Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33673118", "kind": "science-record", "revision": 6, "content_hash": "sha256:85431cfa8e0298d901088303f7755f302c7263eaa018e75a98f58c304c02f506", "created_at": "2026-11-01T15:41:27Z", "updated_at": "2026-11-01T21:24:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059.", "doi": "10.3390/md19020108", "pmid": "33673118", "authors": ["Xiyan Wang", "Thomas Isbrandt", "Mikael Lenz Strube", "Sara Skøtt Paulsen", "Maike Wennekers Nielsen", "Yannick Buijs", "Erwin M Schoof", "Thomas Ostenfeld Larsen", "Lone Gram", "Sheng-Da Zhang"], "journal": "Marine drugs", "year": 2021, "abstract": "Genome mining of pigmented Pseudoalteromonas has revealed a large potential for the production of bioactive compounds and hydrolytic enzymes. The purpose of the present study was to explore this bioactivity potential in a potent antibiotic and enzyme producer, Pseudoalteromonas rubra strain S4059. Proteomic analyses (data are available via ProteomeXchange with identifier PXD023249) indicated that a highly efficient chitin degradation machinery was present in the red-pigmented P. rubra S4059 when grown on chitin. Four GH18 chitinases and two GH20 hexosaminidases were significantly upregulated under these conditions. GH19 chitinases, which are not common in bacteria, are consistently found in pigmented Pseudoalteromonas, and in S4059, GH19 was only detected when the bacterium was grown on chitin. To explore the possible role of GH19 in pigmented Pseudoalteromonas, we developed a protocol for genetic manipulation of S4059 and deleted the GH19 chitinase, and compared phenotypes of the mutant and wild type. However, none of the chitin degrading ability, secondary metabolite profile, or biofilm-forming capacity was affected by GH19 deletion. In conclusion, we developed a genetic manipulation protocol that can be used to unravel the bioactive potential of pigmented pseudoalteromonads. An efficient chitinolytic enzyme cocktail was identified in S4059, suggesting that this strain could be a candidate with industrial potential.", "claims": [{"id": "claim-method", "statement": "To identify proteins with significantly different abundances when S4059 were grown on chitin compared to on mannose, the FDR were estimated using Benjamini–Hochberg method, and a two-tailed unpaired t-test was used with a combination of p-value ≤ 0.05 and Log2 fold-change ≥1.5 [51].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33673118", "locator": "sections[17] \"4.5. Proteomic Data Acquisition\" paragraph 3", "quote": "To identify proteins with significantly different abundances when S4059 were grown on chitin compared to on mannose, the FDR were estimated using Benjamini–Hochberg method, and a two-tailed unpaired t-test was used with a combination of p-value ≤ 0.05 and Log2 fold-change ≥1.5 [51]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Proteomic data are available via ProteomeXchange with identifier PXD023249 (http://www.proteomexchange.org/) and the genome of Pseudoalteromonas rubra S4059 is available at the National Center for Biotechnology Information (NCBI) under the accession number CP045429 (https://www.ncbi.nlm.nih.gov/nuccore/CP045429.1/ (accessed on 23 November 2020)) and CP045430 (https://www.ncbi.nlm.nih.gov/nuccore/CP045430.1/ (accessed on 23 November 2020)). Further inquiries can be directed to the corresponding author/s.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33673118", "locator": "sections[30] \"Data Availability Statement\" paragraph 2", "quote": "Proteomic data are available via ProteomeXchange with identifier PXD023249 (http://www.proteomexchange.org/) and the genome of Pseudoalteromonas rubra S4059 is available at the National Center for Biotechnology Information (NCBI) under the accession number CP045429 (https://www.ncbi.nlm.nih.gov/nuccore/CP045429.1/ (accessed on 23 November 2020)) and CP045430 (https://www.ncbi.nlm.nih.gov/nuccore/CP045430.1/ (accessed on 23 November 2020)). Further inquiries can be directed to the corresponding author/s."}], "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:33673118"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD023249"], "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": {}, "inputs": ["data:geo:PXD023249"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33673118", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/md19020108", "sha256": "sha256:8d8f73c804c7c497b2c19d0f5183ccdb26db76fd36a226f4ad9c2435581e64e9", "bytes": 63381, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/md19020108", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7917724", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD023249", "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=PXD023249", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD023249", "version": null, "note": "Proteomic data are available via ProteomeXchange with identifier PXD023249 (http://www.proteomexchange.org/) and the genome of Pseudoalteromonas rubra S4059 is available at the National Center for Biotechnology Information (NCBI) under the accession number CP045429 (https://www.ncbi.nlm.nih.gov/nuccore/CP045429.1/ (accessed on 23 November 2020)) and CP045430 (https://www.ncbi.nlm.nih.gov/nuccore/CP045430.1/ (accessed on 23 November 2020)). Further inquiries can be directed to the corresponding author/s.