Streptomyces coelicolor
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRD000514
PROVIDER: PRJNA144841 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacteria in the genus Streptomyces are soil dwelling oligotrophs and important producers of secondary metabolites. Previously we showed that global mRNA expression was subject to a series of metabolic and regulatory switches during the life time of a fermentor batch culture of S. coelicolor M145. Here we analyse the proteome from eight time points from the same fermentor culture and, as phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (ΔphoP), defective in the control of phosphate utilisation. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index which also revealed the importance of stress pathway proteins in both cultures. As expected the ΔphoP mutant was deficient in expression of PhoP-dependent genes and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that co-ordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures and these were not confined to the stationary phase.
2011-12-31 | GSE31068 | GEO
Project description:Bacteria in the genus Streptomyces are soil dwelling oligotrophs and important producers of secondary metabolites. Previously we showed that global mRNA expression was subject to a series of metabolic and regulatory switches during the life time of a fermentor batch culture of S. coelicolor M145. Here we analyse the proteome from eight time points from the same fermentor culture and, as phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (M-NM-^TphoP), defective in the control of phosphate utilisation. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index which also revealed the importance of stress pathway proteins in both cultures. As expected the M-NM-^TphoP mutant was deficient in expression of PhoP-dependent genes and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that co-ordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures and these were not confined to the stationary phase. 36 samples, no replicates; one hour resolution from 23-36h and 41-48h; half hour resolution from 36-41h; two hour resolution 48-60h; sample missing for 34 h
2011-12-31 | E-GEOD-31068 | biostudies-arrayexpress
Project description:S. coelicolor was grown in low-phosphate concentration R5 liquid medium which facilitated the transition to a phosphate starvation induced stationary phase and the subsequent induction of the PhoP regulon. The genome wide binding locations of PhoP during phosphate starvation were determined by chromatin-immunopreciptiation followed by hybridisation to high density S. coelicolor DNA microarrays. The use of both wild-type S. coelicolor and phoP-null mutant strains allowed the identification of specific PhoP binding locations.
2012-08-30 | E-MAXD-50 | biostudies-arrayexpress
Project description:S. coelicolor M145 and S. coelicolor ∆argR were grown in MG medium and samples from 3 biological replicates were taken at 32, 42, 49, 56 and 66 hours.
2015-08-19 | GSE58666 | 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:S. coelicolor was grown in low-phosphate concentration R5 liquid medium which facilitated the transition to a phosphate starvation induced stationary phase and the subsequent induction of the PhoP regulon. Global gene expression profiling of a wild-type and a phoP-null mutant was performed using samples isolated, respectively, at 24, 30, 35 and 45 h of growth. RNA was extracted and the resulting cDNA was hybridised to S. coelicolor high density DNA microarrays.
2012-08-30 | E-MAXD-51 | biostudies-arrayexpress
Project description:This data contained within this entry was produced as part of a study that included differential RNA-sequencing. S. coelicolor and E. coli reference strains were grown in batch culture with shaking. The E. coli sample was extracted during mid-exponential growth, while the S. coelicolor sample was extracted at the start of pigmented antibiotic production.
2013-04-20 | E-GEOD-46232 | biostudies-arrayexpress
Project description:Background: 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. Results: Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. Conclusions: Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting. Keywords: time course
2009-12-14 | GSE18489 | 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:The differential RNA-seq data contained within this entry is complemented by global RNA-seq. S. coelicolor and E. coli reference strains were grown in batch culture with shaking. The E. coli sample was extracted during mid-exponential growth, while the S. coelicolor sample was extracted at the start of pigmented antibiotic production. Each of the two samples was incubated with or without TAP (tobacco acid pyrophosphatase) before library construction. Thus, 4 libraries were analysed. TAP treatment allows the cloning and sequencing of 5' ends that were originally triphosphorylated.
2013-05-01 | E-GEOD-46507 | biostudies-arrayexpress