Whole-genome resequencing of Pseudomonas aeruginosa PAO1 after anti-virulence treatments targeting iron uptake
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ABSTRACT:
PROVIDER: PRJEB22899 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2162320.fastq.gz | Fastqsanger.gz | |||
| ERR2162330.fastq.gz | Fastqsanger.gz | |||
| ERR2162321.fastq.gz | Fastqsanger.gz | |||
| ERR2162331.fastq.gz | Fastqsanger.gz | |||
| ERR2162322.fastq.gz | Fastqsanger.gz |
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Project description:We carried out an experimental evolution in human serum as an ex-vivo model and screened evolved lines for the evolution of resistance phenotypes towards two anti-virulence treatments, gallium and flucytosine, which both target the iron scavenging pyoverdine of Pseudomonas aeruginosa (each at 2 different doses). We performed whole-genome sequencing of 16 evolved clones from the different treatment regimes .
2018-09-07 | E-MTAB-6110 | biostudies-arrayexpress
Project description:The gene PA2384 in Pseudomonas aeruginosa PAO1, annotated originally as unknown function, has been previously shown to be dramatically responsive to iron limitation. In the present study, PA2384 is shown by bioinformatics analysis to have a weak similarity to the N-termini DNA binding domain of fur, a well-known ferric uptake regulator. To experimentally investigate the function of PA2384 P. aeruginosa PAO1 recombinant (pUCP20::PA2384) overexpressing PA2384 and PA2384 knock-out mutant PAO1-23844 are constructed and studied. Physiological characterization in a carefully controlled cultivation system shows that the knockout strain needed a longer lag phase to grow and exhibited a significantly reduced production speed of siderophore (pyoverdine and pyochelin) in the stationary phase. Genome-scale transcriptional profiles at different growth stages are compared between the wild type and âPA2384 mutant grown under iron-limiting conditions. The expression of more than 350 genes is affected. Among them, seventy-one genes involved in iron uptake are significantly induced by PA2384. 102 quorum sensing (QS) dependent genes exhibited differential transcription. They include genes related to the biosynthesis of some important virulence factors such as pyocyanin, rhamnolipids and hydrogen cyanide. Transcription of genes responsible for the synthesis of Pseudomonas Quinolone Signal (PQS) is greatly advanced by the knockout of PA2384. We postulate that PA2384 affects QS via PQS. Furthermore, the knockout of PA2384 also results in altered expression of genes involved in electron transfer, central metabolism, phosphorus starvation and translation. It implies that PA2384 may affect more basic physiology than only respond to iron uptake and is a versatile global regulator in P. aeruginosa under iron starvation. Experiment Overall Design: mutant and wilde type biological replicates were analyzed at 3 timepoints
2007-09-21 | E-GEOD-2885 | biostudies-arrayexpress
Project description:The gene PA2384 in Pseudomonas aeruginosa PAO1, annotated originally as unknown function, has been previously shown to be dramatically responsive to iron limitation. In the present study, PA2384 is shown by bioinformatics analysis to have a weak similarity to the N-termini DNA binding domain of fur, a well-known ferric uptake regulator. To experimentally investigate the function of PA2384 P. aeruginosa PAO1 recombinant (pUCP20::PA2384) overexpressing PA2384 and PA2384 knock-out mutant PAO1-23844 are constructed and studied. Physiological characterization in a carefully controlled cultivation system shows that the knockout strain needed a longer lag phase to grow and exhibited a significantly reduced production speed of siderophore (pyoverdine and pyochelin) in the stationary phase. Genome-scale transcriptional profiles at different growth stages are compared between the wild type and ∆PA2384 mutant grown under iron-limiting conditions. The expression of more than 350 genes is affected. Among them, seventy-one genes involved in iron uptake are significantly induced by PA2384. 102 quorum sensing (QS) dependent genes exhibited differential transcription. They include genes related to the biosynthesis of some important virulence factors such as pyocyanin, rhamnolipids and hydrogen cyanide. Transcription of genes responsible for the synthesis of Pseudomonas Quinolone Signal (PQS) is greatly advanced by the knockout of PA2384. We postulate that PA2384 affects QS via PQS. Furthermore, the knockout of PA2384 also results in altered expression of genes involved in electron transfer, central metabolism, phosphorus starvation and translation. It implies that PA2384 may affect more basic physiology than only respond to iron uptake and is a versatile global regulator in P. aeruginosa under iron starvation. Keywords: iron starvation, quorum sensing, time course
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Project description:Analysis of iron-regulated gene expression in Saccharomyces cerevisiae using cDNA microarrays has identified three putative cell wall proteins that are directly regulated by Aft1p, the major iron-dependent transcription factor in yeast. FIT1, FIT2, and FIT3 (for facilitator of iron transport) were more highly expressed in strains grown in low concentrations of iron and in strains in which AFT1-1(up), a constitutively active allele of AFT1, was expressed. Northern blot analysis confirmed that FIT1, FIT2, and FIT3 mRNA transcript levels were increased 60-230-fold in response to iron deprivation in an Aft1p-dependent manner. Fit1p was localized exclusively to the cell wall by indirect immunofluorescence. Deletion of the FIT genes, individually or in combination, resulted in diminished uptake of iron bound to the siderophores ferrioxamine B and ferrichrome, without diminishing the uptake of ferric iron salts, or the siderophores triacetylfusarinine C and enterobactin. FIT-deletion strains exhibited increased expression of Aft1p target genes as measured by a FET3-lacZ reporter gene or by Arn1p Western blotting, indicating that cells respond to the absence of FIT genes by up-regulating systems of iron uptake. Aft1p activation in FIT-deleted strains occurred when either ferrichrome or ferric salts were used as sources of iron during growth, suggesting that the FIT genes enhance uptake of iron from both sources. Enzymatic digestion of the cell wall resulted in the release of significant amounts of iron from cells, and the relative quantity of iron released was reduced in FIT-deletion strains. Fit1p, Fit2p, and Fit3p may function by increasing the amount of iron associated with the cell wall and periplasmic space. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
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Project description:Ferric Citrate Uptake is a Virulence Factor in Uropathogenic Escherichia coli
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Project description:P. aeruginosa PAO1 grown as lawns on Nematode Growth Medium prepared without supplementation (NGM Pi<0.1 mM) has high killing ability against C. elegans, however, no mortality in worms has been observed during 48 hrs when feeding on PAO1 lawns grown on phosphate supplemented full NGM Pi 25 mM, pH 6.0 medium. We used a microarray to define the virulence-related genes in P. aeruginosa grown as lawns in NGM Pi<0.1 mM vs NGM Pi25 mM pH 6.0
2011-07-27 | GSE30967 | GEO
Project description:Our study showed that selected pillararene was able to decrease the level of cell death and demage caused to human A549 epithelial cells by Pseudomonas aeruginosa PAO1 infection. To further understand the protective effects of pillararene during bacterial infections, we analyzed total mRNA isolated from the A549 epithelial cells. Our study showed that pillararene alone had minimal effect on A549 epithelial cells. The addition of PAO1 to A549 cells greatly altered expression levels. The addition of pillararene to infected A549 epithelial cells displayed a concentration-dependent reduction in the inflammatory response.
