GEO DataSets

(Submitter supplied) RNA seq analysis was performed using adpA-deleted and adpA-overexpressed Streptomyces clavuligerus strains to determine its regulatory effect on tunicamycin and other secondary metabolites production

Organism:

Streptomyces clavuligerus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33767

4 Samples

Download data: TXT

(Submitter supplied) tRNA modifications help maintain tRNA structure and facilitate stress responses. Found in all three kingdoms of life, m1A tRNA modification occurs in the T loop of many tRNAs and stabilizes tertiary tRNA structure and impacts translation. M1A in T loop is known to be reversible by three mammalian demethylase enzymes, which bypasses the need of turning over the tRNA molecule to adjust their m1A levels in cells. more...

Organism:

Streptomyces venezuelae

Type:

Other

Platform:

GPL32677

52 Samples

Download data: TSV

(Submitter supplied) Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we hypothesized that a set of genes co-evolved with BGCs to support biosynthetic proficiency must exist in those strains, and that their identification may provide universal strategies to improve the productivity of other strains. more...

Organism:

Streptomyces griseus; Streptomyces rapamycinicus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34215 GPL27559

12 Samples

Download data: CSV

(Submitter supplied) The production of daptomycin (DAP) is precisely regulated by a complex regulatory network in Streptomyces roseosporus (S. roseosporus). Although the most biosynthetic pathway of DAP has been elucidated, the regulatory mechanism of its biosynthesis at transcriptional level is not fully understood. In the present study, a transcriptional regulator DhyR has been identified based on our previous quantification proteomics identification in S. more...

Organism:

Streptomyces filamentosus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34032

2 Samples

Download data: TXT

(Submitter supplied) Background. Transforming waste and non-food materials into bulk biofuels and chemicals represents a major stride in creating a sustainable bioindustry, optimizing the use of resources while reducing environmental footprints. Yet, despite these advancements, the production of high-value natural products often continues to rely on first-generation substrates, underscoring the intricate processes and specific requirements of their biosynthesis. more...

Organism:

Streptomyces lividans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29798

9 Samples

Download data: TXT

(Submitter supplied) We isolated and sequenced mRNA from Streptomyces venezuelae grown on two different solid media that promote different growth behaviour in this bacterial species. The data was analyzed using DeSeq2 to identify genes that undergo changes in expression over time as well as differences in gene expression patterns between the two media conditions.

Organism:

Streptomyces venezuelae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25163

10 Samples

Download data: CSV

(Submitter supplied) Time series data for several S. albus strains engineered to produce nybomycin.

Organism:

Streptomyces albidoflavus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29830

45 Samples

Download data: TXT

(Submitter supplied) To investigate gene expression differences of different tylosin high-producing strains, transcriptomes of three tylosin high-producing engineered strains (TLPH08-2, TLPH11 and TLPH17) and the vector control strain TLSET152 were analyzed by RNA-Seq. Different strains (TLSET152, TLPH08-2, TLPH11 and TLPH17) were harvested at 96 h of fermentationat and then RNA isolation, transcriptome sequencing and data analysis were conducted.

Organism:

Streptomyces xinghaiensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33306

12 Samples

Download data: FASTA, TXT

(Submitter supplied) The terminal compartments of Streptomyces are less prone to transcription than the rest of the chromosome. Indeed, the expression of the highly variable regions enriched in those compartments is generally conditional and often requires an empirical approach to characterize the inducing conditions. For instance, in the context of identifying adequate antibiotic production conditions, an OSMAC (“One Strain Many Compounds”) approach is frequently implemented, based on strain cultivation in different environmental conditions (composition of the medium, growth time, temperature, co-cultures, etc.). more...

Organism:

Streptomyces ambofaciens ATCC 23877

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29484

13 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30648

32 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Streptomycetes are saprophytic bacteria that grow on complex polysaccharides, such as cellulose, starch, chitin and chitosan. For the monomeric building blocks glucose, maltose and N-acetylglucosamine the metabolic pathway is well documented, but that of glucosamine (GlcN) is currently unknown. Importantly, GlcN is lethal to Streptomyces coelicolor nagB mutants, which lack glucosamine-6-phosphate deaminase activity. more...

