Ontology highlight
ABSTRACT:
PROVIDER: PRJNA948046 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23950471_1.fastq.gz | Fastqsanger.gz | |||
| SRR23950471_2.fastq.gz | Fastqsanger.gz |
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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:Background The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of orthology. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle yet crucial differences between these two chromosomes. Results We identified five large S. coelicolor genomic islands (≥25 kb) and 18 smaller islets absent in S. lividans chromosome. Many of these regions show anomalous GC bias and codon usage patterns. Six of them are in close vicinity of tRNA genes while nine are flanked with near perfect repeat sequences indicating that these are probable recent evolutionary acquisitions into S. coelicolor. Embedded within these segments are at least four DNA methylases and two probable methyl-sensing restriction endonucleases. Comparison with S. coelicolor transcriptome and proteome data revealed that some of the missing genes are active during the course of growth and differentiation in S. coelicolor. In particular, a pair of methylmalonyl CoA mutase (mcm) genes involved in polyketide precursor biosynthesis, an acyl-CoA dehydrogenase implicated in timing of actinorhodin synthesis and bldB, a developmentally significant regulator whose mutation causes complete abrogation of antibiotic synthesis belong to this category. Conclusion Our findings provide tangible hints for elucidating the genetic basis of important phenotypic differences between these two streptomycetes. Importantly, absence of certain genes in S. lividans identified here could potentially explain the relative ease of DNA transformations or the conditional lack of actinorhodin synthesis in S. lividans. Further genetic studies based on these results will enable one to target specific sequences in the genetically well-characterized S. coelicolor to adapt it for industrial processes. Keywords: Comparative Genomic Hybridization
2007-06-08 | GSE7167 | GEO
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:The chromosomes of several widely used laboratory derivatives of Streptomyces coelicolor A3(2) were found to have 1.06 Mb inverted repeat sequences at their termini (i.e. long-terminal inverted repeats; L-TIRs), which are 50 times the length of the 22 kb TIRs of the sequenced S. coelicolor strain M145. The L-TIRs include 1005 annotated genes and increase the overall chromosome size to 9.7 Mb. The 1.06 Mb L-TIRs are the longest reported thus far for an actinomycete, and are proposed to represent the chromosomal state of the original soil isolate of S. coelicolor A3(2). S. coelicolor A3(2), M600 and J1501 possess L-TIRs, whereas approximately half the examined early mutants of A3(2) generated by ultraviolet (UV) or X-ray mutagenesis have truncated their TIRs to the 22 kb length. UV radiation was found to stimulate L-TIR truncation. Two copies of a transposase gene (SCO0020) flank 1.04 Mb of DNA in the right L-TIR, and recombination between them appears to generate strains containing short TIRs. This TIR reduction mechanism may represent a general strategy by which transposable elements can modulate the structure of chromosome ends. The presence of L-TIRs in certain S. coelicolor strains represents a major chromosomal alteration in strains previously thought to be genetically similar. A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s). Keywords: dose_response_design
2005-07-26 | GSE2994 | GEO
Project description:We report the DNA binding profile of a novel family of nucleoid-associated protein in Streptomyces coelicolor
2022-04-02 | GSE165795 | GEO
Project description:To identify unique gene expression in cAMP supplemented Streptomyces coelicolor M1146 strain. The genes with different gene expression might be key genes to understand the effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M1146.
2020-11-27 | GSE158811 | GEO
Project description:To identify unique gene expression in cAMP supplemented Streptomyces coelicolor M145 strain. The genes with different gene expression might be key genes to understand the effects of cAMP supplementation on the transcriptome of Streptomyces coelicolor M145.
2020-11-27 | GSE158810 | GEO
Project description:Different pea aphid response differently to stress response with certain genotype producing wing but others changing body colour morph, However, the underlying epigenetic mechanisms remains unclear. Therefore, we used MBD-seq to analyse the epigenomic profile of the four different pea aphid morphs (N116 winged, N116 wingless, N127 red,, N127 pale) to provide insights into the epigenetic profiling (DNA methylation) in regulating this polyphenism. Alternative morphs (N116 winged and N127 pale) were obtained through crowding experiment.
2026-04-10 | E-MTAB-15212 | biostudies-arrayexpress
Project description:Different pea aphid response differently to stress response with certain genotype producing wing but others changing body colour morph, However, the underlying molecular mechanisms remains unclear. Therefore, we used RNA-seq to analyse the transcriptomic profile of the four different pea aphid morphs (N116 winged, N116 wingless, N127 red, N127 pale) to provide insights into the epigenetic profiling (DNA methylation) in regulating this polyphenism. Alternative morphs (N116 winged and N127 pale) were obtained through crowding experiment.
2026-04-10 | E-MTAB-15213 | biostudies-arrayexpress
Project description:GlnK is an important nitrogen sensor protein in Streptomyces coelicolor. Deletion of glnK results in a medium-dependent failure of aerial mycelium and spore formation and loss of antibiotic production. Thus, GlnK is not only a regulator of nitrogen metabolism but also of morphological differentiation and secondary metabolite production. Through a comparative transcriptomic approach between the S. coelicolor wild-type and a S. coelicolor glnK mutant strain, 142 genes were identified that are differentially regulated in both strains. Among these are genes of the ram and rag operon, which are involved in S. coelicolor morphogenesis, as well as, genes involved in gas vesicle biosynthesis and ectoine biosynthesis. Surprisingly, no relevant nitrogen genes were found to be differentially regulated, revealing that GlnK is not an important nitrogen sensor under the tested conditions.
2011-12-31 | GSE30570 | GEO