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Expression data on F0 and F1 strains of Pseudomonas aeruginosa

ABSTRACT: In our study, we seek to understand the differences in growth physiology between wild type P. aeruginosa PAO1 (F0 strain) and its PB1-phage resistant derivative (F1 strain).

ORGANISM(S): Pseudomonas aeruginosa

PROVIDER: GSE75654 | GEO | 2015/12/04

SECONDARY ACCESSION(S): PRJNA304980

REPOSITORIES: GEO

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Expression data on F0 and F1 strains of Pseudomonas aeruginosa

Project description:In our study, we seek to understand the differences in growth physiology between wild type P. aeruginosa PAO1 (F0 strain) and its PB1-phage resistant derivative (F1 strain). F0 and F1 cells were harvested at mid-log for RNA extraction for hybridization to Affymetrix GeneChip P. aeruginosa genome array. A total of 4 biological replicates (4 F0 and 4 F1 samples were used).

2015-12-04 | E-GEOD-75654 | biostudies-arrayexpress

Pseudomonas aeruginosa lasR QS network promotes phage infection by regulating the biosynthesis of LPS and type IV pili by regulating the biosynthesis of LPS and type IV pili

Project description:Purpose: The purpose of this study was to investigate the effect of quorum sensing on phage infection. Methods: We constructed the lasR gene knockout strain of Pseudomonas aeruginosa PAO1 and performed transcriptome sequencing.

2024-04-08 | GSE246747 | GEO

RNA-seq profiling of cultured B16 F0, F1 and F10 cells

Project description:To contrast and compare the transcriptomes of poorly metastatic B16 sub-clones F0 and F1 to the highly metastatic sub-clone F10.

2021-08-31 | GSE182970 | GEO

The PA3040-PA3042 operon influences biofilm formation and bacteriophage survival in Pseudomonas aeruginosa

Project description:Bacteriophages (hereafter “phages”) are ubiquitous predators of bacteria in the natural world, but interest is growing in their development into antibacterial therapy as complement or replacement for antibiotics. However, bacteria have evolved a huge variety of anti-phage defense systems allowing them to resist phage lysis to a greater or lesser extent, and in pathogenic bacteria these inevitably impact phage therapy outcomes. In addition to dedicated phage defense systems, some aspects of the general stress response also impact phage susceptibility, but the details of this are not well known. In order to elucidate these factors in the opportunistic pathogen Pseudomonas aeruginosa, we used the laboratory-conditioned strain PAO1 as host for phage infection experiments as it is naturally poor in dedicated phage defense systems. Screening by transposon insertion sequencing indicated that the uncharacterized operon PA3040-PA3042 was potentially associated with resistance to lytic phages. However, we found that its primary role appeared to be in regulating biofilm formation. Its expression was highly growth-phase dependent and responsive to phage infection and cell envelope stress.

2023-10-30 | GSE246284 | GEO

Interphage competition and biofilms reduce the lytic effect of two phages against Pseudomonas aeruginosa

Project description:Clinical case studies have reported that the combined use of specific lytic phage(s) and antibiotics reduces the severity of difficult-to-treat Pseudomonas aeruginosa infections in many patients. In vitro methods that attempt to reproduce specific pathophysiological conditions can provide a reliable assessment of the antibacterial effects of phages. Here, we measured bacterial killing kinetics and individual phage replication in different growth phases, including biofilms, elucidating factors influencing the efficacy of two phages against the laboratory strain P. aeruginosa PAO1. While two-phage combination treatment effectively eliminated P. aeruginosa in routine broth and in infected human lung cell cultures, the emergence of phage-resistant variants occurred under both conditions. Phage combination displayed initial inhibition of biofilm dispersal, but sustained control was achieved only with a combination of phages and meropenem. In contrast, surface-attached biofilm exhibited tolerance to phage and/or meropenem, suggesting a spatiotemporal variation in antibacterial effect. Moreover, the phage with the shorter lysis time killed P. aeruginosa more rapidly, selecting a specific nucleotide polymorphism that likely conferred a competitive disadvantage and cross resistance to the second phage of the combination. These findings highlight biofilm developmental phase, inter-phage competition and phage resistance as factors limiting the in vitro efficacy of a phage combination. However, their precise impact on the outcome of phage therapy remains uncertain, necessitating validation through phage efficacy trials in order to establish clearer correlations between laboratory assessments and clinical results.

2024-07-17 | GSE271537 | GEO

High-throughput sequencing analysis identify miRNAs in 7dpf F1-zebrafish under Î²-diketone antibiotics exposure to F0-zebrafish

Project description:Small RNA high-throughput sequencing technology was used to characterize the miRNAs in F1-zebrafish after 90-day Î²-diketoneÂ antibiotic (DKA) exposure to F0-zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7-dpf F1-zebrafish were constructed. In total, 10,117,347, 9,818,830 and 12,049,949 raw reads were acquired, respectively, under the different DKA-exposure treatments (0, 6.25 mg/L and 12.5mg/L) from the three miRNAs libraries by Illumina sequencing. Low-quality reads were removed, which included 5' contaminants, those missing the 3' primer or insert tag, sequences with a poly A tail, and those shorter than 17 nt and longer than 25 nt. As a result, 8,141,146 (representing 312,735 unique sequences; control), 8,687,210 (representing 251,508 unique sequences; 6.25 mg/L), and 10,569,566 (representing 441,938 unique sequences; 12.5 mg/L) valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar, and the unique sRNA reads were mainly distributed in the 20-24 nt range, among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads, respectively. The 22-nt sRNAs were the most abundant, with the length distribution of counts of sequ-seqs and unique miRNAs displaying a normal distribution. Sample 1: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7-dpf F1-zebrafish after 90-day DKA exposure to F0-zebrafish at 12.5 mg/L.

2016-07-30 | E-GEOD-85004 | biostudies-arrayexpress

P. aeruginosa PAO1 PA2663 mutant vs. wild type strain

Project description:P. aeruginosa PAO1 wild type and PA2663 mutant strains expression in biofilm cells relative to P. aeruginosa PAO1 wild type strain expression in biofilm cells. All samples cultured in LB with glass wool Keywords: Biofilm

2008-02-22 | GSE9255 | GEO

The repressor C protein, Pf4r, controls superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 filamentous phage and regulates host gene expression

Project description:It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homolog of the P2 phage repressor C. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show that repressor C (Pf4r) is the minimal factor for immunity against reinfection by Pf4 possibly through Pf4r binding to its putative promoter region, and that Pf4r also functions as a transcriptional regulator for expression of host genes. A binding motif for Pf4r was also identified. In wild type P. aeruginosa and Pfr4 complemented Pf4 deficient mutant strains, virulence factor related genes including phenazine and type VI secretion system effectors were upregulated, potentially explaining the reduced virulence of Pf4-deficient P. aeruginosa PAO1. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by MALS analysis where the Pf4r* protein only shows monomer formation. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.

2021-01-31 | GSE154459 | GEO

Pseudomonas aeruginosa

Project description:Expression data from PAO1 and its creBC derivative mutant (PAOΔcreBC)

| PRJNA253371 | ENA

PAO1 strain exposure to thiazolidinedione (TZD) derivative

Project description:The purpose of this study was to define the TZD effect in Pseudomonas aeruginosa. Transcriptional profiling of Pseudomonas aeruginosa wild-type strain,reference strain PAO1, as control Vs. PAO1 strain exposed to a final 0.02mM of TZD derivative ((z)-5-octylidenethiazolidine-2,4-dione).

2014-12-03 | E-MTAB-3144 | biostudies-arrayexpress

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