A wide-ranging Pseudomonas aeruginosa PeptideAtlas build: A useful proteomic resource for a versatile pathogen

Abstract

Pseudomonas aeruginosa is an important opportunistic pathogen with high prevalence in nosocomial infections. This microorganism is a good model for understanding biological processes such as the quorum-sensing response, the metabolic integration of virulence, the mechanisms of global regulation of bacterial physiology, and the evolution of antibiotic resistance. Till now, P. aeruginosa proteomic data, although available in several on-line repositories, were dispersed and difficult to access. In the present work, proteomes of the PAO1 strain grown under very different conditions and from diverse cellular compartments have been analyzed and joined to build the Pseudomonas PeptideAtlas. This resource is a comprehensive mass spectrometry-derived peptide and inferred protein database with 71.3% coverage of the total predicted proteome of P. aeruginosa PAO1. This is the highest published coverage among the eight bacterial PeptideAtlas datasets currently available. The proteins in the Pseudomonas PeptideAtlas cover 84% of metabolic proteins, 71% of proteins involved in genetic information processing, 72% of proteins responsible for environmental information processing, more than 80% of proteins related to quorum sensing and biofilm formation, and 81% of proteins responsible for antimicrobial resistance. It exemplifies a necessary tool for targeted proteomics studies, system-wide observations, and cross-species observational studies. Here we describe how this resource was built and some of the physiologically important proteins of this pathogen. SignificancePseudomonas aeruginosa is among the most versatile bacterial pathogens. Studies of its proteome are very important as they can reveal virulence factors and mechanisms of antibiotic resistance. The construction of a proteomic resource such as the PeptideAtlas enables targeted proteomics studies, system-wide observations, and cross-species observational studies.

The ProteomeXchange consortium at 10 years: 2023 update

“…Using similar workflows, PeptideAtlas has also released species-specific builds based on PX data, including builds for human, Arabidopsis ( 27 ), yeast, rohu ( 28 ) and Pseudomonas aeruginosa ( 29 ). SWATHAtlas ( http://www.swathatlas.org/ ) provides spectral libraries suitable for DIA (Data Independent Acquisition) analysis for over a dozen different species, all validated for quality with DIALib-QC ( 30 ).…”

Deep Profiling of the Proteome Dynamics of Pseudomonas aeruginosa Reference Strain PAO1 under Different Growth Conditions

“…Currently, the most comprehensive build of the peptide atlas of the PAO1 strain proteome (assembled in the year 2021, including 19 experiments of samples cultured under very different conditions and from diverse subcellular fractions) contains 57,747 distinct peptides and 4036 canonical proteins. 23 We also note that most of the individual reports of proteomic analysis of Pseudomonas were limited by the depth of measurement (in most cases in the range of 1000 to 2500 proteins). [9][10][11][12][13][14][15]23 In this study, we aimed to provide a detailed census of the proteome under different culturing states (i.e., different growth stages of planktonic culture as well as planktonic vs biofilm cells) and performed an in-depth analysis of protein clusters related to essential metabolic pathways.…”

“…23 We also note that most of the individual reports of proteomic analysis of Pseudomonas were limited by the depth of measurement (in most cases in the range of 1000 to 2500 proteins). [9][10][11][12][13][14][15]23 In this study, we aimed to provide a detailed census of the proteome under different culturing states (i.e., different growth stages of planktonic culture as well as planktonic vs biofilm cells) and performed an in-depth analysis of protein clusters related to essential metabolic pathways.…”

Biofilm matrix proteome of clinical strain of P. aeruginosa

“…Despite the accepted idea of a pivotal role of matrix in bacterial biofilms little is known about the protein composition of the matrix at a level of proteomes. Moreover, for the well-studied and clinically important biofilm-forming bacteria P. aeruginosa there are only a few studies devoted to matrix proteome of reference strains (mainly PAO1, Table 1), while proteomics of the whole biofilm is better described [4,5]. Vibrio cholerae Matrix LC electrospray ionization and then entered into an LTQ linear ion-trap mass spectrometer (ThermoFisher) 74 [19] Haemophilus influenzae (NTHi) ECM Gel-based LC/MS/MS 60 [20] In a comparative study of liquid culture of PAO1 strain and clinical isolates, it was shown that cystic fibrosis (CF) isolates expressed a narrower range of transporters and a broader set of enzymes of metabolic pathways for the biosynthesis of amino acids, carbohydrates, nucleotides, and polyamines, but this study did not cover biofilm mode of life as well as extracellular matrix composition [6].…”

“…Despite the accepted idea of a pivotal role of matrix in bacterial biofilms little is known about the protein composition of the matrix at a level of proteomes. Moreover, for the well-studied and clinically important biofilm-forming bacteria P. aeruginosa there are only a few studies devoted to matrix proteome of reference strains (mainly PAO1, Table 1), while proteomics of the whole biofilm is better described [4, 5].…”