Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F22%3A00565503" target="_blank" >RIV/61388971:_____/22:00565503 - isvavai.cz</a>
Result on the web
<a href="https://www.mdpi.com/2079-7737/11/12/1729" target="_blank" >https://www.mdpi.com/2079-7737/11/12/1729</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3390/biology11121729" target="_blank" >10.3390/biology11121729</a>
Alternative languages
Result language
angličtina
Original language name
Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation
Original language description
Bacillus subtilis is a model organism used to study molecular processes in prokaryotic cells. Sigma factor B, which associates with RNA polymerase, is one of the transcriptional regulators involved in the cell’s response to environmental stress. This study addresses the key question of how the levels of free SigB, which acts as the actual regulator of gene expression, are controlled. A set of chemical equations describing the network controlling the levels of free SigB was designed, leading to a set of differential equations quantifying the dynamics of the network. Utilizing a microarray-measured gene expression time series then allowed the simulation of the kinetic behavior of the network in real conditions and investigation of the role of phosphatases RsbU/RsbP transmitting the environmental signal and controlling the amounts of free SigB. Moreover, the role of kinetic constants controlling the formation of the molecular complexes, which consequently influence the amount of free SigB, was investigated. The simulation showed that although the total amount of sigma B is relatively high in the unstressed population, the amount of free SigB, which actually controls its regulon, is quite low. The simulation also allowed determination of the proportion of all the network members that were free or bound in complexes. While previously the qualitative features of B. subtilis SigB have been studied in detail, the kinetics of the network have mostly been ignored. In summary, the computational results based on experimental data provide a quantitative insight into the functioning of the SigB-dependent circuit and provide a roadmap for its further exploration in this industrially important bacterium.
Czech name
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Czech description
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Classification
Type
J<sub>SC</sub> - Article in a specialist periodical, which is included in the SCOPUS database
CEP classification
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OECD FORD branch
10602 - Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology
Result continuities
Project
<a href="/en/project/LM2018131" target="_blank" >LM2018131: Czech National Infrastructure for Biological Data</a><br>
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Biology
ISSN
2079-7737
e-ISSN
2079-7737
Volume of the periodical
11
Issue of the periodical within the volume
12
Country of publishing house
CH - SWITZERLAND
Number of pages
12
Pages from-to
11121729
UT code for WoS article
000900495600001
EID of the result in the Scopus database
2-s2.0-85144657039