Pseudomonas aeruginosa PAO1
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ABSTRACT:
PROVIDER: PRJNA140783 | ENA |
REPOSITORIES: ENA
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Project description:Here we examined virulence activation in Pseudomonas aeruginosa in response to the synthetic kappa opioid agonist U-50, 488 in nutrient poor media where growth conditions are limited and density dependent quorum sensing is not activated. We used a microarray to define the virulence-related genes in P. aeruginosa grown in liquid poor nutrient medium to determine the effect of kappa-opioid receptor agonist on virulence/lethal phenotype
2012-05-21 | GSE29946 | GEO
Project description:Here we examined virulence activation in Pseudomonas aeruginosa in response to the synthetic kappa opioid agonist U-50, 488 in nutrient poor media where growth conditions are limited and density dependent quorum sensing is not activated. We used a microarray to define the virulence-related genes in P. aeruginosa grown in liquid poor nutrient medium to determine the effect of kappa-opioid receptor agonist on virulence/lethal phenotype All biological samples for gene expression analysis were prepared in triplicate. P. aeruginosa MPAO1 cells collected from liquid culture at 7 hrs of growth in 1.) 0.1xTY medium containing tryptone 1 g/L and yeast extract, 0.5 g/L, or 2.) 0.1xTY+25 mM potassium phosphate buffer, pH 6.0, or 3.) 0.1xTY+200 uM U-50,488, or 4.) 0.1xTY+ 25 mM potassium phosphate buffer, pH 6.0+ 200 uM U-50,488 were used for RNA isolation. Microarray analysis was performed using Affymetrix P. aeruginosa GeneChips (Affymetrix, Santa Clara, CA) at the University of Chicago Functional Genomics Facility
2012-05-20 | E-GEOD-29946 | biostudies-arrayexpress
Project description:Analysis of Pseudomonas aeruginosa PAO1 treated with 200 µM sphingomyelin. Results provide insight into the response to sphingomyelin in P. aeruginosa.
2017-02-12 | GSE83078 | GEO
Project description:The ParS/ParR two component regulatory system plays important roles for multidrug resistance in Pseudomonas aeruginosa. In this study we report RNA-seq analyses of the transcriptomes of P. aeruginosa PAO1 wild type and par mutants growing in a minimal medium containing 2% casamino acids. This has allowed the quantification of PAO1 transcriptome, and further defines the regulon that is dependent on the ParS/ParR system for expression. Our RNA-seq analysis produced the first estimates of absolute transcript abundance for the 5570 coding genes in P. aeruginosa PAO1. Comparative transcriptomics of P. aeruginosa PAO1 and par mutants identified a total of 464 genes regulated by ParS and ParR. Results also showed that mutations in the parS/parR system abolished the expression of the mexEF-oprN operon by down-regulating the regulatory gene mexS. In addition to affecting drug resistance genes, transcripts of quorum sensing genes (rhlIR and pqsABCDE-phnAB), were significantly up-regulated in both parS and parR mutants. Consistent with these results, a significant portion of the ParS/ParR regulated genes belonged to the MexEF-OprN and quorum sensing regulons. Deletion of par genes also lead to overproduction of phenazines and increased swarming motility, consistent with the up-regulation of quorum sensing genes. Our results established a link among ParS/ParR, MexEF-OprN and quorum sensing in Pseudomonas aeruginosa. Based on these results, we propose a model to illustrate the relationship among these regulatory systems in P. aeruginosa.
