Pseudomonas putida S12
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA271879 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pseudomonas putida S12 is exceptionally tolerant to various organic solvents. To obtain further insight in this bacteriumM-bM-^@M-^Ys primary defence mechanisms towards these potentially harmful substances, we studied its genome wide transcriptional response to sudden addition of toluene. Global gene expression profiles were monitored for 30 minutes after toluene addition. During toluene exposure, high oxygen-affinity cytochrome c oxidase is specifically expressed to provide for an adequate proton gradient supporting solvent efflux mechanisms. Concomitantly, the glyoxylate bypass route was up-regulated, to repair an apparent toluene stress-induced redox imbalance. A knock-out mutant of trgI, a recently identified toluene-repressed gene, was investigated in order to identify TrgI function. Remarkably, upon addition of toluene the number of differentially expressed genes initially was much lower in the trgI-mutant than in the wild-type strain. This suggested that after deletion of trgI cells were better prepared for sudden organic solvent stress. Before, as well as after, addition of toluene many genes of highly diverse functions were differentially expressed in trgI-mutant cells as compared to wild-type cells. This led to the hypothesis that TrgI may not only be involved in the modulation of solvent-elicited responses but in addition may affect basal expression levels of large groups of genes. Differential gene expression after a sudden addition of 5 mM toluene was analysed in early exponential phase cultures (optical density at 600 nm of 0.5-0.6) of P. putida strains S12 (wild-type) and S12M-NM-^TtrgI. Samples were drawn immediately before (t=0) and at set intervals (1, 2, 5, 10 and 30 minutes) after toluene exposure. Duplicat samples were drawn. This resulted in 12 samples per strain, 24 in total.
2015-01-09 | E-GEOD-64791 | biostudies-arrayexpress
Project description:Pseudomonas putida S12 is exceptionally tolerant to various organic solvents. To obtain further insight in this bacterium’s primary defence mechanisms towards these potentially harmful substances, we studied its genome wide transcriptional response to sudden addition of toluene. Global gene expression profiles were monitored for 30 minutes after toluene addition. During toluene exposure, high oxygen-affinity cytochrome c oxidase is specifically expressed to provide for an adequate proton gradient supporting solvent efflux mechanisms. Concomitantly, the glyoxylate bypass route was up-regulated, to repair an apparent toluene stress-induced redox imbalance. A knock-out mutant of trgI, a recently identified toluene-repressed gene, was investigated in order to identify TrgI function. Remarkably, upon addition of toluene the number of differentially expressed genes initially was much lower in the trgI-mutant than in the wild-type strain. This suggested that after deletion of trgI cells were better prepared for sudden organic solvent stress. Before, as well as after, addition of toluene many genes of highly diverse functions were differentially expressed in trgI-mutant cells as compared to wild-type cells. This led to the hypothesis that TrgI may not only be involved in the modulation of solvent-elicited responses but in addition may affect basal expression levels of large groups of genes.
2015-01-09 | GSE64791 | GEO
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:Pseudomonas putida S12 Genome sequencing
| PRJNA222630 | ENA
Project description:Pseudomonas putida S12 Genome sequencing and assembly
| PRJNA171340 | ENA
Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida KT2440 and DOT-T1E in the presence of toluene with the aim to study in more detail the mechanisms involved in toluene response in a toluene-sensitive and a toluene-tolerant strains.
2017-06-04 | GSE86321 | GEO
Project description:To elucidate any observable metabolic alterations during interactions of several strains of Pseudomonas putida (DOT-T1E, and its mutants DOT-T1E-PS28 and DOT-T1E-18) with the aromatic hydrocarbon toluene, metabolomic approaches were employed. Initially, Fourier-transform infrared (FT-IR) spectroscopy, which provided a rapid, high-throughput metabolic fingerprint of P. putida strains, was used to investigate any phenotypic changes resulting from exposure to toluene. Principal component discriminant function analysis (PC-DFA) allowed the differentiation between different conditions of toluene on bacterial cells, which indicated phenotypic changes associated with the presence of the solvent within the cell. Examination of PC-DFA loading plots suggested that the protein and fatty acids groups were responsible for discrimination of responses by P. putida strains to toluene. To identify metabolites of interest, the polar extracts of P. putida cells were analysed using gas chromatography-mass spectrometry (GC-MS) and 15 metabolites of P. putida central metabolic pathways were detected. Multi-block principal component analysis (MB-PCA) indicated that P. putida cultures challenged with toluene were differentially clustered away from the non-challenged cells. Investigation of MB-PCA loading plots and N-way ANOVA for condition | strain×time blocking (dosage of toluene) suggested ornithine as the most significant compound that increased upon solvent exposure. Ornithine presents itself as a major feature which may have important functions in toluene stress tolerance mechanisms.
