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%2F61388971%3A_____%2F19%3A00500022" target="_blank" >RIV/61388971:_____/19:00500022 - isvavai.cz</a>
Result on the web
<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>

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.nnn
Czech name
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Czech description
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Type
J<sub>ost</sub> - Miscellaneous article in a specialist periodical
CEP classification
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OECD FORD branch
20902 - Bioprocessing technologies (industrial processes relying on biological agents to drive the process) biocatalysis, fermentation

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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