Global proteomic profiling of Yersinia ruckeri strains.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28931430", "kind": "science-record", "revision": 8, "content_hash": "sha256:a2f4675544513546a48e37528e33177286f2dab72473f88bb5298b8111bccb94", "created_at": "2026-11-01T15:40:28Z", "updated_at": "2026-11-01T22:43:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Global proteomic profiling of Yersinia ruckeri strains.", "doi": "10.1186/s13567-017-0460-3", "pmid": "28931430", "authors": ["Gokhlesh Kumar", "Karin Hummel", "Timothy J Welch", "Ebrahim Razzazi-Fazeli", "Mansour El-Matbouli"], "journal": "Veterinary research", "year": 2017, "abstract": "Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM) of salmonids. There is little information regarding the proteomics of Y. ruckeri. Herein, we perform whole protein identification and quantification of biotype 1 and biotype 2 strains of Y. ruckeri grown under standard culture conditions using a shotgun proteomic approach. Proteins were extracted, digested and peptides were separated by a nano liquid chromatography system and analyzed with a high-resolution hybrid triple quadrupole time of flight mass spectrometer coupled via a nano ESI interface. SWATH-MS technology and sophisticated statistical analyses were used to identify proteome differences among virulent and avirulent strains. GO annotation, subcellular localization, virulence proteins and antibiotic resistance ontology were predicted using bioinformatic tools. A total of 1395 proteins were identified in the whole cell of Y. ruckeri. These included proteases, chaperones, cell division proteins, outer membrane proteins, lipoproteins, receptors, ion binding proteins, transporters and catalytic proteins. In virulent strains, a total of 16 proteins were upregulated including anti-sigma regulatory factor, arginine deiminase, phosphate-binding protein PstS and superoxide dismutase Cu-Zu. Additionally, several virulence proteins were predicted such as Clp and Lon pro-teases, TolB, PPIases, PstS, PhoP and LuxR family transcriptional regulators. These putative virulence proteins might be used for development of novel targets for treatment of ERM in fish. Our study represents one of the first global proteomic reference profiles of Y. ruckeri and this data can be accessed via ProteomeXchange with identifier PXD005439. These proteomic profiles elucidate proteomic mechanisms, pathogenicity, host-interactions, antibiotic resistance ontology and localization of Y. ruckeri proteins.", "claims": [{"id": "claim-method", "statement": "Differential expression of proteins in each strain was assessed using one-way ANOVA for each protein.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28931430", "locator": "sections[7] \"Data analysis\" paragraph 3", "quote": "Differential expression of proteins in each strain was assessed using one-way ANOVA for each protein."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Shotgun proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [58] with the dataset identifier PXD005439.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28931430", "locator": "sections[17] \"Data deposition\" paragraph 2", "quote": "Shotgun proteomics data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository [58] with the dataset identifier PXD005439."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:28931430"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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