Responses of Pseudomonas aeruginosa to low oxygen
Ontology highlight
ABSTRACT:
ORGANISM(S): Pseudomonas aeruginosa
PROVIDER: GSE6741 | GEO | 2007/05/17
SECONDARY ACCESSION(S): PRJNA98977
REPOSITORIES: GEO
Similar Datasets
Project description:In order to understand how Pseudomonas aeruginosa responds to low oxygen we grew strain PAO1 with 3 different oxygen concentrations: 2%, 0.4% and 0% supplemented with nitrate as an electron acceptor. Gene expression under these conditions was compared to that of cells grown with 20% oxygen. Experiment Overall Design: Transcriptome profiles of Pseudomonas aeruginosa cells grown with 20% oxygen were compared to transcriptome profiles obtained by growing cells with 2%, 0.4% and 0% oxygen (with nitrate as the electron acceptor).
2008-06-15 | E-GEOD-6741 | biostudies-arrayexpress
Project description:The transcription factor Anr regulates the response to low oxygen in P. aeruginosa and is inhibited by oxygen. We used microarrys to compare gene expression in P. aeruginosa PAO1 wild-type with an isogenic anr mutant in order to determine which transcripts are affected by Anr. We grew P. aeruginosa cells as biofilms on CFBE cells in order to model cystic fibrosis airways infections.
2015-11-15 | GSE67006 | GEO
Project description:Chemostats have been used for decades in studying cell growth under controlled environments. Whole transcriptome sequencing by RNA-seq is a relatively new method for gene expression analysis. We utilized both tools for expression analysis of Pseudomonas aeruginosa growing slowly in synthetic cystic fibrosis medium under growth-limiting nitrate and oxygen levels. We established steady-state cultures under two divergent growth rates and found that during slower growth at a doubling time of 9.8 h, 76 known quorum genes were up-expressed while just 11 were down-expressed. Quorum-controlled genes were also more expressed in response to oxygen limitation. 21% of up-expressed genes under slow, oxygen-limited growth are quorum controlled while just 6% are up-expressed under slow, nitrate-limited growth. We found that the autoinducer for regulator RhlR, C4-HSL, is ~3.4 times higher when cells are growing slowly under oxygen limitation while the concentration of the autoinducer for LasR remained unchanged. Experiments with deletion mutants show the importance of rhlR for expression of quorum-controlled genes under slow, oxygen-limited conditions. This is an intriguing observation since P. aeruginosa is likely growing in similar environments in the cystic fibrosis lung, and lasR mutations are known to arise during chronic infection.
2016-12-01 | GSE71880 | GEO
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.
2015-06-29 | GSE68534 | GEO
Project description:Alicycliphilus denitrificans is a versatile, ubiquitous, facultative anaerobic bacterium. A. denitrificans strain BC can use chlorate, nitrate and oxygen as electron acceptor for growth. Cells display a prolonged lag-phase when transferred from nitrate to chlorate and vice versa. Furthermore, cells adapted to aerobic growth do not easily use nitrate or chlorate as electron acceptor. We further investigated these responses of strain BC by differential proteomics, transcript analysis and enzyme activity assays. In nitrate-adapted cells transferred to chlorate and vice versa, appropriate electron acceptor reduction pathways need to be activated. In oxygen-adapted cells, adaptation to the use of chlorate or nitrate is likely difficult due to the poorly active nitrate reduction pathway and low active chlorate reduction pathway. We deduce that the Nar-type nitrate reductase of strain BC also reduces chlorate, which may result in toxic levels of chlorite if cells are transferred to chlorate. Furthermore, the activities of nitrate reductase and nitrite reductase appear to be not balanced when oxygen-adapted cells a shifted to nitrate as electron acceptor, leading to the production of a toxic amount of nitrite. These data suggest that strain BC encounters metabolic challenges in environments with fluctuations in the availability of electron acceptors. Proteomic samples were prepared from Alicycliphilus denitrificans grown in the presence of different electron acceptors: chlorate, nitrate and oxygen. Proteins were separated by a short SDS gel and for each sample 4 in-gel digest slices were prepared. Peptide samples were measured by nLC LTQ-Orbitrap and the data were analysed with MaxQuant using default settings (1% FDR on peptide and protein level) and filtered extra to keep only proteins identified with at least 2 peptides and 1 unique and 1 unmodified peptide.
