Kinetic modelling and meta-analysis of the B. subtilis SigA regulatory network during spore germination and outgrowth

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F17%3A00477942" target="_blank" >RIV/61388971:_____/17:00477942 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11310/17:10362597

Výsledek na webu

<a href="http://dx.doi.org/10.1016/j.bbagrm.2017.06.003" target="_blank" >http://dx.doi.org/10.1016/j.bbagrm.2017.06.003</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.bbagrm.2017.06.003" target="_blank" >10.1016/j.bbagrm.2017.06.003</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Kinetic modelling and meta-analysis of the B. subtilis SigA regulatory network during spore germination and outgrowth

Popis výsledku v původním jazyce

This study describes the meta-analysis and kinetic modelling of gene expression control by sigma factor SigA of Bacillus subtilis during germination and outgrowth based on microarray data from 14 time points. The analysis computationally models the direct interaction among SigA, SigA-controlled sigma factor genes (sigh, sigH, sigD, sigX), and their target genes. Of the > 800 known genes in the SigA regulon, as extracted from databases, 311 genes were analysed, and 190 were confirmed by the kinetic model as being controlled by SigA. For the remaining genes, alternative regulators satisfying kinetic constraints were suggested. The kinetic analysis suggested another 214 genes as potential SigA targets. The modelling was able to (i) create a particular SigA-controlled gene expression network that is active under the conditions for which the expression time series was obtained, and where SigA is the dominant regulator, (ii) suggest new potential SigA target genes, and (iii) fmd other possible regulators of a given gene or suggest a new mechanism of its control by identifying a matching profile of unknown regulator(s). Selected predicted regulatory interactions were experimentally tested, thus validating the model.

Název v anglickém jazyce

Kinetic modelling and meta-analysis of the B. subtilis SigA regulatory network during spore germination and outgrowth

Popis výsledku anglicky

This study describes the meta-analysis and kinetic modelling of gene expression control by sigma factor SigA of Bacillus subtilis during germination and outgrowth based on microarray data from 14 time points. The analysis computationally models the direct interaction among SigA, SigA-controlled sigma factor genes (sigh, sigH, sigD, sigX), and their target genes. Of the > 800 known genes in the SigA regulon, as extracted from databases, 311 genes were analysed, and 190 were confirmed by the kinetic model as being controlled by SigA. For the remaining genes, alternative regulators satisfying kinetic constraints were suggested. The kinetic analysis suggested another 214 genes as potential SigA targets. The modelling was able to (i) create a particular SigA-controlled gene expression network that is active under the conditions for which the expression time series was obtained, and where SigA is the dominant regulator, (ii) suggest new potential SigA target genes, and (iii) fmd other possible regulators of a given gene or suggest a new mechanism of its control by identifying a matching profile of unknown regulator(s). Selected predicted regulatory interactions were experimentally tested, thus validating the model.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2017

Kód důvěrnosti údajů

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

Název periodika

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

ISSN

1874-9399

e-ISSN

—

Svazek periodika

1860

Číslo periodika v rámci svazku

8

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

11

Strana od-do

894-904

Kód UT WoS článku

000407658800008

EID výsledku v databázi Scopus

2-s2.0-85024900599