Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28431522", "kind": "science-record", "revision": 4, "content_hash": "sha256:250dd6f83bd020ab7f70e1103c1d7974a6c99b4fe168accdb0c8f954f666ccf2", "created_at": "2026-11-01T15:40:25Z", "updated_at": "2026-11-01T21:20:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative proteomic analysis of Neisseria meningitidis wildtype and dprA null mutant strains links DNA processing to pilus biogenesis.", "doi": "10.1186/s12866-017-1004-8", "pmid": "28431522", "authors": ["Getachew Tesfaye Beyene", "Shewit Kalayou", "Tahira Riaz", "Tone Tonjum"], "journal": "BMC microbiology", "year": 2017, "abstract": "BACKGROUND: DNA processing chain A (DprA) is a DNA binding protein which is ubiquitous in bacteria, and is required for DNA transformation to various extents among bacterial species. However, the interaction of DprA with competence and recombination proteins is poorly understood. Therefore, the proteomes of whole Neisseria meningitidis (Nm) wildtype and dprA mutant cells were compared. Such a comparative proteomic analysis increases our understanding of the interactions of DprA with other Nm components and may elucidate its potential role beyond DNA processing in transformation.\nRESULTS: Using label-free quantitative proteomics, a total of 1057 unique Nm proteins were identified, out of which 100 were quantified as differentially abundant (P ≤ 0.05 and fold change ≥ |2|) in the dprA null mutant. Proteins involved in homologous recombination (RecA, UvrD and HolA), pilus biogenesis (PilG, PilT1, PilT2, PilM, PilO, PilQ, PilF and PilE), cell division, including core energy metabolism, and response to oxidative stress were downregulated in the Nm dprA null mutant. The mass spectrometry data are available via ProteomeXchange with identifier PXD006121. Immunoblotting and co-immunoprecipitation were employed to validate the association of DprA with PilG. The analysis revealed reduced amounts of PilG in the dprA null mutant and reduced amounts of DprA in the Nm pilG null mutant. Moreover, a number of pilus biogenesis proteins were shown to interact with DprA and /or PilG.\nCONCLUSIONS: DprA interacts with proteins essential for Nm DNA recombination in transformation, pilus biogenesis, and other functions associated with the inner membrane. Inverse downregulation of Nm DprA and PilG expression in the corresponding mutants indicates a link between DNA processing and pilus biogenesis.", "claims": [{"id": "claim-method", "statement": "To identify proteins whose abundance were significantly differentially abundant between the wildtype and ΔdprA mutant, a two tailed unpaired t test was used using a false discovery rate (FDR) value of 0.05 and S0 = 2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28431522", "locator": "sections[14] \"Proteomic analysis\" paragraph 6", "quote": "To identify proteins whose abundance were significantly differentially abundant between the wildtype and ΔdprA mutant, a two tailed unpaired t test was used using a false discovery rate (FDR) value of 0.05 and S0 = 2."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [93] partner repository with the dataset identifier PXD00612. The data can be accessed using the username: reviewer90340@ebi.ac.uk and password: zEcQOQsB.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28431522", "locator": "sections[20] \"ack\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [93] partner repository with the dataset identifier PXD00612. The data can be accessed using the username: reviewer90340@ebi.ac.uk and password: zEcQOQsB."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used label-free quantitative proteomics with a statistical significance threshold of P ≤ 0.05 and a fold-change cutoff of ≥ |2|, and made the source mass-spectrometry data available through ProteomeXchange under identifier PXD006121.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28431522", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using label-free quantitative proteomics, a total of 1057 unique Nm proteins were identified, out of which 100 were quantified as differentially abundant (P ≤ 0.05 and fold change ≥ |2|) in the dprA null mutant."}, {"asset": "source:pmid:28431522", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The mass spectrometry data are available via ProteomeXchange with identifier PXD006121."}, {"asset": "source:pmid:28431522", "locator": "sections[3] \"Predominantly less abundant proteins detected in the Nm ΔdprA mutant\" paragraph 3", "quote": "Using a combination of p ≤ 0.05 and a fold change cutoff of ±2, the analysis resulted in 100 proteins whose abundances were significantly changed (Fig. 2; Additional file 1: Table S1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used label-free quantitative proteomics with a statistical significance threshold of P ≤ 0.05 and a fold-change cutoff of ≥ |2|, and made the source mass-spectrometry data available through ProteomeXchange under identifier PXD006121.", "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:28431522"], "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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"section[6]/table-wrap[1]#Tab4", "version": null, "note": "Selected gene products significantly differentially abundant proteins in the Nm ΔdprA mutant compared to the wildtype when identified by mass spectrometry", "structure": {"pmcid": "PMC5399837", "section_index": 6, "section_title": "Proteins involved in core metabolism are significantly regulated by DprA", "row_count": 27, "column_count": 3}, "table": {"label": "Table 4", "caption": "Selected gene products significantly differentially abundant proteins in the Nm ΔdprA mutant compared to the wildtype when identified by mass spectrometry", "rows": [["Genes", "Protein name/function", "Protein foldchange"], ["Cell division proteins"], ["ftsA", "Cell cycle", "-7"], ["ZipA", "cell septum assembly", "-24"], ["lon", "Lon protease/cell cycle", "-22"], ["ftsZ", "Cell cycle", "-12"], ["minD", "Septum site-determining protein", "-11"], ["Proteins of core metabolism"], ["Glycolysis and TCA cycle"], ["tpiA", "Fructose and mannose metabolism; 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Immunoblotting and co-immunoprecipitation were employed to"], "order_basis": "paper_text_order:1257", "id": "assay:1"}]}