Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptomic consequence of the mutation in the response regulator gene gacA of the two-component regulatory system GacS/GacA in the rhizosphere biocontrol strain Pseudomonas aeruginosa M18

ABSTRACT: To investigate the influence of GacA on the genome-wide transcription of the rhizobacterium P. aeruginosa M18, DNA microarray experiments were carried out to compare the transcriptional profile of M18 with that of the gacA mutant grown to the early stationary phase (OD600 = 5.0 ~ 5.5) in KMB media. When compared with the M18 parental strain, the transcriptomic profile of gacA mutant revealed the significantly differential expression (increased or decreased by at least 2-fold as well as p-value < 0.05) of 839 genes, which represent approximately 15% of all 5696 annotated genes in the M18 genome. Of these 839 genes, 472 were downregulated and 367 genes were upregulated by the gacA mutation. P. aeruginosa M18 and its gacA mutant were grown to OD600=5.0-5.5 (early stationary phase) in KMB medium at 28M-bM-^DM-^C. Three independent experiments were performed at each time.

ORGANISM(S): Pseudomonas aeruginosa M18

SUBMITTER: xianqing Huang

PROVIDER: E-GEOD-43655 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global control of GacA in secondary metabolism, primary metabolism, secretion systems, and motility in the rhizobacterium Pseudomonas aeruginosa M18.

Wei Xue X Huang Xianqing X Tang Lulu L Wu Daqiang D Xu Yuquan Y

Journal of bacteriology 20130524 15

The rhizobacterium Pseudomonas aeruginosa M18 can produce a broad spectrum of secondary metabolites, including the antibiotics pyoluteorin (Plt) and phenazine-1-carboxylic acid (PCA), hydrogen cyanide, and the siderophores pyoverdine and pyochelin. The antibiotic biosynthesis of M18 is coordinately controlled by multiple distinct regulatory pathways, of which the GacS/GacA system activates Plt biosynthesis but strongly downregulates PCA biosynthesis. Here, we investigated the global influence of ...[more]

PMID: 23708134

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Project description:The GacS/GacA signal transduction system is a central regulator in Pseudomonas spp., including the biological control strain P. fluorescens Pf-5, in which GacS/GacA controls the production of secondary metabolites and exoenzymes that suppress plant pathogens. A whole genome oligonucleotide microarray was developed for Pf-5 and used to assess the global transcriptomic consequences of a gacA mutation in P. fluorescens Pf-5. In cultures at the transition from exponential to stationary growth phase, GacA significantly influenced transcript levels of 632 genes, representing more than 10% of the 6147 annotated genes in the Pf-5 genome. Transcripts of genes involved in the production of hydrogen cyanide, the antibiotic pyoluteorin, and the extracellular protease AprA were at a low level in the gacA mutant, whereas those functioning in siderophore production and other aspects of iron homeostasis were significantly higher in the gacA mutant than in wild-type Pf-5. Notable effects of gacA inactivation were also observed in the transcription of genes encoding components of a type VI secretion system and cytochrome C oxidase subunits. Two novel gene clusters expressed under the control of gacA were identified from transcriptome analysis, and we propose global-regulator-based genome mining as an approach to decipher the secondary metabolome of Pseudomonas spp. In this series two conditions have been analyzed. A gacA mutant of Pseudomonas fluorescens Pf-5 was harvested at early (OD 0.5) and late (OD 2.4) time points and compared to wild-type Pf-5 harvested in parallel. For each slide, an experimental RNA sample from a gacA mutant was labeled with Cy3 or Cy5 and was hybridized with a reference RNA sample from wild-type Pf-5 labeled with the other Cy dye. There are six slides per condition. Each condition is represented by three biological replicates. There are two flip-dye replicates for each biological replicate. Each slide contains three replicate spots per gene.

Dataset Information

Transcriptomic consequence of the mutation in the response regulator gene gacA of the two-component regulatory system GacS/GacA in the rhizosphere biocontrol strain Pseudomonas aeruginosa M18

Publications

Global control of GacA in secondary metabolism, primary metabolism, secretion systems, and motility in the rhizobacterium Pseudomonas aeruginosa M18.

Similar Datasets

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