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Morphological differentiation and secondary metabolism responses of Streptomyces coelicolor A3(2) to simulated microgravity based on comparative transcriptomics (2-color)

ABSTRACT: In order to gain a better understanding of the effects of Streptomyces coelicolor A3(2) wild type strain exposed to simulated microgravity condition by clinorotation, we constructed a whole genome microarray to screen simulated microgravity sensitive genes using the Agilent eArray 5.0 program. The genechip was custom designed according to the manufacturer’s recommendations (Agilent, 8*15K). The genome sequences were downloaded from: http://www.ncbi.nlm.nih.gov/genome?Db =genome&Cmd = Search&Term = NC_003888, NC_003903.1, NC_003904.1. Each gene was represented by one 60-nt oligonucleotide probe, and 680 genes associated with morphological differentiation and secondary metabolism out of the total 8116 genes were replicated 9 times each. Cells of Streptomyces coelicolor A3(2) wild type strain were harvested from the colonies grown in JCM42 agar medium at 28°C for 144h (6d) under simulated microgravity (by a rotating clinostat) and 1g control conditions respectively. Total RNA was extracted to conduct the microarray hybridization experiments for two color (Cy3/Cy5).

ORGANISM(S): Streptomyces coelicolor A3(2)

SUBMITTER: Huang Bing

PROVIDER: E-GEOD-53749 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Morphological differentiation and secondary metabolism responses of Streptomyces coelicolor A3(2) to simulated microgravity based on comparative transcriptomics.

Project description:In order to gain a better understanding of the effects of Streptomyces coelicolor A3(2) wild type strain exposed to simulated microgravity condition by clinorotation, we constructed a whole genome microarray to screen simulated microgravity sensitive genes using the Agilent eArray 5.0 program. The genechip was custom designed according to the manufacturerM-bM-^@M-^Ys recommendations (Agilent, 8*15K). The genome sequences were downloaded from: http://www.ncbi.nlm.nih.gov/genome?Db =genome&Cmd = Search&Term = NC_003888, NC_003903.1, NC_003904.1. Each gene was represented by one 60-nt oligonucleotide probe, and 680 genes associated with morphological differentiation and secondary metabolism out of the total 8116 genes were replicated 9 times each. Cells of Streptomyces coelicolor A3(2) wild type strain were harvested from the colonies grown in JCM42 agar medium at 28M-BM-0C for 96h (4d) under simulated microgravity and 1g control conditions. Total RNA was extracted to conduct the microarray hybridization experiments. Three independent experiments were performed in which ASM_1A, ASM_2A, ASM_3A were the test group samples and ANG_1A, ANG_2A, ANG_3A were the control group samples. Differentially expressed genes were selected with PM-oM-<M-^\0.05, FCM-bM-^IM-%2.0 by T-test methods using the independent three sets data.

2014-02-01 | E-GEOD-53748 | biostudies-arrayexpress

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Project description:In order to gain a better understanding of the effects of Streptomyces coelicolor A3(2) wild type strain exposed to spaceflight condition, we constructed a whole genome microarray to screen simulated microgravity sensitive genes using the Agilent eArray 5.0 program. The genechip was custom designed according to the manufacturerM-bM-^@M-^Ys recommendations (Agilent, 8*15K). The genome sequences were downloaded from: http://www.ncbi.nlm.nih.gov/genome?Db =genome&Cmd = Search&Term = NC_003888, NC_003903.1, NC_003904.1. Each gene was represented by one 60-nt oligonucleotide probe, and 680 genes associated with morphological differentiation and secondary metabolism out of the total 8116 genes were replicated 9 times each. Cells of Streptomyces coelicolor A3(2) wild type strain were harvested from the colonies grown in JCM42 agar medium at 23M-BM-10.5M-BM-0C for 16.5 days in spaceflight experiments. Total RNA was extracted to conduct the microarray experiments. The samples labeled in SP12_1 were from the M-bM-^@M-^\M-NM-<g-positionM-bM-^@M-^] and C07_1 from the M-bM-^@M-^\simulated 1g-positionM-bM-^@M-^] inside the BIOBOX for spaceflight during Shenzhou-8 space mission. The samples labeled in DB3_1 were from static 1g position on gound as the control. SP12_1 was test sample; C07_1 and DB3_1 were both samples for control.

2014-02-01 | E-GEOD-53750 | biostudies-arrayexpress

S. coelicolor YSK4425 Time-course Study in R5- medium (Culture#2)

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

S. coelicolor M752 SMM medium time course study

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) M752 mutant strain, which has an in frame deletion of scbR (SCO6265) and compare it to the wild-type M145 strain. scbR encondes a gamma-butyrolactone binding protein (Takano, E., Chakraburtty, R., Nihira, T., Yamada, Y., and Bibb, M. A complex role for the gamma-butyrolactone SCB1 in regulating antibiotic production in Streptomyces coelicolor A3(2). Mol. Microbiol. 2001 41(5), 1015-1028). The time-course study involved analysis of 8 samples (14hr, 15hr, 16hr, 17hr, 19hr, 20hr, 22hr, 39hr). Sample 22hr was 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.

2010-10-25 | E-GEOD-22398 | biostudies-arrayexpress

S. coelicolor LY2517 R5- medium time course study (Culture # 1)

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) deltaSCO2517::kan mutant strain (LY2517) and compare it to the wild-type M145 strain. SCO2517 is a putative two-component system response regulator. The time-course study involved analysis of 6 samples (15h, 22h, 24h, 26h, 35h, 43h). All 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.

2012-12-19 | E-GEOD-21809 | biostudies-arrayexpress

S. coelicolor LY2517 R5- medium time course study (Culture # 2)

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) deltaSCO2517::kan mutant strain (LY2517) and compare it to the wild-type M145 strain. SCO2517 is a putative two-component system response regulator. The time-course study involved analysis of 13 samples (14h, 16h, 18h, 20h, 22h, 24h, 26h, 28h, 30h, 32h, 34h, 37h, 39h). 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-21810 | biostudies-arrayexpress

S. coelicolor Wild Type Time-course Study in R5- medium (Culture#1)

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

S. coelicolor YSK3654 R5- medium time course study

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) deltaSCO3654::apr mutant strain (YSK3654) and compare it to the wild-type M145 strain. SCO3654 is a putative two-component system sensor kinase. The time-course study involved analysis of 9 samples (10h, 13h, 16h, 19h, 22h, 25h, 31h, 35h, 37h). All 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.

2010-10-25 | E-GEOD-21807 | biostudies-arrayexpress

S. coelicolor M145 SMM medium time course study (Culture # 2)

2012-12-19 | E-GEOD-22395 | biostudies-arrayexpress

S. coelicolor WL6268 R5- medium time course study

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) deltaSCO6268::kan mutant strain (WL6268) and compare it to the wild-type M145 strain. SCO6268 is a putative histidine kinase. The time-course study involved analysis of 7 samples (12h, 16h, 18h, 19h, 21h, 25h, 33h). Samples (19h, 21h, 25h, 33h) were analyzed on duplicate arrays (2 technical replicates). Sample 16h was analyzed on triplicate arrays (3 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.

2010-10-25 | E-GEOD-21808 | biostudies-arrayexpress

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