Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The genome of Streptomyces rimosus shows a novel structure compared to other Streptomyces

ABSTRACT: This study compared the genome of Streptomyces rimosus rimosus against that of Streptomyces coelicolor. It also compared 4 strains with changes in oxytetracycline production and derived from G7, the type strain, against G7. Duplicate samples, each replicate may be found in the corresponding supplementary file for the Sample

ORGANISM(S): Streptomyces rimosus

SUBMITTER: Iain Hunter

PROVIDER: E-GEOD-10126 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The genome of Streptomyces rimosus subsp. rimosus shows a novel structure compared to other Streptomyces using DNA/DNA microarray analysis.

Kirby Ralph R Gan Teng-Kuei TK Hunter Iain I Herron Paul P Tilley Emma E

Antonie van Leeuwenhoek 20080227 2

DNA/DNA genome microarray analysis together with genome sequencing suggests that the genome of members of the genus Streptomyces would seem to have a common structure including a linear genomic structure, a core of common syntenous Actinomycete genes, the presence of species specific terminal regions and two intermediate group of syntenous genes that seem to be genus specific. We analyzed Streptomyces species using DNA/DNA microarray comparative genome analysis. Only Streptomyces rimosus failed ...[more]

PMID: 18302004

Similar Datasets

Response of Streptomyces coelicolor to treatment with the antibiotics vancomycin bacitracin and moenomycin A

Project description:To determine the response at the transcriptional level of S. coelicolor cells to treatment with 3 antibiotics that target distinct stages of cell wall biosynthesis, biological triplicate cultures of strain M600 were treated with sub-lethal concentrations (10 µg/ml) of vancomycin, bacitracin or moenomycin A. Samples were taken 0, 30, 60, 90 minutes after addition of the antibiotic. A negative control which received no drug treatment was also performed.

2011-04-29 | E-MEXP-3032 | biostudies-arrayexpress

Global gene transcription analysis in response to changes in chromosome supercoiling in Streptomyces coelicolor

Project description:We address the transcriptional response to both novobiocin-induced rapid chromosome relaxation or long-term topological imbalance, both increased and decreased supercoiling, in environmental antibiotic-producing bacteria belonging to the Streptomyces genus.

2019-06-22 | E-MTAB-8071 | biostudies-arrayexpress

Global gene transcription analysis in Streptomyces coelicolor strains with modification of satKR genes.

Project description:We addressed the transcriptional changes in strains with mutations of satKR (sco3390-3389) genes to elucidate which genes are engaged in restoration of sporulation in non-sporulating Streptomyces coelicolor PS04 strain. Our experiments show that SatR can regulate growth and spore formation in Streptomyces and its activity is independent to DNA supercoiling.

2021-08-21 | E-MTAB-10835 | biostudies-arrayexpress

ChIP-Seq of the Streptomyces venezuelae regulator BldD and its D116A mutant.

Project description:The dimerization and binding of DNA by BldD is affected by its interaction with cyclic di-GMP. The D116A mutant of BldD is partially impaired in its biding of cyclic di-GMP. ChIP-Seq was carried out to determine the difference in the degree of DNA binding by the wild type and D116A mutated BldD in Streptomyces venezuelae.

2017-11-01 | E-MTAB-5328 | biostudies-arrayexpress

The genome of Streptomyces rimosus shows a novel structure compared to other Streptomyces

Project description:This study compared the genome of Streptomyces rimosus rimosus against that of Streptomyces coelicolor. It also compared 4 strains with changes in oxytetracycline production and derived from G7, the type strain, against G7. Keywords: Comparative genomic hybridization

2008-01-11 | GSE10126 | GEO

Genome-wide distribution of AdpA, a global regulator for secondary metabolism and morphological differentiation in Streptomyces [solid]

