Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles.

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Outer membrane vesicles (OMVs) released by this species have been demonstrated to deliver effector proteins such as cytolethal distending toxin (CDT) and leukotoxin (LtxA) into human host cells and to act as triggers of innate immunity upon carriage of NOD1- and NOD2-active pathogen-associated molecular patterns (PAMPs). To improve our understanding of the pathogenicity-associated functions that A. actinomycetemcomitans exports via OMVs, we studied the proteome of density gradient-purified OMVs from a rough-colony type clinical isolate, strain 173 (serotype e) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). This analysis yielded the identification of 151 proteins, which were found in at least three out of four independent experiments. Data are available via ProteomeXchange with identifier PXD002509. Through this study, we not only confirmed the vesicle-associated release of LtxA, and the presence of proteins, which are known to act as immunoreactive antigens in the human host, but we also identified numerous additional putative virulence-related proteins in the A. actinomycetemcomitans OMV proteome. The known and putative functions of these proteins include immune evasion, drug targeting, and iron/nutrient acquisition. In summary, our findings are consistent with an OMV-associated proteome that exhibits several offensive and defensive functions, and they provide a comprehensive basis to further disclose roles of A. actinomycetemcomitans OMVs in periodontal and systemic disease.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [62] via the PRIDE partner repository with the dataset identifier PXD002509 and 10.6019/PXD002509.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26381655", "locator": "sections[8] \"LC-MS/MS analysis and data processing\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [62] via the PRIDE partner repository with the dataset identifier PXD002509 and 10.6019/PXD002509."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used a replicate-consistency criterion: LC-MS/MS-identified proteins detected in at least three of four independent OMV preparations were included, yielding a headline OMV proteome of 151 proteins; the source proteomics data are available through ProteomeXchange under identifier PXD002509.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26381655", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This analysis yielded the identification of 151 proteins, which were found in at least three out of four independent experiments."}, {"asset": "source:pmid:26381655", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD002509."}, {"asset": "source:pmid:26381655", "locator": "sections[14] \"Identification of A. actinomycetemcomitans strain 173 OMV proteins by LC-MS/MS, and their predicted subcellular distribution\" paragraph 2", "quote": "In total, 504 proteins were identified by LC-MS/MS in at least one of the four analyzed independent preparations of A. actinomycetemcomitans strain 173 OMVs. Out of these proteins, 151 were present in three of the four preparations analyzed, and defined as the OMV proteome in the present study (S1 Fig, S1 and S2 Tables)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper used a replicate-consistency criterion: LC-MS/MS-identified proteins detected in at least three of four independent OMV preparations were included, yielding a headline OMV proteome of 151 proteins; the source proteomics data are available through ProteomeXchange under identifier PXD002509.", "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:26381655"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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The listed proteins are discussed in the main text.", "structure": {"pmcid": "PMC4575117", "section_index": 16, "section_title": "Virulence-related mechanisms of A. actinomycetemcomitans vesicles as suggested by proteins identified in the strain 173 OMV proteome", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "Virulence-related mechanisms of A. actinomycetemcomitans vesicles as suggested by proteins identified in the strain 173 OMV proteome.The 151 proteins of the strain 173 OMV proteome identified by LC-MS/MS were manually searched for their earlier reported involvement in A. actinomycetemcomitans offense and defense, and in other bacteria. 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