2013-08-12 | PXD000258 | Pride
Project description:Analysis of Pseudomonas aeruginosa transcriptomes during infection has identified a gene, PA1414 (PAO1 locus tag), that is highly expressed in various types of human infection. This gene was also found to be highly induced under low oxygen conditions, including anaerobic condition as well as static cultivation. Here we compared the proteomes of P. aeruginosa PA14 and the PA1414 mutant during anaerobic cultivation in Brain Heart Infusion (BHI) broth supplemented with 50 mM nitrate to identify the pathways regulated by PA1414.
2022-04-04 | MSV000089197 | MassIVE
Project description:Analysis of Pseudomonas aeruginosa transcriptomes during infection has identified a gene, PA1414 (PAO1 locus tag), that is highly expressed in various types of human infection. This gene was also found to be highly induced under low oxygen conditions, including anaerobic condition as well as static cultivation. Here we compared the proteomes of P. aeruginosa PA14 and the PA1414 mutant during static cultivation in Brain Heart Infusion (BHI) broth supplemented with 50 mM nitrate to identify the pathways regulated by PA1414.
2022-04-04 | MSV000089196 | MassIVE
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 performed high-time-resolution (HTR) transcriptome analyses of Pseudomonas aeruginosa PAO1 (PA) in a continuous cultivation system during the transition from high oxygen tension to low oxygen tension (HLOT) and the reversed transition from low to high oxygen tension (LHOT). From those genes responsive to both transient conditions, we identified 85 essential oxygen-availability responsive genes (EORGs), including the expected ones (arcDABC) encoding enzymes for arginine fermentation. We then predicted a highly accurate regulatory network for the EORGs of PA by integrating information from binding motif searching, literature and inverted HTR datasets. These results not only reveal stringent EORGs of PA and their transcription regulatory network, but also highlight that achieving a high accuracy of the inferred regulatory network might be only feasible for the apparently affected regulators under the given conditions but not for all the expressed regulators in a genome scale. Pseudomonas aeruginosa PAO1 (PA) from a continuous cultivation system during two inverted oxygen-availability transitions were used for RNA extraction and hybridization on Affymetrix P. aeruginosa Genome Array . Our aim is to identify essential oxygen-availability responsive genes and to infer an accurate oxygen-responsive regulatory network. In total, 14 samples were harvested at time points 0, 5, 10, 15, 20, 25, 30, 35, 40, 50, 60, 70, 80 and 90 min after switching from aerobic to microaerobic condition. After reaching a steady state (after about another four bioreactor volume exchange) under these conditions, the culture was shifted from microaerobic back to fully aerobic condition (pO2 set point value from 0.5% to 100%). A similar set of samples were taken during the reversed transition with the same time intervals.
2013-12-10 | E-GEOD-52445 | biostudies-arrayexpress
Project description:We performed high-time-resolution (HTR) transcriptome analyses of Pseudomonas aeruginosa PAO1 (PA) in a continuous cultivation system during the transition from high oxygen tension to low oxygen tension (HLOT) and the reversed transition from low to high oxygen tension (LHOT). From those genes responsive to both transient conditions, we identified 85 essential oxygen-availability responsive genes (EORGs), including the expected ones (arcDABC) encoding enzymes for arginine fermentation. We then predicted a highly accurate regulatory network for the EORGs of PA by integrating information from binding motif searching, literature and inverted HTR datasets. These results not only reveal stringent EORGs of PA and their transcription regulatory network, but also highlight that achieving a high accuracy of the inferred regulatory network might be only feasible for the apparently affected regulators under the given conditions but not for all the expressed regulators in a genome scale.
2013-12-10 | GSE52445 | GEO