Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Escherichia coli proteome analysis to decipher the molecular impact of phosphinic antimicrobials

ABSTRACT: The proteome of Escherichia coli was established by shotgun proteomics and changes upon treatment with phosphinic compounds were measured, highlighting the potential of these new antimicrobials.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Escherichia Coli

SUBMITTER: Jean ARMENGAUD

LAB HEAD: Jean Armengaud

PROVIDER: PXD051418 | Pride | 2024-11-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	F217592.dat	Other
	F217592_p0.05.mzid.gz	Mzid
	F217593.dat	Other
	F217593_p0.05.mzid.gz	Mzid
	F217594.dat	Other

Items per page:

1 - 5 of 61

Publications

Integrated multi-omics unveil the impact of H-phosphinic analogs of glutamate and α-ketoglutarate on Escherichia coli metabolism.

Giovannercole Fabio F Gafeira Gonçalves Luís L Armengaud Jean J Varela Coelho Ana A Khomutov Alex A De Biase Daniela D

The Journal of biological chemistry 20240921 10

Desmethylphosphinothricin (L-Glu-γ-PH) is the H-phosphinic analog of glutamate with carbon-phosphorus-hydrogen (C-P-H) bonds. In L-Glu-γ-PH the phosphinic group acts as a bioisostere of the glutamate γ-carboxyl group allowing the molecule to be a substrate of Escherichia coli glutamate decarboxylase, a pyridoxal 5'-phosphate-dependent α-decarboxylase. In addition, the L-Glu-γ-PH decarboxylation product, GABA-PH, is further metabolized by bacterial GABA ...[more]

PMID: 39307306

Similar Datasets

Terminus DNA loss in the Escherichia coli

Project description:Study of the mechanisms of RecB mutant terminus DNA loss in Escherichia coli. FX158: WT MG1655 FX35: recB- FX37: ruvAB- FX51: matP- MIC18: recB- sbcD- sbcC- MIC20: recB- ruvAB- MIC24: matP- recB- MIC25: recA- recB- MIC31: sbcB- sbcD- MIC34: recA- recD- MIC40: linear chromosome MIC41: linear chromosome recB- MIC42: matP- ftsKC- MIC43: matP- ftsKC- recB- MIC48: recA- Cells were grown in M9 minimal medium supplemented with 0.4 % glucose to exponential phase (0.2 OD 650 nm). Chromosomal DNA was extracted using the Sigma GenElute bacterial genomic DNA kit. 5 μg of DNA were used to generate a genomic library according to Illumina's protocol. The libraries and the sequencing were performed by the High-throughput Sequencing facility of the I2BC (http://www.i2bc.paris-saclay.fr/spip.php?article399&lang=en, CNRS, Gif-sur-Yvette, France). Genomic DNA libraries were made with the ‘Nextera DNA library preparation kit’ (Illumina) following the manufacturer’s recommendations. Library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent technologies). Libraries were pooled in equimolar proportions. 75 bp single reads were generated on an Illumina MiSeq instrument, using a MiSeq Reagent kit V2 (500 cycles) (Illumina), with an expected depth of 217X. An in-lab written MATLAB-based script was used to perform marker frequency analysis. Reads were aligned on the Escherichia coli K12 MG1655 genome using BWA software. Data were normalized by dividing uniquely mapping sequence reads by the total number of reads. Enrichment of uniquely mapping sequence reads in 1 kb non-overlapping windows were calculated and plotted against the chromosomal coordinates.

2017-11-10 | E-MTAB-6122 | biostudies-arrayexpress

Escherichia coli RNA-Seq

Project description:The goal of this study is to compare gene expression data for a well known model organism (Escherichia coli) using different technologies (NGS here, microarray from GSE48776). mRNA profiles of Wild Type and two Mutant Strains (ydcR (b1439) MUTANT and yjiR (b4340) MUTANT), growth in minimal medium, were generated by deep sequencing, in triplicate, using Illumina MiSeq.

