Ontology highlight
ABSTRACT:
PROVIDER: PRJNA602416 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10918230_1.fastq.gz | Fastqsanger.gz | |||
| SRR10918230_2.fastq.gz | Fastqsanger.gz | |||
| SRR10918231_1.fastq.gz | Fastqsanger.gz | |||
| SRR10918231_2.fastq.gz | Fastqsanger.gz | |||
| SRR10918232_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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 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 Genome sequencing
| PRJNA222630 | ENA
Project description:Pseudomonas putida S12 Genome sequencing and assembly
| PRJNA171340 | ENA
Project description:We identified binding sites genome-wide for carbon metabolism transcriptional response regulators in Pseudomonas stutzeri RCH2, Pseudomonas putida KT2240, Pseudomonas fluorescens FW300-N2E2 and FW300-N2C3 by DNA-affinity-purified (DAP) sequencing.
2020-10-01 | GSE157075 | GEO
Project description:Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene
| PRJNA341451 | ENA
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:Sohn2010 - Genome-scale metabolic network of
Pseudomonas putida (PpuMBEL1071)
This model is described in the article:
In silico genome-scale
metabolic analysis of Pseudomonas putida KT2440 for
polyhydroxyalkanoate synthesis, degradation of aromatics and
anaerobic survival.
Sohn SB, Kim TY, Park JM, Lee
SY.
Biotechnol J 2010 Jul; 5(7):
739-750
Abstract:
Genome-scale metabolic models have been appearing with
increasing frequency and have been employed in a wide range of
biotechnological applications as well as in biological studies.
With the metabolic model as a platform, engineering strategies
have become more systematic and focused, unlike the random
shotgun approach used in the past. Here we present the
genome-scale metabolic model of the versatile Gram-negative
bacterium Pseudomonas putida, which has gained widespread
interest for various biotechnological applications. With the
construction of the genome-scale metabolic model of P. putida
KT2440, PpuMBEL1071, we investigated various characteristics of
P. putida, such as its capacity for synthesizing
polyhydroxyalkanoates (PHA) and degrading aromatics. Although
P. putida has been characterized as a strict aerobic bacterium,
the physiological characteristics required to achieve anaerobic
survival were investigated. Through analysis of PpuMBEL1071,
extended survival of P. putida under anaerobic stress was
achieved by introducing the ackA gene from Pseudomonas
aeruginosa and Escherichia coli.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180043.
To cite BioModels Database, please use:
BioModels Database:
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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 | MODEL1507180043 | BioModels
Project description:Alginate, a major exopolysaccharide (EPS) produced by P. putida, is known to create hydrated environments and alleviate the effect of water limitation. In addition to alginate, P. putida is capable of producing cellulose (bcs), putida exopolysaccharide a (pea), and putida exopolysaccharide b (peb). However, unlike alginate, not much is known about their roles under water limitation. Hence, in this study we examined the role of different EPS under water stress. To create environmentally realistic water stress conditions as observed in soil, we used Pressurized Porous Surface Model (PPSM). Our main hypothesis was that under water stress, absence of alginate would be compensated by the other EPS. To test our hypothesis, we investigated colony morphologies and whole genome transcriptomes of P. putida KT2440 WT and its mutants deficient in either alginate or all known EPS A custom-made Nimblegen (WI, USA) whole genome one-color oligonucleotide expression array (12x135K with 45-60 mer probes) of P. putida KT2440 was used to investigate effect of water stress on the differential expression of the whole genome. In this study Pseudomonas putida KT2440 wild type (WT) and two of its mutants deficient either in alginate (Alg-), or all known EPS (EPS-) production were used and grown under dry (water stress) and wet (without water stress) conditions. (Deleted genes in Alg-: PP1277-PP128; in EPS-: PP1277-1288 (alg) + PP2634-2638 (bcs) + PP3132-3142 (pea) + PP1795-1788 (peb)) (Nilsson et al., 2011).39. Nilsson, M., Chiang, W.C., Fazli, M., Gjermansen, M., Givskov, M., and Tolker-Nielsen, T. (2011) Influence of putative exopolysaccharide genes on Pseudomonas putida KT2440 biofilm stability. Environ Microbiol. 13 (5):1 357-1369
2013-12-23 | E-GEOD-53407 | biostudies-arrayexpress