Rule (variable: alphaGLC) Assignment Rule (variable: alphaACT) Assignment Rule (variable: mu) Assignment Rule (variable: k_bm_ACoA)
Assignment Rule (variable: k_bm_AKG) Assignment Rule (variable: k_bm_G6P) Assignment Rule (variable: k_bm_OAA) Assignment Rule (variable: k_bm_PEP)
Assignment Rule (variable: k_bm_PG3) Assignment Rule (variable: k_bm_PYR) Assignment Rule (variable: SS_Me) Assignment Rule (variable: SS_Ppc)
Events
first shift second shift    
Physical entities
Compartments Species
Environment BM ACT GLC
     
Cell ACoA AKG cAMP
FBP G6P GLX
ICT MAL OAA
PEP PG3 PYR
AceA AceB AceK
Acoa2act Acs Akg2mal
CAMPdegr Cya Emp
Eno Fdp GltA
Icd Icd_P Mdh
Me PckA Pdh
PfkA Ppc PpsA
PykF Cra CraFBP
Crp CrpcAMP IclR
PdhR PdhRPYR EIIA
EIIA_P EIICB  
Global parameters
env_M_ACT env_M_GLC env_uc e_AceA_kcat
e_AceA_n e_AceA_L e_AceA_Kict e_AceA_Kpep
e_AceA_Kpg3 e_AceA_Kakg e_AceB_kcat e_AceB_Kglx
e_AceB_Kacoa e_AceB_Kglxacoa e_AceK_kcat_ki e_AceK_kcat_ph
e_AceK_n e_AceK_L e_AceK_Kicd e_AceK_Kicd_P
e_AceK_Kpep e_AceK_Kpyr e_AceK_Koaa e_AceK_Kglx
e_AceK_Kakg e_AceK_Kpg3 e_AceK_Kict e_Acoa2act_kcat
e_Acoa2act_n e_Acoa2act_L e_Acoa2act_Kacoa e_Acoa2act_Kpyr
e_Acs_kcat e_Acs_Kact e_Akg2mal_kcat e_Akg2mal_Kakg
e_CAMPdegr_kcat e_CAMPdegr_KcAMP e_Cya_kcat e_Cya_KEIIA
e_Emp_kcat_f e_Emp_kcat_r e_Emp_Kfbp e_Emp_Kpg3
e_Eno_kcatf e_Eno_kcatr e_Eno_Kpg3 e_Eno_Kpep
e_Fdp_kcat e_Fdp_n e_Fdp_L e_Fdp_Kfbp
e_Fdp_Kpep e_GltA_kcat e_GltA_Koaa e_GltA_Kacoa
e_GltA_Koaaacoa e_GltA_Kakg e_Icd_kcat e_Icd_n
e_Icd_L e_Icd_Kict e_Icd_Kpep e_Mdh_kcat
e_Mdh_n e_Mdh_Kmal e_Me_kcat e_Me_n
e_Me_L e_Me_Kmal e_Me_Kacoa e_Me_Kcamp
e_PckA_kcat e_PckA_Koaa e_PckA_Kpep e_Pdh_kcat
e_Pdh_n e_Pdh_L e_Pdh_Kpyr e_Pdh_KpyrI
