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PTS2for

HPr + EI_P = HPr_P + EI

PTS2rev

HPr_P + EI = HPr + EI_P

PTS3for

IIA + HPr_P = IIA_P + HPr

PTS3rev

IIA_P + HPr = IIA + HPr_P

PTS4for

IICB + IIA_P = IICB_P + IIA

PTS4rev

IICB_P + IIA = IICB + IIA_P

binding_CRP_cAMP

CRP + cAMP = CRP_cAMP

binding_CRP_cAMP_CRPsiteII_crp

CRP_cAMP + CRPsiteII_crp = CRP_cAMP_CRPsiteII_crp

binding_CRP_cAMP_CRPsiteI_crp

CRP_cAMP + CRPsiteI_crp = CRP_cAMP_CRPsiteI_crp

binding_CRP_cAMP_CRPsite_cyaA

CRP_cAMP + CRPsite_cyaA = CRP_cAMP_CRPsite_cyaA

binding_CRP_cAMP_CRPsite_genome

CRP_cAMP + CRPsite_genome = CRP_cAMP_CRPsite_genome

binding_CRP_cAMP_CRPsite_mlcp1

CRP_cAMP + CRPsite_mlcp1 = CRP_cAMP_CRPsite_mlcp1

binding_CRP_cAMP_CRPsite_mlcp2

CRP_cAMP + CRPsite_mlcp2 = CRP_cAMP_CRPsite_mlcp2

binding_CRP_cAMP_CRPsite_ptsGp1

CRP_cAMP + CRPsite_ptsGp1 = CRP_cAMP_CRPsite_ptsGp1

binding_CRP_cAMP_CRPsite_ptsGp2

CRP_cAMP + CRPsite_ptsGp2 = CRP_cAMP_CRPsite_ptsGp2

binding_CRP_cAMP_CRPsite_ptsHp0

CRP_cAMP + CRPsite_ptsHp0 = CRP_cAMP_CRPsite_ptsHp0

binding_CRP_cAMP_CRPsite_ptsHp1

CRP_cAMP + CRPsite_ptsHp1 = CRP_cAMP_CRPsite_ptsHp1

binding_CRP_cAMP_CRPsite_ptsIp0

CRP_cAMP + CRPsite_ptsIp0 = CRP_cAMP_CRPsite_ptsIp0

binding_CRP_cAMP_CRPsite_ptsIp1

CRP_cAMP + CRPsite_ptsIp1 = CRP_cAMP_CRPsite_ptsIp1

binding_IIA_P_CYA

CYA + IIA_P = IIA_P_CYA

binding_IICB_Mlc

IICB + Mlc = IICB_Mlc

binding_Mlc_Mlcsite_mlcp1

Mlc + Mlcsite_mlcp1 = Mlc_Mlcsite_mlcp1

binding_Mlc_Mlcsite_mlcp2

Mlc + Mlcsite_mlcp2 = Mlc_Mlcsite_mlcp2

binding_Mlc_Mlcsite_ptsGp1

Mlc + Mlcsite_ptsGp1 = Mlc_Mlcsite_ptsGp1

binding_Mlc_Mlcsite_ptsGp2

Mlc + Mlcsite_ptsGp2 = Mlc_Mlcsite_ptsGp2

binding_Mlc_Mlcsite_ptsHp0

Mlc + Mlcsite_ptsHp0 = Mlc_Mlcsite_ptsHp0

binding_Mlc_Mlcsite_ptsIp0

Mlc + Mlcsite_ptsIp0 = Mlc_Mlcsite_ptsIp0

decomposition_CRP

CRP = ∅

decomposition_CRP_cAMP

CRP_cAMP = ∅

decomposition_CRP_cAMP_CRPsiteII_crp

CRP_cAMP_CRPsiteII_crp = CRPsiteII_crp

decomposition_CRP_cAMP_CRPsiteI_crp

CRP_cAMP_CRPsiteI_crp = CRPsiteI_crp

decomposition_CRP_cAMP_CRPsite_cyaA

CRP_cAMP_CRPsite_cyaA = CRPsite_cyaA

decomposition_CRP_cAMP_CRPsite_genome

CRP_cAMP_CRPsite_genome = CRPsite_genome

decomposition_CRP_cAMP_CRPsite_mlcp1

CRP_cAMP_CRPsite_mlcp1 = CRPsite_mlcp1

decomposition_CRP_cAMP_CRPsite_mlcp2

CRP_cAMP_CRPsite_mlcp2 = CRPsite_mlcp2

decomposition_CRP_cAMP_CRPsite_ptsGp1

CRP_cAMP_CRPsite_ptsGp1 = CRPsite_ptsGp1

decomposition_CRP_cAMP_CRPsite_ptsGp2

CRP_cAMP_CRPsite_ptsGp2 = CRPsite_ptsGp2

decomposition_CRP_cAMP_CRPsite_ptsHp0

CRP_cAMP_CRPsite_ptsHp0 = CRPsite_ptsHp0

decomposition_CRP_cAMP_CRPsite_ptsHp1

