BSA115-transcription inhibition model
Version 3

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The model represents a hypothetical situation in which an anti-sigmafactor reduces sigB efficacy.

SEEK ID: https://fairdomhub.org/models/49?version=3

1 item is associated with this Model:

bsa_trscrinhib.xml (SBML and XML document - 13.8 KB)

Organism: Bacillus subtilis

Model type: Ordinary differential equations (ODE)

Model format: SBML

Execution or visualisation environment: JWS Online

Model image: No image specified

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Creators and Submitter

Creator

Ulf Liebal

Submitter

Ulf Liebal

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No license - no permission to use unless the owner grants a licence

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Views: 5491 Downloads: 225 Runs: 0

Created: 30th Mar 2011 at 12:31

Last updated: 17th Jan 2013 at 17:31

Version History

Version 3 (latest) Created 18th Dec 2012 at 13:06 by Ulf Liebal

adjusted parameter kxs, model annotation

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People (1)
Programmes (1)
Projects (1)
Investigations (1)
Studies (1)
Assays (1)
Publications (1)

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Ulf Liebal

Projects: BaCell-SysMO

Institutions: University of Rostock

Expertise: Mathematical modelling, Bacillus subtilis, Deterministic modelling of gene regulation networks, stress responses, Systems Biology, sensitivity analysis, Dynamics and Control of Biological Networks, Parameter estimation

Tools: Biochemistry, Computational and theoretical biology, ODE, Matlab, linux, Stochastic models, Deterministic models, Dynamic modelling

Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.

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SysMO

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep

Web page: http://sysmo.net/

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BaCell-SysMO

BaCell-SysMO 2 Modelling carbon core metabolism in Bacillus subtilis – Exploring the contribution of protein complexes in core carbon and nitrogen metabolism.

Bacillus subtilis is a prime model organism for systems biology approaches because it is one of the most advanced models for functional genomics. Furthermore, comprehensive information on cell and molecular biology, physiology and genetics is available and the European Bacillus community (BACELL) has a well-established reputation for applying ...

Programme: SysMO

Public web page: http://www.sysmo.net/index.php?index=53

Organisms: Bacillus subtilis

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The transition from growing to non-growing Bacillus subtilis cells

BaCell-SysMO

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Praveen kumar Sappa

The objective of this project is an integrated understanding the metabolic, proteomic and genetic network that controls the transition from growth to glucose starvation. This transition is a fundamental ecophysiological response that serves as a scientific model for environmental signal integration and is pivotal for industrial fermentations of Bacillus that occur predominantly under nutrient starvation.

Keywords: Glucose starvation, Transcriptomics, Proteomics, Metabolomics,Bacillus subtilis,

Submitter: Praveen kumar Sappa

Studies: B. subtilis Transcription Factor Competition, Batchfermentation exp-starv01_090204, Biphase Batch Fermentation(2009/02/04), Controlled sigmaB induction in shake flask, Transition to starvation in shake flask

Assays: 2D-gelbased analysis of intracellular proteins, Absolute quantification of proteins by the AQUA-technology, B. subtilis Transcription Factor Competition - theoretical interpretation, B. subtilis Transcription Factor Competition - theoretical interpretation, Fermentation-BM5_SysMo, Gene expression(Transcriptome), IPTG induction of sigmaB in BSA115, IPTG induction of sigmaB in BSA115, Relative quantification of proteins by metabolic labeling, Stressosome activation dynamics, metabolome-LCMS

Snapshots: No snapshots

Created: 21st Aug 2009 at 09:18, Last updated: 22nd Nov 2011 at 19:12

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Controlled sigmaB induction in shake flask

BaCell-SysMO

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Ulf Liebal

In this kind of studies sigmaB stress response is induced by the addition of artificial inducers of sigmaB. For example simgaB is downstream of a Pspac promoter and induced by the addition of IPTG. A ctc::lacZ reporter gene is used to monitor sigmaB activity.

Submitter: Ulf Liebal

Investigation: The transition from growing to non-growing Baci...

Assays: IPTG induction of sigmaB in BSA115, IPTG induction of sigmaB in BSA115, Stressosome activation dynamics

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Created: 16th Nov 2009 at 14:52, Last updated: 22nd Nov 2011 at 19:12

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IPTG induction of sigmaB in BSA115

BaCell-SysMO

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Ulf Liebal

We use BSA115 strain which lacks RsbU and RsbW proteins. Therefore, there is limited post-transcriptional regulation of sigmaB activity.

There occurs an unexpected drop in the beta-Gal activity after sigB induction. This modelling effort aims to clarify the reasons.

Submitter: Ulf Liebal

Biological problem addressed: Gene Expression

Investigation: The transition from growing to non-growing Baci...

Study: Controlled sigmaB induction in shake flask

Organisms: Bacillus subtilis : 168 (wild-type / wild-type)

Models: BSA115 Post-transcriptional instability, BSA115-lacz-synth, BSA115-sigB-adaptation, BSA115-transcription inhibition model

SOPs: No SOPs

Data files: 20090915_BSA115-IPTG-assay, Model-representations-BSA115-Experiments and 1 hidden item

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Created: 2nd Feb 2011 at 14:07, Last updated: 8th Nov 2017 at 14:21

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Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis

BaCell-SysMO

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Ulf Liebal

Praveen kumar Sappa

Thomas Millat

Leif Steil

Uwe Voelker

Olaf Wolkenhauer

Abstract (Expand)

In Bacillus subtilis the σB 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 σB activity. In the mutant strain BSA115, σB transcription is inducible by the addition of IPTG and negative control of σB 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 σB 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 σB response. Therefore, we conclude that protein instability following σB 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 σB response.

Authors: , , , , Georg Homuth, ,

Date Published: 2012

Publication Type: Not specified

DOI: 10.1039/C2MB25031D

Citation:

Created: 2nd May 2012 at 11:34, Last updated: 8th Dec 2022 at 17:26

BSA115-transcription inhibition model Version 3

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Version History

Version 3 (latest) Created 18th Dec 2012 at 13:06 by Ulf Liebal

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BSA115-transcription inhibition model
Version 3