Streptomyces coelicolor strain:M1154/pAMX4
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PROVIDER: PRJNA613497 | ENA |
REPOSITORIES: ENA
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Project description:To identify unique gene expression in higher antibiotics producing Streptomyces coelicolor strain, non-producer M1146 and the derivative strain M1146+ACT (M1146 with actinorhodin biosynthetic genes cluster) was choosen for comparative transcriptome analysis. The genes with different gene expression might be key genes important for antibiotics production.
2020-11-27 | GSE155796 | GEO
Project description:SYSTERACT: Systematic Rebuilding of Actinomycetes for Natural Product Formation For several decades antibiotics have saved millions of lives, but their overuse makes them less effective due to increase in bacterial resistance. Because of this major clinical and public health problem, there is an urgent need for new effective antimicrobials. The ERASysAPP project SYSTERACT aims to further develop, the model actinobacterium Streptomyces coelicolor into improved microbial cell factories to heterologously produce diverse bioactive compounds in amounts needed for structural and functional evaluation. Unprecedented systems biology understanding of S. coelicolor is being combined with morphology engineering and improved (de-)regulation and precursor supply to accelerate bioactive compound discovery efforts. By that means, we aim to generate a stepwise improved 'Superhost' for the production of antibiotics in which metabolic bottlenecks and regulatory restriction are greatly mitigated. The optimized strains will be tested concerning their applicability for an improved production of commercially relevant antibiotics and the expression of novel bioactive gene clusters identified in new actinomycete strains and environmental metagenomes. So far two strains, M145 and M1152, have been cultivated for time-resolved 'omics sampling, and a larger number of additional strains are on the list for similar experiments. High quality RNAseq-based transcriptome data have been generated and processed. M145 is the wildtype strain in S. coelicolor (as used in STREAM, see also GSE18489), 3 biol. replicas and M1152 lacks four major biosynthetic gene clusters, undecylprodigine (RED), calcium-dependent antibiotic (CDA), coelimycin (CPK) and actinorhodin (ACT). Contributors: A. Wentzel, W. Wohlleben, G. van Wezel, D van Dissel, O. Wolkenhauer, E. Kerkhoven, N. Spidsoe, K. Nieselt and the SYSTERACT consortium
2019-10-09 | GSE132488 | GEO
Project description:SYSTERACT: Systematic Rebuilding of Actinomycetes for Natural Product Formation For several decades antibiotics have saved millions of lives, but their overuse makes them less effective due to increase in bacterial resistance. Because of this major clinical and public health problem, there is an urgent need for new effective antimicrobials. The ERASysAPP project SYSTERACT aims to further develop, the model actinobacterium Streptomyces coelicolor into improved microbial cell factories to heterologously produce diverse bioactive compounds in amounts needed for structural and functional evaluation. Unprecedented systems biology understanding of S. coelicolor is being combined with morphology engineering and improved (de-)regulation and precursor supply to accelerate bioactive compound discovery efforts. By that means, we aim to generate a stepwise improved 'Superhost' for the production of antibiotics in which metabolic bottlenecks and regulatory restriction are greatly mitigated. The optimized strains will be tested concerning their applicability for an improved production of commercially relevant antibiotics and the expression of novel bioactive gene clusters identified in new actinomycete strains and environmental metagenomes. So far two strains, M145 and M1152, have been cultivated for time-resolved 'omics sampling, and a larger number of additional strains are on the list for similar experiments. High quality RNAseq-based transcriptome data have been generated and processed. M145 is the wildtype strain in S. coelicolor (as used in STREAM, see also GSE18489), 3 biol. replicas and M1152 lacks four major biosynthetic gene clusters, undecylprodigine (RED), calcium-dependent antibiotic (CDA), coelimycin (CPK) and actinorhodin (ACT). Contributors: A. Wentzel, W. Wohlleben, G. van Wezel, D van Dissel, O. Wolkenhauer, E. Kerkhoven, N. Spidsoe, K. Nieselt and the SYSTERACT consortium
2019-10-09 | GSE132487 | GEO
Project description:In order to define the impact of phosphate (Pi) availability on cellular metabolism the project aimed to perform a comparative analysis of the proteomes of two Streptomyces strains with different abilities to produce antibiotics, S. coelicolor and S. lividans as well as of the pptA mutant of S. lividans, grown low (1mM) and high (5mM) phosphate (Pi) availability conditions. Interestingly, in contrast to most Streptomyces species, S. coelicolor produces more antibiotics in Pi proficiency than in Pi limitation, S. lividans does not produce antibiotics in any Pi conditions and the pptA mutant produces antibiotics only in Pi limitation. This in-depth proteomic comparison of three Streptomyces strains (S. coelicolor, S. lividans wt and pptA mutant), in different growth conditions (time and Pi concentration in the medium) was performed on four biological replicates. Protein abundance changes were determined using two label-free mass spectrometry based-quantification methods: spectral count (SC) and MS1 ion intensities named XIC (for eXtracted Ion Current). Our proteomic data reveal for the first time, the impact of Pi availability on the abundance of approximately 4000 proteins of these Streptomyces strains with different abilities to produce antibiotics. The most striking feature differentiating these strains was the much higher abundance of enzymes of the respiratory chain in both phosphate conditions in S. coelicolor compared to the S. lividans strains.
2022-02-04 | PXD029263 | Pride
Project description:We used transcriptome profiling by RNAseq to identify the gene expression signatures elucidated in S. coelicolor in response to the three different glycopeptide compounds that share high degree of structural similarities and the same primary mode of action: dalbavancin, vancomycin and chlorobiphenyl-vancomycin.
2021-02-15 | E-MTAB-9846 | biostudies-arrayexpress
Project description:The rapid rise in antibiotic-resistance of microbial pathogens has brought the attention to new, heterologous approaches to better exploit the vast repertoire of biosynthetic gene clusters in Actinobacteria genomes and the large number of potentially novel bioactive compounds encoded in these. To enable and optimize production of these compounds, a better understanding of -among others- the interplay between primary and secondary metabolism in the selected suitable heterologous production hosts is needed, in our case the model Streptomycete Streptomyces coelicolor. In this study, a genome-scale metabolic model is reconstructed based on several previous metabolic models and refined by including experimental data, in particular proteome data. This new consensus model provides not only a valuable and more accurate mathematical representation to predict steady-state flux distributions in this strain, but also provides a new framework for interpretation and integration of different 'omics' data by the Streptomyces research community for improved strain-specific systems-scale knowledge to be used in targeted strain development, e.g. for efficient new antibiotics production.
2020-09-10 | PXD013178 | Pride
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: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:HupA and HupS are nucleoid associated proteins, homologic to E. coli HU protein. Their binding to DNA changes chromosome structure, protects DNA from damage and influences gene expression. The goal of RNA-seq experiment was to determine HupA and HupS regulons during growth in liquid medium. Dataset contains four strains (hupA, hupS, hupAhupS deletion mutants and wild type), two time points (exponential and stationary growth) and two growth conditions (standard media and osmotic stress).
2024-10-28 | E-MTAB-13846 | biostudies-arrayexpress
Project description:Drug-specific signatures of the glycopeptide antibiotics dalbavancin, vancomycin and chlorobiphenyl-vancomycin in Streptomyces coelicolor
| PRJEB41674 | ENA