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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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

ABSTRACT: 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.

ORGANISM(S): Streptomyces coelicolor A3(2)

SUBMITTER: Yinhua Lu

PROVIDER: E-GEOD-26426 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2011-01-05 | GSE26426 | GEO

Characterization of the RelBbu regulon in Borrelia burgdorferi reveals modulation of glycerol metabolism by (p)ppGpp

Project description:The bacterial stringent response is triggered by deficiencies of available nutrients andother environmental stresses. It is mediated by 5'-triphosphate-guanosine-3'- diphosphate and 5'-diphosphate-guanosine-3'-diphosphate (collectively (p)ppGpp) and generates global changes in gene expression and metabolism that enable bacteria to adapt to and survive these challenges. Borrelia burgdorferi encounters multiple stressors in its cycling between ticks and mammals that could trigger the stringent response. We have previously shown that the B. burgdorferi stringent response is mediated by a single enzyme, RelBbu, with both (p)ppGpp synthase and hydrolase activities, and that a B. burgdorferi 297 relBbu null deletion mutant was defective in adapting to stationary phase, incapable of down-regulating synthesis of rRNA and could not infect mice. We have now used this deletion mutant and microarray analysis to identify genes comprising the rel regulon in B. burgdorferi cultured at 34°C, and found that transcription of genes involved in glycerol metabolism is induced by relBbu. Culture of the wild-type parental strain, the relBbu deletion mutant and its complemented derivative at 34°C and 25°C in media containing glucose or glycerol as principal carbon sources revealed a growth defect in the mutant, most evident at the lower temperature. Transcriptional analysis of the glp operon for glycerol uptake and metabolism in these three strains confirmed that relBbu was necessary and sufficient to increase transcription of this operon in the presence of glycerol at both temperatures, and particularly at 25°C. These results confirm and extend previous findings regarding the stringent response in B. burgdorferi. They also demonstrate that the stringent response regulates glycerol metabolism in this organism and is likely crucial for its optimal growth in ticks.

2015-01-30 | E-MTAB-3029 | 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

A genome-wide transcriptome analysis reveals diverse roles of two-component system DraR-K in physiological and morphological differentiation of Streptomyces coelicolor

Project description:A novel two-component system (TCS) DraR-K was identified previously to play a differential role in antibiotic biosynthesis (ACT, RED and yCPK) of Streptomyces coelicolor M145 on defined minimal medium (MM) conditions. In order to assess whether DraR-K has more global roles, a genome-wide transcriptomic analysis of the wild-type strain M145 and M-bM-^HM-^FdraR-K under the condition of 75 mM glutamine-based MM was performed using DNA microarray. The analysis demonstrated that deletion of draR-K led to the differential expression not only of the biosynthetic gene clusters of ACT, RED and yCPK, but also of other six secondary metabolite biosynthetic clusters, revealing the widely differenital regulation of DraR-K on secondary metabolism of S. coelicolor. Besides, a number of primary metabolism-related genes in the M-bM-^HM-^FdraR-K mutant, such as ureA/B/C/D/G/F, pstSCAB operon and chb gene also exhibited altered expression, which might enable the rebalance of C/N/P ratio under the condition of high concentration of Gln. We also observed that expression of many developmental genes (chpA/B/D/E, ramR/S and rdlA/B) was affected as well after draR-K deletion. Furthermore, the direct role of DraR-K on the transcription of several genes, including cdaR (the pathway-specific activator gene for CDA biosynthesis), chb, and pepA/pepA2 (SCO7336/7337, possibly involved in aerial mycelium development) were validated by electrophoresis mobility shift assays (EMSAs). In summary, our transcriptome analyses revealed the global regulation of DraR-K on physiological and morphological differentiation, especially its differential roles on secondary metabolism of S. coelicolor. The global transcription profiles of M145 and the M-bM-^HM-^FdraR-K mutant was compared using DNA microarray. RNA samples were isolated from these two strains grown on MM supplemented with 75 mM glutamine as the sole nitrogen source at three time points, 36, 48 and 60 h.

2014-03-10 | E-GEOD-55714 | biostudies-arrayexpress

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Project description:This SuperSeries is composed of the following subset Series: GSE22394: S. coelicolor M145 SMM medium time course study (Culture # 1) GSE22395: S. coelicolor M145 SMM medium time course study (Culture # 2) GSE22397: S. coelicolor M145 SMM medium time course study (Culture # 3) Refer to individual Series

2010-10-25 | E-GEOD-22399 | biostudies-arrayexpress

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

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

Transcriptional profiling of Streptomyces coelicolor M145 strain and delta wdpB and delta wdpC mutant strains.

Project description:Transcriptional profiling of Streptomyces coelicolor M145 strain and delta wdpB and delta wdpC mutant strains.

2013-03-26 | E-MTAB-894 | 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

Combined transcriptome analysis and polysome profiling of Streptomyces coelicolor MT1110 in SMMS

Project description:Total RNA, low ribosome density (LRD) and polysome associated RNA were obtained from parallel S.coelicolor cultures of wild type strain MT1110 grown on solid medium SMMS up to rapid growth phase II. The abundance of each RNA in the total RNA, the LRD or polysome pool was quantified by Cydye labeling and hybridization on high density whole genome 105K S.coelicolor DNA microarrays using S.coelicolor M145 as reference.

2018-11-01 | E-MTAB-6206 | biostudies-arrayexpress

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