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:Mechanisms affecting fluoride tolerance in the environmental bacterium Pseudomonas putida.
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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:Fluoride is the anionic form of fluorine, the 13th most abundant element in Earth's crust, and it is toxic to many organisms above a threshold concentration. Environmental bacteria can withstand relatively high fluoride concentrations, but the only mechanism described so far is the CrcB-dependent efflux. CrcB-mediated export is the primary mechanism of F-tolerance in the model environmental bacterium Pseudomonas putida, yet spontaneous NaF-tolerant mutants arise in the absence of the CrcB transporter, showing that this is not the sole pathway of tolerance. We used whole-genome sequencing, proteomic, and transcriptomic analyses to identify mechanisms that affect fluoride tolerance in Pseudomonas putida.
2026-03-30 | PXD068884 | Pride
Project description:Fluoride (F–) is the anionic form of fluorine, the 13th most abundant element in Earth crust, and it is toxic to many organisms above a threshold concentration. Environmental bacteria can withstand relatively high F– concentrations, but the only mechanism described so far is the CrcB dependent efflux. CrcB mediated export is the primary mechanism of F– tolerance in the model environmental bacterium Pseudomonas putida, yet spontaneous NaF-tolerant mutants arise in the absence of the CrcB transporter, showing that this is not the sole pathway of tolerance. We performed a genome wide search for factors affecting F– tolerance in P. putida. Screening >141,000 transposon mutants, we identified PP_3125, a Cro/cI type transcription regulator, as a determinant of high F– tolerance in a strain lacking the CrcB transporter. Proteomic and transcriptomic analyses revealed genes controlled by PP_3125, among which the benzoate transporter BenE-I was linked to the tolerance phenotype. These results show that transporters can adopt moonlighting functions, an aspect unexplored in bacteria. More broadly, the findings reveal alternative fluoride tolerance mechanisms in P. putida and define targets for engineering stress resilient microbial strains for industrial applications.
2026-02-26 | GSE309641 | 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:Common environmental bacterium
| PRJNA37999 | ENA
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