e_Pdh_Kglx e_PfkA_kcat e_PfkA_n e_PfkA_L
e_PfkA_Kg6p e_PfkA_Kpep e_Ppc_kcat e_Ppc_n
e_Ppc_L e_Ppc_Kpep e_Ppc_Kfbp e_PpsA_kcat
e_PpsA_n e_PpsA_L e_PpsA_Kpyr e_PpsA_Kpep
e_PykF_kcat e_PykF_n e_PykF_L e_PykF_Kpep
e_PykF_Kfbp pts_k1 pts_km1 pts_k4
pts_KEIIA pts_Kglc tf_Cra_scale tf_Cra_kfbp
tf_Cra_n tf_Crp_scale tf_Crp_kcamp tf_Crp_n
tf_PdhR_scale tf_PdhR_kpyr tf_PdhR_n g_aceBAK_vcra_unbound
g_aceBAK_vcra_bound g_aceBAK_Kcra g_aceBAK_aceBfactor g_aceBAK_aceKfactor
g_aceBAK_KDNA g_aceBAK_KP g_aceBAK_KPprime g_aceBAK_KG
g_aceBAK_L g_aceBAK_kcat_iclr g_aceBAK_DNA g_aceBAK_vcrp_bound
g_aceBAK_vcrp_unbound g_aceBAK_Kcrp g_acs_vcrp_unbound g_acs_vcrp_bound
g_acs_n g_acs_Kcrp g_akg2mal_vcrp_unbound g_akg2mal_vcrp_bound
g_akg2mal_Kcrp g_akg2mal_n g_emp_vcra_unbound g_emp_vcra_bound
g_emp_Kcra g_emp_vcrp_unbound g_emp_vcrp_bound g_emp_Kcrp
g_eno_vcra_unbound g_eno_vcra_bound g_eno_Kcra g_fdp_vcra_unbound
g_fdp_vcra_bound g_fdp_Kcra g_gltA_vcrp_unbound g_gltA_vcrp_bound
g_gltA_Kcrp g_gltA_n g_icd_vcra_unbound g_icd_vcra_bound
g_icd_Kcra g_mdh_vcrp_unbound g_mdh_vcrp_bound g_mdh_Kcrp
g_pckA_vcra_unbound g_pckA_vcra_bound g_pckA_Kcra g_pdh_vpdhr_unbound
g_pdh_vpdhr_bound g_pdh_Kpdhr g_pfkA_vcra_unbound g_pfkA_vcra_bound
g_pfkA_Kcra g_ppsA_vcra_unbound g_ppsA_vcra_bound g_ppsA_Kcra
g_pykF_vcra_unbound g_pykF_vcra_bound g_pykF_Kcra d_k_degr
bm_k_expr bm_muACT bm_muGLC bm_GLC_ACoA
bm_GLC_AKG bm_GLC_G6P bm_GLC_OAA bm_GLC_PEP
bm_GLC_PG3 bm_GLC_PYR bm_ACT_ACoA bm_ACT_AKG
bm_ACT_G6P bm_ACT_OAA bm_ACT_PEP bm_ACT_PG3
bm_ACT_PYR alphaGLC alphaACT mu
k_bm_ACoA k_bm_AKG k_bm_G6P k_bm_OAA
k_bm_PEP k_bm_PG3 k_bm_PYR SS_Me
SS_Ppc shift1 shift2 GLC_1
GLC_2 ACT_1 ACT_2 BM_1
BM_2      
Reactions (109)
 
