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Pseudomonas putida

ABSTRACT: Common environmental bacterium

PROVIDER: PRJNA12326 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
		Other
	KT.raw.indel.vcf.csi	Raw
	KT.raw.indel.vcf.gz	Vcf
	KT.raw.snp.vcf.csi	Raw

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Transcriptome of Pseudomonas putida KT2440 in response to selenite

Project description:The bacterium Pseudomonas putida KT2440 has the ability to reduce selenite forming nanoparticles of elemental selenium. This is the transcriptome of the organism when cultured in the presence of selenite.

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Expression data from Pseudomonas putida KT2440

Project description:In this study we exploited next-generation Illumina sequencing technology (Wang et al., 2009) to refine the current annotation of the KT2440 genome. Transcriptome sequencing data were queried for yet undescribed small RNAs and ORFs and employed to validate predicted operons and gene coordinates. Expression profiles were measured at 10°C and 30°C to cover the physiologic temperature profile of this mesophilic bacterium. Moreover we compared the sensitivity and specificity of transcriptome data by taking the same RNA preparations for cDNA sequencing and hybridization of Progenika and Affymetrix microarrays. This SuperSeries is composed of the SubSeries listed below.

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Evaluation of Pseudomonas putida KT2440 gene expression in the Arabidopsis thaliana rhizosphere

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

2008-01-11 | GSE9005 | GEO

Pseudomonas putida expression profiles at different stress conditions

Project description:The metabolically versatile Pseudomonas putida strain KT2440 is the first Gram-negative soil bacterium certified as a biosafety strain and is being used for applications in agriculture, biotechnology and bioremediation. P. putida has to cope in its niche with numerous abiotic stresses. The stress response to 4°C, pH 4.5, 0.8 M urea or 45 mM sodium benzoate, respectively, was analyzed by the global mRNA expression profile and screening for stress-intolerant Tn5 transposon mutants. In total we identified 49 gene regions to be differentially expressed and 32 genes in 22 operons to be indispensable for growth during exposure to one or the other abiotic stresses. We propose that stress is sensed by the outer membrane proteins OmlA and FepA and the inner membrane constituents PtsP, PhoPQ and CbrAB. The metabolic response is regulated by the cyo operon, the RelA/SpoT modulon, PcnB and VacB that control mRNA stability and BipA that exerts transcript-specific translational control. The adaptation of the membrane barrier, the uptake of phosphate, the maintenance of intracellular pH and redox status and the translational control of metabolism are the indispensable key mechanisms of the P. putida stress response. Keywords: functional genomics

2006-07-27 | GSE4048 | GEO

Transcription profiling of Pseudomonas putida in the rhizosphere of corn

Project description:It has been performed a genome-wide analysis of gene expression of the root-colonizing bacterium Pseudomonas putida KT2440 in the rhizosphere of corn (Zea mays var. Girona. To identify reliable rhizosphere differentially expressed genes, rhizosphere populations of P. putida bacteria cells were compared with three alternative controls: i) planktonic cells growing exponentially in rich medium (LB), ii) planktonic cells in stationary phase in LB, and iii) sessile populations established in sand microcosms, under the same conditions used to grow inoculated corn plants.

2007-09-02 | E-MEXP-949 | biostudies-arrayexpress

The glycolytic and gluconeogenic transcriptome of Pseudomonas putida KT2440

Project description:Pseudomonas putida KT2440 is a metabolically versatile soil bacterium useful both as a model biodegradative organism and as a host of catalytic activities of biotechnological interest. In this report, we present the high-resolution transcriptome of P. putida grown in different carbon sources as revealed by deep sequencing of the corresponding RNA pools. Examination of the data from growth on glycolytic (glucose, fructose) and gluconeogenic (succinate or glycerol) substrates revealed that > 20% of the P. putida genome is differentially expressed depending on the ensuing metabolic regime. Changes affected not only metabolic genes but also a suite of global regulators, e.g. the rpoS sigma subunit of RNAP, various cold-shock proteins and the three HU histone-like proteins. Specifically, the genes encoding HU subunit variants hupA, hupB and hupN drastically altered their expression levels (and thus their ability to form heterodimeric combinations) under the different growth conditions. Furthermore, we found that the two small RNAs crcZ and crcY, known to inhibit the Crc protein that mediates catabolite repression in P. putida, were both down-regulated by glucose.

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Project description:To undestand the mechanism involved in abitoic stress tolerance of P. Putida (NBAII-RPF 9) the bacterium was grown in liquid LB media overnight and further subjected to saline shock of (1M NaCl) for one hour seperately. The cultures were pelleted with centrifuged for total RNA. The RNA was hybridised in 8X15K Agilent array and image analysis carried out with Agilent Microarray scanner.

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