CRP_cAMP_CRPsite_ptsHp1 = CRPsite_ptsHp1

decomposition_CRP_cAMP_CRPsite_ptsIp0

CRP_cAMP_CRPsite_ptsIp0 = CRPsite_ptsIp0

decomposition_CRP_cAMP_CRPsite_ptsIp1

CRP_cAMP_CRPsite_ptsIp1 = CRPsite_ptsIp1

decomposition_CYA

CYA = ∅

decomposition_EI

EI = ∅

decomposition_EI_P

EI_P = ∅

decomposition_HPr

HPr = ∅

decomposition_HPr_P

HPr_P = ∅

decomposition_IIA

IIA = ∅

decomposition_IIA_P

IIA_P = ∅

decomposition_IICB

IICB = ∅

decomposition_IICB_Mlc

IICB_Mlc = ∅

decomposition_IICB_P

IICB_P = ∅

decomposition_Mlc

Mlc = ∅

decomposition_Mlc_Mlcsite_mlcp1

Mlc_Mlcsite_mlcp1 = Mlcsite_mlcp1

decomposition_Mlc_Mlcsite_mlcp2

Mlc_Mlcsite_mlcp2 = Mlcsite_mlcp2

decomposition_Mlc_Mlcsite_ptsGp1

Mlc_Mlcsite_ptsGp1 = Mlcsite_ptsGp1

decomposition_Mlc_Mlcsite_ptsGp2

Mlc_Mlcsite_ptsGp2 = Mlcsite_ptsGp2

decomposition_Mlc_Mlcsite_ptsHp0

Mlc_Mlcsite_ptsHp0 = Mlcsite_ptsHp0

decomposition_Mlc_Mlcsite_ptsIp0

Mlc_Mlcsite_ptsIp0 = Mlcsite_ptsIp0

decomposition_cAMP

cAMP = ∅

decomposition_mRNA_crp

mRNA_crp = ∅

decomposition_mRNA_crr

mRNA_crr = ∅

decomposition_mRNA_cyaA

mRNA_cyaA = ∅

decomposition_mRNA_mlc

mRNA_mlc = ∅

decomposition_mRNA_ptsG

mRNA_ptsG = ∅

decomposition_mRNA_ptsH

mRNA_ptsH = ∅

decomposition_mRNA_ptsI

mRNA_ptsI = ∅

reaction_CYA_ATP

ATP = cAMP

reaction_EIP_Pyr

EI_P + Pyr = EI + PEP

reaction_EI_PEP

EI + PEP = EI_P + Pyr

reaction_IIA_P_CYA_ATP

ATP = cAMP

reaction_IICB_Glc6P

IICB + Glc6P = IICB_P + Glucose

reaction_IICB_P_Glucose

IICB_P + Glucose = IICB + Glc6P

transcription_CRP_cAMP_CRPsiteI_crp_CRP_cAMP_CRPsiteII_crp_crp

∅ = mRNA_crp

transcription_CRP_cAMP_CRPsite_cyaA_cyaA

∅ = mRNA_cyaA

transcription_CRP_cAMP_CRPsite_mlcp1_Mlc_Mlcsite_mlcp1_mlcp1

∅ = mRNA_mlc

transcription_CRP_cAMP_CRPsite_mlcp2_Mlc_Mlcsite_mlcp2_mlcp2

∅ = mRNA_mlc

transcription_CRP_cAMP_CRPsite_ptsGp1_Mlc_Mlcsite_ptsGp1_ptsGp1

∅ = mRNA_ptsG

transcription_CRP_cAMP_CRPsite_ptsGp2_Mlc_Mlcsite_ptsGp2_ptsGp2

∅ = mRNA_ptsG

transcription_CRP_cAMP_CRPsite_ptsHp0_Mlc_Mlcsite_ptsHp0_ptsHp0

∅ = mRNA_ptsH

transcription_CRP_cAMP_CRPsite_ptsHp1_ptsHp1

∅ = mRNA_ptsH

transcription_CRP_cAMP_CRPsite_ptsIp0_Mlc_Mlcsite_ptsIp0_ptsIp0

∅ = mRNA_ptsI

transcription_CRP_cAMP_CRPsite_ptsIp1_ptsIp1

∅ = mRNA_ptsI

transcription_crp_basal

∅ = mRNA_crp

transcription_crr

∅ = mRNA_crr

transcription_cyaA_basal

∅ = mRNA_cyaA

translation_mRNA_crp

∅ = CRP

translation_mRNA_crr

∅ = IIA

translation_mRNA_cyaA

∅ = CYA

translation_mRNA_ptsG

∅ = IICB

translation_mRNA_ptsH

∅ = HPr

translation_mRNA_ptsI

∅ = EI

translation_mlc

∅ = Mlc

Parameters

Global parameters