 bm_ACoA [ACoA] → ;   {ACT} , {GLC}
 
 bm_AKG [AKG] → ;   {ACT} , {GLC}
 
 bm_G6P [G6P] → ;   {ACT} , {GLC}
 
 bm_OAA [OAA] → ;   {ACT} , {GLC}
 
 bm_PEP [PEP] → ;   {ACT} , {GLC}
 
 bm_PG3 [PG3] → ;   {ACT} , {GLC}
 
 bm_PYR [PYR] → ;   {ACT} , {GLC}
 
 pts_r1 [PEP] + [EIIA] ↔ [PYR] + [EIIA_P];  
 
 pts_r4 [EIIA_P] → [G6P] + [EIIA];   {EIICB} , {GLC}
 
 e_AceK_Ki [Icd] → [Icd_P];   {AKG} , {AceK} , {GLX} , {ICT} , {OAA} , {PEP} , {PG3} , {PYR}
 
 e_AceK_Ph [Icd_P] → [Icd];   {AKG} , {AceK} , {OAA} , {PEP} , {PG3} , {PYR}
 
 tf_Cra [Cra] ↔ [CraFBP];   {FBP}
 
 tf_Crp [Crp] ↔ [CrpcAMP];   {cAMP}
 
 tf_PdhR [PdhR] ↔ [PdhRPYR];   {PYR}
 
 e_AceA [ICT] → [AKG] + [GLX];   {AceA} , {PEP} , {PG3}
 
 e_AceB [ACoA] + [GLX] → [MAL];   {AceB}
 
 e_Acoa2act [ACoA] → ;   {Acoa2act} , {PYR}
 
 e_Acs  → [ACoA];   {ACT} , {Acs}
 
 e_Akg2mal [AKG] → [MAL];   {Akg2mal}
 
 e_CAMPdegr [cAMP] → ;   {CAMPdegr}
 
 e_Cya  → [cAMP];   {Cya} , {EIIA_P}
 
 e_Emp 0.5 × [FBP] ↔ [PG3];   {Emp}
 
 e_Eno [PG3] ↔ [PEP];   {Eno}
 
 e_Fdp [FBP] → [G6P];   {Fdp} , {PEP}
 
 e_GltA [ACoA] + [OAA] → [ICT];   {AKG} , {GltA}
 
 e_Icd [ICT] → [AKG];   {Icd} , {PEP}
 
 e_Mdh [MAL] → [OAA];   {Mdh}
 
 e_Me [MAL] → [PYR];   {ACoA} , {Me} , {cAMP}
 
 e_PckA [OAA] → [PEP];   {PckA}
 
 e_Pdh [PYR] → [ACoA];   {GLX} , {Pdh}
 
 e_PfkA [G6P] → [FBP];   {PEP} , {PfkA}
 
 e_Ppc [PEP] → [OAA];   {FBP} , {Ppc}
 
 e_PpsA [PYR] → [PEP];   {PpsA}
 
 e_PykF [PEP] → [PYR];   {FBP} , {PykF}
 
 g_aceA  → [AceA];   {ACT} , {Cra} , {CrpcAMP} , {GLC} , {GLX} , {IclR} , {PYR}
 
 g_aceB  → [AceB];   {ACT} , {Cra} , {CrpcAMP} , {GLC} , {GLX} , {IclR} , {PYR}
 
 g_aceK  → [AceK];   {ACT} , {Cra} , {CrpcAMP} , {GLC} , {GLX} , {IclR} , {PYR}
 
 g_acoa2act  → [Acoa2act];  
 
 g_acs  → [Acs];   {ACT} , {CrpcAMP} , {GLC}
 
 g_akg2mal  → [Akg2mal];   {ACT} , {CrpcAMP} , {GLC}
 
 g_cAMPdegr  → [CAMPdegr];  
 
 g_cra  → [Cra];  
 
 g_crp  → [Crp];  
 
 g_cya  → [Cya];  
 
 g_emp  → [Emp];   {ACT} , {Cra} , {CrpcAMP} , {GLC}
 
 g_eno  → [Eno];   {ACT} , {Cra} , {GLC}
 
 g_fdp  → [Fdp];   {ACT} , {Cra} , {GLC}
 
 g_gltA  → [GltA];   {ACT} , {CrpcAMP} , {GLC}
 
 g_icd  → [Icd];   {ACT} , {Cra} , {GLC}
 
 g_iclr  → [IclR];  
 
 g_mdh  → [Mdh];   {ACT} , {CrpcAMP} , {GLC}
 
 g_me  → [Me];   {ACT} , {GLC}
 
 g_pckA  → [PckA];   {ACT} , {Cra} , {GLC}
 
 g_pdh  → [Pdh];   {ACT} , {GLC} , {PdhR}
 
 g_pdhr  → [PdhR];  
 
 g_pfkA  → [PfkA];   {ACT} , {Cra} , {GLC}
 
 g_ppc  → [Ppc];   {ACT} , {GLC}
 
 g_ppsA  → [PpsA];   {ACT} , {Cra} , {GLC}
 
 g_pykF  → [PykF];   {ACT} , {Cra} , {GLC}
 
 g_EIIA  → [EIIA];  
 
 g_EIICB  → [EIICB];  
 
 d_AceA [AceA] → ;   {ACT} , {GLC}
 
 d_AceB [AceB] → ;   {ACT} , {GLC}
 
 d_AceK [AceK] → ;   {ACT} , {GLC}
 
 d_Acoa2act [Acoa2act] → ;  
 
 d_Acs [Acs] → ;   {ACT} , {GLC}
 
 d_Akg2mal [Akg2mal] → ;   {ACT} , {GLC}
 
 d_CAMPdegr [CAMPdegr] → ;  
 
 d_Cra [Cra] → ;  
 
 d_CraFBP [CraFBP] → ;  
 
 d_Crp [Crp] → ;  
 
 d_CrpcAMP [CrpcAMP] → ;  
 
 d_Cya [Cya] → ;  
 
 d_Emp [Emp] → ;   {ACT} , {GLC}
 
 d_Eno [Eno] → ;   {ACT} , {GLC}
 
 d_Fdp [Fdp] → ;   {ACT} , {GLC}
 
 d_GltA [GltA] → ;   {ACT} , {GLC}
 
 d_Icd [Icd] → ;   {ACT} , {GLC}
 
 d_Icd_P [Icd_P] → ;   {ACT} , {GLC}
 
 d_IclR [IclR] → ;  
 
