Pseudomonas fluorescens strain:TR3
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA344671 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR4339877_1.fastq.gz | Fastqsanger.gz | |||
| SRR4339877_2.fastq.gz | Fastqsanger.gz |
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Project description:DNA microarray technology was used to survey changes in gene expression in P. fluorescens after mitomycin C (MMC) treatment. As expected, genes associated with the SOS response were upregulated. These include genes coding the recombination involved protein RecA, DNA repair protein RecN, excinuclease ABC subunit A UvrA, and the LexA repressor protein. The expression profile was similar to that which had been shown for E. coli after MMC treatment. Interestingly, expression of 33 bacteriophage-like genes was upregulated two hours after MMC treatment. Those genes are clustered in the chromosome. This result suggests that MMC may induce a prophage resident in the P. fluorescens genome. However, no phage particles were detected in a preparation of P. fluorescens strain DC454 that had been treated with MMC using transmission electron microscopy, and the same preparation failed to produce phage plaques on lawns of any of 10 different Pseudomonas strains tested, suggesting that the 33 bacteriophage-like gene cluster represents a defective prophage. Keywords: time course, stress response
2006-12-11 | GSE5653 | GEO
Project description:The goal of this study was to evaluate the molecular mechanisms by which Brachypodium distachyon grown with and without Pseudomonas fluorescens (P. fluorescens) strain SBW25 respond to Fe deprivation. Fe deprivation induced Brachypodium secretion of phytosiderophores and reduced biomass production while inoculation with P. fluorescens resulted in alterations of extracellular metabolite abundances. Results provide insight into the role of iron in interactions between a host plant and root associated bacteria.
2020-09-22 | GSE158273 | GEO
Project description:Whole genome gene expression study comparing Pseudomonas fluorescens Pf0-1 (Wt) relative to a delta-pst mutant (deletion of the pstSCAB operon) that consitutively expresses the Pho regulon Mutants used in this study are further described in Monds, R.D. Newell, P.D., Gross, R.H., O'Toole, G.A. (2007) Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA. Mol. Microbiol. 63(3): 656-679 A four chip study using total RNA recovered from two independent wild-type cultures of wild type strain Pseudomonas fluorescens Pf0-1 and two independent cultures of Pseudomonas fluorescens Pf0-1 delta pst mutant (deletion of the pstSCAB operon). Each chip measures the expression level of 5733 open reading frames (ORFs) genes from Pseudomonas fluorescens Pf0-1 (Refseq: NC_007492) with twenty 60-mer postive match (PM) probes per gene, with three-fold technical redundancy.
2011-07-13 | E-GEOD-30681 | biostudies-arrayexpress
Project description:Hfq is a transcriptional and translational pleiotropic regulator in several bacteria. RNA-Seq, Ribo-Seq and Proteomic analyses were carried out in the wild-type and a hfq deletion strain of Pseudomonas fluorescens SBW25 with the intention to separate the influence of Hfq on the transcript stability and translation. This submission relates to the RNA-Seq data only. RNA was extracted from two replicate cultures each of SBW25-WT and SBW25-Δhfq strains and, after removal of ribosomal RNA, subjected to RNA-Seq in an Illumina NextSeq500 machine. The resulting sequence data was analysed by mapping to the reference sequence of Pseudomonas fluorescens SBW25 as available in the Genbank accession NC_012660.
2019-02-07 | E-MTAB-5396 | biostudies-arrayexpress
Project description:Pseudomonas species are ubiquitous in plant-associated environments and produce an array of volatiles, enzymes and antimicrobials. The biosynthesis of many metabolites is regulated by the GacS/GacA two-component regulatory system. Transcriptome analysis of Pseudomonas fluorescens SBW25 revealed that 702 genes were differentially regulated (fold change>4, P<0.0001) in a gacS::Tn5 mutant, with 300 and 402 genes up- and down-regulated, respectively. Genes that were significantly down-regulated are involved in viscosin biosynthesis (viscABC), protease production (aprA), motility, biofilm formation, and secretory systems. Genes that were significantly up-regulated are involved in siderophore biosynthesis and oxidative stress. In contrast to previous studies with gac-mutants of other Pseudomonas species/strains, the gacS mutant of SBW25 inhibited growth of oomycete, fungal and bacterial pathogens significantly more than parental strain SBW25. A potential candidate for this enhanced antimicrobial activity was a large nonribosomal peptide synthetase (NRPS) gene cluster predicted to encode for an 8-amino-acid ornicorrugatin-like peptide. Site-directed mutagenesis of an NRPS gene in this cluster, however, did not lead to a reduction in the antimicrobial activity of the gacS mutant. Collectively these results indicate that a mutation in the GacS/GacA regulatory system causes major transcriptional changes in P. fluorescens SBW25 and significantly enhances its antimicrobial activities by yet unknown mechanisms. This expression study used total RNA recovered from four separate wild-type cultures of Pseudomonas fluorescens SBW25 and four separate cultures of the gacS mutant. Expression design was based on the updated genome sequence of Pseudomonas fluorescens SBW25, NC_012660.1 and associated plasmid pQBR0476 with nineteen 60-mer probe per gene. Each probe is replicated 3 times. The design includes random GC and other control probes.
2013-06-17 | E-GEOD-43443 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE29319: Iron-starvation effect on transcriptome of Pseudomonas fluorescens Pf-5: iron(II) chloride GSE29320: Iron-starvation effect on transcriptome of Pseudomonas fluorescens Pf-5: iron(III) chloride Refer to individual Series
2011-05-16 | E-GEOD-29322 | biostudies-arrayexpress
Project description:Whole genome gene expression study comparing Pseudomonas fluorescens Pf0-1 (Wt) relative to a delta-pst mutant (deletion of the pstSCAB operon) that consitutively expresses the Pho regulon Mutants used in this study are further described in Monds, R.D. Newell, P.D., Gross, R.H., O'Toole, G.A. (2007) Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0-1 biofilm formation by controlling secretion of the adhesin LapA. Mol. Microbiol. 63(3): 656-679
2011-07-14 | GSE30681 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE33907: Tannic acid (20 µg/ mL) treatment effect on transcriptome of Pseudomonas fluorescens Pf-5 GSE33908: Tannic acid (160 µg/ mL) treatment effect on transcriptome of Pseudomonas fluorescens Pf-5 Refer to individual Series
2011-11-24 | E-GEOD-33909 | biostudies-arrayexpress
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