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ABSTRACT:
PROVIDER: PRJNA412292 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Identification of transcription start sites in Streptomyces venezuelae genome after 10, 14, 18 and, 24 hours of culture 5' tag RACE. The 4 time points correspond to late vegetative growth, initiation of sporulation, maturation of spores and, completion of sporulation.
2021-07-09 | E-MTAB-10690 | biostudies-arrayexpress
Project description:We identified genome-wide binding regions of NdgR in Streptomyces coelicolor using chromatin immunoprecipitation sequencing (ChIP-seq). We constructed 6×myc-tagged NdgR strain using homologous recombination with myc-tagging vector. Analysis of the sequencing data aligned to Streptomyces coelicolor genome database (NC_003888).
2014-12-29 | GSE59010 | GEO
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
Project description:This SuperSeries is composed of the following subset Series: GSE33992: Streptomyces griseus transcriptome analysis in solid culture with delta adpA, encoding a global transcriptional regulator involved in morphological differentiation and secondary metabolism GSE33993: Streptomyces griseus transcriptome analysis in liquid culture with delta adpA, encoding a global transcriptional regulator involved in morphological differentiation and secondary metabolism GSE34036: Genome-wide distribution of AdpA, a global regulator for secondary metabolism and morphological differentiation in Streptomyces [liquid] GSE34037: Genome-wide distribution of AdpA, a global regulator for secondary metabolism and morphological differentiation in Streptomyces [solid] Refer to individual Series
2012-04-03 | E-GEOD-33994 | biostudies-arrayexpress
Project description:Two component sensor-response regulator systems (TCSs) are very common in the genomes of the Streptomyces species that have been fully sequenced to date. It has been suggested that this large number is an evolutionary response to the variable environment that Streptomyces encounter in soil. Notwithstanding this, TCSs are also more common in the sequenced genomes of other Actinomycetales when these are compared to the genomes of most other eubacteria. In this study, we have used DNA/DNA genome microarray analysis to compare fourteen Streptomyces species and one closely related genus to Streptomyces coelicolor in order to identify a core group of such systems. This core group is compared to the syntenous and non-syntenous TCSs present in the genome sequences of other Actinomycetales in order to separate the systems into those present in Actinomycetales in general, the Streptomyces specific systems and the species specific systems. Horizontal transfer does not seem to play a very important role in the evolution of the TCS complement analyzed in this study. However, cognate pairs do not necessarily seem to evolve at the same pace, which may indicate the evolutionary responses to environmental variation may be reflected differently in sequence changes within the two components of the TCSs. The overall analysis allowed subclassification of the orphan TCSs and the TCS cognate pairs and identification of possible targets for further study using gene knockouts, gene overexpression, reporter genes and yeast two hybrid analysis.
2009-01-31 | GSE13621 | GEO
Project description:The whiH gene is required for the differentiation of aerial hyphae into spores in Streptomyces species. It is a predicted member of the GntR family of transcription factors and has been shown to bind specifically to a sequence in its own promoter. This ChIP-Seq experiment was carried out to determine all the binding sites whiH binds to in the genome of Streptomyces venezuelae. A whiH deletion strain was made and a FLAG tagged whiH protein was expressed in it from a genome-integrated plasmid. Then anti-FLAG antibodies were used for chromatin immunoprecipitation followed by high throughput sequencing. The wild type Streptomyces venezuelae strain (ATCC 10712) was used as a negative control. For both the FLAG-WhiH strain and the WT strain, non-immunoprecipitated (total) DNA was also sequenced to arrive at a background enrichment which could be subtracted from the enrichment in the immunoprecipated sample.
2018-12-31 | E-MTAB-6702 | biostudies-arrayexpress
Project description:To determine the influence of BldM and WhiI on the binding of each other to their respective binding sites in the genome of Streptomyces venezuelae, ChIP-Seq experiments were carried out using polyclonal antibodies against the wild type proteins as well as anti-FLAG antibodies against FLAG-tagged proteins. Null mutants of Streptomyces venezuelae lacking WhiI or BldM were used as controls. The wild tpe strain was used as control in experiments using the anti-FLAG antibodies.
2015-05-19 | E-MTAB-2698 | biostudies-arrayexpress
Project description:Borodina2005 - Genome-scale metabolic network
of Streptomyces coelicolor (iIB711)
This model is described in the article:
Genome-scale analysis of
Streptomyces coelicolor A3(2) metabolism.
Borodina I, Krabben P, Nielsen
J.
Genome Res. 2005 Jun; 15(6):
820-829
Abstract:
Streptomyces are filamentous soil bacteria that produce more
than half of the known microbial antibiotics. We present the
first genome-scale metabolic model of a representative of this
group--Streptomyces coelicolor A3(2). The metabolism
reconstruction was based on annotated genes, physiological and
biochemical information. The stoichiometric model includes 819
biochemical conversions and 152 transport reactions, accounting
for a total of 971 reactions. Of the reactions in the network,
700 are unique, while the rest are iso-reactions. The network
comprises 500 metabolites. A total of 711 open reading frames
(ORFs) were included in the model, which corresponds to 13% of
the ORFs with assigned function in the S. coelicolor A3(2)
genome. In a comparative analysis with the Streptomyces
avermitilis genome, we showed that the metabolic genes are
highly conserved between these species and therefore the model
is suitable for use with other Streptomycetes. Flux balance
analysis was applied for studies of the reconstructed metabolic
network and to assess its metabolic capabilities for growth and
polyketides production. The model predictions of wild-type and
mutants' growth on different carbon and nitrogen sources agreed
with the experimental data in most cases. We estimated the
impact of each reaction knockout on the growth of the in silico
strain on 62 carbon sources and two nitrogen sources, thereby
identifying the "core" of the essential reactions. We also
illustrated how reconstruction of a metabolic network at the
genome level can be used to fill gaps in genome annotation.
This model is hosted on
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and identified by:
MODEL1507180049.
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2015-07-30 | MODEL1507180049 | BioModels
Project description:Investigation of whole genome gene expression level changes in Streptomyces avermitilis delta-aveI mutant, compared to the wild-type strain. The mutants analyzed in this study are further described in Chen L, Lu Y., Chen J, Zhang W, Shu D, Qin Z, Yang S, Jiang W. (2008) Characterization of a negative regulator AveI for avermectin biosynthesis in Streptomyces avermitilis NRRL8165. Appl Microbiol Biotechnol 80(2): 277-86.
2009-07-02 | GSE16892 | GEO
Project description:Streptomyces bingchenggensis is a soil bacterium that produces a family of macrolide antibiotics, milbemycins, which is commercially important in crop protection, human and veterinary medicine. After the complete genome sequence, and annotation, for further development of our gene expression approach to biosynthesis, we have employed whole genome microarray expression profiling as a discovery platform to obtain improved specificity and sensitivity of gene expression analysis, allowing a global and at the same time detailed picture of how gene clusters for secondary metabolism are modulated. In the result, we confirmed the expression mil and nan gene cluster, furthermore, pks3, pks5 and nrps7, nrps8 also showed significant gene expression, but no obvious products detected. In Streptomyces bingchenggensis, there are also corresponding genes belonging to Defense mechanisms, which is much more than other Streptomyces, for the resistance of own metabolites and dealing with complex environmental factors.
2011-09-20 | GSE32205 | GEO