DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor.

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F19%3A00500022" target="_blank" >RIV/61388971:_____/19:00500022 - isvavai.cz</a>

Výsledek na webu

<a href="https://academic.oup.com/nar/article/47/2/621/5146190" target="_blank" >https://academic.oup.com/nar/article/47/2/621/5146190</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gky1018" target="_blank" >10.1093/nar/gky1018</a>

Jazyk výsledku

angličtina

Název v původním jazyce

DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor.

Popis výsledku v původním jazyce

HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation of protein-coding genes with HrdB alone and with a complex of HrdB and a transcriptional cofactor RbpA, using gene expression time series, identified 1694 genes that were under their direct control. When using the HrdB–RbpA complex in the model, an increase of the model fidelity was found for 322 genes. Functional analysis revealed that HrdB controls the majority of gene groups essential for the primary metabolism and the vegetative growth. Particularly, almost all ribosomal protein-coding genes were found in the HrdB regulon. Analysis of promoter binding sites revealed binding motif at the −10 region and suggested the possible role of mono- or di-nucleotides upstream of the −10 element.nnn

Název v anglickém jazyce

DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor.

Popis výsledku anglicky

HrdB in streptomycetes is a principal sigma factor whose deletion is lethal. This is also the reason why its regulon has not been investigated so far. To overcome experimental obstacles, for investigating the HrdB regulon, we constructed a strain whose HrdB protein was tagged by an HA epitope. ChIP-seq experiment, done in 3 repeats, identified 2137 protein-coding genes organized in 337 operons, 75 small RNAs, 62 tRNAs, 6 rRNAs and 3 miscellaneous RNAs. Subsequent kinetic modeling of regulation of protein-coding genes with HrdB alone and with a complex of HrdB and a transcriptional cofactor RbpA, using gene expression time series, identified 1694 genes that were under their direct control. When using the HrdB–RbpA complex in the model, an increase of the model fidelity was found for 322 genes. Functional analysis revealed that HrdB controls the majority of gene groups essential for the primary metabolism and the vegetative growth. Particularly, almost all ribosomal protein-coding genes were found in the HrdB regulon. Analysis of promoter binding sites revealed binding motif at the −10 region and suggested the possible role of mono- or di-nucleotides upstream of the −10 element.nnn

Druh

J_ost - Ostatní články v recenzovaných periodicích

CEP obor

—

OECD FORD obor

20902 - Bioprocessing technologies (industrial processes relying on biological agents to drive the process) biocatalysis, fermentation

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

2019

Kód důvěrnosti údajů

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

Název periodika

Nucleic Acids Research

ISSN

1362-4962

e-ISSN

—

Svazek periodika

47

Číslo periodika v rámci svazku

2

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

13

Strana od-do

621-633

Kód UT WoS článku

000467959100015

EID výsledku v databázi Scopus

2-s2.0-85060625553