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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide maps of the effect of antimicrobial compounds in P. putida DOT-T1E

ABSTRACT: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida DOT-T1E in the presence of antibiotics with different mechanisms of action with the aim to study in more detail the defense mechanisms that bacteria use to resist against toxic compounds. We find that P. putida DOT-T1E responde in a different way against each antimicrobial compound, what clearly shows that bacteria defense in different ways depending on the targets that compounds uses to attack. Our work is the first global transcriptomic analysis done in P. putida DOT-T1E in the presence of a considerable range of antibiotics. P. putida DOT-T1E mRNA profiles in the presence of control condition (LB) and 8 different antibiotics (ampicillin, chloramphenicol, kanamycin, ciprofloxacin, tetracycline, spectinomycin, gentamicin and rifampicin)

ORGANISM(S): Pseudomonas putida DOT-T1E

SUBMITTER: Carlos Molina-Santiago

PROVIDER: E-GEOD-56749 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide maps of the effect of antimicrobial compounds in P. putida DOT-T1E

Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida DOT-T1E in the presence of antibiotics with different mechanisms of action with the aim to study in more detail the defense mechanisms that bacteria use to resist against toxic compounds. We find that P. putida DOT-T1E responde in a different way against each antimicrobial compound, what clearly shows that bacteria defense in different ways depending on the targets that compounds uses to attack. Our work is the first global transcriptomic analysis done in P. putida DOT-T1E in the presence of a considerable range of antibiotics.

2015-01-20 | GSE56749 | GEO

T1E-18 vs T1E-18 Ampicillin

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E-18 grown in the presence of ampicillin (100 ug/ml) compared with the same cells grown in absence of ampicillin.

2013-03-15 | E-MEXP-3824 | biostudies-arrayexpress

T1E vs T1E Indole

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E grown in the presence of indole (300 uM) compared with the same cells grown in absence of indole.

2013-03-20 | E-MEXP-3819 | biostudies-arrayexpress

T1E PS28 vs T1E PS28 Indole

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E PS28 grown in the presence of indole (300 uM) compared with the same cells grown in absence of indole.

2013-03-15 | E-MEXP-3825 | biostudies-arrayexpress

T1E vs T1E Ampicillin

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E grown in the presence of ampicillin (300 ug/ml) compared with the same cells grown in absence of ampicillin

2013-03-15 | E-MEXP-3823 | biostudies-arrayexpress

T1E-18 vs T1E-18 Indole

Project description:Transcriptional profile of Pseudomonas putida DOT-T1E-18 strain grown in the presence of indole (300 uM) compared with the same cells grown in absence of indole.

2013-03-15 | E-MEXP-3822 | biostudies-arrayexpress

Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene

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

Cross-talk between species that do not share often the same environment

Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida DOT-T1E and E. coli growing in co-cultures

2017-10-01 | GSE95310 | GEO

Metabolomics analysis reveals the participation of efflux pumps and ornithine in the response of Pseudomonas putida DOT-T1E cells to challenge with propranolol

Project description:Efflux pumps are critically important membrane components that play a crucial role in strain tolerance in Pseudomonas putida to antibiotics and aromatic hydrocarbons that result in these toxicants being expelled from the bacteria. Here, the effect of propranolol on P. putida was examined by sudden addition of 0.2, 0.4 and 0.6 mg/ml of this β-blocker to several strains of P. putida, including the wild type DOT-T1E and the efflux pump knockout mutants DOT-T1E-PS28 and DOT-T1E-18. Bacterial viability measurements reveal that the efflux pump TtgABC plays a more important role than the TtgGHI pump in strain tolerance to propranolol. Mid-infrared (MIR) spectroscopy was then used as a rapid, high-throughput screening tool to investigate any phenotypic changes resulting from exposure to varying levels of propranolol. Multivariate statistical analysis of these MIR data revealed gradient trends in resultant ordination scores plots, which were related to the concentration of propranolol. MIR illustrated phenotypic changes associated with the presence of this drug within the cell that could be assigned to significant changes that occurred within the bacterial protein components. To complement this phenotypic fingerprinting approach metabolic profiling was performed using gas chromatography mass spectrometry (GC-MS) to identify metabolites of interest during the growth of bacteria following toxic perturbation with the same concentration levels of propranolol. Metabolic profiling revealed that ornithine, which was only produced by P. putida cells in the presence of propranolol, presents itself as a major metabolic feature that has important functions in propranolol stress tolerance mechanisms within this highly significant and environmentally relevant species of bacteria.

2016-08-23 | MTBLS320 | MetaboLights

Metabolic analysis of the response of Pseudomonas putida DOT-T1E strains to toluene using Fourier transform infrared spectroscopy and gas chromatography mass spectrometry

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

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