Microbiology
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.
A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and ResistanceChanges in proteome and phosphoproteome have been determined in E. coli treated with the antibiotics colistin or ciprofloxacin and in a bona-fide mcr-1 positive colistin resistant strain. The results reveal extensive phosphorylation on bacterial proteins and motif specific phosphorylation changes during resistance development. Moreover, regulated sites show high evolutionary conservation, indicating an important biological role. Together, this indicates that phosphorylation mediated signaling could be used as a specific target for drug design.
Comparative Secretome Analyses of Human and Zoonotic Staphylococcus aureus Isolates CC8, CC22, and CC398The proteogenomes and secretomes of dominant human and zoonotic S. aureus lineages CC8, CC22 and CC398 were compared revealing genomic and regulatory differences in the secretion of 869 proteins. In the core secretome, 101 secreted or cell surface anchored virulence factors contribute with 82.4% to total secretome abundance. CC398 isolates showed higher secretion of α- and ß-hemolysins and lower secretion of surface proteins resulting in strong hemolysis and decreased biofilm formation because of lower SigB activity compared to human-specific CC8 and CC22.