Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation

Kód výsledku v 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>

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Quantitative Aspect of Bacillus subtilis σB Regulatory Network—A Computational Simulation

Popis výsledku anglicky

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.

Druh

J_SC - Článek v periodiku v databázi SCOPUS

CEP obor

—

OECD FORD obor

10602 - Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology

Projekt

<a href="/cs/project/LM2018131" target="_blank" >LM2018131: Česká národní infrastruktura pro biologická data</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2022

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

11

Číslo periodika v rámci svazku

12

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

12

Strana od-do

11121729

Kód UT WoS článku

000900495600001

EID výsledku v databázi Scopus

2-s2.0-85144657039