Stressosome activation dynamics
The stressosome is an important sensor of environmental stresses in B. subtilis. It is formed by three protein types that form an icosahedral geometric protein complex. There are uncertanties how protein interactions take place, what the effects on the response behaviour of activation and inhibition of phosphorylation among proteins is, and what kind of proximal signal activates the stressosome in the first place. To answer these questions a computational modelling approach was developed. This approach need to reflect the strict geometric requirements of the stressosome including spatial constraints.
SEEK ID: https://fairdomhub.org/assays/236
Modelling analysis
Projects: BaCell-SysMO
Investigation: The transition from growing to non-growing Bacillus subtilis cells
Study: Controlled sigmaB induction in shake flask
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Biological problem addressed: Signal Induction
Organisms: Bacillus subtilis
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Created: 5th Feb 2014 at 08:44
Last updated: 8th Nov 2017 at 14:21
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Projects: BaCell-SysMO
Institutions: University of Rostock
Modelling of the general stress response activation cascade of sigB in B. subtilis in response to starvation.
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/
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
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
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
The stressosome is composed of three proteins that assemble in the form of an icosahedron. Icosahedra can be modelled in different ways with different abstraction levels regarding the original stressosome structure. The pdf-figure introduces geometric modelling of the stressosome using origami and particle dynamics simulations.
The zip folder contains files that allow simulation of stressosome dynamics. The models are based on a cellular automaton approach. Each protein of RsbR and RsbS is located in the crystal structure of the stressosome. The proteins can be phosphorylated or not and these states determine the future of neighbouring proteins. To simulate the model open the file 'liebal_stressosome-model_12_workflow-matlab.m' in Matlab. It is written in the cell-model, put the cursor into a cell that you wish to ...
Creator: Ulf Liebal
Submitter: Ulf Liebal
Model type: Agent based modelling
Model format: Matlab package
Environment: Matlab
The zip-folder contains files for execution in matlab that allow for the simulation of stressosome dynamics and reproduction of published data on the stressosome. The important file for execution is 'liebal_stressosome-model_12_workflow-matlab.m'.
Creator: Ulf Liebal
Submitter: Ulf Liebal
Model type: Agent based modelling
Model format: Matlab package
Environment: Matlab
Abstract (Expand)
Authors: , , Jon Marles-Wright, ,
Date Published: 2013
Publication Type: Not specified