2016-02-26 | GSE44681 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of farnesol-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Methods:LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 108 CFU/mL. Farnesol was then added at a concentration of either 0 (control) or 0.56 mg/mL, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three farnesol treatment groups, respectively. The cell precipitates were separately snap-frozen at -80ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol. Results: Our RNA-seq results showed that less than 100 genes of P. aeruginosa PAO1 were differentially expressed following farnesol treatment. We found that about 1.7% of all detected genes (96 of 5554 genes) were more than two-fold differentially expressed following farnesol treatment. Conclusions:
2019-10-11 | GSE138731 | GEO
Project description:The ParS/ParR two component regulatory system plays important roles for multidrug resistance in Pseudomonas aeruginosa. In this study we report RNA-seq analyses of the transcriptomes of P. aeruginosa PAO1 wild type and par mutants growing in a minimal medium containing 2% casamino acids. This has allowed the quantification of PAO1 transcriptome, and further defines the regulon that is dependent on the ParS/ParR system for expression. Our RNA-seq analysis produced the first estimates of absolute transcript abundance for the 5570 coding genes in P. aeruginosa PAO1. Comparative transcriptomics of P. aeruginosa PAO1 and par mutants identified a total of 464 genes regulated by ParS and ParR. Results also showed that mutations in the parS/parR system abolished the expression of the mexEF-oprN operon by down-regulating the regulatory gene mexS. In addition to affecting drug resistance genes, transcripts of quorum sensing genes (rhlIR and pqsABCDE-phnAB), were significantly up-regulated in both parS and parR mutants. Consistent with these results, a significant portion of the ParS/ParR regulated genes belonged to the MexEF-OprN and quorum sensing regulons. Deletion of par genes also lead to overproduction of phenazines and increased swarming motility, consistent with the up-regulation of quorum sensing genes. Our results established a link among ParS/ParR, MexEF-OprN and quorum sensing in Pseudomonas aeruginosa. Based on these results, we propose a model to illustrate the relationship among these regulatory systems in P. aeruginosa. A total of 9 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas aeruginosa PAO1 wild type strain (3 replicates); Pseudomonas aeruginosa parS mutant (3 replicates); Pseudomonas aeruginosa parR mutant (3 replicates).
2016-02-26 | E-GEOD-44681 | biostudies-arrayexpress
Project description:P. aeruginosa PAO1 PA2663-UW expression in biofilm cells relative to P. aeruginosa PAO1 WT-UW expression in biofilm cells. All samples cultured in LB with glass wool. Experiment Overall Design: Strains: P. aeruginosa PAO1 wild-type, PA2663 mutant Experiment Overall Design: Medium: LB Experiment Overall Design: Biofilm grown on glass wool Experiment Overall Design: Time: 7 h Experiment Overall Design: Cell type: biofilm
2008-06-19 | E-GEOD-7968 | biostudies-arrayexpress
Project description:Pseudomonas aeruginosa PAO1 contacted with and without poplar roots gene expression Poplar contacted with and without PAO1 gene expression. All samples cultured in 1 x hrp + 0.25 % sucrose Keywords: Contact with different species
2007-03-18 | GSE5887 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of diallyl disulphide-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis. Methods: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 108 CFU/mL. Then DDS was added, with its concentrations were 0 (as control, three biological repeats numbered A1, A2, and A3) and 0.64 mg/mL (three biological repeats numbered B1, B2, and B3) separately, both with a triplicate. All the six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 150 rpm for 5 hours. The cells were then sampled and centrifuged from the three control groups and three DDS treatment groups, respectively. The cell precipitates in the control and DDS-treated groups were quickly separately frozen at -80 ºC. Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol. Results: The RNA sequencing results revealed that a large number of genes in P. aeruginosa PAO1 were differentially expressed after DDS treatment. More than three thousands of genes were differentially expressed, with either up regulated (1649 genes) or down regulated (1725 genes) more than two-fold. Conclusions:
2018-08-21 | GSE118801 | GEO
Project description:Pseudomonas aeruginosa PAO1 contacted with and without poplar roots gene expression Poplar contacted with and without PAO1 gene expression. All samples cultured in 1 x hrp + 0.25 % sucrose Experiment Overall Design: Strains: P. aeruginosa PAO1 WT Experiment Overall Design: Medium: 1 x hrp + 0.25 % sucrose Experiment Overall Design: Biofilm grown on poplar root compared to biofilm grown on glasswool Experiment Overall Design: Poplar roots grown
2008-11-07 | E-GEOD-5887 | biostudies-arrayexpress