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Time course of Streptomyces coelicolor: M145 Control vs. wblA deletion mutant

ABSTRACT: The basic experiment is a comparison of gene transcript levels of Streptomyces coelicolor M145 and its wblA deletion mutant at 6 timepoints (24, 36, 48, 60, 72 and 84 hours) encompassing vegetative growth, aerial growth, and sporulation on solid medium. The wblA mutant is morphologically defective, most of its aerial hyphae failing to show any sign of sporulation-directed attributes, and also overproduces some antibiotics. The microarray analysis was aimed to reveal the major transcriptional changes underpinning or associated with this pleiotropic phenotypic change. Using a fairly stringent cut-off, 291 genes were found to be affected, including developmental genes, antibiotic biosynthetic genes, and genes for primary metabolism. Some genes were over-expressed and others under-expressed in the mutant. Although the largest effects were mostly at timepoints corresponding to aerial growth and early sporulation, some genes were most strongly influenced at earlier timepoints.

ORGANISM(S): Streptomyces coelicolor

PROVIDER: GSE24396 | GEO | 2011/01/28

SECONDARY ACCESSION(S): PRJNA132889

REPOSITORIES: GEO

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Time course of Streptomyces coelicolor: M145 Control vs. wblA deletion mutant

Project description:The basic experiment is a comparison of gene transcript levels of Streptomyces coelicolor M145 and its wblA deletion mutant at 6 timepoints (24, 36, 48, 60, 72 and 84 hours) encompassing vegetative growth, aerial growth, and sporulation on solid medium. The wblA mutant is morphologically defective, most of its aerial hyphae failing to show any sign of sporulation-directed attributes, and also overproduces some antibiotics. The microarray analysis was aimed to reveal the major transcriptional changes underpinning or associated with this pleiotropic phenotypic change. Using a fairly stringent cut-off, 291 genes were found to be affected, including developmental genes, antibiotic biosynthetic genes, and genes for primary metabolism. Some genes were over-expressed and others under-expressed in the mutant. Although the largest effects were mostly at timepoints corresponding to aerial growth and early sporulation, some genes were most strongly influenced at earlier timepoints. M145 vs wblA deletion mutant. 6 timepoints (24, 36, 48, 60, 72 and 84 hours) encompassing vegetative growth, aerial growth, and sporulation, were analysed. Each timepoint comprised 2 technical replicates each of 3 biological replicates. RNA was isolated from triplicated cultures grown on cellophane overlays on MM + mannitol after 24, 36, 48, 60, 72 and 84 hours of incubation. Samples of the RNA were converted to Cy3-labelled cDNA in vitro, and mixed with Cy5-labelled genomic DNA. Each mixture was hybridised to two glass slide microarrays each carrying oligonucleotide probes corresponding to 99% of the genes in the annotated S. coelicolor genome. Thus RNA from each timepoint was compared to the same batch of genomic DNA and the comparison used to arrive at expression values of genes. These expression values were then used to arrive at differential expression between M145 and the wblA deletion mutant for all genes at all six timepoints.

2011-01-28 | E-GEOD-24396 | biostudies-arrayexpress

S.coelicolor_Rok7B7vsM145_MM+mannitol_time_course_expression

Project description:For transcript analysis, total RNA was isolated as described (Noens et al, 2007) from surface-grown mycelia of S. coelicolor M145 and its rok7B7 null mutant, cultivated on MM agar plates with mannitol (1% w/v) as the sole carbon source (plates were covered with cellophane discs). Two independent biological replicate experiments were performed. Samples were taken at 14h (early vegetative growth), 24 h (vegetative growth), 30 h (early aerial growth), 36 h (aerial growth), 42 h (early sporulation) and 54 h (sporulation). Total RNA was purified using the Kirby-mix protocol (Kieser et al, 2000). DNaseI treatment was used to fully remove any traces of DNA. Before use, the RNA samples were checked for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies). cDNA preparation and labeling was performed as previously described (Bucca et al, 1997, Bucca et al, 2009). The filtered data sets were analyzed using rank products analysis (Breitling et al, 2004) via the Rank-ProdIt tool (Laing and Smith, 2010). Differentially expressed genes were identified as demonstrating a > 2 fold change in expression between the parental strain M145 (wild-type) and the rok7B7 mutant.

2014-01-14 | E-MTAB-1465 | biostudies-arrayexpress

Identification of developmentally regulated genes involved in Streptomyces coelicolor sporulation

Project description:The aim of this study was to expand our knowledge about the gene repertoire involved in S. coelicolor sporulation. Here we compare the global transcription patterns of the wildtype (M145) parent and two mutants lacking key regulators of aerial hyphal sporulation (whiA and whiH).

2014-01-31 | E-MTAB-1942 | biostudies-arrayexpress

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

Responsive genes upon deletion of the ohkA gene in Streptomyces coelicolor M145

2011-01-05 | GSE26426 | GEO

Streptomyces coelicolor cells during various developmental stages: wildtype M145 vs. ÎSCO0204.

Project description:Global transcriptional profiling of the SCO0204 null mutant of Streptomyces coelicolor M145 in comparison to the wildtype M145. Goal was to determine the role of SCO0204.

2016-04-14 | E-MTAB-4597 | biostudies-arrayexpress

Differential expression of S. coelicolor M145 vs. tdd8 mutants in R5

Project description:Differential expression data set of S. coelicolor M145, tdd8 deletion mutant and overexpressed tdd8 mutant cultured in R5. RNA samples were collected at the visual onset Red antibiotic production following by cDNA synthesis and labeling. The hybridization was conducted using DNA 104K microarrays (Surrey) using gDNA from S. coelicolor M145 as reference.

2015-06-08 | E-MTAB-2644 | biostudies-arrayexpress

Responsive genes upon deletion of the ohkA gene in Streptomyces coelicolor M145

Project description:Transcription profile analysis between the wild-type strain M145 and the ohkA-deletion mutant to determine the overall transcription changes caused by the deletion of orphan histidine kinase gene ohkA in S.coelicolor. Transcription changes between the ohkA mutant and the wild-type strain M145 were performed at three time points, 48,64,88h.

2011-01-05 | E-GEOD-26426 | biostudies-arrayexpress

Differential expression of S. coelicolor M145 vs. an abrC3 mutant in NB

Project description:Differential expression data set of S. coelicolor M145 and a abrC3 mutant cultured in NB. RNA samples were collected at 36, 48 and 60 hours following cDNA synthesis and labeling. The hybridization was conducted using DNA 104K microarrays (Surrey) using gDNA from S. coelicolor M145 as reference.

2014-01-14 | E-MTAB-1453 | 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

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