Project description:AdpA is a global transcriptional activator triggering morphological differentiation and secondary metabolism in Streptomyces griseus. AdpA influences expression of >1,000 genes, but the overall picture of AdpA regulon has been obscure. Here, we took snapshots of distribution of AdpA across the chromosome in living S. griseus cells by ChIP/ChAP-seq analysis. In both liquid and solid cultures, AdpA bound to similar >1,200 sites, which were located on not only putative regulatory regions (65 %) but also regions (35 %) that appeared not to affect transcription. Transcriptome analysis indicated that approximately 40% of the AdpA binding sites in putative regulatory regions were involved in gene regulation. AdpA was indicated to act as a transcriptional repressor as well as an activator. Expression profiles of AdpA-target genes were very different between liquid and solid cultures in spite of similar AdpA-binding profiles. We therefore concluded that AdpA directly controls >500 genes in cooperation with other regulatory proteins in many cases. In vitro AdpA binding to the selected 304 AdpA-binding sites was examined, revealing several unique characteristics of AdpA regarding its DNA-binding property. This study gave the first experimental insight into the extent of AdpA regulon, indicating many genes under the direct control of AdpA. Time course analysis of genome-wide distribution of AdpA on solid culture

2012-04-03 | E-GEOD-34037 | biostudies-arrayexpress

Identification of desuccinylase ScCobB2 and its desuccinylation substrates in Streptomyces coelicolor

Project description:As a recently discovered protein posttranslational modification in eukaryotes, lysine succinylation has attracted increasing interest due to its ability to regulate several critical cellular processes including catabolism, β-oxidation, and ketogenesis. Nevertheless, understanding of the regulation mechanism is still at an early stage due to the lack of identified specific desuccinylases in most microorganisms.Here, in the model soil bacteria Streptomyces coelicolor, we biochemically characterized a sirtuin-like protein ScCobB2 as a divergent desuccinylase. Based on it, we identified a total of 673 unique succinylated sites, of which 470 sites in 317 proteins were quantified by combining tandem mass tag labeling, antibody affinity enrichment, and LC−MS/MS analysis. Furtheranalyses of the quantitative succinylome revealed that at least 114 proteins representing two major pathways, carbon metabolism and protein biosynthesis, are obviously hypersuccinylated in ∆ScCobB2 cells. We experimentally examined the regulatory roles of ScCobB2 on 13 hypersuccinylated proteins, including glyceraldehyde-3-phosphate dehydrogenase, aconitate hydratase, and several ribosomal proteins, the results of which suggested a high confidence in our quantitative data. This work provided the first discovery of a specificdesuccinylase in bacteria, and demonstrated it has pivotal regulatory role in multiple biological processes for S. coelicolor, laid the foundation for future research of succinylation regulation in other microorganisms.

2019-06-11 | PXD014202 | Pride

Identification by ChIP-Seq of the binding sites of the extracytoplasmic function (ECF) sigma factor SigE in the genome of Streptomyces coelicolor A3(2) M600.

Project description:SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. This ChIP-Seq experiment was carried out to determine the binding sites of SigE under conditions of cell envelope stress induced by 10 ug / ml vancomycin for 30 minutes. A 3xFLAG tagged SigE was introduced in a SigE deletion strain and ChIP-Seq was carried out using M2 (Sigma Aldrich A2220) gel suspension. Non-immunoprecipitated (total) DNA preparations were used for background determination and the wild type M600 was used as the negative control.

2019-04-24 | E-MTAB-7827 | biostudies-arrayexpress

Global transcript levels during growth of Streptomyces venezuelae wild-type strain

Project description:Transcript levels quantified after 10, 15, and 20 hours of gtowth in liquid rich MYM medium

2023-12-24 | E-MTAB-13607 | biostudies-arrayexpress

S. coelicolor M145 SMM medium time course study (Culture # 2)

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) wild type and regulatory mutants. The time-course study involved analysis of 8 samples (15.5hr, 17hr, 19hr, 20.5hr, 22.5hr, 23.5hr, 25hr, 42hr). 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.

2012-12-19 | E-GEOD-22395 | 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