GNPS - Large Pseudomonas UK Collection
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Bruker micrOTOF II
ORGANISM(S): Pseudomonas Fluorescens
SUBMITTER: Tim Maucline, Jacob Malone
PROVIDER: MSV000078803 | GNPS | Fri Aug 08 14:23:00 BST 2014
REPOSITORIES: GNPS
Similar Datasets
Project description:Pseudomonas fluorescens SBW25 cultures were inoculated into the rhizospheres of barley seedlings of the Chevallier and Tipple varieties growing in axenic cultures. Bacterial cells were collected from the rhizosphere one and five days after inculation and RNA extracted from them. Culture used for inoculation (but not exposed to the rhizospheres) were used as control. The aim of the experiment was to determine the changes in gene expression of P. fluorescens SBW25 upon exposure to barley rhizosphere and also to determine if the rhizospehres of the two varieties of Barley had different effects on gene expression of P. fluorescens SBW25.
2023-05-15 | E-MTAB-12918 | biostudies-arrayexpress
Project description:Translational regulation plays a critical role in controlling the environmental responses of diverse bacterial species. In addition to existing, well-established regulatory pathways, the alteration of ribosome function by specific posttranslational modification represents a potential further mechanism for translational control. Although numerous ribosomal proteins undergo diverse posttranslational modifications, in most cases the functional and physiological significance of these changes remains unclear. The datasets presented here support our discovery that the widespread ribosomal modification protein RimK functions as a previously uncharacterized global controller of bacterial mRNA translation. RimK modification of the ribosomal protein RpsF changes both the stability and function of the bacterial ribosome and alters the composition of the bacterial proteome. In addition to multiple ribosomal proteins, rimK deletion in the biocontrol bacterium Pseudomonas fluorescens leads to significantly reduced levels of the important translational regulators Hfq and RsmE. This in turn leads to increased production of ABC transporters, stress response proteins and non-ribosomal peptide synthetases. Deletion of rimK compromises wheat rhizosphere colonization by P. fluorescens and significantly reduces virulence in the phytopathogen Pseudomonas syringae. Critically, the expression of P. fluorescens rimK is not constitutive, but varies throughout wheat rhizosphere colonisation, peaking during initial niche colonisation and declining in the established rhizosphere. Differential modification of the ribosome through temporal control of RimK expression represents a novel regulatory mechanism by which Pseudomonas fine-tunes its proteome to appropriately respond to the surrounding environment.
2016-02-17 | PXD001371 | Pride
Project description:Translational regulation plays a critical role in controlling the environmental responses of diverse bacterial species. In addition to existing, well-established regulatory pathways, the alteration of ribosome function by specific posttranslational modification represents a potential further mechanism for translational control. Although numerous ribosomal proteins undergo diverse posttranslational modifications, in most cases the functional and physiological significance of these changes remains unclear. The datasets presented here support our discovery that the widespread ribosomal modification protein RimK functions as a previously uncharacterized global controller of bacterial mRNA translation. RimK modification of the ribosomal protein RpsF changes both the stability and function of the bacterial ribosome and alters the composition of the bacterial proteome. In addition to multiple ribosomal proteins, rimK deletion in the biocontrol bacterium Pseudomonas fluorescens leads to significantly reduced levels of the important translational regulators Hfq and RsmE. This in turn leads to increased production of ABC transporters, stress response proteins and non-ribosomal peptide synthetases. Deletion of rimK compromises wheat rhizosphere colonization by P. fluorescens and significantly reduces virulence in the phytopathogen Pseudomonas syringae. Critically, the expression of P. fluorescens rimK is not constitutive, but varies throughout wheat rhizosphere colonisation, peaking during initial niche colonisation and declining in the established rhizosphere. Differential modification of the ribosome through temporal control of RimK expression represents a novel regulatory mechanism by which Pseudomonas fine-tunes its proteome to appropriately respond to the surrounding environment.
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Project description:Extracts from 370 Pseudomonas fluorescens isolates from wheat from the United Kingdom.
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Project description:The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescens Pf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA aptamers with specificity for pyoverdine over other siderophores. Two DNA aptamers were isolated, and their features compared. The aptamers were applied to a nanoporous aluminum oxide biosensor and demonstrated to successfully detect PYO-Pf5. This sensor provides a future opportunity to track the locations around plant roots of P. protegens and to monitor PYO-Pf5 production and movement through the soil.
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2011-05-16 | E-GEOD-29322 | biostudies-arrayexpress
Project description:Gene expression patterns of the plant colonizing bacterium,Pseudomonas putida KT2440 were evaluated as a function of growth in the Arabidopsis thaliana rhizosphere. Gene expression in rhizosphere grown P. putida cells was compared to gene expression in non-rhizosphere grown cells. Keywords: Gene expression
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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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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.
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