Time-course transcriptome analysis of non-antibiotics producer and actinorhodin over-producing Streptomyces coelicolor strain
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ABSTRACT:
ORGANISM(S): Streptomyces coelicolor
PROVIDER: GSE155796 | GEO | 2020/11/27
REPOSITORIES: GEO
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Project description:Time-course transcriptome analysis of non-antibiotics producer and actinorhodin over-producing Streptomyces coelicolor strain
| PRJNA655669 | ENA
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: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:The eubacterial species Streptomyces coelicolor proceeds through a complex growth cycle in which morphological differentiation/development is associated with a transition from primary to secondary metabolism and the production of antibiotics. We used DNA microarrays and mutational analysis to investigate the expression of individual genes and multigene antibiotic biosynthetic pathways during these events. We identified expression patterns in biosynthetic, regulatory, and ribosomal protein genes that were associated highly specifically with particular stages of development. A knowledge-based algorithm that correlates temporal changes in expression with chromosomal position identified groups of contiguous genes expressed at discrete stages of morphological development, inferred the boundaries of known antibiotic synthesis gene loci, and revealed novel physical clusters of coordinately regulated genes. Microarray analysis of RNA from cells mutated in genes regulating synthesis of the antibiotics actinorhodin (Act) and undecylprodigiosin (Red) identified proximate and distant sites that contain putative ABC transporter and two-component system genes expressed coordinately with genes of specific biosynthetic pathways and indicated the existence of two functionally and physically discrete regulons in the Red pathway.
2005-06-29 | E-SMDB-837 | biostudies-arrayexpress
Project description:Genome-wide expression analysis of 6 batch cultivations of actinorhodin-producing wild type and recombinant strain of Streptomyces coelicolor
2010-05-25 | E-MTAB-306 | biostudies-arrayexpress
Project description:The Streptomyces coelicolor two genes operon SCO5784-SCO5785 encodes a two-component system which functions in a similar manner to that of the Bacillus subtilis DegS-DegU system. Propagation of the regulatory gene in high copy number results in the overproduction of several extracellular enzymes, among them the major extracellular protease, as well as in a higher level of synthesis of the antibiotic actinorhodin. This two-component system seems to control various processes characterised by the transition from primary to secondary metabolism in S. coelicolor, as determined by proteomic and transcriptomic analices. The presence of the regulatory gene in high copy number in S. coelicolor additionally seems to elicit a stringent response in the bacterial cell. Therefore, we propose renaming S. coelicolor genes SCO5784 and SCO5785 as degS and degU, respectively.
2012-05-04 | GSE23195 | GEO
Project description:To determine the response at the transcriptional level of S. coelicolor cells to treatment with 3 antibiotics that target distinct stages of cell wall biosynthesis, biological triplicate cultures of strain M600 were treated with sub-lethal concentrations (10 µg/ml) of vancomycin, bacitracin or moenomycin A. Samples were taken 0, 30, 60, 90 minutes after addition of the antibiotic. A negative control which received no drug treatment was also performed.
2011-04-29 | E-MEXP-3032 | biostudies-arrayexpress
Project description:The Streptomyces coelicolor two genes operon SCO5784-SCO5785 encodes a two-component system which functions in a similar manner to that of the Bacillus subtilis DegS-DegU system. Propagation of the regulatory gene in high copy number results in the overproduction of several extracellular enzymes, among them the major extracellular protease, as well as in a higher level of synthesis of the antibiotic actinorhodin. This two-component system seems to control various processes characterised by the transition from primary to secondary metabolism in S. coelicolor, as determined by proteomic and transcriptomic analices. The presence of the regulatory gene in high copy number in S. coelicolor additionally seems to elicit a stringent response in the bacterial cell. Therefore, we propose renaming S. coelicolor genes SCO5784 and SCO5785 as degS and degU, respectively. All microarray analyses were performed with RNA samples obtained from three independent cultures grown under identical conditions. Hybridisation assays were carried out with cDNA obtained from RNA extracted at the late exponential phase of growth (24h). The transcriptional profile of wild type (S. coelicolor M145) cells carrying the multicopy plasmid pIJ487 was compared with that of the same strain carrying the degU gene cloned in the same plasmid under the control of its own promoter (S. coelicolor M28). And the transcriptional profile of wild type (S, coelicolor M145) cells was compared to that of the DegU deficient strain (S. coelicolor I32).
2012-05-03 | E-GEOD-23195 | biostudies-arrayexpress
Project description:In actinomycetes, antibiotic production is often associated with a morpho-physiological differentiation program that is regulated by complex molecular and metabolic networks. Many aspects of these regulatory circuits have been already elucidated and many others still deserve further investigations. In this regard, the possible role of many small open-reading frames(smORFs) in actinomycete morpho-physiological differentiation is still elusive. In Streptomyces coelicolor, inactivation of the smORF trpM (SCO2038) - whose product modulates L-tryptophan metabolism - impairs production of antibiotics and morphological differentiation. Indeed, it was demonstrated that TrpM is able to interact with PepA (SCO2179), a putative cytosol aminopeptidase playing a key role in antibiotic production and sporulation. In this work, a S. coelicolor trpM knock-in (Sco-trpMKI) mutant strain was generated by cloning trpM into overexpressing vector to further investigate the role of trpM in actinomycete growth and morpho-physiological differentiation. Results highlighted that trpM: i) stimulates growth and actinorhodin production; ii) decreases calcium-dependent antibiotic production; iii) has no effect on undecylprodigiosin production. Metabolic pathways influenced by trpM knock-in were investigated by combining two-difference in gel electrophoresis/nanoliquid chromatography coupled to electrospray linear ion trap tandem mass spectrometry (2D-DIGE/nanoLC-ESI-LIT- MS/MS) and by LC-ESI-MS/MS procedures, respectively. These analyses demonstrated that over-expression of trpM causes an over-representation of factors involved in protein synthesis and nucleotide metabolism as well as a down-representation of proteins involved in central carbon and amino acid metabolism. At the metabolic level, this corresponded to a differential accumulation pattern of different amino acids - including aromatic ones but tryptophan – and central carbon intermediates. PepA was also down-represented in Sco-trpMKI. The latter was produced as recombinant His- tagged protein and was originally proven having the predicted aminopeptidase activity. Altogether, these results highlight the stimulatory effect of trpM in S. coelicolor growth and actinorhodin biosynthesis, which are elicited through the modulation of various metabolic pathways and PepA representation, further confirming the complexity of regulatory networks that control antibiotic production in actinomycetes.
2020-03-27 | PXD015937 | Pride
Project description: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. However, while ChIP-seq identified 86 CutR binding sites in S. coelicolor none of these are in the actinorhodin BGC, so the effect is indirect. The directly regulated CutR targets identified in this study are implicated in extracellular protein folding, including two of the four highly conserved the HtrA-family foldases, HtrA3 and HtrB and a putative VKOR enzyme which is predicted to recycle DsbA following its catalysis of disulphide bond formation in secreted proteins. We thus tentatively propose a role for CutRS in sensing and responding to protein misfolding outside the cell. Since actinorhodin can oxidise cysteine residues and induce disulphide bond formation in proteins its over production in the ∆cutRS mutant may be a response to protein misfolding on the extracellular face of the membrane.
2023-06-12 | GSE225370 | GEO