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BIOMD0000000217 - Bruggeman2005_AmmoniumAssimilation

 

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Reference Publication
Publication ID: 15819889
Bruggeman FJ, Boogerd FC, Westerhoff HV.
The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica.
FEBS J. 2005 Apr; 272(8): 1965-1985
Molecular Cell Physiology, Institute of Molecular Cell Biology, CRBCS, Vrije Universiteit, Amsterdam, the Netherlands.  [more]
Model
Original Model: JWS logo
Submitter: Lukas Endler
Submission ID: MODEL3579243073
Submission Date: 28 Nov 2008 17:27:48 UTC
Last Modification Date: 09 Aug 2012 16:34:03 UTC
Creation Date: 28 Nov 2008 17:24:29 UTC
Encoders:  Lukas Endler
   Vijayalakshmi Chelliah
   Frank Bruggeman
set #1
bqbiol:hasTaxon Taxonomy Escherichia coli
bqbiol:isVersionOf Gene Ontology ammonia assimilation cycle
Notes

This a model from the article:
The multifarious short-term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replica.
Bruggeman FJ, Boogerd FC, Westerhoff HV. FEBS J. 2005 Apr;272(8):1965-85. 15819889 ,
Abstract:
Ammonium assimilation in Escherichia coli is regulated through multiple mechanisms (metabolic, signal transduction leading to covalent modification, transcription, and translation), which (in-)directly affect the activities of its two ammonium-assimilating enzymes, i.e. glutamine synthetase (GS) and glutamate dehydrogenase (GDH). Much is known about the kinetic properties of the components of the regulatory network that these enzymes are part of, but the ways in which, and the extents to which the network leads to subtle and quasi-intelligent regulation are unappreciated. To determine whether our present knowledge of the interactions between and the kinetic properties of the components of this network is complete - to the extent that when integrated in a kinetic model it suffices to calculate observed physiological behaviour - we now construct a kinetic model of this network, based on all of the kinetic data on the components that is available in the literature. We use this model to analyse regulation of ammonium assimilation at various carbon statuses for cells that have adapted to low and high ammonium concentrations. We show how a sudden increase in ammonium availability brings about a rapid redirection of the ammonium assimilation flux from GS/glutamate synthase (GOGAT) to GDH. The extent of redistribution depends on the nitrogen and carbon status of the cell. We develop a method to quantify the relative importance of the various regulators in the network. We find the importance is shared among regulators. We confirm that the adenylylation state of GS is the major regulator but that a total of 40% of the regulation is mediated by ADP (22%), glutamate (10%), glutamine (7%) and ATP (1%). The total steady-state ammonium assimilation flux is remarkably robust against changes in the ammonium concentration, but the fluxes through GS and GDH are completely nonrobust. Gene expression of GOGAT above a threshold value makes expression of GS under ammonium-limited conditions, and of GDH under glucose-limited conditions, sufficient for ammonium assimilation.

This version of the model originates from JWS online . The original model can be retrieved here .

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.
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.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..

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: 15819889 Submission Date: 28 Nov 2008 17:27:48 UTC Last Modification Date: 09 Aug 2012 16:34:03 UTC Creation Date: 28 Nov 2008 17:24:29 UTC
Mathematical expressions
Reactions
vut1 vur1 vut2 vur2
vut3 vur3 vad vdead
vgdh vgog vgs vgludem
vazgludem vglndem vazglndem vatpase
Rules
Assignment Rule (variable: maxRateGS) Assignment Rule (variable: AdenylationStateGS) Assignment Rule (variable: PIIKG1) Assignment Rule (variable: PIIUMP3KG3)
Physical entities
Compartments Species
compartment PII UTP PIIUMP
PPi GLN PIIUMP2
PIIUMP3 UMP GS
AMP NH4 KG
NADPH GLU NADP
AZGLU ATP ADP
AZglu AZGLN AZgln
P_i    
Global parameters
UT kcatut Kglnut Kutipii
Kutpii Kutpiiump Kututp Kutippi
UR kcatur Kurpiiump Kurump
Kglnur a1 b1 c1
d1 Vad Kadpiikg Kadgln
Kadgs e1 f1 g1
h1 i1 j1 k1
l1 m1 n1 o1
Vdead Kdeadpiikg Kdeadgln Kdeadpiiu
Kdeadgsa Vgdh Kgdhkg Kgdhnh
Kgdhglu Kgdhnadph Kgdhnadp Keqgdh
Kgdhazglu Vgog Kgoggln Kgogkg
Kgognadph Kgogglu Kgognadp Kgogaz
Vgs aamp bamp camp
damp n1amp n2amp Kgseq
Kgsatp Kgsglu Kgsnh Kgsadp
Kgspi Kgsgln Keq Vgludem
Kgludemglu Kgludemeq Kgludemazglu Vglndem
Kglndemgln Kglndemeq Kglndemazgln Vazglndem
Kazglndemazgln Kazglndemeq Kazglndemazinter Vazgludem
Kazgludemazglu Kazgludemeq Kazgludemazinter Vadp
Kadp ATPtot GStot PIItot
Kd1 Kd2 Kd3 Kd1piiump
Kd2piiump Kd3piiump maxRateGS AdenylationStateGS
PIIKG1 PIIUMP3KG3    
Reactions (16)
 
