Quantitative Aspect of Bacillus subtilis σB Regulatory Network on a Proteome Level-A Computational Simulation

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F24%3A00597831" target="_blank" >RIV/61388971:_____/24:00597831 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.mdpi.com/2079-7737/13/8/614" target="_blank" >https://www.mdpi.com/2079-7737/13/8/614</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3390/biology13080614" target="_blank" >10.3390/biology13080614</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Quantitative Aspect of Bacillus subtilis σB Regulatory Network on a Proteome Level-A Computational Simulation

Popis výsledku v původním jazyce

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 dephosphorylate 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 reflected in the time series of protein expression. In this study, the time series of protein expression measured by mass spectrometry were utilized to investigate the role of 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 a 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 performed 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 a quantitative insight into the functioning of the SigB-dependent circuit and offer a template for the quantitative study of similar systemsn

Název v anglickém jazyce

Quantitative Aspect of Bacillus subtilis σB Regulatory Network on a Proteome Level-A Computational Simulation

Popis výsledku anglicky

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 dephosphorylate 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 reflected in the time series of protein expression. In this study, the time series of protein expression measured by mass spectrometry were utilized to investigate the role of 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 a 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 performed 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 a quantitative insight into the functioning of the SigB-dependent circuit and offer a template for the quantitative study of similar systemsn

Druh

J_ost - Ostatní články v recenzovaných periodicích

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

<a href="/cs/project/LM2023055" target="_blank" >LM2023055: Česká národní infrastruktura pro biologická data</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Biology

ISSN

2079-7737

e-ISSN

2079-7737

Svazek periodika

13

Číslo periodika v rámci svazku

8

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

12

Strana od-do

614

Kód UT WoS článku

001307333300001

EID výsledku v databázi Scopus

2-s2.0-85202638017