Pseudomonas putida
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA12326 | ENA |
REPOSITORIES: ENA
Dataset's files
| 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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Similar Datasets
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.
2022-10-01 | GSE214391 | GEO
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.
2011-03-25 | GSE24176 | GEO
Project description:The biological regime of Pseudomonas putida (and any other bacterium) under given environmental conditions results from the hierarchical expression of sets of genes that become turned on and off in response to one or more physicochemical signals. In some cases, such signals are clearly defined, but in many others, cells are exposed to a whole variety of ill-defined inputs that occur simultaneously. Transcriptomic analyses of bacteria passed from a reference condition to a complex niche can thus expose both the type of signals that they experience during the transition and the functions involved in adaptation to the new scenario. In this article, we describe a complete protocol for generation of transcriptomes aimed at monitoring the physiological shift of P. putida between two divergent settings using as a simple case study the change between homogeneous, planktonic lifestyle in a liquid medium and growth on the surface of an agar plate. To this end, RNA was collected from P. putidaKT2440 cells at various times after growth in either condition, and the genome-wide transcriptional outputs were analysed. While the role of individual genes needs to be verified on a case-by-case basis, a gross inspection of the resulting profiles suggested cells that are cultured on solid media consistently had a higher translational and metabolic activity, stopped production of flagella and were conspicuously exposed to a strong oxidative stress. The herein described methodology is generally applicable to other circumstances for diagnosing lifestyle determinants of interest.
2025-01-21 | GSE287362 | GEO
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
Project description:The ability to detect trace amounts of ionizing radiation is a paramount concern for chemical, biological, radiological, nuclear, and explosives (CBRNE) operations and observation of clandestine activities in the event of source relocation and contamination. Microbes respond to environmental stress such as fluctuations in pH and temperature, nutrient limited conditions, and oxidative stress with morphological and behavioral changes, and induced responses are known to persist after the stressor is removed. Innate responses to other external stressors like exposure to low-dose ionizing radiation could be measured and characterized by changes in gene expression and resulting transcriptional changes could by engineered into biosensors to monitor and discern the presence and type of radiation, respectively, in the environment. The current understanding of the biological and transcriptional responses of bacteria to various doses of ionizing radiation is minimal. The work in this study expands upon the findings in our previous study of the response of a model bacterium to low doses of ionizing radiation soil bacterium, Pseudomonas putida KT2440. Following exposure to an approximate absorbed dose rate of 9 mGy d-1 of a 239Pu, 3H, or 55Fe source, RNA-seq analysis revealed key changes in gene expression of P. putida of genes encoding membrane components, central carbon metabolism, DNA repair pathways, and motility. Several genes were differentially expressed genes in P. putida after exposure to multiple radionuclide sources. Moreover, other genes were uniquely differentially expressed by a single radionuclide source. These findings expand upon the limited understanding of the biological response to low doses of ionizing radiation and provide fundamental characterization required to develop discriminatory RNA-based biosensors.
2025-03-31 | GSE213139 | GEO
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
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