Microbiology
Critical Role of a Sheath Phosphorylation Site On the Assembly and Function of an Atypical Type VI Secretion SystemKCl stimulation triggers assembly of the Francisella T6SS in culture. Differential whole cell proteomics reveals that the amounts of the T6SS proteins remain unchanged upon KCl stimulation. A phosphoproteomic analysis identifies a phosphorylation on the T6SS sheath, at site Y139 of IglB. Our data demonstrate that site Y139 of IglB plays a critical role in T6SS biogenesis, providing novel mechanistic insight into the role of sheath phosphorylation in T6SS biogenesis.
Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine LearningWe have developed a new method for the identification of bacterial species causing Urinary Tract Infections. The first training step used DIA analysis on multiple replicates of bacterial inoculates to define a peptide signature by machine learning classifiers. In a second identification step, the signature is monitored by targeted proteomics on unknown samples. This fast, culture-free and accurate method paves the way of the development of new diagnostic approaches limiting the emergence of antimicrobial resistances.
ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolorLysine succinylation is a prevalent protein modification that regulates multiple critical cellular processes. Here, we performed a quantitative succinylome analysis in the model soil bacterium Streptomyces coelicolor after characterization of a specific desuccinylase ScCobB2. Comparison of the ΔScCobB2 to the wild-type succinylome identified a total of 673 unique succinylated sites, and among which, 144 protein sites are statistically hypersuccinylated in ΔScCobB2 cells. Analyses of these hypersuccinylated proteins suggested they are enriched in two major pathways, protein biosynthesis and carbon metabolism. We propose that ScCobB2 has critical regulatory roles in S. coelicolor cellular physiology.
metaQuantome: An Integrated, Quantitative Metaproteomics Approach Reveals Connections Between Taxonomy and Protein Function in Complex MicrobiomesmetaQuantome enables quantitative analysis of the taxonomic and functional state of a microbiome. Leveraging quantitative mass spectrometry data generated from metaproteomic samples along with taxonomic and functional annotations, metaQuantome unravels the complex and hierarchical data structure of taxonomic and functional ontologies. As a result, metaQuantome enables data exploration, tests hypotheses, and generates high-quality visualizations. metaQuantome deciphers the contribution of taxa to a functional process and vice versa. Its accessibility will pave the way for advanced multi-omic analysis of diverse microbiomes.
Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon Sulfolobus islandicusAbout 26% of the total proteins and 44% of the identified proteins were acetylated at lysine residues and the N terminus, respectively, in the hyperthermophilic archaeon Sulfolobus islandicus. A Pat homolog preferentially acetylated a group of acyl-CoA synthetases among the acetylated proteins, whereas an Ard1 homolog exhibited broad substrate specificity. A S. islandicus mutant strain lacking the Pat homolog showed no significant growth defects and that lacking the Ard1 homolog grew more slowly than the parent strain.
The mRNA-bound Proteome of Leishmania mexicana: Novel Genetic Insight into an Ancient ParasiteA comprehensive, quantified identification of the mRNA-binding and whole cell proteomes in the three main Leishmania lifecycle stages, the first such comparison in kinetoplastid parasites, demonstrates trans-regulator RBPs select distinct, specific mRNA target pools in a stage-regulated manner despite equivalent, constitutive transcript levels available. Results further indicate that in L. mexicana parasites, mRNA levels are not a strong predictor of whole cell expression or RNA binding potential of encoded proteins. Included are the first proteomes from the human-infective metacyclic promastigote stage.
Proteomics Reveals Multiple Phenotypes Associated with N-linked Glycosylation in Campylobacter jejuniN-linked protein glycosylation (Pgl) in Campylobacter jejuni is required for chicken colonization and human virulence, yet its biological role remains unknown. pgl gene deletion resulted in a significant rearrangement of the C. jejuni proteome that leads to alterations in crucial phenotypes including stress response, nutrient uptake, electron transport and chemotaxis, and is essential for full activity of the Nap nitrate reductase. N-glycosylation therefore contributes to multiple “virulence” phenotypes in C. jejuni.
Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophilaThe affinity antibody purification combined with LC MS/MS was used to investigate the lysine succinylome profile of A. hydrophila ATCC7966. A total of 666 lysine succinylation proteins were identified and analyzed in depth to better understand its regulatory roles. Lysine succinylation modifications on S-ribosylhomocysteine lyase were further studied and shown to regulate its cellular physiology and affect bacterial quorum sensing behavior of A. hydrophila.
Carcinogenic Helicobacter pylori Strains Selectively Dysregulate the In Vivo Gastric Proteome, Which May Be Associated with Stomach Cancer ProgressionHelicobacter pylori is the strongest risk factor for gastric cancer. Initial interactions between H. pylori and its host occur at the epithelial cell surface, and this activates signaling pathways that drive oncogenesis. This manuscript defines strain-specific gastric epithelial proteomic changes induced by H. pylori in vivo that are critical for initiation of the gastric carcinogenesis. Protein targets were validated in human gastric epithelial cells in vitro, primary human gastric epithelial monolayers, and H. pylori-infected gerbil and human tissue in vivo.