 d_Mdh [Mdh] → ;   {ACT} , {GLC}
 
 d_Me [Me] → ;   {ACT} , {GLC}
 
 d_PckA [PckA] → ;   {ACT} , {GLC}
 
 d_Pdh [Pdh] → ;   {ACT} , {GLC}
 
 d_PdhR [PdhR] → ;  
 
 d_PdhRPYR [PdhRPYR] → ;  
 
 d_PfkA [PfkA] → ;   {ACT} , {GLC}
 
 d_Ppc [Ppc] → ;   {ACT} , {GLC}
 
 d_PpsA [PpsA] → ;   {ACT} , {GLC}
 
 d_PykF [PykF] → ;   {ACT} , {GLC}
 
 d_EIIA [EIIA] → ;  
 
 d_EIIA_P [EIIA_P] → ;  
 
 d_EIICB [EIICB] → ;  
 
 d_ACoA [ACoA] → ;   {ACT} , {GLC}
 
 d_AKG [AKG] → ;   {ACT} , {GLC}
 
 d_cAMP [cAMP] → ;   {ACT} , {GLC}
 
 d_FBP [FBP] → ;   {ACT} , {GLC}
 
 d_G6P [G6P] → ;   {ACT} , {GLC}
 
 d_GLX [GLX] → ;   {ACT} , {GLC}
 
 d_ICT [ICT] → ;   {ACT} , {GLC}
 
 d_MAL [MAL] → ;   {ACT} , {GLC}
 
 d_OAA [OAA] → ;   {ACT} , {GLC}
 
 d_PEP [PEP] → ;   {ACT} , {GLC}
 
 d_PG3 [PG3] → ;   {ACT} , {GLC}
 
 d_PYR [PYR] → ;   {ACT} , {GLC}
 
 env_growth  → [BM];   {ACT} , {GLC}
 
 env_GLCup [GLC] → ;   {BM} , {EIIA_P} , {EIICB}
 
 env_ACTup [ACT] → ;   {Acs} , {BM}
 
 env_ACTex  → [ACT];   {ACoA} , {Acoa2act} , {BM} , {PYR}
 
Rules (12)
 
 Assignment Rule (name: alphaGLC) alphaGLC = GLC/(GLC+pts_Kglc)
 
 Assignment Rule (name: alphaACT) alphaACT = ACT/(ACT+e_Acs_Kact)*(1-GLC/(GLC+pts_Kglc))
 
 Assignment Rule (name: mu) mu = alphaGLC*bm_muGLC+alphaACT*bm_muACT
 
 Assignment Rule (name: k_bm_ACoA) k_bm_ACoA = alphaGLC*bm_GLC_ACoA+alphaACT*bm_ACT_ACoA
 
 Assignment Rule (name: k_bm_AKG) k_bm_AKG = alphaGLC*bm_GLC_AKG+alphaACT*bm_ACT_AKG
 
 Assignment Rule (name: k_bm_G6P) k_bm_G6P = alphaGLC*bm_GLC_G6P+alphaACT*bm_ACT_G6P
 
 Assignment Rule (name: k_bm_OAA) k_bm_OAA = alphaGLC*bm_GLC_OAA+alphaACT*bm_ACT_OAA
 
 Assignment Rule (name: k_bm_PEP) k_bm_PEP = alphaGLC*bm_GLC_PEP+alphaACT*bm_ACT_PEP
 
 Assignment Rule (name: k_bm_PG3) k_bm_PG3 = alphaGLC*bm_GLC_PG3+alphaACT*bm_ACT_PG3
 
 Assignment Rule (name: k_bm_PYR) k_bm_PYR = alphaGLC*bm_GLC_PYR+alphaACT*bm_ACT_PYR
 
 Assignment Rule (name: SS_Me) SS_Me = alphaGLC*0.000999714+alphaACT*0.003399346
 
 Assignment Rule (name: SS_Ppc) SS_Ppc = alphaGLC*0.000999714+alphaACT*0.000279893
 
Events (2)
 
 first shift
GLC = GLC_1
ACT = ACT_1
BM = BM_1
 
 second shift
GLC = GLC_2
ACT = ACT_2
BM = BM_2
 
 Environment Spatial dimensions: 3.0  Compartment size: 1.0
 
   BM
Compartment: Environment
Initial amount: 0.03  (Units: od)
 
 ACT
Compartment: Environment
Initial amount: 0.0  (Units: gram)
 
 GLC
Compartment: Environment
Initial amount: 4.8  (Units: gram)
 
 Cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 ACoA
Compartment: Cell
Initial amount: 0.351972298
 
 AKG
Compartment: Cell
Initial amount: 0.191190619
 
 cAMP
Compartment: Cell
Initial amount: 0.202804098
 
 FBP
Compartment: Cell
Initial amount: 6.57504207
 
 G6P
Compartment: Cell
Initial amount: 1.908140784
 
 GLX
Compartment: Cell
Initial amount: 5.70593E-9
 
 ICT
Compartment: Cell
Initial amount: 0.001408116
 
 MAL
Compartment: Cell
Initial amount: 3.278779135
 
 OAA
Compartment: Cell
Initial amount: 0.050535354
 
 PEP
Compartment: Cell
Initial amount: 0.210455879
 
 PG3
Compartment: Cell
Initial amount: 5.720977255
 
 PYR
Compartment: Cell
Initial amount: 0.863278018
 
 AceA
Compartment: Cell
Initial amount: 0.00472323
 
 AceB
Compartment: Cell
Initial amount: 0.001416969
 
 AceK
Compartment: Cell
Initial amount: 1.41697E-4
 
 Acoa2act
Compartment: Cell
Initial amount: 0.0010
 
 Acs
Compartment: Cell
Initial amount: 0.001096222
 
 Akg2mal
Compartment: Cell
Initial amount: 0.001026848
 
   CAMPdegr
Compartment: Cell
Initial amount: 0.0010
 
 Cya
Compartment: Cell
Initial amount: 0.0010
 
 Emp
Compartment: Cell
Initial amount: 0.011515593
 
 Eno
Compartment: Cell
Initial amount: 0.011552813
 
 Fdp
Compartment: Cell
Initial amount: 1.57492E-4
 
 GltA
Compartment: Cell
Initial amount: 0.001029612
 
 Icd
Compartment: Cell
Initial amount: 0.004290789
 
 Icd_P
Compartment: Cell
Initial amount: 2.20477E-4
 
 Mdh
Compartment: Cell
Initial amount: 0.00345727
 
 Me
Compartment: Cell
Initial amount: 9.99714E-4
 
 PckA
Compartment: Cell
Initial amount: 0.002290892
 
 Pdh
Compartment: Cell
Initial amount: 0.004647401
 
 PfkA
Compartment: Cell
Initial amount: 1.43816E-4
 
 Ppc
Compartment: Cell
Initial amount: 9.99714E-4
 
 PpsA
Compartment: Cell
Initial amount: 9.87493E-4
 
 PykF
Compartment: Cell
Initial amount: 0.005977168
 
 Cra
Compartment: Cell
Initial amount: 2.99098E-4
 
 CraFBP
Compartment: Cell
Initial amount: 0.006990902
 
 Crp
Compartment: Cell
Initial amount: 0.005943273
 
 CrpcAMP
Compartment: Cell
Initial amount: 0.001346727
 
 IclR
Compartment: Cell
Initial amount: 0.00729
 
 PdhR
Compartment: Cell
Initial amount: 0.001163813
 
 PdhRPYR
Compartment: Cell
Initial amount: 0.006126187
 
 EIIA
Compartment: Cell
Initial amount: 0.09647707
 
 EIIA_P
Compartment: Cell
Initial amount: 0.00352292
 
 EIICB
Compartment: Cell
Initial amount: 0.0030
 
Global Parameters (213)
 
