Expression profile of Pseudomonas aeruginosa ÎgcsR PAO1 using RNA-Seq
Ontology highlight
ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa
SUBMITTER: Christopher Nomura
PROVIDER: E-GEOD-76522 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:RNA was isolated from five biological repeats of P.aeruginosa and five biological repeats of P.aeruginosa parR mutant grown in BM2 media contianing glucose as the carbon source, 2 mM MgSO4 and 4 ug/ml indolicidin. Microarray experiments were done using microarray slides and protocols from http://pfgrc.jcvi.org/index.php/microarray/protocols.html
2010-08-31 | E-FPMI-21 | biostudies-arrayexpress
Project description:This study is the first to show transfer of regulatory bacterial sRNAs from bacterial OMVs to host cells. Demonstration of transfer of bacterial sRNA from Pseudomonas aeruginosa OMVs to host cells in two cell types. RNA isolated from PA14 OMV exposed primary human bronchial epithelial cells or CFBE41o- bronchial epithelial cells as well as unexposed control cells was analyzed by small RNA-Seq. Primary cell exposures were performed on two donors and exposures of CFBE41o- cells were done in triplicate.
2016-05-13 | E-GEOD-80421 | biostudies-arrayexpress
Project description:Purpose : The goal of this study was to use RNA Seq to validate transcriptional data of two clinical isolates focussing on a subset of 74 transcript that were selected specifically for Nanostring analysis. Methods : mRNA profiles were generated for the clinical isolates FRD1 and CI224_M, in duplicate, by deep sequencing. Strains were grown for 8 hours in LB medium at 37C prior to RNA harvest. Ribosomal RNA was removed using the Ribi-Zero rRNA Removal Kit (Epicentre). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters. mRNA profiles of liquid cultures grown for 8 hours in LB at 37C were generated for P. aeruginosa clinical isolates FRD1 and CI224_M, each in duplicate, by deep sequencing using Illumina NextSeq.
2016-08-09 | E-GEOD-83773 | biostudies-arrayexpress
Project description:Purpose : The goal of this study was to use RNA Seq to define the regulon of the transciption factor Anr by comparing global transcriptional profiles of Pseudomonas aeruginosa strain PAO1 and a clinical isolate with their isogenic ?anr mutants, grown in colony biofilms at 1% oxygen. Methods : mRNA profiles were generated for laboratory strain PAO1 and for a clinical isolate J215, as well as for ?anr derivatives of each strain, in duplicate, by deep sequencing. Strains were grown for 12 hours in colony biofilms at 1% O2, 5% CO2 prior to RNA harvest. Ribosomal and transfer RNAs were removed using the MICROBExpress kit (Life Technologies). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters. mRNA profiles of 12 hour colony biofilms were generated for P. aeruginosa strains PAO1 WT, PAO1 ?anr, clinical isolate J215, and J215 ?anr, each in duplicate, by deep sequencing using Illumina HiSeq.
2015-06-29 | E-GEOD-68534 | biostudies-arrayexpress
Project description:We found that assassin bugs from the earliest-diverging subfamily of higher Reduviidae (Peiratinae), as well as a subfamily closely related to Triatominae (Stenopodainae) have venom that is highly similar in composition to that produced by previously examined reduviids from Harpactorinae and Reduviinae. This finding suggests that venom composition has been largely stable due to purifying selection among the higher Reduviidae, which is consistent with the ancient origin of venom in the ancestors of Heteroptera 250–300 million years ago (Sunagar and Moran 2015; Walker et al. 2018a). This near homogeneity of venom composition is perhaps surprising considering that reduviid predators have evolved numerous instances of prey specialization and specialized hunting strategies that might be expected to co-evolve with venom. Possibly, further studies focussing on species with more specialized hunting strategies, or different kinds of venom bioactivities, will uncover more nuanced venom adaptations. Alternatively, it is possible that the protease-rich venoms of predatory reduviids are simply well-suited to myriad different hunting strategies. These data are consistent with other examples where venoms are surprisingly similar despite great differences in biology, for example between solitary and eusocial bees. A more detailed picture of venom evolution in Reduviidae would examine venom produced by the early-diverging Phymatine complex as well as venoms of non-reduviid cimicomorphs, prey specialists such as the arachnophagous Emesinae and the myrmecophagous Holoptilinae, and some of the many groups that employ hunting specializations, such as the use of plant resins to catch prey (Hwang and Weirauch 2012). Within Triatominae, examination of saliva produced by additional species from multiple lineages (especially those that switched to blood-feeding independently, if the subfamily is shown to be polyphyletic) and including generalists and specialists on different host taxa and species associated especially with nests and burrows will be informative. The venoms of predatory reduviids such as Zelurus spp. and Opisthacidius spp. that are most closely related to Triatominae, and share some behaviours such as habitation of bird nests by Opisthacidius spp. may also provide more information about the evolution of triatomine saliva.
