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

Result code in 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>
Alternative codes found
RIV/00216208:11110/19:10399264
Result on the web
<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>

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 MINUS SIGN 10 region and suggested the possible role of mono- or di-nucleotides upstream of the MINUS SIGN 10 element.
Czech name
—
Czech description
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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
10606 - Microbiology

Project
<a href="/en/project/LM2015047" target="_blank" >LM2015047: Czech National Infrastructure for Biological Data</a><br>
Continuities
S - Specificky vyzkum na vysokych skolach<br>I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year
2018
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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