Version 1
: Received: 18 June 2024 / Approved: 18 June 2024 / Online: 19 June 2024 (02:49:14 CEST)
How to cite:
Vohradsky, J. Quantitative Aspect of Bacillus subtilis σB Regulatory Network on a Proteome Level – a Computational Simulation. Preprints2024, 2024061285. https://doi.org/10.20944/preprints202406.1285.v1
Vohradsky, J. Quantitative Aspect of Bacillus subtilis σB Regulatory Network on a Proteome Level – a Computational Simulation. Preprints 2024, 2024061285. https://doi.org/10.20944/preprints202406.1285.v1
Vohradsky, J. Quantitative Aspect of Bacillus subtilis σB Regulatory Network on a Proteome Level – a Computational Simulation. Preprints2024, 2024061285. https://doi.org/10.20944/preprints202406.1285.v1
APA Style
Vohradsky, J. (2024). Quantitative Aspect of <em>Bacillus subtilis</em> σB Regulatory Network on a Proteome Level – a Computational Simulation. Preprints. https://doi.org/10.20944/preprints202406.1285.v1
Chicago/Turabian Style
Vohradsky, J. 2024 "Quantitative Aspect of <em>Bacillus subtilis</em> σB Regulatory Network on a Proteome Level – a Computational Simulation" Preprints. https://doi.org/10.20944/preprints202406.1285.v1
Abstract
Bacillus subtilis is a model organism used to study molecular processes in Gram-positive bacteria. Sigma factor B, which associates with RNA polymerase, is one of the transcriptional regulators involved in the cell’s response to environmental stress. Experiments have proven that the amounts of free σB (SigB) are controlled by a system of anti- (RsbW) and anti-anti-sigma (RsbV) factors expressed from the same operon as SigB. Moreover, the phosphorylation state of RsbV is controlled by phosphatases RsbP and RsbU, which directly dephosphorylates RsbV. A set of chemical equations describing the network controlling the levels of free SigB was converted to a set of differential equations quantifying the dynamics of the network. The solution of these equations allowed the simulation of the kinetic behavior of the network and its components under real conditions. In this study, the time series of protein expression measured by mass spectrometry were utilized to investigate the role of the phosphatases RsbU/RsbP in transmitting the environmental signal. Additionally, the influence of kinetic constants and the amounts of other network components on the functioning of the network was investigated. A comparison with the same simulation performed using transcriptomic dataset showed that while the time series between the proteomic and transcriptomic datasets) are not correlated, the results are the same. This indicates that when modeling is done within one dataset, it does not matter whether the data come from the mRNA or protein level. In summary, the computational results based on experimental data provide quantitative insight into the functioning of the SigB-dependent circuit and offer a template for the quantitative study of similar systems.
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
