Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic description of a classic model of carbon catabolic repression in Streptomyces coelicolor:Glk effect

ABSTRACT: The aim of this work was to use a high density microarray approach in Streptomyces coelicolor M145 and a glk substituted mutant (ScoZm)derived from it, to evaluate the paradigmatic model proposed for CCR in Streptomyces

ORGANISM(S): S. coelicolor_M145_strain

SUBMITTER: alba romero

PROVIDER: E-MTAB-3602 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor.

Romero-Rodríguez Alba A Rocha Diana D Ruiz-Villafan Beatriz B Tierrafría Víctor V Rodríguez-Sanoja Romina R Segura-González Daniel D Sánchez Sergio S

BMC microbiology 20160427

<h4>Background</h4>In the genus Streptomyces, one of the most remarkable control mechanisms of physiological processes is carbon catabolite repression (CCR). This mechanism regulates the expression of genes involved in the uptake and utilization of alternative carbon sources. CCR also affects the synthesis of secondary metabolites and morphological differentiation. Even when the outcome effect of CCR in different bacteria is the same, their essential mechanisms can be quite different. In several ...[more]

PMID: 27121083

Similar Datasets

Transcriptomic description of a classic model of carbon catabolic repression in Streptomyces coelicolor: Glucose effect

Project description:The aim of this work was to use a high density microarray approach in Streptomyces coelicolor M145 using a represive condition (RM) (0.5%agar+0.5%glucose) and non-repressive condition (NRM) (agar 1%)

2016-04-02 | E-MTAB-3603 | biostudies-arrayexpress

Transcriptome data for Streptomyces coelicolor at 2 growth stage

Project description:Transcriptome analysis of Streptomyces coelicolor MT1110 cultures grown in SMM + 0.5% casaminoacids at 30?C up to mid exponential and stationary phase. Total RNA was extracted from both stages of growth, labelled with Cy3-dCTP and mixed with genomic DNA from S. coelicolor M145 labelled with Cy5-dCTP that was used as common reference in an indirect type of microarray experiment. Labelled Cy3/Cy5-dCTP samples were hybridized onto SCO-Chip2-v2 High Density IJISS arrays.

2020-08-01 | E-MAXD-61 | 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

Transcriptional analysis between Streptomyces clavuligerus ATCC 27064 and a mutant altered in antibiotic production

Project description:The objective was to analyze the differential expression between the wild strain and the Streptomyces clavuligerus ΔclaR::aac mutant Six experimental conditions were assayed, two strains (Streptomyces clavuligerus ATCC 27064, S. clavuligerus ΔclaR::aac) in three culture times (22.5h, 46.5h and 60 h). Two biological replicates for each condition.

2015-08-05 | E-GEOD-66683 | biostudies-arrayexpress

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

Global distribution of RNA polymerase in Streptomyces coelicolor

Project description:Genome wide ChIP-chip analysis of RNA Polymerase binding sites in Streptomyces coelicolor MT1110 cultures grown in SMM + 0.5% casaminoacids at 30C up to mid exponential and stationary phase. Chromatin extracted from rifampicin and formaldehyde treated cultures was incubated with anti ? subunit of core RNA polymerase of E.coli monoclonal antibodies and the DNA purified from anti RNA Polymerase IP and mock IP samples was labelled with either Cy3 or Cy5- dCTP and hybridized in an direct type of microarray experiment onto SCO-Chip2-v2 High Density IJISS arrays

2020-08-01 | E-MAXD-60 | biostudies-arrayexpress

sRNA scr5239 involved in important feedback loop of S. coelicolor central metabolism

Project description:The project is focused on the highly conserved sRNA scr5329 in Streptomyces coelicolor. A proteomics approach revealed that the sRNA regulates several metabolic enzymes, among them the Phosphoenolpyruvate-Carboxykinase (PEPCK), a key enzyme of the central carbon metabolism. The sRNA scr5239 promotes its degradation on the post-transcriptional level. The expression itself is dependent on the global transcriptional regulator DasR, which is N-acetylglucosamine-responsive thereby creating a feedback regulation. By post-transcriptional regulation of PEPCK and likely more targets, scr5239 adds an additional layer to the DasR regulatory network, providing a tool to control the metabolism in dependency to the carbon source.

2020-01-28 | PXD016811 | Pride

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 gene expression analysis by RNA-Seq for the bldC deletion strain and the wild type of Streptomyces venezuelae strain NRRL B-65442 after 10 and 14 hours of culture

Project description:The BldC gene is required for the formation of aerial hyphae in Streptomyces venezuelae. It is a 68 amino acid DNA-binding protein related to the MerR family of transcription factors. BldC deletion strains are bald because they initiate sporulation prematurely, omitting the formation of aerial hyphae altogether. This RNA-Seq experiment was carried out to determine and quantify effect of BldC on the expression of all genes in the S. venezuelae genome after 10 and 14 hours of culture.

2019-01-14 | E-MTAB-7457 | biostudies-arrayexpress

S. coelicolor M752 SMM medium time course study

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data