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%2F44555601%3A13440%2F18%3A43893858" target="_blank" >RIV/44555601:13440/18:43893858 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11110/19:10399264

Výsledek na webu

<a href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1018/5146190" target="_blank" >https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky1018/5146190</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 MINUS SIGN 10 region and suggested the possible role of mono- or di-nucleotides upstream of the MINUS SIGN 10 element.

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 MINUS SIGN 10 region and suggested the possible role of mono- or di-nucleotides upstream of the MINUS SIGN 10 element.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10606 - Microbiology

Projekt

<a href="/cs/project/LM2015047" target="_blank" >LM2015047: Česká národní infrastruktura pro biologická data</a><br>

Návaznosti

S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2018

Kód důvěrnosti údajů

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

Název periodika

Nucleic Acids Research

ISSN

0305-1048

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