Pseudomonas aeruginosa strain:L6-1
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ABSTRACT:
PROVIDER: PRJNA305457 | ENA |
REPOSITORIES: ENA
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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:Pseudomonas aeruginosa (P. aeruginosa) lung infection is a significant cause of mortality in patients with cystic fibrosis (CF). Most CF patients acquire unique P. aeruginosa strains from the environment; however clonal strains have been identified in CF communities in several countries. Two clonal strains infect 10% to 40% of patients in three CF clinics in mainland eastern Australia. The expression profiles of four planktonically-grown isolates of one Australian clonal strain (AES-2), and four non–clonal CF P. aeruginosa isolates were compared to each other and to the reference strain PAO1 using the Affymetrix P. aeruginosa PAO1 genome array, to gain insight into properties mediating the enhanced infectivity of AES-1. The isolates were subsequently grown as 3-day old biofilms and similarly extracted for RNA and compared as above. Data analysis was carried out using BIOCONDUCTOR software. Keywords: Comparative strain hybridization
2009-02-05 | GSE10304 | GEO
Project description:Lentimicrobium sp. L6 strain:L6 Genome sequencing and assembly
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Project description:To gain insights into the mechanisms by which RC301 compensates for the deficiency in the NPR-1 controlled immune and behavioral responses of strain DA650, we determine the whole-genome expression profile of these two strains upon exposure to Pseudomonas aeruginosa strain PA14
2017-06-10 | GSE86431 | 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.
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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:Chromosome segregation in Pseudomonas aeruginosa is assisted by the tripartite ParAB-parS system, composed of an ATPase (ParA), a DNA-binding protein (ParB), and its target parS sequence(s). ParB forms a nucleoprotein complex around four parSs (parS1-parS4), which is positioned within the cell by ParA. Remarkably, ParB of P. aeruginosa binds to multiple heptanucleotides (half-parSs) scattered in the genome. In this work we analysed the transcriptome of P. aeruginosa with mutated 25 half-parSs forming the strongest ParB ChIP-seq peaks. Inactivation of ParB binding to even a small fraction of these sites modulated the gene expression, however this effect is most likely indirect. Overall this work suggests complex relation between ParB binding to genome and P. aeruginosa transcriptome.
2023-08-03 | GSE233235 | GEO
Project description:We identified PhaF as an RNA binding protein in Pseudomonas aeruginosa. In order to identify the different target transcripts of PhaF, we carried out the CLIP (Crosslinking and immunoprecipitation) and CLAP-Seq (Covalent linkage affinity purification) approaches, which utilizes UV irradiation to crosslink PhaF with the transcripts that are in close vicinity to it. For CLIP-Seq experiments, we used the Pseudomonas aeruginosa PAO1 strain along with a derivative of PAO1 that harbors a C-terminal VSVG tag on PhaF. In order to determine the importance of the C-terminal domain (CTD) of PhaF on RNA binding, we used PAO1ΔphaF strains carrying plasmids that express a C-terminal VSVG tagged version of PhaF-CTD (pPhaF-CTD-V), along with a control strain that carries the same plasmid (pPhaF-CTD) but without the VSVG tag. For CLAP-Seq experiments, we used the Pseudomonas aeruginosa PAO1 strain along with a derivative of PAO1 that harbors a C-terminal Halo tag on PhaF. All the strains were subjected to UV irradiation, lysed, immunoprecipitated using either anti-VSVG-antibody coated beads or Magne Halo tagged beads. Following immunoprecipitation, the RNAs were purified. We also purified Total (Tot) RNA (samples collected before immunoprecipitation) from the PAO1 strains harboring the C-terminal VSVG tag on PhaF. The purified RNA samples were converted to cDNA libraries, which were subsequently sequenced using the Illumina NextSeq. The sequences were mapped to the genome to identify the target transcripts. In a separate series of experiments we also carried out RNA-Seq to identify the genes that are differentially regulated using Pseudomonas aeruginosa PAO1 and PAO1ΔphaF strains. The isolated RNA was sent to SeqCenter (Pittsburgh, PA) and the sequences obtained were mapped to the genome and DESeq analysis was performed.
2026-01-12 | GSE298077 | GEO