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The P. aeruginosa PA14 transcriptome recorded under 14 different experimental conditions

ABSTRACT: We analyzed the transcriptional profile of P.aeruginosa PA14 grown under 14 different environmental conditions. These included conditions of growth within biofilms, at various temperatures, osmolarities and phosphate concentrations, under anaerobic conditions, attached to a surface and conditions encountered within the eukaryotic host. We found that >30% of the PA14 genome was differentially regulated at least under one of the 14 environmental conditions (referred to as the adaptive transcriptome). Most of the genes were also differentially regulated upon sigma factor hyper expression and/or inactivation (GEO accession number GSE54999) and many of those belonged to primary alternative sigma factor regulons.

ORGANISM(S): Pseudomonas aeruginosa

PROVIDER: GSE55197 | GEO | 2015/06/16

SECONDARY ACCESSION(S): PRJNA238880

REPOSITORIES: GEO

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The P. aeruginosa PA14 transcriptome recorded under 14 different experimental conditions

Project description:We analyzed the transcriptional profile of P.aeruginosa PA14 grown under 14 different environmental conditions. These included conditions of growth within biofilms, at various temperatures, osmolarities and phosphate concentrations, under anaerobic conditions, attached to a surface and conditions encountered within the eukaryotic host. We found that >30% of the PA14 genome was differentially regulated at least under one of the 14 environmental conditions (referred to as the adaptive transcriptome). Most of the genes were also differentially regulated upon sigma factor hyper expression and/or inactivation (GEO accession number GSE54999) and many of those belonged to primary alternative sigma factor regulons. The samples of P. aeruginosa PA14 wild type strain were cultivated under 14 different experimental conditions and were analyzed by RNA-seq. For each condition, at least two biological replicates were generated Please note that PA14 is our standard lab strain used for all generated data in this records. There is no mutation introduced for any of those experiments, and thus, the descriptions only highlight the growth conditions.

2015-06-16 | E-GEOD-55197 | biostudies-arrayexpress

Transcription profiling of P.aeruginosa PA14 and P.aeruginosa PA14 metR::phoA

Project description:Five biological repeats of P.aeruginosa PA14 and five biological repeats of P.aeruginosa PA14 metR::phoA were grown in liquid BM2 swarming media containing 62mM potassium phosphate buffer [pH7], 2 mM MgSO4, 10uM FeSO4, 0.4% (wt/vol) glucose, and 0.1% (wt/vol) casamino acids. Microarray experiments were done using microarray slides and protocols from TIGR on samples taken from mid-log phase (OD600 0.4-0.5)cells.

2009-08-20 | E-FPMI-19 | biostudies-arrayexpress

Transcription profiling of P.aeruginosa PA14 and P.aeruginosa PA14 metR::phoA grown on swarming plates

Project description:Four biological repeats of P.aeruginosa PA14 and four biological repeats of P.aeruginosa PA14 metR::phoA were grown in BM2 swarming media plates containing 62mM potassium phosphate buffer [pH7], 2 mM MgSO4, 10uM FeSO4, 0.4% (wt/vol) glucose, 0.1% (wt/vol) casamino acids and 0.5% agar. Microarray experiments were done using microarray slides and protocols from TIGR on samples harvested from the dendritic swarm colony growth, 2 to 3 mm of the swarm zone edge.

2009-08-20 | E-FPMI-20 | biostudies-arrayexpress

Proteomics of Pseudomonas aeruginosa PAO1 and PA14

Project description:Recent studies have shown that the concentrations of proteins expressed from orthologous genes are often conserved across organisms, and to a greater extent than the abundances of the corresponding mRNAs. However, such studies have not distinguished between evolutionary (e.g., sequence divergence) and environmental (e.g., growth condition) effects on the regulation of steady-state protein and mRNA abundances. Here we systematically investigated the transcriptome and proteome of two closely related Pseudomonas aeruginosa strains, PAO1 and PA14, under identical experimental conditions, thus controlling for environmental effects. For 703 genes observed by both shotgun proteomics and microarray experiments, we find that the protein-to-mRNA ratios are highly correlated between orthologous genes in the two strains, to an extent comparable to protein and mRNA abundances. In spite of this high molecular similarity between PAO1 and PA14, we found that several metabolic, virulence, and antibiotic resistance genes are differentially expressed between the two strains, mostly at the protein but not at the mRNA level. Our data demonstrate that post-transcriptional regulation is important for understanding the discordance between mRNA and protein abundance.

