Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene
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PROVIDER: PRJNA341451 | ENA |
REPOSITORIES: ENA
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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: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 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 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:Solvent tolerant bacteria from hydrocarbon contaminated habitats
| PRJEB41203 | ENA
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: Not available
| S-EPMC103577 | biostudies-literature
Project description:Transcriptional profiles of a chlorhexidine tolerant Salmonella Typhimurium were compared to its, chlorhexidine sensitive, isogenic progenitor isolate. RNA was extracted from mid-log phase cells from both isolates, without chlorhexidine exposure and following exposure to 1 µg/ ml of chlorhexidine for 30 minutes. Transcriptional profiles of the tolerant isolate were compared to the sensitive isolate, with and without chlorhexidine exposure.
2015-06-06 | GSE59566 | GEO
Project description: Not available
| S-EPMC194927 | biostudies-literature
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