Pseudomonas aeruginosa strain:LMG 1272
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA552675 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| VIYL01.dat.gz | Other | |||
| VIYL01.fasta.gz | Fasta.gz | |||
| VIYL01.master.dat | Other | |||
| SRR10198149_1.fastq.gz | Fastqsanger.gz |
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Project description:Pseudomonas aeruginosa is an opportunistic pathogen which causes acute and chronic infections that are difficult to treat. Comparative genomic analysis has showed a great genome diversity among P. aeruginosa clinical strains and revealed important regulatory traits during chronic adaptation. While current investigation of epigenetics of P. aeruginosa is still lacking, understanding the epigenetic regulation may provide biomarkers for diagnosis and reveal important regulatory mechanisms. The present study focused on characterization of DNA methyltransferases (MTases) in a chronically adapted P. aeruginosa clinical strain TBCF10839. Single-molecule real-time sequencing (SMRT-seq) was used to characterize the methylome of TBCF. RCCANNNNNNNTGAR and TRGANNNNNNTGC were identified as target motifs of DNA MTases, M.PaeTBCFI and M.PaeTBCFII, respectively.
2023-07-22 | GSE209530 | GEO
Project description:This study addresses the impact of zinc limitation on the opportunistic human pathogen, Pseudomonas aeruginosa. Zinc limitation was assessed in the P. aeruginosa PAO1 strain using an isogenic deletion mutant lacking the periplasmic, zinc solute-binding protein, znuA (PA5498). ZnuA delivers bound zinc to its cognate ABC transporter, ZnuBC, for import into the cytoplasm. Our transcriptional analyses revealed P. aeruginosa to possess a multitude of zinc acquisition mechanisms, each of which were highly up-regulated in the zinc-deficient znuA mutant strain. P. aeruginosa also utilized zinc-independent paralogues of zinc-dependent genes to maintain cellular function under zinc limitation. Together, these data reveal the complex transcriptional response and versatility of P. aeruginosa to zinc depletion.
2017-01-01 | GSE60177 | GEO
Project description:Background: Pantoea ananatis LMG 2665T synthesizes and utilizes acyl homoserine lactones (AHLs) for signaling. In this strain, short chain AHLs (C4 to C8) are produced by the EanI/R quorum sensing (QS) system that is involved in pathogenicity and biofilm formation. The complete set of genes regulated by the EanI/R system in P. ananatis LMG 2665T is still not fully known. In the present study, RNA-seq was used to analyze the transcriptome profiles controlled by the EanI/R system in this strain by comparing the wild type strain and its QS mutant 2665T ean∆I/R during lag and log stages. The RNA seq data was validated by RT qPCR. Results: The results showed that the EanI/R regulon in P. ananatis LMG 2665T comprised 144 genes, constituting 3.3% of the whole transcriptome under the experimental conditions in this study. The majority of genes regulated by the EanI/R system included genes for flagella assembly, bacterial chemotaxis, pyruvate metabolism, two component system, metabolic pathways, microbial metabolism and biosynthesis of secondary metabolites. Conclusions: This is the first study to identify the EanI/R QS regulon in P. ananatis LMG 2665T. Functional analysis of genes regulated the EanI/R system in LMG 2665T could help unveil genes that play a vital role in pathogenesis and survival strategies of this pathogen.
2018-10-31 | GSE87207 | GEO
Project description:Analysis of a SigX knockout mutant of Pseudomonas aeruginosa H103 strain in minimal medium with glucose as carbon source (M9G). SigX, one of the 19 extra-cytoplasmic function sigma factors of P. aeruginosa, was only known to be involved in transcription of the gene encoding the major outer membrane protein OprF in Pseudomonas aeruginosa. Deletion of the ECF sigma factor sigX gene provide insights into the SigX role in several virulence and biofilm- related phenotypes in Pseudomonas aeruginosa.
2014-01-01 | GSE51076 | GEO
Project description:We compared gene expression in wild-type P. aeruginosa strain CF18 relative to P. aeruginosa CF18 gacA mutant.
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Project description:Analysis of a SigX knockout mutant of Pseudomonas aeruginosa H103 strain in LB.
2018-12-01 | GSE117438 | GEO
Project description:We have isolated and characterized several bacteriophages infecting Pseudomonas aeruginosa distantly related to Felix O1 virus and proposed they form a new subfamily named Felixounavirinae. The infectious cycle of bacteriophages belonging to this subfamily has not been studied yet in terms of gene expression. The present study reports the RNA-Seq analysis of bacteriophage PAK_P3 infecting PAK strain of P. aeruginosa. RNA profile of Host and Phage at 0min, 3.5min and 13 min after infection of Pseudomonas aeruginosa PAK strain with the Pseudomonas phage PAK P3. Three biological replicates for each time point.
2016-07-20 | E-GEOD-76513 | biostudies-arrayexpress
Project description:The transcriptome of two different Pseudomonas aeruginosa mutant strains were compared to the Pseudomonas aeruginosa wild type strain in the stationary growth phase
2010-04-24 | E-MEXP-2606 | biostudies-arrayexpress
Project description:Representatives of two families of bacterial Par proteins, ParA and ParB, are encoded by the majority of bacterial chromosomes in the close vicinity of oriC. ParA(Soj) and ParB(Spo0J) proteins of Pseudomonas aeruginosa are both important for optimal growth, nucleoids segregation, cell division and different types of motility. Comparative transcriptome analysis of parAnull, parBnull mutants versus parental PAO1161 strain of P. aeruginosa demonstrated global changes in genes expression pattern in logarithmic phase of planktonic cultures grown on rich medium. The set of genes that were similarly regulated in both mutant strains as compared to the wild-type strain as well as two sets of genes uniquely affected in the particular mutant were defined suggesting that ParA and ParB may act in common and independently. In general, many genes involved in cell division, DNA and RNA processing and metabolic processes were down-regulated in mutant cells, in contrast genes which products play a role in adaptation, protection, motility, cell-to-cell signaling as well as signal transduction increased their expression in par mutant cells. Besides their role in chromosome segregation, ParA and ParB seem to have the potential to regulate genes transcription. The altered expression of a large number of genes encoding known or predicted transcriptional regulators and genes coding for products involved in c-di-GMP signalling, suggests that the part of observed global changes in genes expression pattern in parAnull and parBnull mutants might be the effect of indirect regulation mediated by regulatory genes under ParA and ParB control. The extended regulatory network provides the mechanism to modulate genes expression in response to the stage of the chromosome segregation process and cell cycle. Pseudomonas aeruginosa PAO1161 (leu, r-, RifR), derivative of PAO1, as a control (reference) strain, Pseudomonas aeruginosa PAO1161 parA1-40::smh (parAnull) and Pseudomonas aeruginosa PAO1161 parB1-18::TcR (parBnull) disruption mutant strains were used in the experiments. Three independent biological replicates of total RNA were isolated for each strain from logarithmic (Log) phase of planktonic culture grown on rich medium (L broth) at 37oC. In total, nine samples of RNA were prepared.
2014-02-12 | E-GEOD-47031 | biostudies-arrayexpress
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. Keywords: Comparison of transcriptome profiles
2007-05-17 | GSE6741 | GEO