ArticleNucleic acids research2019
DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 34 citations in OpenAlex.
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- Transcriptional analysis of genes associated with glycolysis in Streptomyces coelicolor M145.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Molecular basis of Streptomyces ECF σShbA factors transcribing principal σHrdB genes.Nucleic acids research · 2025Article
- An Overview of Lsr2 Repressor Effect inMicroorganisms · 2024Article
- Structural insights into transcription activation of theiScience · 2024Article
- RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria.Nucleic acids research · 2024Article
- Structural and functional characterization of AfsR, an SARP family transcriptional activator of antibiotic biosynthesis in Streptomyces.PLoS biology · 2024Article
- Harnessing regulatory networks in Actinobacteria for natural product discovery.Journal of industrial microbiology & biotechnology · 2024Review
- σCommunications biology · 2024Article
- The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145.Scientific reports · 2023Article
- Comparative Proteomic Analysis of Transcriptional and Regulatory Proteins Abundances inInternational journal of molecular sciences · 2022Article
- Comparative and pangenomic analysis of the genus Streptomyces.Scientific reports · 2022Article
- An extended catalogue of ncRNAs in Streptomyces coelicolor reporting abundant tmRNA, RNase-P RNA and RNA fragments derived from pre-ribosomal RNA leader sequences.Archives of microbiology · 2022Article
- Structural basis of Streptomyces transcription activation by zinc uptake regulator.Nucleic acids research · 2022Article
- Mycothiol Peroxidase Activity as a Part of the Self-Resistance Mechanisms against the Antitumor Antibiotic Cosmomycin D.Microbiology spectrum · 2022Article
- RIViT-seq enables systematic identification of regulons of transcriptional machineries.Nature communications · 2022Article
- Identification of Group II Intron RmInt1 Binding Sites in a Bacterial Genome.Frontiers in molecular biosciences · 2022Article
- Ms1 RNA Interacts With the RNA Polymerase Core inFrontiers in microbiology · 2022Article
- High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters.ACS synthetic biology · 2021Article
- Chemotranscriptomic Profiling Defines Drug-Specific Signatures of the Glycopeptide Antibiotics Dalbavancin, Vancomycin and Chlorobiphenyl-Vancomycin in a VanB-Type-Resistant Streptomycete.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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