Transcription profiling of Streptomyces coelicolor strain M653 in a time series after ppGpp synthesis activation by thiostrepton
Ontology highlight
ABSTRACT:
ORGANISM(S): Streptomyces coelicolor
SUBMITTER: Andrew Hesketh
PROVIDER: E-MEXP-1119 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:As a control for the effect of thiostrepton on gene expression in Streptomyces coelicolor, cultures of strain M667 [DrelA tipAp::] that lacks the truncated relA gene downstream of the thiostrepton-inducible promoter were treated with thiostrepton. Samples were harvested at 30 min intervals following induction for comparison to a control set of samples from aliquots of the same cultures that were not induced.
2007-08-01 | E-MEXP-1120 | biostudies-arrayexpress
Project description:Comparison of the Streptomyces coelicolor relA mutant strain M570 with the parental strain M600 during growth on MYM agar.
2007-08-01 | E-MEXP-1098 | biostudies-arrayexpress
Project description:Hypoxia imposes a challenge upon most of the filamentous fungi that require oxygen for proliferation. Here, we used whole genome DNA microarrays to investigate global transcriptional changes in Aspergillus nidulans gene expression after exposure to hypoxia followed by normoxia. Aeration affected the expression of 2,864 genes (27% of the total number of genes in the fungus), of which 50% were either induced or repressed under hypoxic conditions. Up-regulated genes included those for glycolysis, ethanol production, the tricarboxylic acid (TCA) cycle, and for the γ-aminobutyrate (GABA) shunt that bypasses two steps of the TCA cycle. Ethanol and lactate production under hypoxic conditions indicated that glucose was fermented to these compounds via the glycolytic pathway. Since the GABA shunt bypasses the NADH-generating reaction of the TCA cycle catalyzed by oxoglutarate dehydrogenase, hypoxic A. nidulans cells eliminated excess NADH. Hypoxia down-regulated some genes involved in transcription initiation by RNA polymerase II, and lowered the cellular mRNA content. These functions were resumed by reoxygenation, indicating that A. nidulans controls global transcription to adapt to a hypoxic environment. This study is the first to show that hypoxia elicits systematic transcriptional responses in A. nidulans. We transferred A. nidulans cells from normoxic to hypoxic conditions for 6 h, and then back to normoxic conditions to examine the effect of hypoxia on gene expression. Total RNA was prepared for DNA microarray analysis from the cells after 3 and 6 h of exposure to hypoxia, followed by 3 and 6 h of reoxygenation.
2010-08-14 | E-GEOD-23605 | biostudies-arrayexpress
Project description:Hypoxia imposes stress on filamentous fungi that require oxygen to proliferate. Global transcription analysis of Aspergillus oryzae grown under hypoxic conditions found that the expression of about 50% of 4,244 affected genes was either induced or repressed more than 2-fold. A comparison of these genes with the hypoxically-regulated genes of A. nidulans (Masuo et al., Mol. Gen. Genet. 2010, 284:415-424) based on their predicted amino acid sequences classified them as bi-directional best hit (BBH), one-way best hit (extra homolog: EH) and no-hit (non-syntenic genes: NSG) genes. Clustering analysis of the BBH genes indicated that A. oryzae and A. nidulans down-regulated global translation and transcription under hypoxic conditions, respectively. Under hypoxic conditions, both fungi up-regulated genes for alcohol fermentation and the γ-aminobutyrate shunt of the tricarboxylate cycle, whereas A. oryzae up-regulated the glyoxylate pathway, indicating that both fungi eliminate NADH accumulation under hypoxic conditions. The A. oryzae NS genes included specific genes for secondary and nitric oxide metabolism under hypoxic conditions. This comparative transcriptomic analysis discovered common and strain-specific responses to hypoxia in hypoxic Aspergillus species. We transferred A. oryzae cells from normoxic to hypoxic conditions for 6 h, and then back to normoxic conditions to examine the effect of hypoxia on gene expression. Total RNA was prepared for DNA microarray analysis from the cells after 1, 3, and 6 h of exposure to hypoxia, followed by 1, 3, and 6 h of reoxygenation.
2011-07-30 | E-GEOD-31046 | biostudies-arrayexpress
Project description:Transcriptional profiling of S. coelicolor comparing control untreated cells with ciprofloxacin treated cells. Two-condition experiment, Control Vs CIP treatment. Biological replicates: 3 control, One dye swap replicate. four samples and three biological replicate to study the response of S. coleicolor cells to ciprofloxacin
2014-01-01 | E-GEOD-49788 | biostudies-arrayexpress
Project description:Description: In Streptomyces coelicolor the Zur repressor controls genes involved in zinc uptake and alternative ribosomal proteins that lack structural zinc. This experiment provides global gene expression patterns of M145 and S121 (zur deletion) grown in NMMP plus glucose medium to mid-log phase. The data reveal that Zur also controls genes involved in production of a non-ribosomally encoded siderophore-related peptide designated coelibactin.
