Liebal2012 - B.subtilis transcription inhibition model
An important transcription factor of B.subsilis is sigma B . Liebal et al. (2012) have performed experiments in B.subtilis wild type and mutant straits to test and validate a mathematical model of the dynamics of sigma B activity. The following three models are constructed and their ability to fit the experimental data were tested. 1) Transcription inhibition model (MODEL1212180000), 2) sigma B proteolysis model (MODEL1302080000) and 3) Post-transcriptional instability model (MODEL1302080001). This model corresponds to the Transcription inhibition model (MODEL1212180000).
This model is described in the article:
Abstract:
In Bacillus subtilis the σ(B) mediated general stress response provides protection against various environmental and energy related stress conditions. To better understand the general stress response, we need to explore the mechanism by which the components interact. Here, we performed experiments in B. subtilis wild type and mutant strains to test and validate a mathematical model of the dynamics of σ(B) activity. In the mutant strain BSA115, σ(B) transcription is inducible by the addition of IPTG and negative control of σ(B) activity by the anti-sigma factor RsbW is absent. In contrast to our expectations of a continuous β-galactosidase activity from a ctc::lacZ fusion, we observed a transient activity in the mutant. To explain this experimental finding, we constructed mathematical models reflecting different hypotheses regarding the regulation of σ(B) and β-galactosidase dynamics. Only the model assuming instability of either ctc::lacZ mRNA or β-galactosidase protein is able to reproduce the experiments in silico. Subsequent Northern blot experiments revealed stable high-level ctc::lacZ mRNA concentrations after the induction of the σ(B) response. Therefore, we conclude that protein instability following σ(B) activation is the most likely explanation for the experimental observations. Our results thus support the idea that B. subtilis increases the cytoplasmic proteolytic degradation to adapt the proteome in face of environmental challenges following activation of the general stress response. The findings also have practical implications for the analysis of stress response dynamics using lacZ reporter gene fusions, a frequently used strategy for the σ(B) response.
Figure 3a of the reference article has been reproduced. beta-galactosidase (lacz in model) activity at different concentrations of IPTG (100M, 200M and 1000M) has been reproduced. SED-ML (Simulation Experiment Description Markup Language) file is available for this model (see curation tab).
This model is hosted on BioModels Database and identified by: MODEL1212180000 .
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models .
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.
-
Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis.
- Liebal UW, Sappa PK, Millat T, Steil L, Homuth G, Völker U, Wolkenhauer O
- Molecular bioSystems , 6/ 2012 , Volume 8 , pages: 1806-1814 , PubMed ID: 22511268
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, Germany. ulf.liebal@uni-rostock.de
- In Bacillus subtilis the σ(B) mediated general stress response provides protection against various environmental and energy related stress conditions. To better understand the general stress response, we need to explore the mechanism by which the components interact. Here, we performed experiments in B. subtilis wild type and mutant strains to test and validate a mathematical model of the dynamics of σ(B) activity. In the mutant strain BSA115, σ(B) transcription is inducible by the addition of IPTG and negative control of σ(B) activity by the anti-sigma factor RsbW is absent. In contrast to our expectations of a continuous β-galactosidase activity from a ctc::lacZ fusion, we observed a transient activity in the mutant. To explain this experimental finding, we constructed mathematical models reflecting different hypotheses regarding the regulation of σ(B) and β-galactosidase dynamics. Only the model assuming instability of either ctc::lacZ mRNA or β-galactosidase protein is able to reproduce the experiments in silico. Subsequent Northern blot experiments revealed stable high-level ctc::lacZ mRNA concentrations after the induction of the σ(B) response. Therefore, we conclude that protein instability following σ(B) activation is the most likely explanation for the experimental observations. Our results thus support the idea that B. subtilis increases the cytoplasmic proteolytic degradation to adapt the proteome in face of environmental challenges following activation of the general stress response. The findings also have practical implications for the analysis of stress response dynamics using lacZ reporter gene fusions, a frequently used strategy for the σ(B) response.
