DNA mapping and kinetic modeling of the HrdB regulon inStreptomyces coelicolor

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.

The Transcription Unit Architecture of Streptomyces lividans TK24

“…From the functional analysis, we hypothesized that genes exploiting promoters with 18- or 19-nt spacer are regulated by housekeeping σ factors, as their enriched functions are related to fundamental processes, including cellular resource metabolisms, translation and transcription. Based on the published ChIP-Seq and dRNA-Seq results in the genetically close organism S. coelicolor , we examined this hypothesis (Jeong et al, 2016; Smidova et al, 2019). The binding specificity of S. lividans ’ hrdB , a housekeeping σ factor, was assumed to be the same as the S. coelicolor ’ hrdB since their amino acid sequences are identical.…”

“…Spacer length was calculated when the two promoter elements were found for one TSS. For the promoter motif of S. coelicolor ’ hrdB regulons, hrdB target genes and their primary TSSs were collected from published ChIP-Seq and dRNA-Seq data (Jeong et al, 2016; Smidova et al, 2019). The promoter motifs of S. lividans were found by similar methods using the MEME suite oops option.…”

Chemotranscriptomic Profiling Defines Drug-Specific Signatures of the Glycopeptide Antibiotics Dalbavancin, Vancomycin and Chlorobiphenyl-Vancomycin in a VanB-Type-Resistant Streptomycete

“…The principal sigma factor in S. coelicolor is sigma factor HrdB and is required for cell viability. The regulon of genes controlled by HrdB includes those required for primary metabolism and vegetative cell growth ( Smidova et al, 2019 ). Genes dependent on HrdB for their transcription are significantly over-represented in the groups of genes down-regulated in response to at least one of the glycopeptide antibiotics ( Table 2 ), consistent with a decrease in active growth following the treatments.…”

“…Where necessary, operon structure was taken from Charaniya et al (2007) . Dependence of transcription on sigma HrdB was assigned using the data published in Smidova et al (2019) . Pairwise Tanimoto similarity scores for the glycopeptide antibiotic structures were obtained from ChEBI ( Hastings et al, 2016 ).…”

Recent Advances in the Heterologous Biosynthesis of Natural Products from Streptomyces

“…There are three types of promoters in Streptomyces. A type I promoter includes the −10 element (5′-TANNNT-3′) and −35 element (5′-TTGNC-3′) with an 18-19 nucleotide spacer length [157,158], such as the hrdB promoter from S. coelicolor [159]. In contrast, a type II promoter contains the −10 element, similar to type I, and other elements (5′-TGTC-3′) with a different spacer length [160], and a type III does not display the typical −10 and −35 sequences that are present in different types [157,161].…”