   env_M_ACT
Value: 60.05
Constant
 
   env_M_GLC
Value: 180.156
Constant
 
   env_uc
Value: 9.5E-7
Constant
 
   e_AceA_kcat
Value: 614.0
Constant
 
   e_AceA_n
Value: 4.0
Constant
 
   e_AceA_L
Value: 50100.0
Constant
 
   e_AceA_Kict
Value: 0.022
Constant
 
   e_AceA_Kpep
Value: 0.055
Constant
 
   e_AceA_Kpg3
Value: 0.72
Constant
 
   e_AceA_Kakg
Value: 0.827
Constant
 
   e_AceB_kcat
Value: 47.8
Constant
 
   e_AceB_Kglx
Value: 0.95
Constant
 
   e_AceB_Kacoa
Value: 0.755
Constant
 
   e_AceB_Kglxacoa
Value: 0.719
Constant
 
   e_AceK_kcat_ki
Value: 3.4E12
Constant
 
   e_AceK_kcat_ph
Value: 1.7E9
Constant
 
   e_AceK_n
Value: 2.0
Constant
 
   e_AceK_L
Value: 1.0E8
Constant
 
   e_AceK_Kicd
Value: 0.043
Constant
 
   e_AceK_Kicd_P
Value: 0.643
Constant
 
   e_AceK_Kpep
Value: 0.539
Constant
 
   e_AceK_Kpyr
Value: 0.038
Constant
 
   e_AceK_Koaa
Value: 0.173
Constant
 
   e_AceK_Kglx
Value: 0.866
Constant
 
   e_AceK_Kakg
Value: 0.82
Constant
 
   e_AceK_Kpg3
Value: 1.57
Constant
 
   e_AceK_Kict
Value: 0.137
Constant
 
   e_Acoa2act_kcat
Value: 3079.0
Constant
 
   e_Acoa2act_n
Value: 2.0
Constant
 
   e_Acoa2act_L
Value: 639000.0
Constant
 
   e_Acoa2act_Kacoa
Value: 0.022
Constant
 
   e_Acoa2act_Kpyr
Value: 0.022
Constant
 
   e_Acs_kcat
Value: 340.0
Constant
 
   e_Acs_Kact
Value: 0.0010
Constant
 
   e_Akg2mal_kcat
Value: 1530.0
Constant
 
   e_Akg2mal_Kakg
Value: 0.548
Constant
 
   e_CAMPdegr_kcat
Value: 1000.0
Constant
 
   e_CAMPdegr_KcAMP
Value: 0.1
Constant
 
   e_Cya_kcat
Value: 993.0
Constant
 
   e_Cya_KEIIA
Value: 0.0017
Constant
 
   e_Emp_kcat_f
Value: 1000.0
Constant
 
   e_Emp_kcat_r
Value: 848.0
Constant
 
   e_Emp_Kfbp
Value: 5.92
Constant
 
   e_Emp_Kpg3
Value: 16.6
Constant
 
   e_Eno_kcatf
Value: 695.0
Constant
 
   e_Eno_kcatr
Value: 522.0
Constant
 
   e_Eno_Kpg3
Value: 4.76
Constant
 
   e_Eno_Kpep
Value: 1.11
Constant
 
   e_Fdp_kcat
Value: 192.0
Constant
 
   e_Fdp_n
Value: 4.0
Constant
 
   e_Fdp_L
Value: 4000000.0
Constant
 
   e_Fdp_Kfbp
Value: 0.0030
Constant
 
   e_Fdp_Kpep
Value: 0.3
Constant
 
   e_GltA_kcat
Value: 1614.0
Constant
 
   e_GltA_Koaa
Value: 0.029
Constant
 
   e_GltA_Kacoa
Value: 0.212
Constant
 
   e_GltA_Koaaacoa
Value: 0.029
Constant
 
   e_GltA_Kakg
Value: 0.63
Constant
 
   e_Icd_kcat
Value: 695.0
Constant
 
   e_Icd_n
Value: 2.0
Constant
 
   e_Icd_L
Value: 127.0
Constant
 
   e_Icd_Kict
Value: 1.6E-4
Constant
 
   e_Icd_Kpep
Value: 0.334
Constant
 
   e_Mdh_kcat
Value: 773.0
Constant
 
   e_Mdh_n
Value: 1.7
Constant
 
   e_Mdh_Kmal
Value: 10.1
Constant
 
   e_Me_kcat
Value: 1879.0
Constant
 
   e_Me_n
Value: 1.33
Constant
 
   e_Me_L
Value: 104000.0
Constant
 
   e_Me_Kmal
Value: 0.00624
Constant
 
   e_Me_Kacoa
Value: 3.64
Constant
 
   e_Me_Kcamp
Value: 6.54
Constant
 
   e_PckA_kcat
Value: 55.5
Constant
 
   e_PckA_Koaa
Value: 0.184
Constant
 
   e_PckA_Kpep
Value: 1000.0
Constant
 
   e_Pdh_kcat
Value: 1179.0