2016-08-23 | MTBLS319 | MetaboLights
Project description:To gain an insight into molecular mechanisms underlying plant-microbe interactions gene expression changes in rice plants in response to a plant growth promoting rhizobacteria such as the Pseudomonas putida, root transcriptome analysis through microarray technology was performed from rice roots in response to P. putida RF3. Species of Pseudomonas are well known as biocontrol agents hence defense response and genes related to root exudation of phytochemicals were analysed in detail. For treatment of rice plants with P. putida, aseptically germinated rice seedlings from half strength MS medium were transferred to flasks containing Hoaglands’ nutrient solution, treated with P. putida and incubated for 48 hours in growth chamber in an orbital shaker. Gene expression changes in rice roots were then analyzed by microarray experiment. Untreated roots served as control. Data analysis revealed defense responsive genes to be upregulated with greater fold changes. In addition to defense response genes, few genes involved in secondary metabolism were also upregulated significantly. Validation of microarray data was performed using real time PCR for defense responsive genes (OsPBZ, OsPR101a, OsCHIA, etc). Detailed analysis of the differentially expressed genes reveal the role of P. putida RF3 in inducing systemic resistance in plants thereby immunizing the rice plants against future attacks by pests/pathogens. Our study enhances the current understanding on gene expression changes occurring during plant-microbe associations and thus demonstrates the potential of P. putida RF3 as a biocontrol agent.
2017-12-01 | GSE99881 | 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:Nogales2008 - Genome-scale metabolic network
of Pseudomonas putida (iJN746)
This model is described in the article:
A genome-scale metabolic
reconstruction of Pseudomonas putida KT2440: iJN746 as a cell
factory.
Nogales J, Palsson BØ, Thiele
I.
BMC Syst Biol 2008; 2: 79
Abstract:
BACKGROUND: Pseudomonas putida is the best studied pollutant
degradative bacteria and is harnessed by industrial
biotechnology to synthesize fine chemicals. Since the
publication of P. putida KT2440's genome, some in silico
analyses of its metabolic and biotechnology capacities have
been published. However, global understanding of the
capabilities of P. putida KT2440 requires the construction of a
metabolic model that enables the integration of classical
experimental data along with genomic and high-throughput data.
The constraint-based reconstruction and analysis (COBRA)
approach has been successfully used to build and analyze in
silico genome-scale metabolic reconstructions. RESULTS: We
present a genome-scale reconstruction of P. putida KT2440's
metabolism, iJN746, which was constructed based on genomic,
biochemical, and physiological information. This
manually-curated reconstruction accounts for 746 genes, 950
reactions, and 911 metabolites. iJN746 captures
biotechnologically relevant pathways, including
polyhydroxyalkanoate synthesis and catabolic pathways of
aromatic compounds (e.g., toluene, benzoate, phenylacetate,
nicotinate), not described in other metabolic reconstructions
or biochemical databases. The predictive potential of iJN746
was validated using experimental data including growth
performance and gene deletion studies. Furthermore, in silico
growth on toluene was found to be oxygen-limited, suggesting
the existence of oxygen-efficient pathways not yet annotated in
P. putida's genome. Moreover, we evaluated the production
efficiency of polyhydroxyalkanoates from various carbon sources
and found fatty acids as the most prominent candidates, as
expected. CONCLUSION: Here we presented the first genome-scale
reconstruction of P. putida, a biotechnologically interesting
all-surrounder. Taken together, this work illustrates the
utility of iJN746 as i) a knowledge-base, ii) a discovery tool,
and iii) an engineering platform to explore P. putida's
potential in bioremediation and bioplastic production.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180068.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180068 | BioModels