2014-05-08 | PXD000684 | Pride

Expression data from Arabidopsis seedlings treated with Pseudomonas aeruginosa (strain PA14)

Project description:Early stages of host microbe adaptations involve 'system status changes' (rewiring of pre-existing cellular signaling networks and components) of the host and microbe. We posited that under certain environmental conditions these changes leads to maladaptations and favor emergence of new infectious diseases, and these adaptations will have characteristic signatures representative of the adaptation. Here using Arabidopsis seedlings in a submerged environment treated with P. aerugionsa, we show one such rewired regulation where the master two-component regulator GacA (previously shown to act upstream of quorum sensing, including the regulator LasR, that in turn controls a subset of virulence factors) is completely dispensable. The gacA mutant behaves similar to wild type P. aeruginosa (strain PA14) by a number of read-outs. Consistent with that, the gene expression data here indicates that the transcriptome pattern of the host is identical when treated with wild type PA14 or PA14-gacA mutant. Single time point (10 day old Arabidopsis seedlings infected with wild type PA14 or mutant bacteria PA14DgacA, and analyzed 24h after infection) with two independent experimenal replicates per treatment

2011-01-22 | E-GEOD-26084 | biostudies-arrayexpress

Expression data from Arabidopsis seedlings treated with Pseudomonas aeruginosa (strain PA14)

2011-01-22 | GSE26084 | GEO

Proteomics of Pseudomonas aeruginosa PAO1 and PA14

2018-08-29 | MSV000082863 | MassIVE

Gene expression in the small intestine of mice colonized with Pseudomonas aeruginosa

Project description:Celiac disease (CeD) is a food sensitivity characterized by a breakdown of oral tolerance to gluten proteins in genetically predisposed individuals, although the underlying mechanisms are incompletely understood. To evaluate a functional role of bacterial proteases in CeD, we colonized germ-free or clean SPF mice with P.aeruginosa PA14 or P.aeruginosa PA14 disrupted in lasB gene (elastase). We show gluten-independent, PAR-2 mediated upregulation of inflammatory pathways by LasB in C57BL/6 mice without villus blunting. In mice expressing CeD risk genes, P. aeruginosa elastase synergized with gluten to induce more severe inflammation that was associated with moderate villus blunting.

2019-02-01 | GSE125983 | GEO

Transcription analysis of the sensor kinase PA4398 in Pseudomonas aeruginosa PA14 under swarming conditions.

Project description:In this experiment the transcriptional profile of the Pseudomonas aeruginosa PA14 two-component sensor kinase PA4398 was investigated under swarming conditions using DNA microarrays. To this aim three independent cultures of the PA14 wild-type and the PA4398 mutant were grown until mid-log phase in Luria-Bertani broth following an incubation on BM2-swarm plates containing 0.1 % (wt/vol) casaminoacids and 0.5 % (wt/vol) agar for 20 h at 37 °C. Subsequent total RNA was extracted from the leading edge of dendritic swarm colonies and analyzed by microarrays.

2015-01-02 | E-MTAB-2540 | biostudies-arrayexpress

Regulation of Energy Metabolism by the Extracytoplasmic Function (ECF) σ factors of Arcobacter butzleri

Project description:The extracytoplasmic function (ECF) σ factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. The emerging pathogen Arcobacter butzleri possesses seven putative pairs of σ/anti-σ factors belonging to the ECF family. Here, we report the identification of the genes regulated by five out of the seven A. butzleri ECF σ factors. Three of the ECF σ factors play an apparent role in transport, energy generation and the maintainance of redox balance. Several genes like the nap, sox and tct genes are regulated by more than one ECF σ factor indicating that the A. butzleri ECF σ factors form a network of overlapping regulons. In contrast to other eubacteria, these A. butzleri ECF regulons appear to primarily regulate responses to changing environments in order to meet metabolic needs instead of an obvious role in stress adaptation.

2011-12-31 | GSE34089 | GEO

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