2024-07-30 | PXD050854 | Pride
Project description:LFQ proteome datasets of Pseudomonas aeruginosa type strain PA14 cultured at different enviromental conditions: Exponential-, transition- and stationary(12 h and 24 h)growth phases. Biofilm (24 h and 48 h), low osmolarity conditions (control = exponential phase), iron starvation and respective control, Sub-MIC ciproflox treatment and respective control.
2018-11-20 | PXD010200 | Pride
Project description:Membrane protein and phospholipid (PL) compositions change in response to environmental cues and during infections. Covalent modification (e.g., unsaturation and cyclopropanation) and remodeling the acyl chain length of PLs is an important bacterial adaptation mechanism. However, little is known about which bacterial pathways are regulated in response to the alteration of PL composition. Here, we show that P. aeruginosa PlaF, which modulates membrane PL composition, is important for biofilm biogenesis, and we performed whole-cell quantitative proteomics of P. aeruginosa wild-type and ∆plaF biofilms to identify pathways regulated by PlaF. The results revealed profound alterations in the abundance of 14 two-component systems (TCS), including the PprA-PprB, which controls the transition to biofilm. Activation of PprA-the PprB system observed by proteomics was confirmed by mRNA quantification. Furthermore, we have observed a unique phosphorylation pattern of transcriptional regulators, transporters and metabolic enzymes, and differential production of nine proteases in ∆plaF, indicating that PlaF-mediated virulence adaptation involves complex transcriptional and post-transcriptional regulation. Moreover, proteomics revealed that the pyoverdin-mediated iron uptake pathway proteins were depleted in ∆plaF, which agrees with decreased concentrations of extracellular pyoverdine and intracellular iron in ∆plaF and is likely responsible for its prolonged lag phase due to reduced iron uptake. Conversely, the accumulation of proteins from alternative iron-uptake systems in ∆plaF suggests that PlaF may function as a switch between different iron-acquisition pathways. The observation that ∆plaF accumulates PL-acyl chain modifying enzymes and PlsX, an initiator of de novo PL synthesis, reveals novel insights into the relationship between degradation, covalent modification and biosynthesis of PLs for membrane homeostasis. Although the precise mechanism by which PlaF simultaneously affects multiple pathways remains to be elucidated, we suggest that PlaF-catalyzed degradation of PLs is a signal which is amplified by proteins of TCS, phosphorylation and proteolytic degradation systems to elicit the global adaptive response in P. aeruginosa.
2023-04-25 | PXD037737 | Pride
Project description:The opportunistic pathogen Pseudomonas aeruginosa is among the main colonizers of the lungs of cystic fibrosis (CF) patients. We have isolated and sequenced several P. aeruginosa isolates from the sputum of CF patients and used phenotypic, genomic and proteomic analyses to compare these CF derived strains with each other and with the model strain PAO1.
2015-10-14 | PXD002865 | Pride
Project description:P. aeruginosa was described to sense xenosiderophores in the extracellular environment, leading to a regulation of genes encoding the siderophore uptake proteins. Data presented here allowed to characterize the proteomic response of P. aeruginosa in presence of different xenosiderophores. PAO1 strain was grown under iron-starvation conditions with or without addition of xenosiderophores. Proteomic analyses were performed on bacterial lysates in biological triplicates.
2020-02-17 | PXD011950 | Pride
Project description:Pseudomonas aeruginosa is a major opportunistic human pathogen which employs a myriad of virulence factors. In people with cystic fibrosis (CF) P. aeruginosa frequently colonises the lungs and becomes a chronic infection that evolves to become less virulent over time, but often adapts to favour persistence in the host with alginate-producing mucoid, slow-growing, and antibiotic resistant phenotypes emerging. Cysteamine is an endogenous aminothiol which has been shown to prevent biofilm formation, reduce phenazine production, and potentiate antibiotic activity against P. aeruginosa, and has been investigated in clinical trials as an adjunct therapy for pulmonary exacerbations of CF. Here we demonstrate (for the first time in a prokaryote) that cysteamine prevents glycine utilisation by P. aeruginosa in common with reported activity blocking the glycine cleavage system in human cells. Despite the inhibition of glycine metabolism, cysteamine inhibits hydrogen cyanide (HCN) production by P. aeruginosa, implicating interference in the regulation of virulence. Cysteamine impaired chemotaxis and reductions in pyocyanin and exopolysaccharide production in cysteamine-treated P. aeruginosa and reduced toxicity of secreted factors in a Galleria mellonella model. Thus, cysteamine has additional potent anti-virulence properties targeting P. aeruginosa, further supporting its therapeutic potential in CF and other infections.
2021-08-19 | PXD027156 | Pride