Constant
 
   e_Pdh_n
Value: 2.65
Constant
 
   e_Pdh_L
Value: 3.4
Constant
 
   e_Pdh_Kpyr
Value: 0.128
Constant
 
   e_Pdh_KpyrI
Value: 0.231
Constant
 
   e_Pdh_Kglx
Value: 0.218
Constant
 
   e_PfkA_kcat
Value: 908000.0
Constant
 
   e_PfkA_n
Value: 4.0
Constant
 
   e_PfkA_L
Value: 9.5E7
Constant
 
   e_PfkA_Kg6p
Value: 0.022
Constant
 
   e_PfkA_Kpep
Value: 0.138
Constant
 
   e_Ppc_kcat
Value: 5635.0
Constant
 
   e_Ppc_n
Value: 3.0
Constant
 
   e_Ppc_L
Value: 5200000.0
Constant
 
   e_Ppc_Kpep
Value: 0.048
Constant
 
   e_Ppc_Kfbp
Value: 0.408
Constant
 
   e_PpsA_kcat
Value: 1.32
Constant
 
   e_PpsA_n
Value: 2.0
Constant
 
   e_PpsA_L
Value: 1.0E-79
Constant
 
   e_PpsA_Kpyr
Value: 0.00177
Constant
 
   e_PpsA_Kpep
Value: 0.0010
Constant
 
   e_PykF_kcat
Value: 5749.0
Constant
 
   e_PykF_n
Value: 4.0
Constant
 
   e_PykF_L
Value: 100000.0
Constant
 
   e_PykF_Kpep
Value: 5.0
Constant
 
   e_PykF_Kfbp
Value: 0.413
Constant
 
   pts_k1
Value: 116.0
Constant
 
   pts_km1
Value: 46.3
Constant
 
   pts_k4
Value: 2520.0
Constant
 
   pts_KEIIA
Value: 0.0085
Constant
 
   pts_Kglc
Value: 0.0012
Constant
 
   tf_Cra_scale
Value: 100.0
Constant
 
   tf_Cra_kfbp
Value: 1.36
Constant
 
   tf_Cra_n
Value: 2.0
Constant
 
   tf_Crp_scale
Value: 1.0E8
Constant
 
   tf_Crp_kcamp
Value: 0.895
Constant
 
   tf_Crp_n
Value: 1.0
Constant
 
   tf_PdhR_scale
Value: 100.0
Constant
 
   tf_PdhR_kpyr
Value: 0.164
Constant
 
   tf_PdhR_n
Value: 1.0
Constant
 
   g_aceBAK_vcra_unbound
Value: 1.9E-9
Constant
 
   g_aceBAK_vcra_bound
Value: 2.0E-6
Constant
 
   g_aceBAK_Kcra
Value: 0.00365
Constant
 
   g_aceBAK_aceBfactor
Value: 0.3
Constant
 
   g_aceBAK_aceKfactor
Value: 0.03
Constant
 
   g_aceBAK_KDNA
Value: 2.19
Constant
 
   g_aceBAK_KP
Value: 0.897
Constant
 
   g_aceBAK_KPprime
Value: 0.00301
Constant
 
   g_aceBAK_KG
Value: 0.00488
Constant
 
   g_aceBAK_L
Value: 923.0
Constant
 
   g_aceBAK_kcat_iclr
Value: 9.3E-4
Constant
 
   g_aceBAK_DNA
Value: 1.0
Constant
 
   g_aceBAK_vcrp_bound
Value: 2.3E-10
Constant
 
   g_aceBAK_vcrp_unbound
Value: 2.0E-8
Constant
 
   g_aceBAK_Kcrp
Value: 0.341
Constant
 
   g_acs_vcrp_unbound
Constant
 
   g_acs_vcrp_bound
Value: 1.2E-6
Constant
 
   g_acs_n
Value: 2.31
Constant
 
   g_acs_Kcrp
Value: 0.0047
Constant
 
   g_akg2mal_vcrp_unbound
Constant
 
   g_akg2mal_vcrp_bound
Value: 1.4E-6
Constant
 
   g_akg2mal_Kcrp
Value: 0.091
Constant
 
   g_akg2mal_n
Value: 0.74
Constant
 
   g_emp_vcra_unbound
Value: 6.2E-7
Constant
 
   g_emp_vcra_bound
Constant
 
   g_emp_Kcra
Value: 0.09
Constant
 
   g_emp_vcrp_unbound
Constant
 
   g_emp_vcrp_bound
Value: 4.7E-7
Constant
 
   g_emp_Kcrp
Value: 0.012
Constant
 
   g_eno_vcra_unbound
Value: 6.8E-7
Constant
 
   g_eno_vcra_bound
Constant
 
   g_eno_Kcra
Value: 0.016
Constant
 
   g_fdp_vcra_unbound
Constant
 
   g_fdp_vcra_bound
Value: 4.5E-8
Constant
 
   g_fdp_Kcra
Value: 0.00118
Constant
 
