Streptomyces coelicolor A3(2)
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ABSTRACT:
PROVIDER: PRJNA189845 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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
Project description:During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix GeneChip and a high-resolution time-series of fermenter-grown samples. This time series was conducted using medium leading to glutamate depletion and the cultivation conditions as published in Nieselt et al. BMC Genomics 2010, performed with the Streptomyces coelicolor wild type strain M145E.
2011-12-31 | GSE30569 | GEO
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 RNA-seq data of our study.
2020-03-28 | GSE136167 | GEO
Project description:We studied the influence of copper in physiological and morphological differentiation of Streptomyces coelicolor. We demonstrate differences in phenotype (germination, growth rate, antibiotic production) and genetic expression between a strain mutated at copper chaperone CopZ (SCO2730::Tn5062), the wild-type strain and a wild-type strain sporulated in a media with 80µM CuSO4. These differences are correlated with the cytosolic copper. Our results demonstrate a pleiotropic effect of copper modulating S. coelicolor development.
2018-12-31 | GSE111126 | GEO
Project description:Streptomyces coelicolor A3(2) shotgun proteomics. S. coelicolor A3(2) was fermented in GYM.
2022-03-23 | MSV000089111 | MassIVE
Project description:Transcriptome time-courses during the S. coelicolor germination were used to reveal processes that underlie the gene expression at the transcriptional level within transition from dormancy to vegetative growth.
2013-08-01 | GSE44415 | GEO
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
Project description:Alam2010 - Genome-scale metabolic network of
Streptomyces coelicolor
This model is described in the article:
Metabolic modeling and
analysis of the metabolic switch in Streptomyces
coelicolor.
Alam MT, Merlo ME, STREAM
Consortium, Hodgson DA, Wellington EM, Takano E, Breitling
R.
BMC Genomics 2010; 11: 202
Abstract:
BACKGROUND: The transition from exponential to stationary
phase in Streptomyces coelicolor is accompanied by a major
metabolic switch and results in a strong activation of
secondary metabolism. Here we have explored the underlying
reorganization of the metabolome by combining computational
predictions based on constraint-based modeling and detailed
transcriptomics time course observations. RESULTS: We
reconstructed the stoichiometric matrix of S. coelicolor,
including the major antibiotic biosynthesis pathways, and
performed flux balance analysis to predict flux changes that
occur when the cell switches from biomass to antibiotic
production. We defined the model input based on observed
fermenter culture data and used a dynamically varying objective
function to represent the metabolic switch. The predicted
fluxes of many genes show highly significant correlation to the
time series of the corresponding gene expression data.
Individual mispredictions identify novel links between
antibiotic production and primary metabolism. CONCLUSION: Our
results show the usefulness of constraint-based modeling for
providing a detailed interpretation of time course gene
expression data.
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2015-07-30 | MODEL1507180005 | BioModels
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