Bacteria
Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal InterfaceProteomics and metaproteomics are important tools for studying the spatiotemporal heterogeneous ecosystem in our gut. We review strategies and their applications to gut ecology studies, such as building a dynamical model of the MLI.
Open Database Searching Enables the Identification and Comparison of Bacterial Glycoproteomes without Defining Glycan Compositions Prior to SearchingWe assess the ability of open searching (OS) to analyze bacterial glycoproteomes. We find OS readily identifies known and unknown glycans within samples. Using OS, we compared glycan use across eight Burkholderia species confirming the conservation of glycan use and highlight how low frequency glycans can be identified in OS data sets. Importantly, OS is not without caveats; leading to lower assignment scores and under reporting multiply glycosylated peptides. This supports the value of OS followed by focused searching approaches.
Proteomics of Campylobacter jejuni Growth in Deoxycholate Reveals Cj0025c as a Cystine Transport Protein Required for Wild-type Human Infection PhenotypesGrowth in the bile salt component deoxycholate (DOC) results in a profound change in the Campylobacter jejuni proteome that is reflected in phenotypic alterations including increased virulence, antibiotic resistance, and nutrient transport. A significantly induced protein was Cj0025c, which shares sequence similarity with TcyP cystine transporters from other bacteria. We show that Cj0025c is required for cystine uptake and deletion of cj0025c results in a sulfur-starved proteome and loss of wild-type phenotypes including human cell invasion, motility and helical morphology.
The Aspergillus fumigatus Secretome Alters the Proteome of Pseudomonas aeruginosa to Stimulate Bacterial Growth: Implications for Co-infectionThe growth of Pseudomonas aeruginosa increased exponentially when exposed to the culture filtrates produced by Aspergillus fumigatus and by co-cultures of A. fumigatus and P. aeruginosa in a nutrient-poor, nitrate-rich medium. Qualitative proteomic analysis of the A. fumigatus culture filtrates identified several secreted proteases and peptidases, including known human allergens. LFQ proteomics performed on P. aeruginosa exposed to the culture filtrates identified changes in several pathways and processes including an increase in outer-membrane proteins and stress response proteins.
Ionizing Radiation-induced Proteomic Oxidation in Escherichia coliMeasurement of ionizing radiation induced proteome-wide oxidative modification in both E. coli and the highly radiation resistant D. radiodurans. Although E. coli has several IR-induced oxidation events, D. radiodurans is virtually unaffected by IR treatment. An active site cysteine in the enzyme GAPDH within the glycolytic pathway was the largest IR-induced change in E coli, a result that replicated in human cells, suggesting GAPDH is partially responsible for IR response in higher organisms.
Proteomic Analysis of Salmonella-modified Membranes Reveals Adaptations to Macrophage HostsThe proteome of Salmonella-modified membranes has been extracted using an affinity-based proteome approach. The data highlight communalities between the compartment in epithelial and phagocytic cells, but also provide evidence for cell-specific adaptations in Salmonella pathogen-containing compartments. These observations provide novel insights into the mechanisms of host-dependent differences in the pathophysiology of Salmonella infections.
Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based ProteotypingPeptide biomarker candidates for the respiratory tract pathogens Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis and Staphylococcus aureus are presented. First, bacterial cultures representing the genetic variability in each of the four species, were analyzed. The peptide biomarker candidates were then experimentally verified to be present in a clinical situation by analyzing true positive clinical samples. The most promising peptide biomarkers were used in a targeted MS mode, demonstrating their use for future clinical implementation.
Citrullinome of Porphyromonas gingivalis Outer Membrane Vesicles: Confident Identification of Citrullinated PeptidesThe citrullinome of P. gingivalis outer membrane vesicles (OMV) has been explored by a novel two-dimensional separation system combined with high resolution mass spectrometry and in-house build software. Analysis of OMVs from wild-type and two PPAD mutants resulted in confident discrimination based on citrullinated peptides. In the wild-type citrullinome 78 proteins were identified having a total of 161 validated citrullination sites. A single citrullination was identified in the C351A mutant and none in the ΔPPAD mutant.