Streptomyces coelicolor
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ABSTRACT:
PROVIDER: PRJNA154767 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE30569: Metabolic switching in Streptomyces coelicolor wild type, time series under glutamate depletion condition GSE30570: Metabolic switching in Streptomyces coelicolor time series under glutamate depletion of mutant SCglnK-3. Refer to individual Series
2011-12-31 | E-GEOD-30571 | biostudies-arrayexpress
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: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. 30 samples, no replicates; one hour resolution from 20-32h and 40-42h; half our resolution from 32-40 h; two hour resolution 44-58h; sample missing for 29 and 34 h
2011-12-31 | E-GEOD-30569 | biostudies-arrayexpress
Project description:Metabolic switching in Streptomyces coelicolor Timeseries 1
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Project description:Expression time-series from Streptomyces coelicolor germination
| PRJNA189845 | ENA
Project description:Time-series transcription microarray data of Streptomyces coelicolor M145
| PRJNA232582 | ENA
Project description:Metabolic switching of the PII protein GlnK in Streptomyces coelicolor
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Project description:Time-series transcription microarray data of Streptomyces coelicolor M145-OA
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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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MODEL1507180005.
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2015-07-30 | MODEL1507180005 | BioModels
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