2010-10-13 | E-MAXD-56 | biostudies-arrayexpress
Project description:Time-dependent gene expression patterns during development and antibiotic production on solid growth medium (SMM) comparing a M600 bldA deletion mutant with wild-type M600 of S.coelicolor A3(2). Eight time points matched in all three replicates of both wild-type and mutant were picked to span the entire Streptomyces growth curve.
2008-06-05 | E-MAXD-27 | biostudies-arrayexpress
Project description:The sirA gene encodes a member of sirtuin protein that is NAD(+)-dependent histone deacetylase (HDAC) and ubiquitous in eukaryote. DNA microarray analyses for Aspergillus nidulans FGSCA26 (WT) strain and Gene disruptant of sirA (SirAd) indicated that genes for synthesizing secondary metabolic products such as sterigmatocystin, penicillin G, emericellamide, aspernidine A, xanthone, austinol, and siderophores are down-regulated by SirA. Aspergillus nidulans WT and SirAd strains were cultured in 200 ml of GMM at 30°C for 24, 48, and 72 h, and their total RNA was purified as described above.
2016-08-09 | E-GEOD-85319 | biostudies-arrayexpress
Project description:Mutations in the cysB, sconB and sconC genes affect sulfur metabolism in Aspergillus nidulans in different ways. Mutation of cysB blocks synthesis of cysteine by the main pathway leaving only the less effective alternative route. Mutations of sconB or sconC affect subunits of the SCF ubiquitin ligase complex, a negative controller of METR transcription factor, resulting in specific activation of a number of sulfur assimilation and metabolism genes, ultimately leading to elevated levels of cysteine and glutathione in scon mutants. We compared transcriptomes of these three mutants with that of a wild type strain finding that expression of a few hundred genes is altered at least twofold indicating a major reorganization of cellular metabolism. Despite the different effects of the cysB and scon mutations on sulfur metabolism they affect expression of overlapping sets of genes. We identified categories of the Functional Catalogue assigned to the differentially expressed genes and selected categories most enriched among the up- and down-regulated gene groups. Besides those involved in sulfur metabolism, many up-regulated genes are related to stress responses. The two-component signal transduction system is most enriched in genes up-regulated in the cysB, sconB and sconC mutants. This category contains histidine kinases that sense and transduce environmental signals to a cascade of protein kinases. Genes encoding heat shock proteins are also up-regulated, as are genes of the glutamate degradation pathway. The latter, also known as the GABA shunt, is induced by oxidative stress. A large group of up-regulated genes are involved in carbohydrate and energy metabolism, including genes coding for enzymes of trehalose and glycerol synthesis. Genes coding for enzymes of alcohol fermentation, which are induced in response to anaerobic stress, are also up-regulated in the mutants studied. The altered expression of the carbohydrate metabolism genes is accompanied by changes in sugar accumulation in mycelia and conidia of the mutants. Among the down-regulated genes the most numerous are those encoding membrane proteins and enzymes involved in secondary metabolism, including the penicillin biosynthesis cluster. Genes coding for lysozyme are down-regulated too. As secondary metabolites often inhibit growth of other organisms, lowered expression of genes responsible for their synthesis suggests a decreased response to biotic stress in the mutants studied. Comparison of transcriptomes of the filamentous fungus Aspergillus nidulans strains bearing mutations in the cysB, sconB or sconC genes, affecting sulfur metabolism in different ways, with that of the wild type (WT) strain. Three biological replicates of WT vs cysB and WT vs sconC comparisons were performed and four biological replicates of WT vs sconB comparison were done. Each biological replicate had two technical replicates with dye swapping. A total of twenty individual hybridizations were made.
2014-02-14 | E-GEOD-54130 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M752 mutant strain, which has an in frame deletion of scbR (SCO6265) and compare it to the wild-type M145 strain. scbR encondes a gamma-butyrolactone binding protein (Takano, E., Chakraburtty, R., Nihira, T., Yamada, Y., and Bibb, M. A complex role for the gamma-butyrolactone SCB1 in regulating antibiotic production in Streptomyces coelicolor A3(2). Mol. Microbiol. 2001 41(5), 1015-1028). The time-course study involved analysis of 8 samples (14hr, 15hr, 16hr, 17hr, 19hr, 20hr, 22hr, 39hr). Sample 22hr was analyzed on duplicate arrays (2 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.
2010-10-25 | E-GEOD-22398 | biostudies-arrayexpress