Try the new BioModels platform (beta)
BioModels Database logo

BioModels Database

spacer

BIOMD0000000240 - Veening2008_DegU_Regulation

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 18414485
Veening JW, Igoshin OA, Eijlander RT, Nijland R, Hamoen LW, Kuipers OP.
Transient heterogeneity in extracellular protease production by Bacillus subtilis.
Mol. Syst. Biol. 2008; 4: 184
Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.  [more]
Model
Original Model: http://www.nature.com/msb/...
Submitter: Lukas Endler
Submission ID: MODEL8237240421
Submission Date: 02 Dec 2008 17:09:30 UTC
Last Modification Date: 04 Apr 2014 15:38:28 UTC
Creation Date: 02 Dec 2008 16:57:44 UTC
Encoders:  Vijayalakshmi Chelliah
   Jan-Willem Veening
   Oleg A Igoshin
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:isVersionOf Gene Ontology endospore formation
Gene Ontology entry of bacterium into host cell
set #3
bqbiol:hasTaxon Taxonomy Octodon degus
set #4
bqbiol:hasTaxon Taxonomy Bacillus subtilis
Notes

This a model from the article:
Transient heterogeneity in extracellular protease production by Bacillus subtilis.
Veening JW, Igoshin OA, Eijlander RT, Nijland R, Hamoen LW, Kuipers OP Mol. Syst. Biol. 2008 ; Volume: 4 : 184 18414485,
Abstract:
The most sophisticated survival strategy Bacillus subtilis employs is the differentiation of a subpopulation of cells into highly resistant endospores. To examine the expression patterns of non-sporulating cells within heterogeneous populations, we used buoyant density centrifugation to separate vegetative cells from endospore-containing cells and compared the transcriptome profiles of both subpopulations. This demonstrated the differential expression of various regulons. Subsequent single-cell analyses using promoter-gfp fusions confirmed our microarray results. Surprisingly, only part of the vegetative subpopulation highly and transiently expresses genes encoding the extracellular proteases Bpr (bacillopeptidase) and AprE (subtilisin), both of which are under the control of the DegU transcriptional regulator. As these proteases and their degradation products freely diffuse within the liquid growth medium, all cells within the clonal population are expected to benefit from their activities, suggesting that B. subtilis employs cooperative or even altruistic behavior. To unravel the mechanisms by which protease production heterogeneity within the non-sporulating subpopulation is established, we performed a series of genetic experiments combined with mathematical modeling. Simulations with our model yield valuable insights into how population heterogeneity may arise by the relatively long and variable response times within the DegU autoactivating pathway.


This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 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: 18414485 Submission Date: 02 Dec 2008 17:09:30 UTC Last Modification Date: 04 Apr 2014 15:38:28 UTC Creation Date: 02 Dec 2008 16:57:44 UTC
Mathematical expressions
Reactions
AprEdeg AprEsyn DimerAss DimerDis
degradation1 degradation2 degradation3 degradationmRNA
dephosphorylation mRNAAprEdeg mRNAAprEsyn phosphorylation
synthesisDegU synthesismRNA    
Rules
Assignment Rule (variable: kphos) Assignment Rule (variable: kdephos) Assignment Rule (variable: DegU_Total)  
Physical entities
Compartments Species
univ AprE DegU DegUP
Dim mAprE mDegU
Global parameters
Imax Io Irmax Iro
K Kdim Kr Kr1
R V ka kd
kdeg kdegA kdegm kdephos
kphos ksyn ksyn1 p
q kphosratiokdephos DegU_Total  
Reactions (14)
 
 AprEdeg [AprE] → ;  
 
 AprEsyn  → [AprE];   {mAprE}
 
 DimerAss 2.0 × [DegUP] → [Dim];  
 
 DimerDis [Dim] → 2.0 × [DegUP];  
 
 degradation1 [DegU] → ;  
 
 degradation2 [DegUP] → ;  
 
 degradation3 [Dim] → ;  
 
 degradationmRNA [mDegU] → ;  
 
 dephosphorylation [DegUP] → [DegU];  
 
 mRNAAprEdeg [mAprE] → ;  
 
 mRNAAprEsyn  → [mAprE];   {Dim}
 
 phosphorylation [DegU] → [DegUP];  
 
 synthesisDegU  → [DegU];   {mDegU}
 
 synthesismRNA  → [mDegU];   {Dim}
 
Rules (3)
 
 Assignment Rule (name: kphos) kphos = ratio*p
 
 Assignment Rule (name: kdephos) kdephos = q/ratio
 
 Assignment Rule (name: DegU_Total) DegU_Total = DegU+DegUP+2*Dim
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 AprE
Compartment: univ
Initial amount: 0.0
 
 DegU
Compartment: univ
Initial amount: 10.0
 
 DegUP
Compartment: univ
Initial amount: 0.0
 
 Dim
Compartment: univ
Initial amount: 0.0
 
 mAprE
Compartment: univ
Initial amount: 0.0
 
 mDegU
Compartment: univ
Initial amount: 0.0
 
Global Parameters (23)
 
 Imax
Value: 0.048
Constant
 
 Io
Value: 0.004
Constant
 
 Irmax
Value: 0.4
Constant
 
 Iro
Value: 0.02
Constant
 
 K
Value: 7.0
Constant
 
 Kdim
Value: 12.0
Constant
 
 Kr
Value: 7.0
Constant
 
 Kr1
Value: 7.0
Constant
 
   R
Value: 7.0
Constant
 
   V
Value: 1.0
Constant
 
 ka
Value: 0.025
Constant
 
 kd
Value: 0.1
Constant
 
 kdeg
Value: 4.0E-4
Constant
 
 kdegA
Value: 1.0E-4
Constant
 
 kdegm
Value: 0.01
Constant
 
  kdephos
Value: NaN
 
  kphos
Value: NaN
 
 ksyn
Value: 0.04
Constant
 
 ksyn1
Value: 0.04
Constant
 
   p
Value: 0.15
Constant
 
   q
Value: 0.004
Constant
 
   kphosratiokdephos
Value: 0.026666667
Constant
 
   DegU_Total
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000240

Curator's comment: (updated: 21 Dec 2009 14:51:58 GMT)

Figure 7A and 7B is reproduced here. We got the following useful information for curation from the authors. In the paper, the x-axis is mislabelled by a factor of 5, and also the values for 3 of the parameters are incorrect in the paper. The parameters and their correct values are 1) Kdim (K1 for aprE, in the paper)= 12, 2) kphos (kph, in the paper) = 0.004, and 3) kdephos (kdeph, in the paper) = 0.15.
All these are implemented in the model. The model was simulated and integrated using Copasi

spacer
spacer