PTS2for
PTS2rev
PTS3for
PTS3rev
PTS4for
PTS4rev
binding_CRP_cAMP
binding_CRP_cAMP_CRPsiteII_crp
binding_CRP_cAMP_CRPsiteI_crp
binding_CRP_cAMP_CRPsite_cyaA
binding_CRP_cAMP_CRPsite_genome
binding_CRP_cAMP_CRPsite_mlcp1
binding_CRP_cAMP_CRPsite_mlcp2
binding_CRP_cAMP_CRPsite_ptsGp1
binding_CRP_cAMP_CRPsite_ptsGp2
binding_CRP_cAMP_CRPsite_ptsHp0
binding_CRP_cAMP_CRPsite_ptsHp1
binding_CRP_cAMP_CRPsite_ptsIp0
binding_CRP_cAMP_CRPsite_ptsIp1
binding_IIA_P_CYA
binding_IICB_Mlc
binding_Mlc_Mlcsite_mlcp1
binding_Mlc_Mlcsite_mlcp2
binding_Mlc_Mlcsite_ptsGp1
binding_Mlc_Mlcsite_ptsGp2
binding_Mlc_Mlcsite_ptsHp0
binding_Mlc_Mlcsite_ptsIp0
decomposition_CRP
decomposition_CRP_cAMP
decomposition_CRP_cAMP_CRPsiteII_crp
decomposition_CRP_cAMP_CRPsiteI_crp
decomposition_CRP_cAMP_CRPsite_cyaA
decomposition_CRP_cAMP_CRPsite_genome
decomposition_CRP_cAMP_CRPsite_mlcp1
decomposition_CRP_cAMP_CRPsite_mlcp2
decomposition_CRP_cAMP_CRPsite_ptsGp1
decomposition_CRP_cAMP_CRPsite_ptsGp2
decomposition_CRP_cAMP_CRPsite_ptsHp0
decomposition_CRP_cAMP_CRPsite_ptsHp1
decomposition_CRP_cAMP_CRPsite_ptsIp0
decomposition_CRP_cAMP_CRPsite_ptsIp1
decomposition_CYA
decomposition_EI
decomposition_EI_P
decomposition_HPr
decomposition_HPr_P
decomposition_IIA
decomposition_IIA_P
decomposition_IICB
decomposition_IICB_Mlc
decomposition_IICB_P
decomposition_Mlc
decomposition_Mlc_Mlcsite_mlcp1
decomposition_Mlc_Mlcsite_mlcp2
decomposition_Mlc_Mlcsite_ptsGp1
decomposition_Mlc_Mlcsite_ptsGp2
decomposition_Mlc_Mlcsite_ptsHp0
decomposition_Mlc_Mlcsite_ptsIp0
decomposition_cAMP
decomposition_mRNA_crp
decomposition_mRNA_crr
decomposition_mRNA_cyaA
decomposition_mRNA_mlc
decomposition_mRNA_ptsG
decomposition_mRNA_ptsH
decomposition_mRNA_ptsI
reaction_CYA_ATP
reaction_EIP_Pyr
reaction_EI_PEP
reaction_IIA_P_CYA_ATP
reaction_IICB_Glc6P
reaction_IICB_P_Glucose
transcription_CRP_cAMP_CRPsiteI_crp_CRP_cAMP_CRPsiteII_crp_crp
transcription_CRP_cAMP_CRPsite_cyaA_cyaA
transcription_CRP_cAMP_CRPsite_mlcp1_Mlc_Mlcsite_mlcp1_mlcp1
transcription_CRP_cAMP_CRPsite_mlcp2_Mlc_Mlcsite_mlcp2_mlcp2
transcription_CRP_cAMP_CRPsite_ptsGp1_Mlc_Mlcsite_ptsGp1_ptsGp1
transcription_CRP_cAMP_CRPsite_ptsGp2_Mlc_Mlcsite_ptsGp2_ptsGp2
transcription_CRP_cAMP_CRPsite_ptsHp0_Mlc_Mlcsite_ptsHp0_ptsHp0
transcription_CRP_cAMP_CRPsite_ptsHp1_ptsHp1
transcription_CRP_cAMP_CRPsite_ptsIp0_Mlc_Mlcsite_ptsIp0_ptsIp0
transcription_CRP_cAMP_CRPsite_ptsIp1_ptsIp1
transcription_crp_basal
transcription_crr
transcription_cyaA_basal
translation_mRNA_crp
translation_mRNA_crr
translation_mRNA_cyaA
translation_mRNA_ptsG
translation_mRNA_ptsH
translation_mRNA_ptsI
translation_mlc