Organism:

Streptomyces coelicolor A3(2)

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30648

8 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Streptomycetes are saprophytic bacteria that grow on complex polysaccharides, such as cellulose, starch, chitin and chitosan. For the monomeric building blocks glucose, maltose and N-acetylglucosamine the metabolic pathway is well documented, but that of glucosamine (GlcN) is currently unknown. Importantly, GlcN is lethal to Streptomyces coelicolor nagB mutants, which lack glucosamine-6-phosphate deaminase activity. more...

Organism:

Streptomyces coelicolor A3(2)

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30648

24 Samples

Download data: TXT

(Submitter supplied) CutRS was the first two-component system to be identified in Streptomyces species and is highly conserved in this genus. It was reported >25 years ago that deletion of cutRS increases the production of the antibiotic actinorhodin in Streptomyces coelicolor but despite this early work the function of CutRS has remained enigmatic until now. Here we show that deletion of cutRS upregulates the production of the actinorhodin biosynthetic enzymes up to 260-fold in the cutRS mutant, explaining the increase in actinorhodin production. more...

Organism:

Streptomyces coelicolor

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29790

12 Samples

Download data: BEDGRAPH

(Submitter supplied) The present work provides a multi-omics systems-wide view on S. rimosus. Using genomics, transcriptomics, proteomics, and metabolomics, we compared the wild type with an OTC-overproducing derivative, previously obtained by classical mutagenesis. The integration of the data provided a deep insight into the underlying metabolic and regulatory networks that mediate high-level OTC formation. Strikingly, the overproducer revealed a synergistically activated supply of acetyl-CoA and malonyl CoA and increased abundance of various CoA thioesters.

Organism:

Streptomyces rimosus subsp. rimosus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33407

9 Samples

Download data: TSV

(Submitter supplied) Streptomyces avermitilis is a avermectin producer.Since the avermectin biosynthesis rate has a increased significantly in P3 fermentation stage( P1,24–96 h; P2:96–192 h, P3:192–240 h), but the sugar absorption rate decreased significantly in P3 fermentation stage, in order to improve the titer of avermectins, we conducted transcriptomic analysis of Streptomyces avermitilis S0 in fourth and eighth day, and selected native promoters with appropriate temple using to express sugar transporters.

Organism:

Streptomyces avermitilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33244

4 Samples

Download data: FASTA, TXT

(Submitter supplied) When cultivated on ISP2 plates for sporulation, the gra-orf32 deletion mutant of Streptomyces vietnamensis produced much more granaticins than in liquid or on solid YEME. The transcriptome analysis showed that the transcription levels of more than 1,600 genes were significantly changed (p < 0.05, log2 fold change >1). Amongst them, 872 genes were upregulated and 762 genes were downregulated on ISP2 plates, compared to those on YEME plates. more...

Organism:

Streptomyces vietnamensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32907

6 Samples

Download data: TXT

(Submitter supplied) To gain insights into the processes underlying adaptation to phage infection, we performed RNA-seq analysis of infected mycelium from the plaque interface of S. venezuelae wild type harvested 24 h and 72 h after infection with Alderaan.

Organism:

Streptomyces venezuelae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32677

8 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Streptomyces clavuligerus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32587

6 Samples

Download data: XLSX

(Submitter supplied) PAS-LuxR transcriptional regulators are highly conserved enzymes governing polyene macrolide antifungal biosynthesis. One of such regulators PteF, is located in the polyene macrolide filipin gene cluster from Streptomyces avermitilis and its mutation leads to a drastic decrease in filipin production as well as a severe loss of oligomycin production, an ATP-synthase inhibitor of macrolide structure, and a delay in sporulation. more...

Organism:

Streptomyces avermitilis

Type:

Expression profiling by array

Platform:

GPL17101

12 Samples

Download data: TXT, XLSX

(Submitter supplied) To investigate the effect of bldA deletion on gene expression in Streptomyces iranensis with respect to secondary metabolite cluster genes

Organism:

Streptomyces iranensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32214

8 Samples

Download data: TSV