Submitter of this revision: administrator
Modellers: administrator, Ulf Liebal
Metadata information
BioModels Database BIOMD0000000461
Gene Ontology regulation of proteolysis
isDescribedBy (1 statement)
hasTaxon (1 statement)
Connected external resources
SBGN view in Newt Editor
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
|||
| BIOMD0000000461_url.xml | SBML L2V4 representation of Liebal2012 - B.subtilis transcription inhibition model | 18.06 KB | Preview | Download |
Additional files |
|||
| BIOMD0000000461-SEDML.xml | This SED-ML file can be used to reproduce the curation result (for example, figure 3a of the reference publication), by loading it into SED-ML Web Tools (http://sysbioapps.dyndns.org/SED-ML_Web_Tools/). | 4.27 KB | Preview | Download |
| BIOMD0000000461-biopax2.owl | Auto-generated BioPAX (Level 2) | 9.45 KB | Preview | Download |
| BIOMD0000000461-biopax3.owl | Auto-generated BioPAX (Level 3) | 12.05 KB | Preview | Download |
| BIOMD0000000461.m | Auto-generated Octave file | 3.28 KB | Preview | Download |
| BIOMD0000000461.pdf | Auto-generated PDF file | 146.87 KB | Preview | Download |
| BIOMD0000000461.png | Auto-generated Reaction graph (PNG) | 38.39 KB | Preview | Download |
| BIOMD0000000461.sci | Auto-generated Scilab file | 1.31 KB | Preview | Download |
| BIOMD0000000461.svg | Auto-generated Reaction graph (SVG) | 10.36 KB | Preview | Download |
| BIOMD0000000461.vcml | Auto-generated VCML file | 910.00 Bytes | Preview | Download |
| BIOMD0000000461.xpp | Auto-generated XPP file | 1.58 KB | Preview | Download |
| BIOMD0000000461_urn.xml | Auto-generated SBML file with URNs | 17.64 KB | Preview | Download |
- Model originally submitted by : Ulf Liebal
- Submitted: Dec 18, 2012 2:48:57 PM
- Last Modified: Dec 21, 2018 5:19:00 PM
Revisions
-
Version: 3
- Submitted on: Dec 21, 2018 5:19:00 PM
- Submitted by: administrator
- With comment: Include the additional files provided by the submitter in the original submission: BIOMD0000000461-SEDML.xml
-
Version: 2
- Submitted on: May 30, 2014 5:05:28 PM
- Submitted by: Ulf Liebal
- With comment: Current version of Liebal2012 - B.subtilis transcription inhibition model
-
Version: 1
- Submitted on: Dec 18, 2012 2:48:57 PM
- Submitted by: Ulf Liebal
- With comment: Original import of bsatrscrinhib
(*) You might be seeing discontinuous
revisions as only public revisions are displayed here. Any private revisions
of this model will only be shown to the submitter and their collaborators.
: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| IPTG isopropyl beta-D-thiogalactopyranoside |
100.0 mol |
| sigb IPR006288 |
0.0 mol |
| x inhibitor |
0.0 mol |
| lacz Beta-galactosidase 12 ; beta-galactosidase activity |
0.0 mol |
| Reactions | Rate | Parameters |
|---|---|---|
| IPTG => sigb; IPTG, sigb | IPTG*kbs-kbd*sigb | kbd = 0.044; kbs = 100.0 |
| sigb => x; x, sigb | (-kxd*x)+kxs*sigb/(1+x) | kxd = 9.0; kxs = 0.76 |
| sigb => lacz; x, lacz, sigb, x | (-kzd*lacz)+kzs*sigb/(1+x) | kzs = 4.0E-4; kzd = 0.041 |
(added: 08 Feb 2013, 13:23:47, updated: 08 Feb 2013, 13:23:47)