Pseudomonas putida strain:1312
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA382790 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The entire set of flagellar structural components and flagellar-specific transcriptional regulators, as well as much of the core chemotaxis machinery, is encoded into a >70 kbp cluster in Pseudomonas putida KT2440 genome. We have performed RNA-seq of the wild-type strain in order to identify operon boundaries and promoters location in this cluster.
2021-05-05 | GSE173832 | GEO
Project description:KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria not known to have a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC homologs found in environmental Pseudomonas species. We characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. Through phenotypic assays and transcriptomics, we show that KaiC is involved in osmotic and oxidative stress resistance in P. putida and in biofilm production in both P. putida and P. protegens.
2023-01-04 | GSE221044 | GEO
Project description:Transcription profiling of Pseudomonas putida PP3546 mutant
2013-04-02 | E-MEXP-3655 | biostudies-arrayexpress
Project description:Pseudomonas putida S12 is an inherently solvent-tolerant strain and constitutes a promising platform for biotechnology applications in whole-cell biocatalysis of aromatic compounds. The genome of P. putida S12 consists of a 5.8 Mbp chromosome and a 580 kbp megaplasmid pTTS12. pTTS12 encodes several genes which enable the tolerance to various stress conditions, including the main solvent efflux pump SrpABC. Removal (curing) of megaplasmid pTTS12 and subsequent loss of solvent efflux pump SrpABC caused a significant reduction in solvent tolerance of the resulting strain. In this study, we succeeded in restoring solvent tolerance in the megaplasmid-cured P. putida S12 using adaptive laboratory evolution (ALE) and molecular analysis to investigate the intrinsic solvent tolerance of P. putida S12. RNA-seq was performed to study the global transcriptomic response of the solvent-adapted plasmid-cured P. putida S12 in the presence of toluene. This analysis revealed the downregulation of ATP synthase, flagella and other RND efflux pumps, which indicates the importance of maintaining proton motive force during solvent stress.
2021-02-24 | GSE144045 | 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:Transcriptome of the wildtype or evolved Pseudomonas putida KT2440
2020-07-08 | GSE149827 | GEO
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:Pseudomonas putida strain LWPZF Genome sequencing and assembly
| PRJNA695031 | 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
Project description:Pseudomonas species have become promising cell factories for the production of natural products due to their inherent robustness. Here, we explored membrane adaptations of Pseudomonas putida KT2440, in particular outer membrane vesicle (OMV) formation in response to 1-octanol, PQS and prodigiosin, causing chemical membrane stress via RNA-seq of mRNA. Pseudomonas putida wild type KT2440 (Nelson et al. 2002) and the derived strains P. putida pig21 were cultivated in biological triplicates under continuous shaking (130 rpm) at 30 °C in 10 mL LB (lysogeny broth) medium (10 g L-1 tryptone, 5 g L-1 yeast extract, 10 g L-1 sodium chloride; Carl Roth®, Karlsruhe, Germany). Antibiotics were added to the culture medium when appropriate to the following final concentrations: 25 µg mL-1 kanamycin, 25 µg mL-1 irgasan, 25 µg mL-1 gentamicin, 50 µg mL-1 tetracycline. For chemical induction of OMV formation, P. putida KT2440 was exposed to 1 mM 1-octanol or 50 µM PQS (Pseudomonas quinolone signal) after reaching the logarithmic growth phase. For transcriptome analysis, cells were cultivated as described above, the cell pellet was harvested after 7 h, adjusted to an optical density (OD700 nm) of 1 and flash frozen . Total RNA was isolated from 3 biological replicates using Quick-RNA Miniprep Plus kit (Zymo Research). The samples were treated with DNase (Zymo Research) and RNA was again purified with an RNA Clean&Concentrator-5 kit (Zymo Research). Ribosomal rRNA was removed with a riboPOOL for bacteria (siTOOLs Biotech GmbH). The purity of RNA and removal of rRNA was then tested with an Agilent RNA Pico 6000 kit and an Agilent 2100 Bioanalyzer (Agilent Technologies). TruSeq Stranded mRNA Sample Preparation guide (Illumina) was then used to construct the cDNA library. The constructed cDNA library was then sequenced with Illumina NextSeq500 high output mode paired end using a read length of 75 bases.
2023-01-09 | E-MTAB-12470 | biostudies-arrayexpress