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BIOMD0000000222 - Singh2006_TCA_Ecoli_glucose

 

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Reference Publication
Publication ID: 16887020
Singh VK, Ghosh I.
Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets.
Theor Biol Med Model 2006; 3: 27
Bioinformatics Centre, University of Pune, Pune-411007, India. vivek@bioinfo.ernet.in  [more]
Model
Original Model: BIOMD0000000222.xml.origin
Submitter: Indira Ghosh
Submission ID: MODEL8583955822
Submission Date: 29 Sep 2006 22:47:42 UTC
Last Modification Date: 20 Dec 2010 09:47:18 UTC
Creation Date: 29 Sep 2006 22:47:42 UTC
Encoders:  Vijayalakshmi Chelliah
   Vivek Kumar Singh
set #1
bqbiol:isVersionOf KEGG Pathway ko00020
bqbiol:isHomologTo Reactome REACT_1785
bqbiol:occursIn Taxonomy Escherichia coli
bqbiol:hasVersion Gene Ontology tricarboxylic acid cycle
Gene Ontology glyoxylate cycle
Notes

This a model from the article:
Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drugtargets.
Singh VK , Ghosh I Theor Biol Med Model 2006 Aug 3;3:27 16887020 ,
Abstract:
BACKGROUND: Targeting persistent tubercule bacilli has become an important challenge in the development of anti-tuberculous drugs. As the glyoxylate bypass is essential for persistent bacilli, interference with it holds the potential for designing new antibacterial drugs. We have developed kinetic models of the tricarboxylic acid cycle and glyoxylate bypass in Escherichia coli and Mycobacterium tuberculosis, and studied the effects of inhibition of various enzymes in the M. tuberculosis model. RESULTS: We used E. coli to validate the pathway-modeling protocol and showed that changes in metabolic flux can be estimated from gene expression data. The M. tuberculosis model reproduced the observation that deletion of one of the two isocitrate lyase genes has little effect on bacterial growth in macrophages, but deletion of both genes leads to the elimination of the bacilli from the lungs. It also substantiated the inhibition of isocitrate lyases by 3-nitropropionate. On the basis of our simulation studies, we propose that: (i) fractional inactivation of both isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 is required for a flux through the glyoxylate bypass in persistent mycobacteria; and (ii) increasing the amountof active isocitrate dehydrogenases can stop the flux through the glyoxylate bypass, so the kinase that inactivates isocitrate dehydrogenase 1 and/or the proposed inactivator of isocitrate dehydrogenase 2 is a potential target for drugs against persistent mycobacteria. In addition, competitive inhibition of isocitrate lyases along with a reduction in the inactivation of isocitrate dehydrogenases appears to be a feasible strategy for targeting persistent mycobacteria. CONCLUSION: We used kinetic modeling of biochemical pathways to assess various potential anti-tuberculous drug targets that interfere with the glyoxylate bypass flux, and indicated the type of inhibition needed to eliminate the pathogen. The advantage of such an approach to the assessment of drug targets is that it facilitates the study of systemic effect(s) of the modulation of the target enzyme(s) in the cellular environment.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team.
For more information see the terms of use .
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 16887020 Submission Date: 29 Sep 2006 22:47:42 UTC Last Modification Date: 20 Dec 2010 09:47:18 UTC Creation Date: 29 Sep 2006 22:47:42 UTC
Mathematical expressions
Reactions
CS ACN ICD KDH
ScAS SDH FUM MDH
ICL MS SYN  
Physical entities
Compartments Species
cell aca oaa coa
cit icit akg
sca suc fa
mal gly biosyn
Reactions (11)
 
 CS [aca] + [oaa] ↔ [coa] + [cit];  
 
 ACN [cit] ↔ [icit];  
 
 ICD [icit] ↔ [akg];  
 
 KDH [akg] ↔ [sca];  
 
 ScAS [sca] ↔ [suc];  
 
 SDH [suc] ↔ [fa];  
 
 FUM [fa] ↔ [mal];  
 
 MDH [mal] ↔ [oaa];  
 
 ICL [icit] ↔ [suc] + [gly];  
 
 MS [gly] + [aca] ↔ [mal] + [coa];  
 
 SYN [akg] ↔ [biosyn];   {icit}
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 aca
Compartment: cell
Initial concentration: 0.5
 
 oaa
Compartment: cell
Initial concentration: 0.0040
 
 coa
Compartment: cell
Initial concentration: 1.0E-4
 
 cit
Compartment: cell
Initial concentration: 3.0
 
 icit
Compartment: cell
Initial concentration: 0.018
 
 akg
Compartment: cell
Initial concentration: 0.2
 
 sca
Compartment: cell
Initial concentration: 0.04
 
 suc
Compartment: cell
Initial concentration: 0.6
 
 fa
Compartment: cell
Initial concentration: 0.3
 
 mal
Compartment: cell
Initial concentration: 1.8
 
 gly
Compartment: cell
Initial concentration: 4.0
 
   biosyn
Compartment: cell
Initial concentration: 0.1
 
CS (6)
 
