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ABSTRACT:
PROVIDER: PRJNA836759 | ENA |
REPOSITORIES: ENA
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Project description:ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.
2019-12-20 | GSE137648 | GEO
Project description:Transcriptome of the wildtype or evolved Pseudomonas putida KT2440
2020-07-08 | GSE149827 | 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.
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2015-07-30 | MODEL1507180068 | BioModels
Project description:Transcriptome profiling of Pseudomonas putida KT2440 comparing cells exposed for 1 hour to DIMBOA from maize (Zea mays) to unexposed cells
2012-07-09 | GSE36489 | 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:Genome-wide scanning of gene expression by microarray techniques was successfully performed on RNA extracted from a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1, which contains a chloroaromatic degrading plasmid, in the presence or absence of 3-chlorobenzoic acid (3CB). The genes showing significant changes in their expression in both triplicate microarray analyses using amplified RNA and single microarray analysis using unamplified RNA were investigated. Pathway analysis revealed that the benzoate degradation pathway underwent the most significant changes following treatment with 3CB. Analysis based on categorization of differentially expressed genes against 3CB revealed new findings about the cellular responses of the bacteria to 3CB, including upregulation of the genes specifically involved in transport of 3CB, and induction of a K+/H+ antiporter complex, an universal stress protein, two cytochrome P450 proteins and an efflux transporter. Downregulated expression of some genes involved in carbon metabolism and the genes belong to a prophage in the presence of 3CB was observed. This study demonstrated the applicability of the method of soil RNA extraction for microarray analysis through a proof-of-concept experiment using a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1. A study using total RNA extracted from soil cultures of Pseudomonas putida KT2440/pSL1. Each chip measures the expression level of 5,341 genes from the Pseudomonas putida KT2440 genome with two sets of six 60-mer probes per gene.
2011-03-29 | E-GEOD-28215 | biostudies-arrayexpress
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: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:Plasmid-free Pseudomonas putida KT2440 compared with the same strain harbouring NAH7 plasmid; all the cells were grown in minimal medium M9 with glucose
2012-07-27 | E-MEXP-3412 | biostudies-arrayexpress
Project description:The completely sequenced catabolic plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon the recipient strain Pseudomonas putida KT2440. To study the coordinated expression of pCAR1 with its host chromosome, transcriptome of the transconjugant strain KT2440(pCAR1) was analyzed at growth with carbazole as the sole carbon source compared to succinate as an alternative carbon source. Next, horizontal gene transfer of a plasmid potentially alters the transcriptome of its host chromosome. Transcriptome of the transconjugant strain KT2440(pCAR1) was compared to the parental strain KT2440 at the same growth conditions. Furthermore, pCAR1 encodes a possible global regulator designated ORF70, which belongs to the MvaT family of H-NS-like nucleoid-associated proteins in Pseudomonas. To investigate the regulon under the control of ORF70, transcriptome of KT2440(pCAR1deltaORF70) was compared to the parental strain KT2440(pCAR1) at the same growth conditions. Keywords: Comparative transcriptome analysis
2007-05-01 | GSE7650 | GEO