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Cells. 2019 Sep 23;8(10). pii: E1129. doi: 10.3390/cells8101129.

The Core Proteome of Biofilm-Grown Clinical Pseudomonas aeruginosa Isolates.

Author information

1
Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany. jelena.erdmann@twincore.de.
2
Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School, Hannover 30625, Germany. jelena.erdmann@twincore.de.
3
Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany. janne.thoeming@twincore.de.
4
Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany. sarah.pohl@twincore.de.
5
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig 38124, Germany. sarah.pohl@twincore.de.
6
Research Core Unit Proteomics and Institute of Toxicology, Hannover Medical School, Hannover 30625, Germany. Pich.Andreas@mh-hannover.de.
7
Institute of Clinical Chemistry, Bioanalytics, University Medical Center Göttingen, Göttingen 37075, Germany. christof.lenz@med.uni-goettingen.de.
8
Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, Göttingen 37077, Germany. christof.lenz@med.uni-goettingen.de.
9
Institute for Molecular Bacteriology, TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover 30625, Germany. susanne.haeussler@helmholtz-hzi.de.
10
Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig 38124, Germany. susanne.haeussler@helmholtz-hzi.de.

Abstract

Comparative genomics has greatly facilitated the identification of shared as well as unique features among individual cells or tissues, and thus offers the potential to find disease markers. While proteomics is recognized for its potential to generate quantitative maps of protein expression, comparative proteomics in bacteria has been largely restricted to the comparison of single cell lines or mutant strains. In this study, we used a data independent acquisition (DIA) technique, which enables global protein quantification of large sample cohorts, to record the proteome profiles of overall 27 whole genome sequenced and transcriptionally profiled clinical isolates of the opportunistic pathogen Pseudomonas aeruginosa. Analysis of the proteome profiles across the 27 clinical isolates grown under planktonic and biofilm growth conditions led to the identification of a core biofilm-associated protein profile. Furthermore, we found that protein-to-mRNA ratios between different P. aeruginosa strains are well correlated, indicating conserved patterns of post-transcriptional regulation. Uncovering core regulatory pathways, which drive biofilm formation and associated antibiotic tolerance in bacterial pathogens, promise to give clues to interactions between bacterial species and their environment and could provide useful targets for new clinical interventions to combat biofilm-associated infections.

KEYWORDS:

DIA; SWATH; bacteria; mass spectrometry; microbiology

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