Expression time-series from Streptomyces coelicolor germination
Ontology highlight
ABSTRACT:
ORGANISM(S): Streptomyces coelicolor A3(2)
PROVIDER: GSE44415 | GEO | 2013/08/01
SECONDARY ACCESSION(S): PRJNA189845
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptome time-courses during the S. coelicolor germination were used to reveal processes that underlie the gene expression at the transcriptional level within transition from dormancy to vegetative growth. Samples from 13 time points at the initial 5.5 h (30 min time intervals) of germination. 2-3 biological (and technical) replicates for each time point. Altogether 37 samples.
2013-08-01 | E-GEOD-44415 | biostudies-arrayexpress
Project description:We studied the influence of copper in physiological and morphological differentiation of Streptomyces coelicolor. We demonstrate differences in phenotype (germination, growth rate, antibiotic production) and genetic expression between a strain mutated at copper chaperone CopZ (SCO2730::Tn5062), the wild-type strain and a wild-type strain sporulated in a media with 80µM CuSO4. These differences are correlated with the cytosolic copper. Our results demonstrate a pleiotropic effect of copper modulating S. coelicolor development.
2018-12-31 | GSE111126 | GEO
Project description:Based on the chromosomal locations of genes inferred from sequence analysis to be essential for the viability of Streptomyces coelicolor, Bentley et al. (Bentley et al., 2002) have suggested that a 4.9 Mb central region of the linear S. coelicolor chromosome encodes core functions expressed during vegetative growth of this species, while 1.5 Mb and 2.3 Mb chromosomal DNA segments lateral to this core encode auxiliary functions proposed to be required under other growth conditions. To examine this hypothesis and experimentally identify genes expressed during vegetative growth of S. coelicolor cultures, we used DNA microarrays to measure globally the abundance of S. coelicolor transcripts in cells growing in liquid medium. We found that, overall, genes corresponding to the 4.9 Mb core region of the S. coelicolor M145 chromosome were more highly expressed under non-limiting growth conditions than genes in the 1.5 Mb left and 2.3 Mb right chromosome arms, supporting the notion of the core versus auxiliary organization of genes on the chromosome. To examine how this chromosomal distribution of transcripts changes under other growth conditions, we also measured gene expression changes during stationary phase and several stress conditions. During stationary phase, the composition of S. coelicolor transcripts appears to shift from large quantities of growth-related transcripts encoded in the core region to those of less characterized genes, which may be essential for differentiation and other physiological responses, encoded throughout the chromosome. After temperature and osmotic upshifts, we found that S. coelicolor transiently induces a set of several hundred genes located throughout the chromosome, which may function in response mechanisms common to the two stress conditions. Keywords: all_pairs
2005-07-12 | GSE2921 | GEO
Project description:The process of Saccharomyces cerevisiae spore germination includes breakage of dormancy, morphological changes and resumption of vegetative growth. We have determined the global transcriptional response during the first two hours of spore germination in response to rich growth medium and glucose alone, and identified possible transcription factors regulating the different transcriptional programs.
2012-12-18 | GSE29960 | GEO
Project description:Based on the chromosomal locations of genes inferred from sequence analysis to be essential for the viability of Streptomyces coelicolor, Bentley et al. (Bentley et al., 2002) have suggested that a 4.9 Mb central region of the linear S. coelicolor chromosome encodes core functions expressed during vegetative growth of this species, while 1.5 Mb and 2.3 Mb chromosomal DNA segments lateral to this core encode auxiliary functions proposed to be required under other growth conditions. To examine this hypothesis and experimentally identify genes expressed during vegetative growth of S. coelicolor cultures, we used DNA microarrays to measure globally the abundance of S. coelicolor transcripts in cells growing in liquid medium. We found that, overall, genes corresponding to the 4.9 Mb core region of the S. coelicolor M145 chromosome were more highly expressed under non-limiting growth conditions than genes in the 1.5 Mb left and 2.3 Mb right chromosome arms, supporting the notion of the core versus auxiliary organization of genes on the chromosome. To examine how this chromosomal distribution of transcripts changes under other growth conditions, we also measured gene expression changes during stationary phase and several stress conditions. During stationary phase, the composition of S. coelicolor transcripts appears to shift from large quantities of growth-related transcripts encoded in the core region to those of less characterized genes, which may be essential for differentiation and other physiological responses, encoded throughout the chromosome. After temperature and osmotic upshifts, we found that S. coelicolor transiently induces a set of several hundred genes located throughout the chromosome, which may function in response mechanisms common to the two stress conditions.
