DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolor Article Swipe
Klára Šmídová
,
Alice Ziková
,
Jiří Pospíšil
,
Marek Schwarz
,
Jan Bobek
,
Jiří Vohradský
·
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gky1018
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gky1018
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.
Related Topics
Concepts
Regulon
Biology
Streptomyces coelicolor
Gene
Genetics
Operon
Sigma factor
Ribosomal binding site
Promoter
Regulation of gene expression
Gene expression
RNA
Ribosome
Escherichia coli
Mutant
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gky1018
- OA Status
- gold
- Cited By
- 34
- References
- 72
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2899112317
All OpenAlex metadata
Raw OpenAlex JSON
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https://openalex.org/W2899112317Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/nar/gky1018Digital Object Identifier
- Title
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DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolorWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2018Year of publication
- Publication date
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2018-10-11Full publication date if available
- Authors
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Klára Šmídová, Alice Ziková, Jiří Pospíšil, Marek Schwarz, Jan Bobek, Jiří VohradskýList of authors in order
- Landing page
-
https://doi.org/10.1093/nar/gky1018Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
- OA URL
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https://doi.org/10.1093/nar/gky1018Direct OA link when available
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Regulon, Biology, Streptomyces coelicolor, Gene, Genetics, Operon, Sigma factor, Ribosomal binding site, Promoter, Regulation of gene expression, Gene expression, RNA, Ribosome, Escherichia coli, MutantTop concepts (fields/topics) attached by OpenAlex
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34Total citation count in OpenAlex
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2025: 3, 2024: 6, 2023: 4, 2022: 9, 2021: 5Per-year citation counts (last 5 years)
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72Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| sustainable_development_goals[0].score | 0.5899999737739563 |
| sustainable_development_goals[0].display_name | Life in Land |
| citation_normalized_percentile.value | 0.76812724 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |