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Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344.

ABSTRACT: Here, we report the whole-genome sequence and annotation of Pseudomonas kilonensis 1855-344 (previously known as P. fluorescens 1855-344). The genome contains an octopine oxidase gene cluster consistent with the ability to utilize octopine. A biosynthetic gene cluster was identified for mangotoxin and aryl-polyene using the antiSMASH server.

SUBMITTER: Eng WW

PROVIDER: S-EPMC4432341 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature

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Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344.

Eng Wilhelm Wei Han WW Gan Han Ming HM Gan Huan You HY Hudson André O AO Savka Michael A MA

Genome announcements 20150514 3

Here, we report the whole-genome sequence and annotation of Pseudomonas kilonensis 1855-344 (previously known as P. fluorescens 1855-344). The genome contains an octopine oxidase gene cluster consistent with the ability to utilize octopine. A biosynthetic gene cluster was identified for mangotoxin and aryl-polyene using the antiSMASH server. ...[more]

PMID: 25977435

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Pseudomonas kilonensis strain:1855-344

Project description:Pseudomonas kilonensis strain:1855-344 Genome sequencing and assembly

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Genome sequence of the biocontrol strain Pseudomonas fluorescens F113.

Project description:Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) that has biocontrol activity against fungal plant pathogens and is a model for rhizosphere colonization. Here, we present its complete genome sequence, which shows that besides a core genome very similar to those of other strains sequenced within this species, F113 possesses a wide array of genes encoding specialized functions for thriving in the rhizosphere and interacting with eukaryotic organisms.

| S-EPMC3294817 | biostudies-literature

Complete Genome Sequence of Biocontrol Strain Pseudomonas fluorescens LBUM223.

Project description:Pseudomonas fluorescens LBUM223 is a plant growth-promoting rhizobacterium (PGPR) with biocontrol activity against various plant pathogens. It produces the antimicrobial metabolite phenazine-1-carboxylic acid, which is involved in the biocontrol of Streptomyces scabies, the causal agent of common scab of potato. Here, we report the complete genome sequence of P. fluorescens LBUM223.

| S-EPMC4424314 | biostudies-literature

Characterization of the SOS response of Pseudomonas fluorescens strain DC454 using whole genome transcript analysis

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

Novel lectin-like bacteriocins of biocontrol strain Pseudomonas fluorescens Pf-5.

Project description:Bacteriocin LlpA, produced by Pseudomonas sp. strain BW11M1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (A. H. A. Parret, G. Schoofs, P. Proost, and R. De Mot, J. Bacteriol. 185:897-908, 2003). Biocontrol strain Pseudomonas fluorescens Pf-5 contains two llpA-like genes, named llpA1(Pf-5) and llpA2(Pf-5). Recombinant Escherichia coli cells expressing llpA1(Pf-5) or llpA2(Pf-5) acquired bacteriocin activity and secreted a 31-kDa protein cross-reacting with LlpA(BW11M1) antibodies. Antibacterial activity of the recombinant proteins was evidenced by gel overlay assays. Analysis of the antimicrobial spectrum indicated that LlpA1(Pf-5) and LlpA2(Pf-5) are able to inhibit P. fluorescens strains, as well as the related mushroom pathogen Pseudomonas tolaasii. LlpA-type bacteriocins are characterized by a domain structure consisting of tandem monocot mannose-binding lectin (MMBL) domains. Molecular phylogeny of these MMBL domains suggests that the individual MMBL domains within an LlpA protein have evolved separately toward a specific, as yet unknown, function or, alternatively, were acquired from different ancestral sources. Our observations are consistent with earlier observations, which hinted that MMBL-like bacteriocins represent a new family of antibacterial proteins, probably with a novel mode of action.

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Unusual extracellular appendages deployed by the model strain Pseudomonas fluorescens C7R12.

Project description:Pseudomonas fluorescens is considered to be a typical plant-associated saprophytic bacterium with no pathogenic potential. Indeed, some P. fluorescens strains are well-known rhizobacteria that promote plant growth by direct stimulation, by preventing the deleterious effects of pathogens, or both. Pseudomonas fluorescens C7R12 is a rhizosphere-competent strain that is effective as a biocontrol agent and promotes plant growth and arbuscular mycorrhization. This strain has been studied in detail, but no visual evidence has ever been obtained for extracellular structures potentially involved in its remarkable fitness and biocontrol performances. On transmission electron microscopy of negatively stained C7R12 cells, we observed the following appendages: multiple polar flagella, an inducible putative type three secretion system typical of phytopathogenic Pseudomonas syringae strains and densely bundled fimbria-like appendages forming a broad fractal-like dendritic network around single cells and microcolonies. The deployment of one or other of these elements on the bacterial surface depends on the composition and affinity for the water of the microenvironment. The existence, within this single strain, of machineries known to be involved in motility, chemotaxis, hypersensitive response, cellular adhesion and biofilm formation, may partly explain the strong interactions of strain C7R12 with plants and associated microflora in addition to the type three secretion system previously shown to be implied in mycorrhizae promotion.

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Draft Genome Sequence of the Phenazine-Producing Pseudomonas fluorescens Strain 2-79.

Project description:Pseudomonas fluorescens strain 2-79, a natural isolate of the rhizosphere of wheat (Triticum aestivum L.), possesses antagonistic potential toward several fungal pathogens. We report the draft genome sequence of strain 2-79, which comprises 5,674 protein-coding sequences.

| S-EPMC4384134 | biostudies-literature

Secondary metabolites help biocontrol strain Pseudomonas fluorescens CHA0 to escape protozoan grazing.

Project description:In soil ecosystems, bacteria must cope with predation activity, which is attributed mainly to protists. The development of antipredation strategies may help bacteria maintain higher populations and persist longer in the soil. We analyzed the interaction between the root-colonizing and biocontrol strain Pseudomonas fluorescens CHA0 and three different protist isolates (an amoeba, a flagellate, and a ciliate). CHA0 produces a set of antibiotics, HCN, and an exoprotease. We observed that protists cannot grow on CHA0 but can multiply on isogenic regulatory mutants that do not produce the extracellular metabolites. The in vitro responses to CHA0 cells and its exoproducts included growth inhibition, encystation, paralysis, and cell lysis. By analyzing the responses of protists to bacterial supernatants obtained from different isogenic mutants whose production of one or more exometabolites was affected and also to culture extracts with antibiotic enrichment, we observed different contributions of the phenolic antifungal compound 2,4-diacetylphloroglucinol (DAPG) and the extracellular protease AprA to CHA0 toxicity for protists and to the encystation-reactivation cycle. The grazing pressure artificially produced by a mixture of the three protists in a microcosm system resulted in reduced colonization of cucumber roots by a regulatory isogenic CHA0 mutant unable to produce toxins. These results suggest that exometabolite production in biocontrol strain CHA0 may contribute to avoidance of protist grazing and help sustain higher populations in the rhizosphere, which may be a desirable and advantageous trait for competition with other bacteria for available resources.

| S-EPMC1636139 | biostudies-literature

Cell-associated hemolysis activity in the clinical strain of Pseudomonas fluorescens MFN1032.

Project description:BACKGROUND: MFN1032 is a clinical Pseudomonas fluorescens strain able to grow at 37 degrees C. MFN1032 cells induce necrosis and apoptosis in rat glial cells at this temperature. This strain displays secretion-mediated hemolytic activity involving phospholipase C and cyclolipopeptides. Under laboratory conditions, this activity is not expressed at 37 degrees C. This activity is tightly regulated and is subject to phase variation. RESULTS: We found that MFN1032 displays a cell-associated hemolytic activity distinct from the secreted hemolytic activity. Cell-associated hemolysis was expressed at 37 degrees C and was only detected in vitro in mid log growth phase in the presence of erythrocytes. We studied the regulation of this activity in the wild-type strain and in a mutant defective in the Gac two-component pathway. GacS/GacA is a negative regulator of this activity. In contrast to the Pseudomonas fluorescens strains PfO-1 and Pf5, whose genomes have been sequenced, the MFN1032 strain has the type III secretion-like genes hrcRST belonging to the hrpU operon. We showed that disruption of this operon abolished cell-associated hemolytic activity. This activity was not detected in P.fluorescens strains carrying similar hrc genes, as for the P. fluorescens psychrotrophic strain MF37. CONCLUSIONS: To our knowledge this the first demonstration of cell-associated hemolytic activity of a clinical strain of Pseudomonas fluorescens. Moreover, this activity seems to be related to a functional hrpU operon and is independent of biosurfactant production. Precise link between a functional hrpU operon and cell-associated hemolytic activity remains to be elucidated.

| S-EPMC2871272 | biostudies-literature

Enzymes involved in vinyl acetate decomposition by Pseudomonas fluorescens PCM 2123 strain.

Project description:Esterases are widely used in food processing industry, but there is little information concerning enzymes involved in decompositions of esters contributing to pollution of environment. Vinyl acetate (an ester of vinyl alcohol and acetic acid) is a representative of volatile organic compounds (VOCs) in decomposition, of which hydrolyses and oxidoreductases are mainly involved. Their activities under periodically changing conditions of environment are essential for the removal of dangerous VOCs. Esterase and alcohol/aldehyde dehydrogenase activities were determined in crude cell extract from Pseudomonas fluorescens PMC 2123 after vinyl acetate induction. All examined enzymes exhibit their highest activity at 30-35 °C and pH 7.0-7.5. Esterase preferably hydrolyzed ester bonds with short fatty chains without plain differences for C2 or C4. Comparison of Km values for alcohol and aldehyde dehydrogenases for acetaldehyde suggested that this metabolite was preferentially oxidized than reduced. Activity of alcohol dehydrogenase reducing acetaldehyde to ethanol suggested that one mechanism of defense against the elevated concentration of toxic acetaldehyde could be its temporary reduction to ethanol. Esterase activity was inhibited by phenylmethanesulfonyl fluoride, while β-mercaptoethanol, dithiothreitol, and ethylenediaminetetraacetic acid had no inhibitor effect. From among metal ions, only Mg(2+) and Fe(2+) stimulated the cleavage of ester bond.

| S-EPMC3936133 | biostudies-literature

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