Actinomycetes
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1042969 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR26895547_1.fastq.gz | Fastqsanger.gz | |||
| SRR26895547_2.fastq.gz | Fastqsanger.gz | |||
| SRR26895548_1.fastq.gz | Fastqsanger.gz | |||
| SRR26895548_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 13 |
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Project description:Actinomycete genomes contain a plethora of orphan gene clusters encoding unknown secondary metabolites, and representing a huge unexploited pool of chemical diversity. The explosive increase in genome sequencing and the massive advance of bioinformatic tools have revolutionized the rationale for natural product discovery from actinomycetes. In this context, we applied a genome mining approach to discover a group of unique catecholate-hydroxamate siderophores termed as qinichelins from Streptomyces sp. MBT76. Quantitative proteomics statistically correlated a gene cluster of interest (qch) to its unknown chemotype (qinichelin), after which structural elucidation of isolated qinichelin was assisted by bioinformatics analysis and verified by MS2 and NMR experiments. Strikingly, intertwined functional crosstalk among four separately located gene clusters was implicated in the biosynthesis of qinichelins.
2018-10-24 | PXD006577 | Pride
Project description:We provide a manually-curated genome mining analysis of the bacterial plant pathogen Streptomyces scabiei. The expression of the deduced biosynthetic gene clusters was assessed by a RNAseq approach, and their potential to be induced by the virulence elicitors cellobiose and cellotriose was estimated by comparing mRNA levels before and after elicitor addition. Finally, we performed metabolomic analyzes to evaluate how the production of known specialized metabolites responds to virulence elicitors, in correlation (or not) with the transcriptomic data
2021-08-08 | GSE181490 | GEO
Project description:A complex programme of regulation governs gene expression during development of the morphologically and biochemically complex eubacterial genus Streptomyces. Earlier work has suggested a model in which 'higher level' pleiotropic regulators activate 'pathway-specific' regulators located within chromosomal gene clusters encoding biosynthesis of individual antibiotics. We used mutational analysis and adventitious overexpression of key Streptomyces coelicolor regulators to investigate functional interactions among them. We report here that cluster-situated regulators (CSRs) thought to be pathway-specific can also control other antibiotic biosynthetic gene clusters, and thus have pleiotropic actions. Surprisingly, we also find that CSRs exhibit growth-phase-dependent control over afsR2/afsS, a 'higher level' pleiotropic regulatory locus not located within any of the chromosomal gene clusters it targets, and further demonstrate that cross-regulation by CSRs is modulated globally and differentially during the S. coelicolor growth cycle by the RNaseIII homologue AbsB. Our results, which reveal a network of functional interactions among regulators that govern production of antibiotics and other secondary metabolites in S. coelicolor, suggest that revision of the currently prevalent view of higher-level versus pathway-specific regulation of secondary metabolism in Streptomyces species is warranted.
2005-12-02 | E-SMDB-3554 | biostudies-arrayexpress
Project description: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. We show here that genes co-evolved with natural product BGCs in Streptomyces can be identified by phylogenomics analysis. Among the 597 genes that co-evolved with polyketide BGCs, 11 genes in the “coenzyme” category have been examined, including a gene cluster encoding for the co-factor pyrroloquinoline quinone (PQQ). When the pqq gene cluster was engineered into 11 Streptomyces strains, it enhanced production of 16,385 metabolites, including 36 known natural products with up to 40-fold improvement and several activated silent gene clusters. This study provides a new engineering strategy for improving polyketide production and discovering new biosynthetic gene clusters.
