Proteomics based analysis of the nicotine catabolism in Paenarthrobacter nicotinovorans pAO1.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30390017", "kind": "science-record", "revision": 7, "content_hash": "sha256:a393105f1922f337f961cab38b6c48885006833712bb3dae88e8c4037ead5d69", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:00:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomics based analysis of the nicotine catabolism in Paenarthrobacter nicotinovorans pAO1.", "doi": "10.1038/s41598-018-34687-y", "pmid": "30390017", "authors": ["Marius Mihăşan", "Cornelia Babii", "Roshanak Aslebagh", "Devika Channaveerappa", "Emmalyn Dupree", "Costel C Darie"], "journal": "Scientific reports", "year": 2018, "abstract": "Paenarthrobacter nicotinovorans is a nicotine-degrading microorganism that shows a promising biotechnological potential for the production of compounds with industrial and pharmaceutical importance. Its ability to use nicotine was linked to the presence of the catabolic megaplasmid pAO1. Although extensive work has been performed on the molecular biology of nicotine degradation in this bacterium, only half of the genes putatively involved have been experimentally linked to nicotine. In the current approach, we used nanoLC-MS/MS to identify a total of 801 proteins grouped in 511 non-redundant protein clusters when P. nicotinovorans was grown on citrate, nicotine and nicotine and citrate as the only carbon sources. The differences in protein abundance showed that deamination is preferred when citrate is present. Several putative genes from the pAO1 megaplasmid have been shown to have a nicotine-dependent expression, including a hypothetical polyketide cyclase. We hypothesize that the enzyme would hydrolyze the N1-C6 bond from the pyridine ring with the formation of α-keto- glutaramate. Two chromosomally-encoded proteins, a malate dehydrogenase, and a D-3-phosphoglycerate dehydrogenase were shown to be strongly up-regulated when nicotine was the sole carbon source and could be related to the production the α-keto-glutarate. The data have been deposited to the ProteomeXchange with identifier PXD008756.", "claims": [{"id": "claim-method", "statement": "Significance was assessed using the Fisher’s Exact test and the p-values were further adjusted using the Benjamini and Hochberg correction to account for multiple comparisons30.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30390017", "locator": "sections[13] \"Data analysis\" paragraph 4", "quote": "Significance was assessed using the Fisher’s Exact test and the p-values were further adjusted using the Benjamini and Hochberg correction to account for multiple comparisons30."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the dataset identifier PXD008756.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30390017", "locator": "sections[18] \"Availability of Materials and Data\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the dataset identifier PXD008756."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:30390017"], "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_unresolved", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD008756"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {"e_value": "199 (putative cyclases, E-value = 9"}, "inputs": ["data:geo:PXD008756"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_unresolved"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30390017", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-018-34687-y", "sha256": "sha256:36a64b21a92d110c2738e51894cf342ae8f1d47a0cd814b3e195d407e8b5691c", "bytes": 38876, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-018-34687-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6214936", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD008756", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD008756", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD008756", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the dataset identifier PXD008756.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the dataset identifier PXD008756.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30390017:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:720f166faf37dffc6b2ffbbe11cb26995b634de30fe140f8538caafa014dacc3", "bytes": 719, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Distribution of the shared and specific non-redundant proteins identified in the cell free lysates of Paenarthrobacter nicotinovorans pAO1.", "structure": {"pmcid": "PMC6214936", "section_index": 3, "section_title": "Proteins identification overview", "row_count": 7, "column_count": 6}, "table": {"label": "Table 1", "caption": "Distribution of the shared and specific non-redundant proteins identified in the cell free lysates of Paenarthrobacter nicotinovorans pAO1.", "rows": [["Proteome", "Dimension (sequences)", "Proteins", "Total number of proteins"], ["Citrate", "Nicotine", "Nicotine and Citrate"], ["Paenarthrobacter aureus TC1", "4565", "332", "306", "218", "397"], ["Paenarthrobacter nicotinovorans", "4722", "377", "369", "268", "482"], ["Specific to P. nicotinovorans", "—", "66", "85", "62", "115"], ["pAO1 megaplasmid", "175", "1", "21", "27", "28"], ["Total number of non-redundant proteins", "—", "398", "391", "279", "511"]], "row_count": 7, "column_count": 6, "numeric_cells": 23, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:30390017:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8e5b0f7e6398ac2268e302af3001661ac4e654418f86c2e183f438e754157273", "bytes": 2879, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#Tab2", "version": null, "note": "Differentially regulated pAO1-encoded proteins during the growth of Paenarthrobacter nicotinovorans on different carbon sources.", "structure": {"pmcid": "PMC6214936", "section_index": 4, "section_title": "Differentially regulated plasmid-encoded proteins in