PXD029140

PXD029140 is an original dataset announced via ProteomeXchange.

Title	Impacts of resistance gene knock-outs on the proteome
Description	The spread of antibiotic resistance has developed to all known antibiotics. Extended spectrum β-lactamase-producing bacteria are particularly problematic, as they are resistant to a wide range of commonly used antibiotics. Resistance to β-lactams is known to be multifactorial, although the underlying mechanisms generally are poorly understood but critical factors for effective therapy against infections, especially for multi-resistant pathogenic bacteria. In the present study, a plasmid-based homologous recombination system was used to target and delete specific β-lactamase genes (i.e., the blaOXA-1, blaTEM-1 or the ESBL blaCTX-M15) of the clinical strain ESBL Escherichia coli CCUG 73778, generating three “knock-out” clone variants, each one lacking only one of the β-lactamases. The objective was to determine the genotypic impacts of each gene loss on the phenotypic antibiotic resistance and proteome of the bacterium. Quantitative proteomic analyses performed on the three clone variants and the original strain, using tandem mass tags (TMT) and bottom-up liquid chromatography tandem mass spectrometry (LC-MS/MS), after exposure to different concentrations of cefadroxil. Variation of the proteome in each clone variant was determined, to establish the relative importance of each resistance gene and better understand the genetic and proteomic responses and mechanisms of the resistance phenotypes. The knockout of blaCTX-M-15 was observed to have the greatest impact in protein expression, with the knockout of blaOXA-1 also effecting a marked but lower degree of changes. Proteins known to be associated with antibiotic resistance, cell membrane integrity, cellular stress, gene expression and hypothetical/unknown function proteins, among others, demonstrated distinct differences in expression levels (Fold change >1-5 or <-1.5), that may be related to aspects of compensation for the mutant resistance phenotypes. The present study provides a framework to study the impacts of targeted loss of antibiotic resistance genes in clinically relevant strains for understanding the mechanisms of phenotypic antibiotic resistance.
HostingRepository	PRIDE
AnnounceDate	2023-01-04
AnnouncementXML	Submission_2023-01-04_04:53:49.434.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	ProteomicsCore Facility
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-15 03:21:40	ID requested
⏵ 1	2023-01-04 04:53:49	announced

Dataset with its publication pending

submitter keyword: Escherichia coli,antibiotic resistance, β-lactamase, quantitative proteomics, tandem mass tag, LC-MS/MS

EdwardMoore
contact affiliation	Professor,Department of Infectious Diseases, University of Gothenburg; Box 480, 40530 Göteborg, Sweden
contact email	edward.moore@gu.se
lab head
ProteomicsCore Facility
contact affiliation	SAMBIO Core Facilities, Sahgrenska Academy, University of Gothenburg
contact email	gupcf@outlook.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/01/PXD029140

PRIDE project URI

• PRIDE
  1. PXD029140
     1. Label: PRIDE project
     2. Name: Impacts of resistance gene knock-outs on the proteome