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Succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440.

ABSTRACT: The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis. This dataset is related to PXD007089.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Pseudomonas Putida Kt2440

TISSUE(S): Cell Lysate

SUBMITTER: Saori Kosono

LAB HEAD: Saori Kosono

PROVIDER: PXD007133 | Pride | 2018-11-21

REPOSITORIES: Pride

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Proteome and acylome analyses of the functional interaction network between the carbazole-degradative plasmid pCAR1 and host Pseudomonas putida KT2440.

Vasileva Delyana D Suzuki-Minakuchi Chiho C Kosono Saori S Yoshida Minoru M Okada Kazunori K Nojiri Hideaki H

Environmental microbiology reports 20180416 3

Understanding the interplay between a plasmid and its host system is a bottleneck towards prediction of the fate of plasmid-harbouring strains in the natural environments. Here, we studied the impact of the conjugative plasmid pCAR1, involved in carbazole degradation, on the proteome of Pseudomonas putida KT2440 using SILAC method. Furthermore, we investigated two acyl lysine modifications (acetylation and succinylation) that respond to the metabolic status of the cell and are implicated in regu ...[more]

PMID: 29573367

Similar Datasets

Succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440 (2).

Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis. This dataset is related to PXD007090.

2018-11-21 | PXD007722 | Pride

Proteome, acetylome and succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440

Project description:The impact of the conjugative plasmid pCAR1, which is involved in carbazole degradation, on the proteome, acetylome, and succinylome of host Pseudomonas putida KT2440 was investigated using a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative analysis.

2018-09-24 | PXD007089 | Pride

Proteome, acetylome and succinylome analysis of pCAR1-free and pCAR1-harbouring Pseudomonas putida KT2440 (2)

2018-11-22 | PXD007090 | Pride

Proteomic analysis of E. coli K-12 LE392, P. putida KT2440 under exposure of six non-antibiotic pharmaceuticals

Project description:The goals of this study are to use SWATH-MS to detect bacterial proteomic profiles of E. coli K-12 LE392 with conjugative RP4 plasmid, P. putida KT2440, and their protein response under the exposure of six kinds of non-antibiotic pharmaceuticals, i.e., ibuprofen (ibu), naproxen (nap), gemfibrozil (gem), iopromide (iop), diclofenac (dic), propanolol (pro). Each treatment condition was conducted in triplicate. By comparing the proteomic profiles of experimental groups and control group, the effects of these non-antibiotic pharmaceuticals on translational levels can be revealed.

2022-02-15 | PXD012642 | Pride

The effect of multiple phaJ deletions Pseudomonas putida KT2440 on polyhydroxyalkanoates synthesis

Project description:Pseudomonas putida KT2440 is a well-known model organism for the medium chain length (mcl) PHA accumulation. (R)-Specific enoyl-coenzyme A hydratase (PhaJ) was considered to be the main supplier of monomers for PHA synthesis by converting the -oxidation intermediate, trans-2-enoyl-CoA to (R)-3-hydroxyacyl-CoA when fatty acids (FA) are used. Three PhaJ homologues, PhaJ1, PhaJ4 and MaoC are annotated in P. putida KT2440. To investigate the relationship of fatty acids - PHA metabolism and the role of each PhaJ in PHA biosynthesis in P. putida KT2440, a series of P. putida KT2440 knockouts was obtained. PHA content and monomer composition in WT and mutants under different growth conditions were analysed. However, when all three PhaJ homologues were deleted, the mutant still accumulated PHA up to 10.7 % of the cell dry weight (CDW). To identify other potential PHA monomer suppliers by analysing the proteome of the phaJ1maoCphaJ4. The proteomes of the WT, phaJ1phaJ4 and phaJ1maoCphaJ4 strains in MSM medium with octanoate under nitrogen limited condition were detected. In addition, we found that the deletion of PhaJ1 in P. putida KT2440 has a negative impact on the PHA accumulation in cells cultivated on glucose with nitrogen limitation conditions. It seems PhaJ1 also mediates the synthesis of PHA when glucose was used as the carbon and energy source. To investigate the role of PhaJ1 in PHA accumulation with glucose, the proteomes of P. putida KT2440 wild type, phaJ1, phaJ1phaJ4 and phaJ1maoCphaJ4 mutant growing on glucose were detected and compared.

