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Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation
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SYSNO ASEP 0565503 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation Author(s) Vohradský, Jiří (MBU-M) RID, ORCID Article number 11121729 Source Title Biology. - : MDPI
Roč. 11, č. 12 (2022)Number of pages 12 s. Language eng - English Country CH - Switzerland Keywords Bacillus subtilis sigma B ; computer simulation ; regulatory network Subject RIV EA - Cell Biology OECD category Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology R&D Projects LM2018131 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Method of publishing Open access Institutional support MBU-M - RVO:61388971 UT WOS 000900495600001 EID SCOPUS 85144657039 DOI 10.3390/biology11121729 Annotation 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. Workplace Institute of Microbiology Contact Eliška Spurná, eliska.spurna@biomed.cas.cz, Tel.: 241 062 231 Year of Publishing 2023 Electronic address https://www.mdpi.com/2079-7737/11/12/1729
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