CGH of Streptomyces coelicolor versus S. lividans 66 and TK24
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ABSTRACT: Comparative genomic hybridization analysis of Streptomyces coelicolor A3(2) versus Streptomyces lividans 66 and Streptomyces lividans TK24 using high density 105,000 x 60-mer ink-jet in situ synthesized arrays.
Project description:S. coelicolor was grown in low-phosphate concentration R5 liquid medium which facilitated the transition to a phosphate starvation induced stationary phase and the subsequent induction of the PhoP regulon. Global gene expression profiling of a wild-type and a phoP-null mutant was performed using samples isolated, respectively, at 24, 30, 35 and 45 h of growth. RNA was extracted and the resulting cDNA was hybridised to S. coelicolor high density DNA microarrays.
Project description:Global transcriptional profiling of the SCO0204 null mutant of Streptomyces coelicolor M145 in comparison to the wildtype M145. Goal was to determine the role of SCO0204.
Project description:A genome-wide transcriptomic analysis of the response of the model streptomycete Streptomyces coelicolor A3(2) M145 to fermentor culture in Modified Evans Media limited, respectively, for nitrogen, phosphate and carbon
Project description:Global ChIP-chip analysis of HspR repressor binding sites in Streptomyces coelicolor MT1110 cultures grown in YEME plus 10% sucrose at 30?C up to early stationary phase. Chromatin extracted from formaldehyde treated cultures was incubated with anti HspR polyclonal antibodies and the DNA purified from anti HspR IP and mock IP samples was labelled with either Cy3 or Cy5- dCTP and hybridized in an indirect and direct type of microarray experiment onto SCO-Chip2-v1 and SCO-Chip2-v2 High Density IJISS arrays, developed in collaboration with Oxford Gene Technology.
Project description:Transcription profiling by array using Streptomyces coelicolor oligomerics array to compare the gene expression of streptomyces lividans adpA mutant to the wild type at early stationary phase in YEME medium.
Project description:Transcriptome analysis of Streptomyces coelicolor MT1110 cultures grown in SMM + 0.5% casaminoacids at 30?C up to mid exponential and stationary phase. Total RNA was extracted from both stages of growth, labelled with Cy3-dCTP and mixed with genomic DNA from S. coelicolor M145 labelled with Cy5-dCTP that was used as common reference in an indirect type of microarray experiment. Labelled Cy3/Cy5-dCTP samples were hybridized onto SCO-Chip2-v2 High Density IJISS arrays.
Project description:In Streptomyces coelicolor the SigR sigma factor controls genes involved in coping with the deleterious formation of disulphide bonds in cellular proteins. This experiment provides global gene expression patterns of M600 and J2139 (sigR deletion) grown in NMMP plus glucose medium to mid-log phase then treated with diamide. The data reveal that sigR activates, directly or indirectly, more than 65 transcription units, encoding functions that include thiol-disulphide oxidoreductases, thiol buffers, and ATP-dependent proteases. The sigR regulon partially overlaps the ClgR and HspR regulons, that include functions for protein degradation and protein refolding. Diamide also leads to the transient down-regulation of central metabolic gene expression, in particular ribosomal protein expression.
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.
Project description:Global regulation by the Streptomyces coelicolor atypical MerR-like transcription factor BldC. BldC is a transcriptional regulator essential for morphological development and antibiotic production in Streptomyces coelicolor. Here we identify the BldC regulon by means of chromatin immunoprecipitation (ChIP) microarray analysis. The BldC regulon encompasses at least 201 transcriptional units, which include many genes that play key roles in Streptomyces development (e.g., bldC itself, bldB, bldM, whiB, whiD, whiI, sigF, smeA-sffA, hupS), antibiotic production (e.g., afsK) and stress response (e.g., clpB, nsrR, sigE, sigF). All BldC-binding sites identified by ChIP-chip are present in the promoters of the target genes. In vitro DNA-binding experiments show that BldC is capable of binding DNA specifically in the absence of other proteins and suggest that BldC is a minor-groove DNA-binding protein. The regulon of BldC partially overlaps with that of the pleiotropic regulator BldD. BldC and BldD bind to distinct sites in the promoter region of smeA, where they simultaneously repress its transcription. ChIP-chip experiment using an anti-BldC antibody and a total DNA control. Comparison of IP in wild-type strain vs. IP in a bldC null mutant strain.
Project description:Description: In Streptomyces coelicolor the Zur repressor controls genes involved in zinc uptake and alternative ribosomal proteins that lack structural zinc. This experiment provides global gene expression patterns of M145 and S121 (zur deletion) grown in NMMP plus glucose medium to mid-log phase. The data reveal that Zur also controls genes involved in production of a non-ribosomally encoded siderophore-related peptide designated coelibactin.