2005-06-20 | E-SMDB-3219 | biostudies-arrayexpress
Project description:Expression time-series from Streptomyces coelicolor germination
| PRJNA189845 | ENA
Project description:During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix GeneChip and a high-resolution time-series of fermenter-grown samples. This time series was conducted using medium leading to glutamate depletion and the cultivation conditions as published in Nieselt et al. BMC Genomics 2010, performed with the Streptomyces coelicolor wild type strain M145E.
2011-12-31 | GSE30569 | GEO
Project description:Seed maturation, dormancy and germination are distinct physiological processes. Transition from maturation to dormancy, and from dormancy into germination are not only critical developmental phases in the plant life cycle but are also important agricultural traits. These developmental processes and their phase transitions are fine determined and coordinately regulated by genetic makeup and environmental cues. SCARECROW-LIKE15 (SCL15) has been demonstrated to be essential for repressing the seed maturation programme in vegetative tissues (Gao et al., Nat Commun, 2015, 6:7243). Here we report that SCL15 is also important for seed dormancy maintenance, germination timing and seed vigor performance based on the effects of SCL15 mutation on plant germination, growth and reproduction when compared with wild type Arabidopsis and over-expression lines 35S:SCL15 and Napin:SCL15. Seed dormancy is enhanced by the mutation of SCL15 in a GA signaling dependent way, indicating that SCL15 plays a negative role for primary dormancy release. Seed germination is positively regulated by SCL15 through interaction with ABA, GA and auxin signaling. SCL15 acts as positive regulator of seed vigor and effect of SCL15 mRNA abundance on seed reserve accumulation and seed development during late embryogenesis may contribute to the seed vigor performance.
2020-11-04 | GSE160707 | GEO
Project description:The present work aimed at providing noval reference genes (RGs) for streptomycetes by global quantitative analysis of gene expression profile. By using the time-series microarray data obtained in different culture medium (SMM in the present work and modified R5 from publication), the stably expressed genes of S. coelicolor were screened. Further statistical, bioinformatic and biological function analysis picked out 13 candidate RGs. According to qRT-PCR assays, 5 genes with high stability were selected and used for validation in other streptomycetes to assess their prevalence. Additionally, the absolute gene expression level reflcted by RNA-seq was also taken into consideration in the present work to guide the appropriate RGs selection for streptomycetes.
2013-12-31 | GSE53562 | GEO
Project description:Based on the chromosomal locations of genes inferred from sequence analysis to be essential for the viability of Streptomyces coelicolor, Bentley et al. (Bentley et al., 2002) have suggested that a 4.9 Mb central region of the linear S. coelicolor chromosome encodes core functions expressed during vegetative growth of this species, while 1.5 Mb and 2.3 Mb chromosomal DNA segments lateral to this core encode auxiliary functions proposed to be required under other growth conditions. To examine this hypothesis and experimentally identify genes expressed during vegetative growth of S. coelicolor cultures, we used DNA microarrays to measure globally the abundance of S. coelicolor transcripts in cells growing in liquid medium. We found that, overall, genes corresponding to the 4.9 Mb core region of the S. coelicolor M145 chromosome were more highly expressed under non-limiting growth conditions than genes in the 1.5 Mb left and 2.3 Mb right chromosome arms, supporting the notion of the core versus auxiliary organization of genes on the chromosome. To examine how this chromosomal distribution of transcripts changes under other growth conditions, we also measured gene expression changes during stationary phase and several stress conditions. During stationary phase, the composition of S. coelicolor transcripts appears to shift from large quantities of growth-related transcripts encoded in the core region to those of less characterized genes, which may be essential for differentiation and other physiological responses, encoded throughout the chromosome. After temperature and osmotic upshifts, we found that S. coelicolor transiently induces a set of several hundred genes located throughout the chromosome, which may function in response mechanisms common to the two stress conditions. Keywords: all_pairs An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.
2005-07-12 | E-GEOD-2921 | biostudies-arrayexpress