   g_gltA_vcrp_unbound
Constant
 
   g_gltA_vcrp_bound
Value: 2.3E-6
Constant
 
   g_gltA_Kcrp
Value: 0.04
Constant
 
   g_gltA_n
Value: 1.07
Constant
 
   g_icd_vcra_unbound
Value: 1.1E-7
Constant
 
   g_icd_vcra_bound
Value: 8.5E-7
Constant
 
   g_icd_Kcra
Value: 0.00117
Constant
 
   g_mdh_vcrp_unbound
Constant
 
   g_mdh_vcrp_bound
Value: 9.1E-6
Constant
 
   g_mdh_Kcrp
Value: 0.06
Constant
 
   g_pckA_vcra_unbound
Constant
 
   g_pckA_vcra_bound
Value: 2.5E-6
Constant
 
   g_pckA_Kcra
Value: 0.00535
Constant
 
   g_pdh_vpdhr_unbound
Value: 3.6E-7
Constant
 
   g_pdh_vpdhr_bound
Value: 1.3E-9
Constant
 
   g_pdh_Kpdhr
Value: 0.0034
Constant
 
   g_pfkA_vcra_unbound
Value: 8.2E-7
Constant
 
   g_pfkA_vcra_bound
Value: 6.6E-9
Constant
 
   g_pfkA_Kcra
Value: 6.3E-7
Constant
 
   g_ppsA_vcra_unbound
Constant
 
   g_ppsA_vcra_bound
Value: 3.3E-6
Constant
 
   g_ppsA_Kcra
Value: 0.017
Constant
 
   g_pykF_vcra_unbound
Value: 3.9E-7
Constant
 
   g_pykF_vcra_bound
Value: 2.1E-9
Constant
 
   g_pykF_Kcra
Value: 0.0023
Constant
 
   d_k_degr
Value: 2.8E-5
Constant
 
   bm_k_expr
Value: 20000.0
Constant
 
   bm_muACT
Value: 5.6E-5
Constant
 
   bm_muGLC
Value: 1.8E-4
Constant
 
   bm_GLC_ACoA
Value: 1.88
Constant
 
   bm_GLC_AKG
Value: 0.978
Constant
 
   bm_GLC_G6P
Value: 0.154
Constant
 
   bm_GLC_OAA
Value: 6.4
Constant
 
   bm_GLC_PEP
Value: 0.423
Constant
 
   bm_GLC_PG3
Value: 0.049
Constant
 
   bm_GLC_PYR
Value: 0.553
Constant
 
   bm_ACT_ACoA
Value: 0.108
Constant
 
   bm_ACT_AKG
Value: 0.056
Constant
 
   bm_ACT_G6P
Value: 0.076
Constant
 
   bm_ACT_OAA
Value: 1.43
Constant
 
   bm_ACT_PEP
Value: 0.047
Constant
 
   bm_ACT_PG3
Value: 0.066
Constant
 
   bm_ACT_PYR
Value: 5.185
Constant
 
   alphaGLC  
 
   alphaACT  
 
   mu  
 
   k_bm_ACoA  
 
   k_bm_AKG  
 
   k_bm_G6P  
 
   k_bm_OAA  
 
   k_bm_PEP  
 
   k_bm_PG3  
 
   k_bm_PYR  
 
   SS_Me  
 
   SS_Ppc  
 
   shift1
Value: 8.15   (Units: hours)
Constant
 
   shift2
Value: 27.85   (Units: hours)
Constant
 
   GLC_1
Constant
 
   GLC_2
Value: 3.0   (Units: gram_per_litre)
Constant
 
   ACT_1
Value: 5.0   (Units: gram_per_litre)
Constant
 
   ACT_2
Value: 3.0   (Units: gram_per_litre)
Constant
 
   BM_1
Value: 0.03
Constant
 
   BM_2
Value: 5.0E-4
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000244

Curator's comment: (updated: 15 Mar 2010 02:17:49 GMT)

Reproduction of figure 3 of the original article using RoadRunner (SBW 2.7.10). Integration was performed until 159 000 sec ~ 44.17 h simulation time.

As the model uses events to simulate the medium changes, a solver supporting these is required. Alternatively the simulations can be performed piecewise until the time points of growth medium changes and continuing after manual changes of the concentrations of GLC, ACT and BM. With Copasi this can be done using the "update model" option under time course.

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