2013-07-12 | E-GEOD-48829 | biostudies-arrayexpress

Transcription Profiling of the Persister Phenotype in Escherichia Coli

Project description:When bacteria are challenged with antimicrobials, small numbers of cells may survive treatment. These so-called persister cells are not mutants, but are a set of phenotypic variants which, after re-growth exhibit the same susceptibility properties as their progenitor populations. The presence of persisters may determine the effective therapeutic dose of antibiotics and account for the intractability of biofilm-related infections. In the current investigation, Escherichia coli persister cells were isolated without prior exposure to antimicrobials, using fluorescence-assisted cell sorting of a strain, labelled with a chromosomal green fluorescent protein marker. Levels of persistence were inversely proportional to fluorescence intensity in the gfp-tagged E. coli population, and separated persister cells showed enhanced expression of two groups of genes located in the e14 and CP4-6 cryptic prophage regions when analysed by DNA microarray.

2013-10-13 | E-MEXP-3511 | biostudies-arrayexpress

Global gene expression in ocular isolates of Escherichia coli with potential to form biofilm

Project description:The results of this study would unravel the identity of genes that are differentially regulated during biofilm formation and establish whether the differentially regulated genes are related to increased resistance to antimicrobials and or virulence.

2016-04-29 | GSE77872 | GEO

Molecular changes in the proteome of Bacillus cereus cells upon mutation of the tspO gene.

Project description:The proteome of Bacillus cereus mutated in the TspO gene was established by shotgun proteomics and compared to the proteome of Bacillus cereus wild type strain (ATCC14579) to characterize the molecular modifications induced by the mutation.

2024-05-02 | PXD048360 | Pride

Shotgun proteomic cartography of Bacillus pumilus spores

Project description:The proteome of Bacillus pumilus spores was established by shotgun proteomics to better characterize this biological material used as indicator to assess the effectiveness of decontamination procedures.

2023-12-21 | PXD044078 | Pride

Shotgun proteomic cartography of Bacillus atrophaeus spores

Project description:The proteome of Bacillus atrophaeus spores was established by shotgun proteomics to better characterize this biological material used as indicator to assess the effectiveness of decontamination procedures.

2023-12-21 | PXD044079 | Pride

Human proteome changes upon Mopeia mammarenavirus (MOPV) infection.

Project description:The proteome of human cells infected with Mopeia mammarenavirus(MOPV) was analyzed and compared to the proteome of control cells.

2024-11-13 | PXD053439 | Pride

Impact of suppression of the SOS response on protein expression in clinical isolates of Escherichia coli under antimicrobial pressure of ciprofloxacin

Project description:Suppression of the SOS response in combination with drugs has been proposed as a potential target to tackle antimicrobial resistance. The SOS response is the pathway used to repair bacterial DNA damage induced by antimicrobials such as quinolones. The extent of lexA-regulated protein expression and other associated systems under pressure of agents that damage bacterial DNA in clinical isolates remains unclear. The aim of this study was to assess the impact of this strategy on the proteome profile of Escherichia coli clinical strains.

2024-04-04 | PXD050358 | Pride

Rho and NusG suppress pervasive antisense transcription in Escherichia coli [RNA-seq].

Project description:Despite the prevalence of antisense transcripts in bacterial transcriptomes, little is known about how their synthesis is controlled. We report that a major function of the Escherichia coli termination factor Rho and its co-factor NusG is suppression of ubiquitous antisense transcription genome-wide. Rho binds C-rich unstructured nascent RNA (high C/G ratio) prior to its ATP-dependent dissociation of transcription complexes. NusG is required for efficient termination at minority subsets (~20%) of both antisense and sense Rho-dependent terminators with lower C/G ratio sequences. In contrast, a widely studied nusA deletion proposed to compromise Rho-dependent termination had no effect on antisense or sense Rho-dependent terminators in vivo. Global co-localization of the nucleoid-associated protein H-NS with Rho-dependent terminators and genetic interactions between hns and rho suggest that H-NS aids Rho in suppression of antisense transcription. The combined actions of Rho, NusG, and H-NS appear to be analogous to the Sen1-Nrd1-Nab3 and nucleosome systems that suppress antisense transcription in eukaryotes. RNA-seq experiments were performed on ribosome-depleted RNA from cells treated with 20 ug/ml bicyclomycin or untreated cells. The series contains 4 datasets.

2012-11-01 | E-GEOD-41939 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data