Pseudomonas putida
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA292321 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2149467.fastq.gz | Fastqsanger.gz | |||
| SRR2149468.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2 [tiling array]
| PRJNA292322 | ENA
Project description:High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2
| PRJNA292319 | ENA
Project description:Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond the ir coding regions, i.e., the 3â-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA-seq confirmed these data at a single-nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural 16 retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer. Genome Analyzer IIx system (1x75bp) was used for sequencing total RNA extracted from P. putida (mt-2) containing the plasmid pWW0, in two different physiological states (treated with m-xylene and in C-runout condition).
2016-07-07 | E-GEOD-71852 | biostudies-arrayexpress
Project description:A sub-genomic array of structural and regulatory genes of the TOL plasmid pWW0 of Pseudomonas putida mt-2 has been taiolored for inferring the genetic network of m-xylene metabolism through expression profiling of xyl genes. To this end we visualized the response to m-xylene, o-xylene, 3MBA and to a heat shock.
2006-01-01 | E-MEXP-305 | biostudies-arrayexpress
Project description:Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond the ir coding regions, i.e., the 3’-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA-seq confirmed these data at a single-nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural 16 retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer.
2016-07-07 | GSE71852 | GEO
Project description:Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally-encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond the ir coding regions, i.e., the 3'-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA-seq confirmed these data at a single-nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural 16 retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer.
2016-07-07 | GSE71851 | GEO
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: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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To the extent possible under law, all copyright and related or
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the public domain worldwide. Please refer to
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2015-07-30 | MODEL1507180068 | BioModels
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:Pseudomonas putida KT2440 is a metabolically versatile soil bacterium useful both as a model biodegradative organism and as a host of catalytic activities of biotechnological interest. In this report, we present the high-resolution transcriptome of P. putida grown in different carbon sources as revealed by deep sequencing of the corresponding RNA pools. Examination of the data from growth on glycolytic (glucose, fructose) and gluconeogenic (succinate or glycerol) substrates revealed that > 20% of the P. putida genome is differentially expressed depending on the ensuing metabolic regime. Changes affected not only metabolic genes but also a suite of global regulators, e.g. the rpoS sigma subunit of RNAP, various cold-shock proteins and the three HU histone-like proteins. Specifically, the genes encoding HU subunit variants hupA, hupB and hupN drastically altered their expression levels (and thus their ability to form heterodimeric combinations) under the different growth conditions. Furthermore, we found that the two small RNAs crcZ and crcY, known to inhibit the Crc protein that mediates catabolite repression in P. putida, were both down-regulated by glucose. cDNA libraries from Pseudomonas supplemented with different carbon sources (glucose, glycerol, fructose, succinate) were sequenced using HiSeq 2000 to yield 91 paired-end reads. Gene expression values were compared.
2013-07-23 | E-GEOD-46491 | biostudies-arrayexpress