DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11110%2F19%3A10399264" target="_blank" >RIV/00216208:11110/19:10399264 - isvavai.cz</a>
Alternative codes found
RIV/44555601:13440/18:43893858
Result on the web
<a href="https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=L7aYYXdHSj" target="_blank" >https://verso.is.cuni.cz/pub/verso.fpl?fname=obd_publikace_handle&handle=L7aYYXdHSj</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nar/gky1018" target="_blank" >10.1093/nar/gky1018</a>
Alternative languages
Result language
angličtina
Original language name
DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10600 - Biological sciences
Result continuities
Project
<a href="/en/project/LM2015047" target="_blank" >LM2015047: Czech National Infrastructure for Biological Data</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Nucleic Acids Research
ISSN
0305-1048
e-ISSN
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Volume of the periodical
47
Issue of the periodical within the volume
2
Country of publishing house
GB - UNITED KINGDOM
Number of pages
13
Pages from-to
621-633
UT code for WoS article
000467959100015
EID of the result in the Scopus database
2-s2.0-85060625553