2024-03-01 | GSE256209 | GEO
Project description:Genomes of Actinomycetes strains that contain enediyne biosynthetic gene clusters
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Project description:A complex programme of regulation governs gene expression during development of the morphologically and biochemically complex eubacterial genus Streptomyces. Earlier work has suggested a model in which 'higher level' pleiotropic regulators activate 'pathway-specific' regulators located within chromosomal gene clusters encoding biosynthesis of individual antibiotics. We used mutational analysis and adventitious overexpression of key Streptomyces coelicolor regulators to investigate functional interactions among them. We report here that cluster-situated regulators (CSRs) thought to be pathway-specific can also control other antibiotic biosynthetic gene clusters, and thus have pleiotropic actions. Surprisingly, we also find that CSRs exhibit growth-phase-dependent control over afsR2/afsS, a 'higher level' pleiotropic regulatory locus not located within any of the chromosomal gene clusters it targets, and further demonstrate that cross-regulation by CSRs is modulated globally and differentially during the S. coelicolor growth cycle by the RNaseIII homologue AbsB. Our results, which reveal a network of functional interactions among regulators that govern production of antibiotics and other secondary metabolites in S. coelicolor, suggest that revision of the currently prevalent view of higher-level versus pathway-specific regulation of secondary metabolism in Streptomyces species is warranted. Groups of assays that are related as part of a time series. Computed
2006-02-01 | E-GEOD-4138 | biostudies-arrayexpress
Project description: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. We show here that genes co-evolved with natural product BGCs in Streptomyces can be identified by phylogenomics analysis. Among the 597 genes that co-evolved with polyketide BGCs, 11 genes in the “coenzyme” category have been examined, including a gene cluster encoding for the co-factor pyrroloquinoline quinone (PQQ). When the pqq gene cluster was engineered into 11 Streptomyces strains, it enhanced production of 16,385 metabolites, including 36 known natural products with up to 40-fold improvement and several activated silent gene clusters. This study provides a new engineering strategy for improving polyketide production and discovering new biosynthetic gene clusters.
2024-02-12 | PXD049454 |
Project description:A complex programme of regulation governs gene expression during development of the morphologically and biochemically complex eubacterial genus Streptomyces. Earlier work has suggested a model in which 'higher level' pleiotropic regulators activate 'pathway-specific' regulators located within chromosomal gene clusters encoding biosynthesis of individual antibiotics. We used mutational analysis and adventitious overexpression of key Streptomyces coelicolor regulators to investigate functional interactions among them. We report here that cluster-situated regulators (CSRs) thought to be pathway-specific can also control other antibiotic biosynthetic gene clusters, and thus have pleiotropic actions. Surprisingly, we also find that CSRs exhibit growth-phase-dependent control over afsR2/afsS, a 'higher level' pleiotropic regulatory locus not located within any of the chromosomal gene clusters it targets, and further demonstrate that cross-regulation by CSRs is modulated globally and differentially during the S. coelicolor growth cycle by the RNaseIII homologue AbsB. Our results, which reveal a network of functional interactions among regulators that govern production of antibiotics and other secondary metabolites in S. coelicolor, suggest that revision of the currently prevalent view of higher-level versus pathway-specific regulation of secondary metabolism in Streptomyces species is warranted. Groups of assays that are related as part of a time series. Keywords: time_series_design
2006-02-02 | GSE4138 | GEO
Project description:Mining of fungal genomes uncovered their great potential for the production of novel secondary metabolites (SMs). However most of them stay silent under standard laboratory cultivation conditions. Co-cultivation of fungi with organism that occur in their natural habitat has shown to be trigger for the activation of such silent SM gene clusters. Recently, we showed that the cultivation of Aspergillus nidulans with the bacterium Streptomyces rapamycinicus leads to the activation of the orsellinic acid gene cluster. Hence we decided to study this interaction further to gain insight into the regulation of SM gene clusters and more specifically to study the chromatin remodelling network actuve upon co-cultivation of the two organisms. This study gives novel insight into the regulation of the orsellinic acid gene cluster and the interaction of the two organisms. To the best of our knowledge this is the first report of mapping the chromatin landscape of microbial interactions, making this study a role model for the analysis of similar systems.
2018-10-12 | E-MTAB-5819 | biostudies-arrayexpress
Project description:In order to explore the role of LaeA in secondary metabolite biosynthetic gene clusters’ regulation, toxin production, and virulence of Valsa mali, TMT-based proteomic analysis of wildtype, LaeA deletion mutant and overexpression mutant were performed. Totally, 4,299 proteins (FDR < 0.01) were identified by searching against the Valsa mali protein sequence database.
2021-09-09 | PXD021783 | Pride