 Vf_cs
Value: 91.2   (Units: mM_per_min)
Constant
 
 Kaca_cs
Value: 0.03   (Units: mM)
Constant
 
 Koaa_cs
Value: 0.07   (Units: mM)
Constant
 
 Vr_cs
Value: 0.912   (Units: mM_per_min)
Constant
 
 Kcoa_cs
Value: 0.3   (Units: mM)
Constant
 
 Kcit_cs
Value: 0.7   (Units: mM)
Constant
 
ACN (4)
 
 Vf_acn
Value: 91.2   (Units: mM_per_min)
Constant
 
 Kcit_acn
Value: 1.7   (Units: mM)
Constant
 
 Vr_acn
Value: 0.912   (Units: mM_per_min)
Constant
 
 Kicit_acn
Value: 3.33   (Units: mM)
Constant
 
ICD (4)
 
 Vf_icd
Value: 14.72   (Units: mM_per_min)
Constant
 
 Kicit_icd
Value: 0.0080   (Units: mM)
Constant
 
 Vr_icd
Value: 0.1472   (Units: mM_per_min)
Constant
 
 Kakg_icd
Value: 0.13   (Units: mM)
Constant
 
KDH (4)
 
 Vf_kdh
Value: 35.84   (Units: mM_per_min)
Constant
 
 Kakg_kdh
Value: 0.1   (Units: mM)
Constant
 
 Vr_kdh
Value: 0.3584   (Units: mM_per_min)
Constant
 
 Ksca_kdh
Value: 1.0   (Units: mM)
Constant
 
ScAS (4)
 
 Vf_scas
Value: 3.5   (Units: mM_per_min)
Constant
 
 Ksca_scas
Value: 0.02   (Units: mM)
Constant
 
 Vr_scas
Value: 0.035   (Units: mM_per_min)
Constant
 
 Ksuc_scas
Value: 5.0   (Units: mM)
Constant
 
SDH (4)
 
 Vf_sdh
Value: 7.38   (Units: mM_per_min)
Constant
 
 Ksuc_sdh
Value: 0.02   (Units: mM)
Constant
 
 Vr_sdh
Value: 7.31   (Units: mM_per_min)
Constant
 
 Kfa_sdh
Value: 0.4   (Units: mM)
Constant
 
FUM (4)
 
 Vf_fum
Value: 44.64   (Units: mM_per_min)
Constant
 
 Kfa_fum
Value: 0.15   (Units: mM)
Constant
 
 Vr_fum
Value: 37.2   (Units: mM_per_min)
Constant
 
 Kmal_fum
Value: 0.04   (Units: mM)
Constant
 
MDH (4)
 
 Vf_mdh
Value: 356.64   (Units: mM_per_min)
Constant
 
 Kmal_mdh
Value: 2.6   (Units: mM)
Constant
 
 Vr_mdh
Value: 353.11   (Units: mM_per_min)
Constant
 
 Koaa_mdh
Value: 0.04   (Units: mM)
Constant
 
ICL (5)
 
 Vf_icl
Value: 1.9   (Units: mM_per_min)
Constant
 
 Kicit_icl
Value: 0.604   (Units: mM)
Constant
 
 Vr_icl
Value: 0.019   (Units: mM_per_min)
Constant
 
 Ksuc_icl
Value: 0.59   (Units: mM)
Constant
 
 Kgly_icl
Value: 0.13   (Units: mM)
Constant
 
MS (6)
 
 Vf_ms
Value: 1.9   (Units: mM_per_min)
Constant
 
 Kgly_ms
Value: 2.0   (Units: mM)
Constant
 
 Kaca_ms
Value: 0.01   (Units: mM)
Constant
 
 Vr_ms
Value: 0.019   (Units: mM_per_min)
Constant
 
 Kmal_ms
Value: 1.0   (Units: mM)
Constant
 
 Kcoa_ms
Value: 0.1   (Units: mM)
Constant
 
SYN (4)
 
 Vf_icd
Value: 14.72   (Units: mM_per_min)
Constant
 
 Kicit_icd
Value: 0.0080   (Units: mM)
Constant
 
 Vr_icd
Value: 0.1472   (Units: mM_per_min)
Constant
 
 Kakg_icd
Value: 0.13   (Units: mM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000222

Curator's comment: (updated: 07 Jul 2009 16:17:50 BST)

This model corresponds to the E.coli growth on glucose model, reported in the publication. Steady state fluxes computed based on the simulation (Table 2 - Column 2)and that compared to the experimental fluxes (Table 3 - Column 3), reported in the reference publication is reproduced here.

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