2023-05-10 | PXD037932 | Pride

The effect of multiple phaJ deletions Pseudomonas putida KT2440 on polyhydroxyalkanoates synthesis (part2)

Project description:Pseudomonas putida KT2440 is a well-known model organism for the medium chain length (mcl) PHA accumulation. (R)-Specific enoyl-coenzyme A hydratase (PhaJ) was considered to be the main supplier of monomers for PHA synthesis by converting the -oxidation intermediate, trans-2-enoyl-CoA to (R)-3-hydroxyacyl-CoA when fatty acids (FA) are used. Three PhaJ homologues, PhaJ1, PhaJ4 and MaoC are annotated in P. putida KT2440. To investigate the relationship of fatty acids - PHA metabolism and the role of each PhaJ in PHA biosynthesis in P. putida KT2440, a series of P. putida KT2440 knockouts was obtained. PHA content and monomer composition in WT and mutants under different growth conditions were analysed. However, when all three PhaJ homologues were deleted, the mutant still accumulated PHA up to 10.7 % of the cell dry weight (CDW). To identify other potential PHA monomer suppliers by analysing the proteome of the phaJ1maoCphaJ4. The deletion of (R)-3-hydroxydecanoyl-ACP:CoA transacylase (PhaG), which connects de novo FA and PHA synthesis pathways, while causing further 1.8-fold decrease in PHA content, did not abolish PHA accumulation. Further proteome analysis revealed quinoprotein alcohol dehydrogeanses PedE and PedH as potential monomer suppliers, but when these were deleted PHA level remained at 2.2 – 14.8 % CDW depending on the fatty acid used, and whether nitrogen limitation was applied. To identify the other non-specific dehydrogenases supply monomers for PHA synthesis, we analysed the proteome of the sextuple mutant under nitrogen limiting and non-limiting conditions.

2023-05-10 | PXD037937 | Pride

Proteomic analysis of E. coli K-12 LE392, P. putida KT2440 under exposure of carbamazepine

Project description:The goals of this study are to use SWATH-MS to detect bacterial proteomic profiles of wild-type E. coli K-12 LE392, P. putida KT2440, and their quantitative protein response under the exposure of antiepileptic drug carbamazepine. Three concentrations of carbamazepine were applied, which were 0.05 mg/L, 10.0 mg/L and 50.0 mg/L. The group without dosing carbamazepine was the control group. Each concentration was conducted in triplicate. By comparing the proteomic profiles of experimental groups and control group, the effects of carbamazepine on bacterial translational levels can be revealed.

2018-10-10 | PXD009279 | Pride

Bacillus subtilis acetylome and succinylome

Project description:The two major acyl-modifications on lysine residues, acetylation and succinylation, were analyzed in the gram-positive model bacterium Bacillus subtilis. To identify and quantify the changes in acetylation and succinylation in response to the carbon source, a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomic analysis of cells grown on glucose or citrate was performed.

2015-07-02 | PXD001615 | Pride

RNA-seq of Pseudomonas putida KT2440 and the derived strain P. putida pig21 treated with 1-octanol and PQS (Pseudomonas quinolone signal), causing chemical membrane stress.

Project description:Pseudomonas species have become promising cell factories for the production of natural products due to their inherent robustness. Here, we explored membrane adaptations of Pseudomonas putida KT2440, in particular outer membrane vesicle (OMV) formation in response to 1-octanol, PQS and prodigiosin, causing chemical membrane stress via RNA-seq of mRNA. Pseudomonas putida wild type KT2440 (Nelson et al. 2002) and the derived strains P. putida pig21 were cultivated in biological triplicates under continuous shaking (130 rpm) at 30 °C in 10 mL LB (lysogeny broth) medium (10 g L-1 tryptone, 5 g L-1 yeast extract, 10 g L-1 sodium chloride; Carl Roth®, Karlsruhe, Germany). Antibiotics were added to the culture medium when appropriate to the following final concentrations: 25 µg mL-1 kanamycin, 25 µg mL-1 irgasan, 25 µg mL-1 gentamicin, 50 µg mL-1 tetracycline. For chemical induction of OMV formation, P. putida KT2440 was exposed to 1 mM 1-octanol or 50 µM PQS (Pseudomonas quinolone signal) after reaching the logarithmic growth phase. For transcriptome analysis, cells were cultivated as described above, the cell pellet was harvested after 7 h, adjusted to an optical density (OD700 nm) of 1 and flash frozen . Total RNA was isolated from 3 biological replicates using Quick-RNA Miniprep Plus kit (Zymo Research). The samples were treated with DNase (Zymo Research) and RNA was again purified with an RNA Clean&Concentrator-5 kit (Zymo Research). Ribosomal rRNA was removed with a riboPOOL for bacteria (siTOOLs Biotech GmbH). The purity of RNA and removal of rRNA was then tested with an Agilent RNA Pico 6000 kit and an Agilent 2100 Bioanalyzer (Agilent Technologies). TruSeq Stranded mRNA Sample Preparation guide (Illumina) was then used to construct the cDNA library. The constructed cDNA library was then sequenced with Illumina NextSeq500 high output mode paired end using a read length of 75 bases.

2023-01-09 | E-MTAB-12470 | biostudies-arrayexpress

Transcriptome of Pseudomonas putida KT2440 harboring plasmid RP4 during conjugative transfer

Project description:We analyzed gene expression during conjugative transfer of plasmid RP4. Pairs of rifampicin-susceptible (RifS) and -resistance (RifR) strains of Pseudomonas putida KT2440 were conjugated for 10 minute on filter membrane in the presence of rifampicin to discriminate the expression changes in the donor and recipient cells.

2020-03-13 | GSE146879 | GEO

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