2023-02-27 | GSE182847 | GEO
Project description:The budding yeast S. cerevisiae responds to depletion of iron in the environment by activating Aft1p, the major iron-dependent transcription factor, and by transcribing systems involved in the uptake of iron. Here we have studied the transcriptional response to iron deprivation, and have identified new Aft1p target genes. We find that other metabolic pathways are regulated by iron: biotin uptake and biosynthesis, nitrogen assimilation, and purine biosynthesis. Two enzymes active in these pathways, biotin synthase and glutamate synthase, require an iron-sulfur cluster for activity. Iron deprivation activates transcription of the biotin importer and simultaneously represses transcription of the entire biotin biosynthetic pathway. Multiple genes involved in nitrogen assimilation and amino acid metabolism are induced by iron deprivation, while glutamate synthase, a key enzyme in nitrogen assimilation, is repressed. A CGG palindrome within the promoter of glutamate synthase confers iron-regulated expression, suggesting control by a transcription factor of the binuclear zinc cluster family. We provide evidence that yeast subjected to iron deprivation undergo a transcriptional remodeling, resulting in a shift from iron-dependent to parallel, but iron-independent, metabolic pathways. A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s). Using regression correlation
2006-02-07 | E-GEOD-4196 | biostudies-arrayexpress
Project description:b-Oxidative enzymes for fatty acid degradation (Fad) of long-chain fatty acid (LCFA), a component of lung surfactant phosphatidylcholine, are induced in vivo during lung infection in cystic fibrosis patients, which could contribute to nutrient acquisition and pathogenesis of Pseudomonas aeruginosa. In addition, fatty acid biosynthesis (Fab) is essential for the syntheses of two virulence controlling acylated-homoserine-lactone molecules in this organism. We mapped the promoter regions of the fadBA5-operon (PA3014 and PA3013) and a fadE homologue (PA2815) involved in Fad and the fabAB-operon involved in Fab. Focusing on the transposon mutagenesis of strain PAO1 carrying the PfadBA5-lacZ fusion, we identified a regulator for the fadBA5-operon to be PsrA (PA3006). Transcriptome analysis of the DpsrA mutant indicates its importance in regulating b-oxidative enzymes, which confirms a previous proteomic study. We further showed that induction of the fadBA-operon responds to LCFA signals, and this induction requires the presence of PsrA, suggesting that PsrA binds to LCFA to derepress fadBA5. Electrophoresis mobility shift assay indicate specific binding of PsrA to the fadBA5-promoter region. This binding is disrupted by specific LCFA (C18:1D9, C16:0, and to a lesser extent C14:0), but not by the first intermediate of b-oxidation, acyl-CoA. We proposed that PsrA is a Fad-regulator that binds and responds to LCFA signals in Pseudomonas aeruginosa. Keywords: Pseudomonas aeruginosa, wild-type PAO1 compared to PAO1-psrA::Tn
2008-02-14 | GSE8083 | GEO
Project description:The budding yeast S. cerevisiae responds to depletion of iron in the environment by activating Aft1p, the major iron-dependent transcription factor, and by transcribing systems involved in the uptake of iron. Here we have studied the transcriptional response to iron deprivation, and have identified new Aft1p target genes. We find that other metabolic pathways are regulated by iron: biotin uptake and biosynthesis, nitrogen assimilation, and purine biosynthesis. Two enzymes active in these pathways, biotin synthase and glutamate synthase, require an iron-sulfur cluster for activity. Iron deprivation activates transcription of the biotin importer and simultaneously represses transcription of the entire biotin biosynthetic pathway. Multiple genes involved in nitrogen assimilation and amino acid metabolism are induced by iron deprivation, while glutamate synthase, a key enzyme in nitrogen assimilation, is repressed. A CGG palindrome within the promoter of glutamate synthase confers iron-regulated expression, suggesting control by a transcription factor of the binuclear zinc cluster family. We provide evidence that yeast subjected to iron deprivation undergo a transcriptional remodeling, resulting in a shift from iron-dependent to parallel, but iron-independent, metabolic pathways. A dose response design type examines the relationship between the size of the administered dose and the extent of the response of the organism(s). Keywords: dose_response_design
2006-02-08 | GSE4196 | GEO