 vut1 [PII] + [UTP] ↔ [PIIUMP] + [PPi];   {GLN} , {PIIUMP2} , {PIIUMP3}
 
 vur1 [PIIUMP] ↔ [PII] + [UMP];   {GLN} , {PIIUMP2} , {PIIUMP3}
 
 vut2 [PIIUMP] + [UTP] ↔ [PIIUMP2] + [PPi];   {GLN} , {PII} , {PIIUMP3}
 
 vur2 [PIIUMP2] ↔ [PIIUMP] + [UMP];   {GLN} , {PIIUMP3}
 
 vut3 [PIIUMP2] + [UTP] ↔ [PIIUMP3] + [PPi];   {GLN} , {PII} , {PIIUMP}
 
 vur3 [PIIUMP3] ↔ [PIIUMP2] + [UMP];   {GLN} , {PIIUMP}
 
 vad [GS] ↔ [AMP];   {GLN} , {PII} , {KG}
 
 vdead [AMP] ↔ [GS];   {GLN} , {PII} , {PIIUMP3} , {KG}
 
 vgdh [NH4] + [KG] + [NADPH] ↔ [GLU] + [NADP];  
 
 vgog [GLN] + [NADPH] + [KG] ↔ 2.0 × [GLU] + [NADP];   {AZGLU}
 
 vgs [GLU] + [ATP] + [NH4] ↔ [P_i] + [GLN] + [ADP];   {AMP}
 
 vgludem [GLU] ↔ [AZGLU];  
 
 vazgludem [AZGLU] ↔ [AZglu];  
 
 vglndem [GLN] ↔ [AZGLN];  
 
 vazglndem [AZGLN] ↔ [AZgln];  
 
 vatpase [ADP] ↔ [ATP];  
 
Rules (4)
 
 Assignment Rule (name: vAPP_GS) maxRateGS = aamp*camp/((1+12^n1amp*(AMP/(bamp*GStot))^n1amp)*(1+12^n2amp*(AMP/(damp*GStot))^n2amp))*Vgs
 
 Assignment Rule (name: nAMP) AdenylationStateGS = 12*AMP/GStot
 
 Assignment Rule (name: PIIKG1) PIIKG1 = 3*PII*KG/Kd1/(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3))
 
 Assignment Rule (name: PIIUMP3KG3) PIIUMP3KG3 = PIIUMP3*KG^3/(Kd1piiump*Kd2piiump*Kd3piiump)/(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))
 
   compartment Spatial dimensions: 3.0  Compartment size: 1.0
 
 PII
Compartment: compartment
Initial concentration: 0.003
 
 UTP
Compartment: compartment
Initial concentration: 0.5
Constant
 
   PIIUMP
Compartment: compartment
Initial concentration: 0.0
 
 PPi
Compartment: compartment
Initial concentration: 0.05
Constant
 
 GLN
Compartment: compartment
Initial concentration: 1.0
 
   PIIUMP2
Compartment: compartment
Initial concentration: 0.0
 
   PIIUMP3
Compartment: compartment
Initial concentration: 0.0
 
 UMP
Compartment: compartment
Initial concentration: 0.01
Constant
 
 GS
Compartment: compartment
Initial concentration: 0.014
 
 AMP
Compartment: compartment
Initial concentration: 0.0
 
 NH4
Compartment: compartment
Initial concentration: 0.05
Constant
 
 KG
Compartment: compartment
Initial concentration: 0.2
Constant
 
 NADPH
Compartment: compartment
Initial concentration: 0.15
Constant
 
 GLU
Compartment: compartment
Initial concentration: 1.0
 
 NADP
Compartment: compartment
Initial concentration: 0.05
Constant
 
   AZGLU
Compartment: compartment
Initial concentration: 1.0
 
 ATP
Compartment: compartment
Initial concentration: 2.685
 
 ADP
Compartment: compartment
Initial concentration: 2.685
 
   AZglu
Compartment: compartment
Initial concentration: 0.1
Constant
 
   AZGLN
Compartment: compartment
Initial concentration: 1.0
 
   AZgln
Compartment: compartment
Initial concentration: 0.1
Constant
 
 P_i
Compartment: compartment
Initial concentration: 10.0
 
Global Parameters (98)
 
