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Streptomyces tsukubensis NRRL18488

ABSTRACT: RNA-seq Transcriptional Profiling of the FK506 Biosynthetic Gene Cluster in Streptomyces tsukubaensis NRRL18488 and General Analysis of the Transcriptome

PROVIDER: PRJNA357641 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5115251.fastq.gz	Fastqsanger.gz
	SRR5115252.fastq.gz	Fastqsanger.gz
	SRR5115253.fastq.gz	Fastqsanger.gz
	SRR5115254.fastq.gz	Fastqsanger.gz
	SRR5115255.fastq.gz	Fastqsanger.gz

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RNA-seq Transcriptional Profiling of the FK506 Biosynthetic Gene Cluster in Streptomyces tsukubaensis NRRL18488 and General Analysis of the Transcriptome

Project description:FK506 (tacrolimus) is a valuable immunosuppressant produced by several Streptomyces strains. In the genome of the wild type producer Streptomyces tsukubaensis NRRL18488 FK506 biosynthesis is encoded by a gene cluster that spans 83.5 kilobases. A whole transcriptome differential shotgun sequencing of S. tsukubaensis was performed to analyze transcription at two different time points; before and during active FK506 production. In total 8,914 transcription start sites were identified in either condition, which enabled precise determination of the 5'-UTR length of the corresponding transcripts as well as the identification of two consensus sequence motifs in the promoter regions. The transcription start sites of all gene operons within the FK506 cluster were identified, including three examples of leaderless RNA transcripts. These data provide detailed insight into the transcription of the FK506 biosynthetic gene cluster and supports future regulatory studies and genetic manipulations.

2017-07-05 | GSE92480 | GEO

Streptomyces tsukubaensis: transcriptomic response to tacrolimus repressing carbon sources

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

Genome-wide transcriptome response of Streptomyces tsukubaensis to N-acetylglucosamine

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

Streptomyces tsukubensis

Project description:Streptomyces tsukubaensis overview

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Ribosome pausing at the AT-rich codons regulates the protein expression of secondary metabolite gene clusters in the Streptomyces tsukubaensis NRRL 18488

Project description:Streptomyces tsukubaensis NRRL 18488 is the preferred strain for the production of immunosuppressant agent tacrolimus (FK506). To take full advantage of its genetic potential, systematic understanding of secondary metabolism and related regulatory mechanisms is highly demanded. Here, to this end, we complete its 7.9 Mbp linear genome sequence followed by integrating with multi-omics measurements. With accurate reannotation of FK506 gene cluster, total 2,389 transcription start sites were determined by using primary transcriptome analysis. Integrated analysis of transcriptome and translatome data revealed that secondary metabolic gene clusters, especially FK506 cluster, undergo translational control with decrease in translational efficiency according to the growth. Furthermore, we demonstrated that SD motif has little correlation with ribosome pausing but AT-rich codons delay the translational elongation. Strong ribosome pausing was observed in the rare TTA codon in FK506 cluster. This comprehensive genome-scale analysis provides insight to the translational regulation of secondary metabolism in S. tsukubaensis.

2019-10-16 | GSE97637 | GEO

Streptomyces tsukubensis strain:F601

Project description:Streptomyces tsukubaensis Genome sequencing and assembly

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Streptomyces tsukubensis NRRL18488

Project description:Streptomyces tsukubaensis: transcriptomic response to tacrolimus repressing carbon sources

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Project description:Ribosome pausing at the AT-rich codons regulates the protein expression of secondary metabolite gene clusters in the Streptomyces tsukubaensis NRRL 18488

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Transcription Start Site (TSS) mapping and total RNAseq of Streptomyces scabies wild-type (WT) versus Streptomyces scabies ΔbtmL

Project description:The aim of this experiment was to map the transcription start sites (TSSs) in the bottromycin biosynthetic gene cluster from Streptomyces scabies, qualitatively assess the expression levels of this cluster within the bacterium's transcriptome and evaluate whether deletion of a potential regulatory gene in the cluster, btmL affects gene cluster expression.

2020-02-19 | E-MTAB-8236 | biostudies-arrayexpress

ChIP-Seq of Cluster situated regulators (ForJ, ForF and ForZ) of the formicamycin BGC in Streptomyces formicae

Project description:ForJ, ForF and ForZ are cluster situated regulators of the formicamycin biosynthetic gene cluster in Streptomyces forimcae. This ChIP Sequencing experiment was conducted to identify where in the genome these regulators bind in order to identify which transcripts they might regulate.

2019-05-31 | E-MTAB-8006 | biostudies-arrayexpress

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