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Streptomyces coelicolor A3(2)

ABSTRACT: RNA-seq in polysome fractions

PROVIDER: PRJDB14415 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR408738_1.fastq.gz	Fastqsanger.gz
	DRR408738_2.fastq.gz	Fastqsanger.gz
	DRR408739_1.fastq.gz	Fastqsanger.gz
	DRR408739_2.fastq.gz	Fastqsanger.gz

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Streptomyces coelicolor A3(2) SigR regulon

2012-06-03 | GSE33593 | GEO

Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism.

Project description:Streptomyces are filamentous soil bacteria that produce more than half of the known microbial antibiotics. We present the first genome-scale metabolic model of a representative of this group--Streptomyces coelicolor A3(2). The metabolism reconstruction was based on annotated genes, physiological and biochemical information. The stoichiometric model includes 819 biochemical conversions and 152 transport reactions, accounting for a total of 971 reactions. Of the reactions in the network, 700 are unique, while the rest are iso-reactions. The network comprises 500 metabolites. A total of 711 open reading frames (ORFs) were included in the model, which corresponds to 13% of the ORFs with assigned function in the S. coelicolor A3(2) genome. In a comparative analysis with the Streptomyces avermitilis genome, we showed that the metabolic genes are highly conserved between these species and therefore the model is suitable for use with other Streptomycetes. Flux balance analysis was applied for studies of the reconstructed metabolic network and to assess its metabolic capabilities for growth and polyketides production. The model predictions of wild-type and mutants' growth on different carbon and nitrogen sources agreed with the experimental data in most cases. We estimated the impact of each reaction knockout on the growth of the in silico strain on 62 carbon sources and two nitrogen sources, thereby identifying the "core" of the essential reactions. We also illustrated how reconstruction of a metabolic network at the genome level can be used to fill gaps in genome annotation.

| S-EPMC1142472 | biostudies-literature

Transcriptome profiles of Streptomyces coelicolor A3(2) wild type treated with kanamycin and iron

Project description:We determine genes that responsible for iron induced resistance to kanamycin in Streptomyces coelicolor. Iron acts as a inducing agent for resistance to bactericidal antibiotics with concentration dependent manner. Identification of iron-dependent differentially expressed genes in wild-type by RNA-seq identified more than 100 genes. This series encompasses the RNA-seq data of our study.

2022-03-10 | GSE168567 | GEO

Genome-wide identification of WblC (WhiB7) binding sites in Streptomyces coelicolor A3(2) treated with tetracycline

Project description:We determined Streptomyces coelicolor genes that are directly regulated by WblC (or WhiB7), an actinobacterial transcription factor that activates expression of intrinsic resistance in response to translation-inhibitory antibiotic stress. Identification of differentially expressed genes in wblC mutant by RNA-seq and WblC binding sites in wild type by ChIP-seq identified more than 300 genes as WblC regulon. This series encompasses the ChIP-seq data of our study.

2020-03-28 | GSE136166 | GEO

Replisome trafficking in growing vegetative hyphae of Streptomyces coelicolor A3(2).

Project description:We observed movies of replisome trafficking during Streptomyces coelicolor growth. A replisome(s) in the spore served as a replication center(s) until hyphae reached a certain length, when a tip-proximal replisome formed and moved at a fixed distance behind the tip at a speed equivalent to the extension rate of the tip.

| S-EPMC3067586 | biostudies-literature

Biosynthesis of the sesquiterpene antibiotic albaflavenone in Streptomyces coelicolor A3(2).

Project description:Cytochrome P450 170A1 (CYP170A1) is encoded by the sco5223 gene of the Gram-positive, soil-dwelling bacterium Streptomyces coelicolor A3(2) as part of a two-gene cluster with the sco5222 gene. The SCO5222 protein is a sesquiterpene synthase that catalyzes the cyclization of farnesyl diphosphate to the novel tricyclic hydrocarbon, epi-isozizaene (Lin, X., Hopson, R., and Cane, D. E. (2006) J. Am. Chem. Soc. 128, 6022-6023). The presence of CYP170A1 (sco5223) suggested that epiisozizaene might be further oxidized by the transcriptionally coupled P450. We have now established that purified CYP170A1 carries out two sequential allylic oxidations to convert epi-isozizaene to an epimeric mixture of albaflavenols and thence to the sesquiterpene antibiotic albaflavenone. Gas chromatography/mass spectrometry analysis of S. coelicolor culture extracts established the presence of albaflavenone in the wild-type strain, along with its precursors epi-isozizaene and the albaflavenols. Disruption of the CYP170A1 gene abolished biosynthesis of both albaflavenone and the albaflavenols, but not epi-isozizaene. The combined results establish for the first time the presence of albaflavenone in S. coelicolor and clearly demonstrate that the biosynthesis of this antibiotic involves the coupled action of epi-isozizaene synthase and CYP170A1.

| S-EPMC2276382 | biostudies-literature

Synthetic RNA Silencing of Actinorhodin Biosynthesis in Streptomyces coelicolor A3(2).

Project description:We demonstrate the first application of synthetic RNA gene silencers in Streptomyces coelicolor A3(2). Peptide nucleic acid and expressed antisense RNA silencers successfully inhibited actinorhodin production. Synthetic RNA silencing was target-specific and is a new tool for gene regulation and metabolic engineering studies in Streptomyces.

| S-EPMC3694883 | biostudies-literature

Transcriptome profiles of Streptomyces coelicolor A3(2) wild type and wblC (whiB7) mutant treated with tetracycline

2020-03-28 | GSE136167 | GEO

ANTIBIOTICS OVERPRODUCTION IN STREPTOMYCES COELICOLOR A3(2) MEDIATED BY PHOSPHOFRUCTOKINASE A2 DELETION

Project description:Gene expression analysis of S. coelicolor M145 and the delta_pfkA2 mutant. RNA samples were taken in the early exponential phase during growth in fermentors in defined mineral medium. Keywords: cell type, gene expression, genetic modification

2008-05-01 | GSE7686 | GEO

Streptomyces coelicolor A3(2) SigR regulon

Project description:We determined the genomic locations of the SigR binding sites by chromatin immuno-precipitation of cross-linked DNA and hybridization on a tilling oligonucleotide array after 20 minutes of diamide treatment on cell cultures. Three independent biological samples were prepared separately from the wild-type cells and pooled before hybridization on a single array. Three more independent biological samples were prepared from sigR deletion mutant cells, pooled, and hybridized on another single array. After normalization, the signal from the mutant cells was subtracted from the signal from the wild-type cells to recover SigR specific signal.

2012-06-02 | E-GEOD-33593 | biostudies-arrayexpress

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