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ABSTRACT:
INSTRUMENT(S): LTQ
ORGANISM(S): Streptomyces Spp.
SUBMITTER: Dr. Erin E. Carlson
PROVIDER: MSV000078789 | GNPS | Wed Jul 30 06:23:00 BST 2014
REPOSITORIES: GNPS
Similar Datasets
Project description: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
2024-07-01 | GSE243267 | GEO
Project description:The present work aimed at selecting appropriate native temporal promoters with the identical profile of the cumate-inducible promoter under the optimal induction condition. This strategy enabled us to optimized the expression of biosynthetic gene cluster of desired secondary metabolites in Streptomyces, while avoid the use of inducer during fermentation. By clustering the genes with quite similar transcriptional profile with that of gfp controlled by the cumate-inducible promoter based on time-series microarray data, 50 qualified genes were identified, which were controlled by 24 putative promoters. Then, the cumate-inducible promoter were replaced by the 24 native temporal promoters, and fermentation results showed the good performance of these promoters compared to that of the cumate-inducible promoter. Therefore, our strategy could be used to fine-tune the expression of target BGCs for production improvement.
2020-06-01 | GSE100343 | GEO
Project description:RNAs are often studied in non-native sequence contexts to facilitate structural studies. However, seemingly innocuous changes to an RNA sequence may perturb the native structure and generate inaccurate or ambiguous structural models. To facilitate the investigation of native RNA secondary structure by selective 2′ hydroxyl acylation analyzed by primer extension (SHAPE), we engineered an approach that couples minimal enzymatic steps to RNA chemical probing and mutational profiling (MaP) reverse transcription (RT) methods - a process we call template switching and mutational profiling (Switch-MaP). In Switch-MaP, RT templates and additional library sequences are added post-probing through ligation and template switching, capturing reactivities for every nucleotide. For a candidate SAM-I riboswitch, we compared RNA structure models generated by the Switch-MaP approach to those of traditional primer-based MaP, including RNAs with or without appended structure cassettes. Primer-based MaP masked reactivity data in the 5′ and 3′ ends of the RNA, producing ambiguous ensembles inconsistent with the conserved SAM-I riboswitch secondary structure. Structure cassettes enabled unambiguous modeling of an aptamer construct but introduced non-native interactions in the full-length riboswitch. In contrast, Switch-MaP provided reactivity data for each nucleotide in each RNA and enabled unambiguous modeling of secondary structure, consistent with the conserved SAM-I fold. Switch-MaP is an alternative approach to primer-based and cassette-based chemical probing methods that precludes primer masking and the formation of alternative secondary structures due to non-native sequence elements.
2024-12-26 | GSE274121 | GEO
Project description:To avoid the complex switches and to reduce the limitations of different metabolic stages on the synthesis of metabolites, we designed a Streptomyces self-sustained system (StSS) that contains two functional modules, the primary metabolism module (PM) and the secondary metabolism module (SM). Here, the transcriptomic of hrdB regulatory strain in the secondary metabolism was analyzed.
2021-06-19 | GSE178472 | GEO
Project description:The goal was to study the dfactionation of different lignocelullose (glucose, wheat bran, wheat straw) by Streptomyces coelicolor A3(2) and the corresponding production of secondary metabolites. This was performed by multi-omic experiment such as transcriptomic/metabolomic and leads to the production of new metabolites. For that, the strain Streptomyces coelicolor A3(2) was subjected to two carbon sources in triplicate (wheat bran and glucose as control). Enzymatic activities were studied at different times and the expression of CAZYmes was studied by transcriptomic in order to detect which enzymes are needed for each carbon source
2020-10-01 | E-MTAB-8971 | biostudies-arrayexpress
Project description:Streptomycetes are major producers of a wide variety of secondary metabolites that serve as bioactive compounds. Many secondary metabolites are produced in response to environmental signals such as biotic and abiotic stresses. In this study, we identified salinity stress as one of the stimuli activating secondary metabolism in the model Streptomyces species, Streptomyces coelicolor. Comparative metabolomics revealed overproduction of several known secondary metabolites, most notably undecylprodigiosin and coelimycin P1, in addition to their biosynthetic intermediates and derivatives as well as many unknown metabolites. Transcriptomic analysis revealed activation of diverse biological processes including potassium uptake, compatible solute production and phosphate limitation stress response through conserved and species-specific mechanisms, presumably to overcome the salinity stress. This stress response leads to activation of a variety of regulatory and metabolic pathways required for production of secondary metabolites including activation of conserved metabolic pathways for energy and substrate supply and species-specific secondary metabolites biosynthetic gene clusters. Furthermore, several promoter sequences contributing to upregulation of secondary metabolism induced by salinity stress were identified. Overall, our data show how S. coelicolor copes with the salinity stress and tailors the cellular metabolism toward secondary metabolism in a conserved and species-specific manner.
The work (proposal:https://doi.org/10.46936/10.25585/60008131) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
2025-08-13 | MSV000098817 | MassIVE
Project description:Lincomycin is a lincosamide antibiotic that forms cross-links within the peptidyl transferase loop region of the 23S rRNA of the 50S subunit of the bacterial ribosome, thereby inhibiting protein synthesis. We have previously reported that lincomycin at concentrations below the minimum inhibitory concentration potentiates the production of secondary metabolites in actinomycete strains. We aimed to elucidate the fundamental mechanisms underlying lincomycin induction of secondary metabolism in actinomycetes. Therefore, the dose-dependent response of lincomycin on gene expression of the model actinomycetes Streptomyces coelicolor A3(2) and possible relationships to secondary metabolism have been investigated.
2018-03-02 | E-MTAB-6434 | biostudies-arrayexpress
Project description:Streptomyces coelicolor normally produce spores with a relatively high heterogeneity, which will produce genetically heterogeneous sub-populations. These sub-populations often exert massive chromosome amplifications and deletions. Cells with gross chromosomal changes produce an increased diversity of secondary metabolites and secrete significantly more antibiotics; however, these changes come at the cost of dramatically reduced individual fitness, providing direct evidence for a trade-off between secondary metabolite production and fitness. We propose that antibiotic production in colonies of the multicellular bacterium Streptomyces coelicolor is coordinated by a division of labour. This proteomics survey will provide more detailed insights into how these chromosomal changed strains behave under normal growth condition.
2020-05-26 | PXD014413 | Pride
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:This study utilized comparative global gene expression microarray analysis to evaluate the effects of a compound including garlic-derived secondary metabolites on intestinal immunity of chicken. Two-condition experiment, Garlic metabolites-fed chickens vs. Non-treated control chickens. Biological replicates: 2 control replicates, 2 Garlic metabolites-fed replicates with dye-switching.
2012-03-07 | E-GEOD-36302 | biostudies-arrayexpress