Fixed species

Initial values

Functions and Rules

Assignment rules

TMlcsite_ptsIp0 = Mlcsite_ptsIp0 + Mlc_Mlcsite_ptsIp0

TCRPsite_cyaA = CRPsite_cyaA + CRP_cAMP_CRPsite_cyaA

TCRPsiteII_crp = CRPsiteII_crp + CRP_cAMP_CRPsiteII_crp

TCRPsite_ptsGp2 = CRPsite_ptsGp2 + CRP_cAMP_CRPsite_ptsGp2

TMlcsite_ptsGp2 = Mlcsite_ptsGp2 + Mlc_Mlcsite_ptsGp2

TCRPsite_ptsHp0 = CRPsite_ptsHp0 + CRP_cAMP_CRPsite_ptsHp0

TMlcsite_ptsHp0 = Mlcsite_ptsHp0 + Mlc_Mlcsite_ptsHp0

TCRPsite_ptsHp1 = CRPsite_ptsHp1 + CRP_cAMP_CRPsite_ptsHp1

TCRPsite_ptsIp0 = CRPsite_ptsIp0 + CRP_cAMP_CRPsite_ptsIp0

TCRPsite_ptsIp1 = CRPsite_ptsIp1 + CRP_cAMP_CRPsite_ptsIp1

TMlcsite_mlcp1 = Mlcsite_mlcp1 + Mlc_Mlcsite_mlcp1

TCRPsite_mlcp1 = CRPsite_mlcp1 + CRP_cAMP_CRPsite_mlcp1

TMlcsite_mlcp2 = Mlcsite_mlcp2 + Mlc_Mlcsite_mlcp2

TCRPsite_mlcp2 = CRPsite_mlcp2 + CRP_cAMP_CRPsite_mlcp2

TMlcsite_ptsGp1 = Mlcsite_ptsGp1 + Mlc_Mlcsite_ptsGp1

TCRPsite_ptsGp1 = CRPsite_ptsGp1 + CRP_cAMP_CRPsite_ptsGp1

TCRPsiteI_crp = CRPsiteI_crp + CRP_cAMP_CRPsiteI_crp

Function definitions

Events

Trigger: geq(time, 500)

Delay:

Assignments:

  • Glucose = 2.000000e-09

Constraints

Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.


Species:

Reactions:

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Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli.

  • Yousuke Nishio
  • Yoshihiro Usuda
  • Kazuhiko Matsui
  • Hiroyuki Kurata
Mol. Syst. Biol. 2008; 4 : 160
Abstract
The phosphotransferase system (PTS) is the sugar transportation machinery that is widely distributed in prokaryotes and is critical for enhanced production of useful metabolites. To increase the glucose uptake rate, we propose a rational strategy for designing the molecular architecture of the Escherichia coli glucose PTS by using a computer-aided design (CAD) system and verified the simulated results with biological experiments. CAD supports construction of a biochemical map, mathematical modeling, simulation, and system analysis. Assuming that the PTS aims at controlling the glucose uptake rate, the PTS was decomposed into hierarchical modules, functional and flux modules, and the effect of changes in gene expression on the glucose uptake rate was simulated to make a rational strategy of how the gene regulatory network is engineered. Such design and analysis predicted that the mlc knockout mutant with ptsI gene overexpression would greatly increase the specific glucose uptake rate. By using biological experiments, we validated the prediction and the presented strategy, thereby enhancing the specific glucose uptake rate.
The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000571) Biomodels notes: Figure 3A of the reference publication has been reproduced here: simulated time course for IIAGlc protein in response to glucose depletion in the PTS for 1000 minutes. JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.