   UT
Value: 6.0E-4
Constant
 
   kcatut
Value: 137.0
Constant
 
   Kglnut
Value: 0.07
Constant
 
   Kutipii
Value: 0.0018
Constant
 
   Kutpii
Value: 0.003
Constant
 
   Kutpiiump
Value: 0.0035
Constant
 
   Kututp
Value: 0.04
Constant
 
   Kutippi
Value: 0.1135
Constant
 
   UR
Value: 6.0E-4
Constant
 
   kcatur
Value: 5.5
Constant
 
   Kurpiiump
Value: 0.0023
Constant
 
   Kurump
Value: 8.4
Constant
 
   Kglnur
Value: 0.07
Constant
 
   a1
Value: 1.0E-22
Constant
 
   b1
Value: 0.5166
Constant
 
   c1
Value: 0.5974
Constant
 
   d1
Value: 0.0387
Constant
 
   Vad
Value: 0.5
Constant
 
   Kadpiikg
Value: 1.052E-5
Constant
 
   Kadgln
Value: 0.9714
Constant
 
   Kadgs
Value: 0.001703
Constant
 
   e1
Value: 1.0E-22
Constant
 
   f1
Value: 2.766
Constant
 
   g1
Value: 3.323
Constant
 
   h1
Value: 0.2148
Constant
 
   i1
Value: 1.0E-22
Constant
 
   j1
Value: 1.0E-22
Constant
 
   k1
Value: 1.0E-22
Constant
 
   l1
Value: 0.02316
Constant
 
   m1
Value: 0.8821
Constant
 
   n1
Value: 8.491
Constant
 
   o1
Value: 0.8791
Constant
 
   Vdead
Value: 0.5
Constant
 
   Kdeadpiikg
Value: 2.274E-6
Constant
 
   Kdeadgln
Value: 0.04444
Constant
 
   Kdeadpiiu
Value: 1.805E-5
Constant
 
   Kdeadgsa
Value: 2.015E-4
Constant
 
   Vgdh
Value: 360.0
Constant
 
   Kgdhkg
Value: 0.32
Constant
 
   Kgdhnh
Value: 1.1
Constant
 
   Kgdhglu
Value: 10.0
Constant
 
   Kgdhnadph
Value: 0.04
Constant
 
   Kgdhnadp
Value: 0.042
Constant
 
   Keqgdh
Value: 1290.0
Constant
 
   Kgdhazglu
Value: 2.5
Constant
 
   Vgog
Value: 85.0
Constant
 
   Kgoggln
Value: 0.175
Constant
 
   Kgogkg
Value: 0.007
Constant
 
   Kgognadph
Value: 0.0015
Constant
 
   Kgogglu
Value: 11.0
Constant
 
   Kgognadp
Value: 0.0037
Constant
 
   Kgogaz
Value: 0.65
Constant
 
   Vgs
Value: 600.0
Constant
 
   aamp
Value: 10.0
Constant
 
   bamp
Value: 2.3667
Constant
 
   camp
Value: 0.1012
Constant
 
   damp
Value: 10.8688
Constant
 
   n1amp
Value: 1.1456
Constant
 
   n2amp
Value: 19.2166
Constant
 
   Kgseq
Value: 460.0
Constant
 
   Kgsatp
Value: 0.35
Constant
 
   Kgsglu
Value: 4.1
Constant
 
   Kgsnh
Value: 0.1
Constant
 
   Kgsadp
Value: 0.0585
Constant
 
   Kgspi
Value: 3.7
Constant
 
   Kgsgln
Value: 5.65
Constant
 
   Keq
Value: 460.0   (Units: dimensionless)
Constant
 
   Vgludem
Value: 120.0
Constant
 
   Kgludemglu
Value: 8.0
Constant
 
   Kgludemeq
Value: 1.0E10
Constant
 
   Kgludemazglu
Value: 0.5
Constant
 
   Vglndem
Value: 70.0
Constant
 
   Kglndemgln
Value: 2.0
Constant
 
   Kglndemeq
Value: 1.0E10
Constant
 
   Kglndemazgln
Value: 0.25
Constant
 
   Vazglndem
Value: 20.0
Constant
 
   Kazglndemazgln
Value: 1.0
Constant
 
   Kazglndemeq
Value: 1.0E10
Constant
 
   Kazglndemazinter
Value: 0.5
Constant
 
   Vazgludem
Value: 30.0
Constant
 
   Kazgludemazglu
Value: 0.3
Constant
 
   Kazgludemeq
Value: 1.0E10   (Units: dimensionless)
Constant
 
   Kazgludemazinter
Value: 0.5   (Units: dimensionless)
Constant
 
   Vadp
Value: 100.0
Constant
 
   Kadp
Value: 0.5
Constant
 
   ATPtot
Value: 5.37
Constant
 
   GStot
Value: 0.014
Constant
 
   PIItot
Value: 0.003
Constant
 
   Kd1
Value: 0.005
Constant
 
   Kd2
Value: 0.15
Constant
 
   Kd3
Value: 0.15
Constant
 
   Kd1piiump
Value: 0.025
Constant
 
   Kd2piiump
Value: 0.15
Constant
 
   Kd3piiump
Value: 0.15
Constant
 
   maxRateGS
Value: NaN
 
   AdenylationStateGS
Value: NaN
 
   PIIKG1
Value: NaN
 
   PIIUMP3KG3
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000217

Curator's comment: (updated: 29 Jun 2009 12:45:35 BST)

Figure 2 of the reference publication is reproduced. For generating figures A,C,E and G - [KG]=0.2mM and for the figures B,D,F and H - [KG]=1.0mM. The model was simulated and run using Copasi v4.5.

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