Streptomyces jumonjinensis and Streptomyces katsurahamanus
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ABSTRACT:
PROVIDER: PRJNA542368 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Clavulanic acid is a clinically-important secondary metabolite used in treatment of infectious diseases. We aimed to decipher complex regulatory mechanisms acting in clavulanic acid biosynthesis through the analysis of transcriptome- and proteome-wide alterations in an industrial clavulanic acid overproducer Streptomyces clavuligerus, namely DEPA and its wild-type counterpart NRRL3585.
2022-11-02 | PXD032272 | Pride
Project description:To investigate the function of organic nitrogen on clavulanic acid biosynthesis in Streptomyces clavuligerus, we established F613-1 strain cells cultured in MH fermentation medium and ML fermentation medium. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different medium at three time points.
2022-08-25 | GSE211765 | GEO
Project description:To increase production of the important pharmaceutical compounds, both mutagenesis approaches and rational engineering have been extensively applied. Mutagenesis approaches are most popular in industry, but their effects have not yet been studied very well. Here, we used microarrays to compare the transcriptomes of the S. clavuligerus wild type (ATCC 27064) strain and the DS48802 clavulanic acid high-producer strain, which has been obtained by classical strain improvement (mutagenesis). Streptomyces clavuligerus strains were grown in shake flasks. RNA was extracted after 70h and hybridized to microarrays.
2010-11-10 | E-GEOD-24033 | biostudies-arrayexpress
Project description:Streptomyces clavuligerus F613-1 produces a clinically important β-lactamase inhibitor, clavulanic acid (CA). The biosynthesis pathway of CA has been basically elucidated, however, the global regulation of CA biosynthesis remains unclear. In order to further elucidate the regulatory mechanism of clavulanic acid synthesis, TCS RS07910/07915 which is next to the CA biosynthetic gene cluster was deleted in Streptomyces clavuligerus. F613-1. Deletion of RS07910/07915 results in decreased the production of CA, but the phenotype was not affected. Both the transcriptome and ChIP-seq data revealed that the TCS RS07910/07915 mainly regulate genes involved in primary metabolism (such as fatty acid degradation, glyceraldehyde 3-phosphate (G3P) metabolism, arginine biosynthesis) and CA biosynthesis. EMSA assays revealed that RS07915 could bind to the promoter fragments of argG, argC, oat1, oat2, ceaS1 and claR in vitro, indicating that RS07915 could direct regulate the biosynthesis genes of arginine and CA. This study indicated that RS07910/07915 is a pleiotropy regulatory TCS, RS07910/07915 could directly affect the biosynthesis of CA, and indirectly affect CA production through affecting primary metabolism of arginine and G3P (precursors of CA).
2018-08-30 | GSE119208 | GEO
Project description:Bacterial genomic plasticity and instability carry multiple functional genetic information in Streptomyces secondary metabolism. Our previously publication has reported an effective industrial Streptomyces strain, with a unique phenotype of the high clavulanic acid yield. The complete genome of strain F163-1 harboring a 136.9-kb giant region of plasticity (RGP) was sequenced. The chromosome and plasmid are densely packed by an exceptionally huge variety of potential secondary metabolic gene clusters, excluding production of putative antibiotics. Intriguingly, architecture and size differences of plasmid pSCL4 between F613-1 and ATCC 27064 suggest the pSCL4 plasmid evolving from pSCL4-like and pSCL2-like extrachromosomal replicons, in addition to the previously proposed ATCC 27064 mega-plasmid formation hypothesis through recombination between the smaller F613-1 pSCL4 plasmid arm regions and the linear chromosome. Comparative genomics systemically investigate secondary metabolism capacitates in this study indicates that frequent exchange of genetic materials between Streptomyces replicons may shape remarkable diversities of secondary metabolite repertoires. Consequently, the F613-1 strain seems to have evolved its specific genomic architectures and genetic patterns to meet the requirement in subsequent industrial processes.
2017-10-10 | GSE104738 | GEO
Project description:In this work, we identified glucose and glycerol as tacrolimus repressing carbon sources in the important species Streptomyces tsukubaensis. A genome-wide analysis of the transcriptomic response to glucose and glycerol additions was performed using microarray technology. The transcriptional time series obtained allowed us to compare the transcriptomic profiling of S. tsukubaensis growing under tacrolimus producing and non-producing conditions. The analysis revealed important and different metabolic changes after the additions and a lack of transcriptional activation of the fkb cluster. In addition, we detected important differences in the transcriptional response to glucose between S. tsukubaensis and the model species Streptomyces coelicolor. A number of genes encoding key players of morphological and biochemical differentiation were strongly and permanently downregulated by the carbon sources. Finally, we identified several genes showing transcriptional profiles highly correlated to that of the tacrolimus biosynthetic pathway regulator FkbN that might be potential candidates for the improvement of tacrolimus production
2017-10-12 | GSE99752 | GEO
Project description:Chitin is the second most abundant biopolymer present in soils and is utilized by antibiotic-producing Streptomyces species. Its monomer, N-acetylglucosamine (NAG), regulates the developmental program of the model organism Streptomyces coelicolor. NAG blocks differentiation when growing on rich medium whilst it promotes development on poor culture media. We report here the negative effect of NAG on tacrolimus (FK506) production in Streptomyces tsukubaensis NRRL 18488 growing on a defined rich medium. Using microarrays technology, we found that GlcNAc represses the transcription of fkbN, encoding the main transcriptional activator of the tacrolimus biosynthetic cluster, and of ppt1, encoding a phosphopantheteinyltransferase involved in tacrolimus biosynthesis. On the contrary, NAG stimulated transcription of genes related to amino acid and nucleotide biosynthesis, DNA replication, RNA translation, glycolysis, pyruvate metabolism, and key gene members of the PHO regulon. The results obtained support those previously reported for S. coelicolor, but some important differences were observed
2020-02-08 | GSE110393 | GEO
Project description:We performed ribosome profiling which is the deep-sequencing of mRNA fragments protected by translating ribosome for two Streptomyces species through different growth phases to provide the translatome data
2020-03-03 | GSE138278 | GEO
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: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