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Proteome, acetylome and 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 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Pseudomonas Putida Kt2440

TISSUE(S): Cell Lysate, Cell Line Cell

SUBMITTER: Saori Kosono

LAB HEAD: Saori Kosono

PROVIDER: PXD007089 | Pride | 2018-09-24

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	160226_QE_428_Kosono_01_TP_log.mgf	Mgf
	160226_QE_428_Kosono_01_TP_log.raw	Raw
	160226_QE_428_Kosono_01_TP_log_silac.msf	Msf
	160226_QE_428_Kosono_02_TP_stat.mgf	Mgf
	160226_QE_428_Kosono_02_TP_stat.raw	Raw

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1 - 5 of 18

Publications

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

Proteome, acetylome and 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 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.

2018-11-22 | PXD007090 | Pride

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 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.

2018-11-21 | PXD007133 | Pride

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

2018-11-21 | PXD007722 | Pride

Human brain global proteome and succinylome analyses

Project description:This is about the global proteome and global succinylome of human brain tissues.

2021-12-08 | PXD015124 | Pride

Transcription profiling of E. coli biofilm to assess the global gene impact of a natural F conjugative plasmid-carrying E.coli biofilm

Project description:we examined the three different mature biofilms and searched the genes which promoted the rapid biofilm formation when their population hosing the plasmids. We investigate the global transcriptional differences between the non-conjugative or conjugative plasmid-carrying and plasmid-free strains.

2007-05-15 | E-MEXP-953 | biostudies-arrayexpress

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

Transcription profiling of rat liver display strain-specific, hereditary and AHR-Dependent Components

Project description:Background; The rat is a major model organism in toxicogenomics and pharmacogenomics, and the use of steady-state hepatic mRNA levels to predict and understand drug toxicity and mechanism is well-established. Surprisingly, the inter- and intra-strain variability of rat mRNA expression has not been evaluated, nor has the extent of its hereditability been established. We address these issues by studying three rat strains (Long-Evans, Hans/Wistar, and Sprague-Dawley) and two F2 lines derived from Long-Evans x Hans/Wistar crosses. Results; Using three independent techniques â variance analysis, linear modelling, and unsupervised pattern recognition â we characterize large amounts of both intra- and inter-strain variability in mRNA levels. Importantly, both sources of variability are highly non-random, and are enriched for specific functional groups. Specific transcription-factor binding-sites are enriched in their promoter regions, and these genes occur in âislandsâ throughout the rat genome. Using the two F2 crosses we study the hereditability of hepatic mRNA levels and show that the majority of rat genes appear to exhibit directional genetics, with only a small fraction having evidence for interacting loci. Finally, a comparison of inter-strain heterogeneity between mouse and rat orthologs shows more heterogeneity in rats than mice, and find that rat and mouse heterogeneity are uncorrelated. Conclusions; Our results establish that hepatic mRNA levels are relatively homogeneous within rat strains, but highly variable between them. This variability may be related to increased activity specific transcription-factors, and has clear functional consequences. Future toxicogenomic and pharmacogenomic studies may take advantage of this phenomenon by surveying panels of rat strains. Experiment Overall Design: We profiled the basal mRNA levels in three strains and two lines of rat, each using four biological replicates.

2009-11-28 | E-GEOD-10448 | biostudies-arrayexpress

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

Transcription profiling of pNCF (non-conjugative factor of F plasmid) carrying E.coli biofilm

Project description:Three E.coli affymetrix antisense arrays were used to examine the global gene expression of pNCF carrying E.coli biofilm. The pNCF is the derivative of only 65 kb non-conjugative factor of F plasmid. It was introduced to E.coli MG1655 strains before prepare the biofilm samples. The biofilms were cultured under the continuous flow cell system using MOP minimal medium supplemented with 0.02% glucose at 37C. The total RNA was extracted directly from the chamber after 48h of incubation for further array procedures according to the manufacture manual.

2007-09-01 | E-MEXP-1145 | biostudies-arrayexpress

Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast

Project description:In eukaryotes, the conjugation of proteins to the small ubiquitin-like modifier SUMO regulates numerous cellular functions. A proportion of SUMO conjugates are targeted for degradation by SUMO-targeted ubiquitin ligases (STUbLs) and it has been proposed that the ubiquitin-selective chaperone Cdc48/p97-Ufd1-Npl4 facilitates this process. However, the extent to which the two pathways overlap, and how the substrates are selected, remains unknown. Here, we address these questions in fission yeast through proteome-wide analyses of SUMO modification sites. We identify over a thousand sumoylated lysines in a total of 468 proteins and quantify changes occurring in the SUMO modification status when the STUbL or Ufd1 pathways are compromised by mutations. The data suggest the coordinated processing of several classes of SUMO conjugates, many dynamically associated with centromeres or telomeres. They provide new insights into subnuclear organization and chromosome biology, and, altogether, constitute an extensive resource for the molecular characterization of SUMO function and dynamics.

2015-10-30 | PXD002972 | Pride

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