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Transcriptional analysis of wild-type and delta_dasR mutant of Streptomyces coelicolor grown in soil amended with chitin

ABSTRACT: Genome-wide microarray analysis was performed using RNA extracted from soil cultures of Streptomyces coelicolor A3(2) in the presence or absence of chitin. The vast majority of genes in chitin and amino sugar metabolism, as well as many other genes for carbon and energy, nitrogen and sulfur metabolism, were differentially expressed in response to addition of chitin. Moreover, the gene expressions of eight gene clusters for secondary metabolites were also significantly up-regulated in the chitin amended soil. To reveal the role of a pleiotropic transcriptional regulator, DasR, which has been reported to be involved in regulation of chitin metabolism, antibiotic production and morphological differentiation, the gene expression patterns of wild type and dasR mutant in soil amended with chitin were compared by microarray analysis. The dasR mutation resulted in up-regulation of four antibiotic gene clusters and down-regulation of chitin metabolism.

ORGANISM(S): Streptomyces coelicolor A3(2)

PROVIDER: GSE39164 | GEO | 2012/11/07

SECONDARY ACCESSION(S): PRJNA170126

REPOSITORIES: GEO

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Transcriptional analysis of wild-type and delta_dasR mutant of Streptomyces coelicolor grown in soil amended with chitin

Project description:Genome-wide microarray analysis was performed using RNA extracted from soil cultures of Streptomyces coelicolor A3(2) in the presence or absence of chitin. The vast majority of genes in chitin and amino sugar metabolism, as well as many other genes for carbon and energy, nitrogen and sulfur metabolism, were differentially expressed in response to addition of chitin. Moreover, the gene expressions of eight gene clusters for secondary metabolites were also significantly up-regulated in the chitin amended soil. To reveal the role of a pleiotropic transcriptional regulator, DasR, which has been reported to be involved in regulation of chitin metabolism, antibiotic production and morphological differentiation, the gene expression patterns of wild type and dasR mutant in soil amended with chitin were compared by microarray analysis. The dasR mutation resulted in up-regulation of four antibiotic gene clusters and down-regulation of chitin metabolism. A study using total RNA extracted from soil cultures of Streptomyces ceolicolor A3(2). A whole genome microarray of S. coelicolor (NimbleGen Custom Prokaryotic Gene Expression 72K 4-plex Arrays) was designed and manufactured by Roche (Roche NimbleGen, Madison, WI). Each array contained four sets of 8 sequence-specific 60-mer probes per gene corresponding to 7825 genes from the S. coelicolor A3(2) genome.

2012-11-07 | E-GEOD-39164 | biostudies-arrayexpress

Metabolic switching in Streptomyces coelicolor Timeseries 1

Project description:Background: 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. Results: Surprisingly, we find that the metabolic switch actually consists of multiple finely orchestrated switching events. Strongly coherent clusters of genes show drastic changes in gene expression already many hours before the classically defined transition phase where the switch from primary to secondary metabolism was expected. The main switch in gene expression takes only 2 hours, and changes in antibiotic biosynthesis genes are delayed relative to the metabolic rearrangements. Furthermore, global variation in morphogenesis genes indicates an involvement of cell differentiation pathways in the decision phase leading up to the commitment to antibiotic biosynthesis. Conclusions: Our study provides the first detailed insights into the complex sequence of early regulatory events during and preceding the major metabolic switch in S. coelicolor, which will form the starting point for future attempts at engineering antibiotic production in a biotechnological setting. Keywords: time course

2009-12-14 | GSE18489 | GEO

Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor

Project description:A complex programme of regulation governs gene expression during development of the morphologically and biochemically complex eubacterial genus Streptomyces. Earlier work has suggested a model in which 'higher level' pleiotropic regulators activate 'pathway-specific' regulators located within chromosomal gene clusters encoding biosynthesis of individual antibiotics. We used mutational analysis and adventitious overexpression of key Streptomyces coelicolor regulators to investigate functional interactions among them. We report here that cluster-situated regulators (CSRs) thought to be pathway-specific can also control other antibiotic biosynthetic gene clusters, and thus have pleiotropic actions. Surprisingly, we also find that CSRs exhibit growth-phase-dependent control over afsR2/afsS, a 'higher level' pleiotropic regulatory locus not located within any of the chromosomal gene clusters it targets, and further demonstrate that cross-regulation by CSRs is modulated globally and differentially during the S. coelicolor growth cycle by the RNaseIII homologue AbsB. Our results, which reveal a network of functional interactions among regulators that govern production of antibiotics and other secondary metabolites in S. coelicolor, suggest that revision of the currently prevalent view of higher-level versus pathway-specific regulation of secondary metabolism in Streptomyces species is warranted. Groups of assays that are related as part of a time series. Keywords: time_series_design

2006-02-02 | GSE4138 | GEO

Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor

2006-02-01 | E-GEOD-4138 | biostudies-arrayexpress

Metabolic switching in Streptomyces coelicolor Timeseries 1

2010-05-18 | E-GEOD-18489 | biostudies-arrayexpress

Metabolic switching in Streptomyces coelicolor wild type, time series under glutamate depletion condition

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

Metagenome of chitin-amended soil

Project description:Soil metagenome sampled from a chitin-amended agricultural field

| PRJEB11634 | ENA

The Streptomyces coelicolor DegS-DegU-like regulon

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

Streptomyces coelicolor A3(2)

Project description:Transcriptional analysis of wild-type and delta_dasR mutant of Streptomyces coelicolor grown in soil amended with chitin

| PRJNA170126 | ENA

Plant response to chitin 4mer

Project description:Analysis of 14-day-old Columbia-0 seedlings treated with chito-tetramer.Results provide insight into the signaling pathways involved in plant devlopment in response to the four-mer. Chitin is the second biopolymer most abundant at nature, after cellulose, forming part of insect exosqueletons, crustacean shells, krill and fungal spores where is present as a high molecular weight molecule. Previously we showed that Arabidopsis defense related clusters of genes were induced by high molecular weight chitin (CHH) or 8mer oligosaccharides similarly (Ramonell et al., 2005), some of those genes were essential for effective defense against phytopathogenic fungus (Berrocal-Lobo et al., 2010). At this work we show that differentially, a chitin oligosaccharide of lower molecular weight (4mer), induce genes in Arabidopsis related principally to vegetative growth, development and carbon and nitrogen metabolism.

2017-02-17 | GSE83858 | GEO

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