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Chip-seq to identify HrdB regulated genes in Streptomyces coelicolor

ABSTRACT: Chip-seq to identify HrdB regulated genes in Streptomyces coelicolor

PROVIDER: PRJEB27299 | ENA |

REPOSITORIES: ENA

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Chip-seq to identify HrdB regulated genes in Streptomyces coelicolor

Project description:Chip-seq to identify the HrdB (SCO5820) binding sites and regulated genes in Streptomyces coelicolor. The HrdB gene was tagged on genome by HA (Human Influenza hemagglutinin derived) epitope (TAC CCG TAC GAT GTG CCG GAT TAC GCG). We have 3 replicates with HrdB tagged by HA and 2 replicates with wild-type strain as controls. Chip-seq experiment was conducted using antibody against HA tag in vegetative growth phase (see protocols).

2018-10-14 | E-MTAB-6926 | biostudies-arrayexpress

Effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M1146 strain

Project description:To identify unique gene expression in cAMP supplemented Streptomyces coelicolor M1146 strain. The genes with different gene expression might be key genes to understand the effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M1146.

2020-11-27 | GSE158811 | GEO

Effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M145 strain

Project description:To identify unique gene expression in cAMP supplemented Streptomyces coelicolor M145 strain. The genes with different gene expression might be key genes to understand the effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M145.

2020-11-27 | GSE158810 | GEO

The regulation and role of SCO2027, iron importer protein in Streptomyces coelicolor

Project description:We determined genes that directly or indirectly regulated by CatR (or PerR), and hydrogen peroxide regulon in Streptomyces coelicolor.

2021-07-01 | GSE164218 | GEO

Genome-wide binding site profiling of NdgR in Streptomyces coelicolor

Project description:We identified genome-wide binding regions of NdgR in Streptomyces coelicolor using chromatin immunoprecipitation sequencing (ChIP-seq). We constructed 6×myc-tagged NdgR strain using homologous recombination with myc-tagging vector. Analysis of the sequencing data aligned to Streptomyces coelicolor genome database (NC_003888).

2014-12-29 | GSE59010 | GEO

Chip-seq to identify σE dependent genes in EtOH stressed and unstressed Streptomyces coelicolor A3(2)

Project description:Chip-seq experiment used to identify the binding sites of alternative σ factor σE in Streptomyces coelicolor. We access the binding sites with and without EtOH stress condition (see methods). To capture the binding of σE, the σE gene was tagged on genome by HA (Human Influenza hemagglutinin derived) epitope (TAC CCA TAC GAC GTC CCA GAC TAC GCT) on its C-terminus, wild type strain without tagged σE served as negative control.

2023-11-29 | E-MTAB-10987 | biostudies-arrayexpress

Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145

Project description:This work was carried out to elucidate the proteins that are regulated by the two-component system CutRS in Streptomyces coelicolor M145 and how this response changes in the presence of glucose. A comparison of the whole cell proteomes of Streptomyces coelicolor M145 WT and Streptomyces coelicolor M145 ∆cutRS on both DNA (no glucose) and DNAD (with glucose) was made.

2023-06-16 | PXD040579 | Pride

Metabolic switching of the PII protein GlnK in Streptomyces coelicolor

Project description:GlnK is an important nitrogen sensor protein in Streptomyces coelicolor. Deletion of glnK results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic production. Thus, GlnK is not only a regulator of nitrogen metabolism but also of morphological differentiation and secondary metabolite production. Through a comparative transcriptomic approach between the S. coelicolor wild-type and a S. coelicolor glnK mutant strain, 142 genes were identified that are differentially regulated in both strains. Among these are genes of the ram and rag operon, which are involved in S. coelicolor morphogenesis, as well as, genes involved in gas vesicle biosynthesis and ectoine biosynthesis. Surprisingly, no relevant nitrogen genes were found to be differentially regulated, revealing that GlnK is not an important nitrogen sensor under the tested conditions.

2011-12-31 | GSE30570 | GEO

Streptomyces coelicolor A3(2) strain M600 wild type transcriptome ChIP-chip with the bldC null mutant

Project description:Global regulation by the Streptomyces coelicolor atypical MerR-like transcription factor BldC. BldC is a transcriptional regulator essential for morphological development and antibiotic production in Streptomyces coelicolor. Here we identify the BldC regulon by means of chromatin immunoprecipitation (ChIP) microarray analysis. The BldC regulon encompasses at least 201 transcriptional units, which include many genes that play key roles in Streptomyces development (e.g., bldC itself, bldB, bldM, whiB, whiD, whiI, sigF, smeA-sffA, hupS), antibiotic production (e.g., afsK) and stress response (e.g., clpB, nsrR, sigE, sigF). All BldC-binding sites identified by ChIP-chip are present in the promoters of the target genes. In vitro DNA-binding experiments show that BldC is capable of binding DNA specifically in the absence of other proteins and suggest that BldC is a minor-groove DNA-binding protein. The regulon of BldC partially overlaps with that of the pleiotropic regulator BldD. BldC and BldD bind to distinct sites in the promoter region of smeA, where they simultaneously repress its transcription.

2013-01-01 | GSE28908 | GEO

The Streptomyces coelicolor DegS-DegU-like regulon

Project description:The Streptomyces coelicolor two genes operon SCO5784-SCO5785 encodes a two-component system which functions in a similar manner to that of the Bacillus subtilis DegS-DegU system. Propagation of the regulatory gene in high copy number results in the overproduction of several extracellular enzymes, among them the major extracellular protease, as well as in a higher level of synthesis of the antibiotic actinorhodin. This two-component system seems to control various processes characterised by the transition from primary to secondary metabolism in S. coelicolor, as determined by proteomic and transcriptomic analices. The presence of the regulatory gene in high copy number in S. coelicolor additionally seems to elicit a stringent response in the bacterial cell. Therefore, we propose renaming S. coelicolor genes SCO5784 and SCO5785 as degS and degU, respectively.

2012-05-04 | GSE23195 | GEO

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