P. nicotinovorans in the presence of nicotine", "row_count": 22, "column_count": 9}, "table": {"label": "Table 2", "caption": "Differentially regulated pAO1-encoded proteins during the growth of Paenarthrobacter nicotinovorans on different carbon sources.", "rows": [["", "Protein", "UniProt ID", "Compared growth conditions"], ["Nicotine vs Citrate", "Nicotine and Citrate vs Citrate", "Nicotine vs Nicotine and Citrate"], ["Fold Change", "Fisher’s exact test (p < 0.00245)", "Fold Change", "Fisher’s exact test (p < 0.00077)", "Fold Change", "Fisher’s exact test (p < 0.00249)"], ["1", "2,6-dihydropseudooxynicotine hydrolase, DHPONH", "DHPON_PAENI", "INF", "<0.00010", "INF", "<0.00010", "3", "<0.00010"], ["2", "2,6-dihydroxypyridine 3-monooxygenase, DHPH", "DHPH_PAENI", "INF", "<0.00010", "INF", "<0.00010", "2.8", "<0.00010"], ["3", "2-oxoglutaramate amidase, NIT", "NIT_PAENI", "INF", "<0.00010", "INF", "<0.00010", "2.3", "0.011"], ["4", "4-methylaminobutanoate oxidase (formaldehyde-forming), MABO", "MABO1_PAENI", "INF", "0.00013", "n.d", "—", "INF", "<0.00010"], ["5", "4-methylaminobutanoate oxidase (methylamine-forming), MAO", "MABO2_PAENI", "INF", "<0.00010", "INF", "<0.00010", "3.9", "<0.00010"], ["6", "6-hydroxy-L-nicotine oxidase 6-HLNO", "Q93NH4_PAENI", "INF", "<0.00010", "INF", "0.00029", "27", "<0.00010"], ["7", "6-hydroxypseudooxynicotine dehydrogenase complex subunit alpha, KDHA", "KDHA_PAENI", "INF", "<0.00010", "INF", "<0.00010", "4.2", "<0.00010"], ["8", "Bifunctional protein FolD", "Q8GAI4_PAENI", "INF", "0.00069", "n.d", "—", "INF", "0.0002"], ["9", "Formyltetrahydrofolate deformylase, PurU", "Q8GAI2_PAENI", "INF", "0.0017", "n.d", "—", "INF", "0.0014"], ["10", "Hypothetical polyketide cyclase, PKC", "Q93NG4_PAENI", "INF", "<0.00010", "INF", "<0.00010", "1.4", "0.15"], ["11", "NAD(P)H-Nicotine Blue (4,4′,5,5′-tetrahydroxy-3,3′-diazadiphenoquinone-(2,2′)) Oxidoreductase, NBOR", "Q8GAJ2_PAENI", "INF", "<0.00010", "INF", "<0.00010", "1.4", "0.23"], ["12", "Nicotine dehydrogenase large subunit NDHL", "Q93NH5_PAENI", "INF", "<0.00010", "INF", "0.00031", "3.1", "0.0058"], ["13", "Nicotine dehydrogenase medium subunit, NDHM", "Q59127_PAENI", "INF", "<0.00010", "INF", "<0.00010", "2.7", "0.0078"], ["14", "Nicotine dehydrogenase small subunit, NDHS", "Q59129_PAENI", "INF", "<0.00010", "INF", "0.00031", "3.1", "0.0058"], ["15", "ORF106, putative molybdenum transport ATPase, MODC", "Q93NG5_PAENI", "INF", "0.0011", "INF", "<0.00010", "1.5", "0.25"], ["16", "ORF78, putative carbon monoxide dehydrogenase subunit G, COXG", "Q93NG2_PAENI", "INF", "<0.00010", "INF", "<0.00010", "2", "0.00017"], ["17", "ORF76, putative carbon monoxide dehydrogenase subunit D, COXD", "Q93NG0_PAENI", "INF", "<0.00010", "INF", "<0.00010", "1.5", "0.24"], ["18", "Succinate-semialdehyde dehydrogenase SsaDH", "SSDH_PAENI", "INF", "<0.00010", "INF", "0.00023", "7.4", "0.00013"], ["19", "ORF92, hypothetical DUF948 domain-containing protein", "Q8GAH6_PAENI", "INF", "0.00032", "n.d", "—", "INF", "0.00014"]], "row_count": 22, "column_count": 9, "numeric_cells": 110, "header_rows": 3, "locator": "section[4]/table-wrap[1]#Tab2"}}], "gaps": ["asset:data:geo:PXD008756 not downloaded", "asset:data:geo:PXD008756 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {"e_value": "199 (putative cyclases, E-value = 9"}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "BLAST"}}, {"id": "method-2", "family": null, "specific": null, "label": "Fisher’s Exact test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Significance was assessed using the Fisher’s Exact test and the p-values were further adjusted using the Benjamini and Hochberg correction to account for multiple comparisons30."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PXD008756"], "resolved_accessions": [], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the MassIVE partner repository with the dataset identifier PXD008756."], "basis": "The paper names PXD008756, but the accession does not resolve in the repository (not_in_proteomexchange), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:30390017", "data:geo:PXD008756", "asset:table:pmid:30390017:1", "asset:table:pmid:30390017:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD008756"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 32246, "completion_tokens": 953, "cached_tokens": 793}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:30390017", "type": "paper", "label": "pmid:30390017"}, {"id": "source:pmid:30390017", "type": "manuscript", "label": "PMID 30390017 full text"}, {"id": "data:geo:PXD008756", "type": "dataset", "label": "GEO PXD008756"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30390017", "type": "paper", "label": "pmid:30390017"}, {"id": "source:pmid:30390017", "type": "manuscript", "label": "PMID 30390017 full text"}, {"id": "data:geo:PXD008756", "type": "dataset", "label": "GEO PXD008756"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30390017", "type": "extraction", "used": ["source:pmid:30390017"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD008756", "type": "accession_resolution", "used": ["data:geo:PXD008756"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:30390017", "parent_hash": "sha256:aa27a2fb8903ddff78abae5fab4e5f4398ca9200ae82170542397bdc794ebb55", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD008756 licence not read", "asset:data:geo:PXD008756 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_unresolved"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Proteomics based analysis of the nicotine catabolism in", "of Materials and Data The mass spectrometry proteomics data have been deposited to the ProteomeXcha", "le 2. Availability of Materials and Data The mass spectrometry proteomics data have been deposited to the P"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["BLAST"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}