S. coelicolor YSK3225 R5- Medium Time-course Study (Culture #1)
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ABSTRACT:
ORGANISM(S): Streptomyces coelicolor
SUBMITTER: Karthik Jayapal
PROVIDER: E-GEOD-8108 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) afsS::apr mutant strain (YSK4425) and compare it to wild-type M145 strain. The regulatory protein encoded by afsS is known to affect antibiotic biosynthesis (Floriano, B., Bibb, M. 1996. afsR is a pleiotropic but conditionally required regulatory gene for antibiotic production in Streptomyces coelicolor A3(2). Mol Microbiol, 21, 385-96). Keywords: Time course The time-course study involved analysis of 14 samples (15h, 17h, 19h, 21h, 23h, 25h, 28h, 31h, 32h, 35h, 37h, 38h, 41h, 45h). Of these, 15h, 17h, 19h, 21h, 23h, 25h, 32h, 41h, and 45h samples were analyzed on duplicate arrays (2 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.
2010-06-10 | E-GEOD-8160 | biostudies-arrayexpress
Project description:Many biological processes are intrinsically dynamic, incurring profound changes at both molecular and physiological levels. Systems analyses of such processes incorporating large-scale transcriptome or proteome profiling can be quite revealing. Although consistency between mRNA and proteins is often implicitly assumed in such studies, instances of divergent trends are frequently observed indicating the existence of post-transcriptional regulation. Here, we present a comparative transcriptome and proteome analysis of growth and stationary phase adaptation in Streptomyces coelicolor, taking the time-dynamics of process into consideration. These processes are of immense interest in streptomycetes as they encompass the physiological transformations eliciting biosynthesis of many naturally occurring therapeutic agents. A shotgun proteomics approach based on mass spectrometric analysis of isobaric stable isotope labeled peptides iTRAQ(TM) enabled identification and rapid quantification of approximately 14% of the theoretical proteome of S. coelicolor. Independent principal component analyses of this and DNA microarray-derived transcriptome data revealed that the prominent patterns in both protein and mRNA domains are surprisingly well correlated. Despite this general consensus, by employing a systematic concordance analysis we estimated that over 30% of the analyzed genes likely exhibited significantly divergent patterns, of which nearly one-third displayed even opposing trends. Integrating this data with biological information, we discovered that certain groups of functionally related genes were co-regulated independently as mRNA and/or proteins despite observations of apparent mRNA-protein discordance. This clearly suggests that post-transcriptional regulatory mechanisms are prominent even amongst prokaryotes while reaffirming the plausibility of such mechanisms acting in a concerted fashion at a protein complex or sub-pathway level. Keywords: Time course Time-course study involved analysis of 8 samples (7h, 11h, 14h, 16h, 22h, 26h, 34h, 38h). Of these, 14h, 22h, 26h and 38h were analyzed in duplicate arrays. All arrays used cDNA labeled with Alexa647 and gDNA labeled with Cy3.
2010-06-11 | E-GEOD-7172 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M145 wild type and disruption mutants of regulatory genes (afsS and absA1) known to affect antibiotic biosynthesis. Keywords: Time course The time-course study involved analysis of 6 samples (15h, 22h, 24h, 26h, 35h, 43h). Of these, 15h and 22h were analyzed in duplicate arrays. Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.
2010-06-10 | E-GEOD-8084 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarray methods to investigate the temporal transcriptome profiles of S. coelicolor A3(2) âabsA1::apr mutant strain and compared with the M145 Wild-type strain (series submitted separately). Keywords: Time course Time-course study involved analysis of 6 samples (18h, 24h, 26h, 28h, 32h and 42h). All arrays used cDNA labeled with Alexa647 and gDNA labeled with Cy3.
2010-06-10 | E-GEOD-8109 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarray methods to investigate the temporal transcriptome profiles of S. coelicolor A3(2) âafsS::apr mutant strain and compared with the M145 Wild-type strain (series submitted separately). Keywords: Time course Time-course study involved analysis of 8 samples (16h, 20h, 22h, 24h, 26h, 31h, 37h and 40h). All arrays used cDNA labeled with Alexa647 and gDNA labeled with Cy3.
2010-06-10 | E-GEOD-8110 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M145 wild type and disruption mutants of regulatory genes (afsS and absA1) known to affect antibiotic biosynthesis. Keywords: Time course The time-course study involved analysis of 9 samples (10h, 13h, 16h, 19h, 22h, 25h, 31h, 35h, 37h). Of these, the 16h sample was analyzed on three arrays (3 technical replicates). All other samples were analyzed on duplicate arrays (2 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.
2010-06-11 | E-GEOD-8086 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) M145 wild type and disruption mutants of regulatory genes (afsS and absA1) known to affect antibiotic biosynthesis. Keywords: Time course The time-course study involved analysis of 13 samples (10h, 13h, 14h, 16h, 18h, 20h, 22h, 24h, 27h, 29h, 32h, 34h, 37h). Of these, 13h, 14h, 16h, 18h, 20h, 22h, 24h, 32h, and 37h sample were analyzed on duplicate arrays (2 technical replicates). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.
2010-06-11 | E-GEOD-8107 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants. The time-course study involved analysis of 8 samples (15.5hr, 17hr, 19hr, 20.5hr, 22.5hr, 23.5hr, 25hr, 42hr). Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.
2012-12-19 | E-GEOD-22395 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants. The time-course study involved analysis of 8 samples (14hr, 14.5hr, 15.5hr, 17.5hr, 18.5hr, 20hr, 34hr, 40hr). Sample 14hr was analyzed on 5 arrays. Sample 14.5hr was analyzed on 3 arrays. Sample 20hr was analyzed on 2 arrays. Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.
2012-12-19 | E-GEOD-22397 | biostudies-arrayexpress
Project description:Antibiotic biosynthesis in Streptomyces species is controlled by a complex genetic and biochemical network of global and pathway specific regulators. Details of their precise interactions in mediating temporal and spatial expression of secondary metabolite genes remain poorly defined. In this study, we employed whole-genome microarrays to investigate the temporal transcriptome profiles of S. coelicolor A3(2) wild type and regulatory mutants. The time-course study involved analysis of 9 samples (14hr, 15hr, 16hr, 17hr, 18hr, 19hr, 20hr, 21hr, 40hr). Samples (14hr, 15hr, 17hr, 20hr, 40hr) were analyzed on 2 arrays. Samples (18hr, 19hr, 21hr) were analyzed on 3 arrays. Genomic DNA of S. coelicolor wild type (M145) was used as a reference for all the arrays. cDNA was labeled with Alexa647 and genomic DNA was labeled with Cy3.
2012-12-19 | E-GEOD-22394 | biostudies-arrayexpress