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Proteomic data are available via ProteomeXchange with identifier PXD023249 (http://www.proteomexchange.org/) and the genome of Pseudoalteromonas rubra S4059 is available at the National Center for Biotechnology Information (NCBI) under the accession number CP045429 (https://www.ncbi.nlm.nih.gov/nuccore/CP045429.1/ (accessed on 23 November 2020)) and CP045430 (https://www.ncbi.nlm.nih.gov/nuccore/CP045430.1/ (accessed on 23 November 2020)). Further inquiries can be directed to the corresponding author/s.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Chitin degradation machinery and secondary metabolite profiles in the marine bacterium Pseudoalteromonas rubra S4059", "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:33673118:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cd82d165729f8bd0b8414038c4048f61151f43956b3ebb306169d89168a04c20", "bytes": 845, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#marinedrugs-19-00108-t001", "version": null, "note": "The chitinolytic machinery in Pseudoalteromonas rubra S4059 according to the prediction of the proteome from Uniprot (Proteome ID UP000305729). The signal peptide was predicted using amino acid sequence by SignalIP-5.0 (http://www.cbs.dtu.dk/services/SignalP/ (accessed on 22 September 2018)).", "structure": {"pmcid": "PMC7917724", "section_index": 3, "section_title": "2.1. In Silico Analysis of Chitin Degrading Machinery and Bioactive Potential in P. rubra S4059", "row_count": 15, "column_count": 3}, "table": {"label": "Table 1", "caption": "The chitinolytic machinery in Pseudoalteromonas rubra S4059 according to the prediction of the proteome from Uniprot (Proteome ID UP000305729). The signal peptide was predicted using amino acid sequence by SignalIP-5.0 (http://www.cbs.dtu.dk/services/SignalP/ (accessed on 22 September 2018)).", "rows": [["Glycoside Hydrolase Type", "Accession", "Signal Peptide"], ["GH18", "A0A5S3USE2", "Y"], ["", "A0A5S3V351", "Y"], ["", "A0A5S3V6T3", "Y"], ["", "A0A5S3V0U4", "Y"], ["", "A0A5S3USH6", "Y"], ["", "A0A5S3V3K3", "Y"], ["", "A0A5S3V378", "Y"], ["GH19", "A0A5S3UX38", "Y"], ["", "A0A5S3UPT5", "N"], ["GH20", "A0A5S3UX95", "Y"], ["", "A0A5S3UV09", "Y"], ["", "A0A5S3V1X9", "Y"], ["LPMO", "A0A5S3UTD1", "Y"], ["", "A0A5S3V4S2", "Y"]], "row_count": 15, "column_count": 3, "numeric_cells": 8, "header_rows": 1, "locator": "section[3]/table-wrap[1]#marinedrugs-19-00108-t001"}}], "gaps": ["asset:data:geo:PXD023249 not downloaded", "asset:data:geo:PXD023249 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Benjamini–Hochberg false discovery rate estimation combined with a two-tailed unpaired t-test, using p-value ≤ 0.05 and log2 fold-change ≥ 1.5.", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "To identify proteins with significantly different abundances when S4059 were grown on chitin compared to on mannose, the FDR were estimated using Benjamini–Hochberg method, and a two-tailed unpaired t-test was used with a combination of p-value ≤ 0.05 and Log2 fold-change ≥1.5 [51]."}}], "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Benjamini–Hochberg false discovery rate estimation combined with a two-tailed unpaired t-test, using p-value ≤ 0.05 and log2 fold-change ≥ 1.5.), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": "R1", "reachable": true, "accessions": ["PXD023249"], "resolved_accessions": ["PXD023249"], "statements": ["Proteomic data are available via ProteomeXchange with identifier PXD023249 (http://www.proteomexchange.org/) and the genome of Pseudoalteromonas rubra S4059 is available at the National Center for Biotechnology Information (NCBI) under the accession number CP045429 (https://www.ncbi.nlm.nih.gov/nuccore/CP045429.1/ (accessed on 23 November 2020)) and CP045430 (https://www.ncbi.nlm.nih.gov/nuccore/CP045430.1/ (accessed on 23 November 2020)). Further inquiries can be directed to the corresponding author/s."], "basis": "The paper names PXD023249 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33673118", "data:geo:PXD023249", "asset:table:pmid:33673118:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD023249"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:27:32Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 54290, "completion_tokens": 2141, "cached_tokens": 792}}, "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:33673118", "type": "paper", "label": "pmid:33673118"}, {"id": "source:pmid:33673118", "type": "manuscript", "label": "PMID 33673118 full text"}, {"id": "data:geo:PXD023249", "type": "dataset", "label": "GEO PXD023249"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33673118", "type": "paper", "label": "pmid:33673118"}, {"id": "source:pmid:33673118", "type": "manuscript", "label": "PMID 33673118 full text"}, {"id": "data:geo:PXD023249", "type": "dataset", "label": "GEO PXD023249"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33673118", "type": "extraction", "used": ["source:pmid:33673118"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD023249", "type": "accession_resolution", "used": ["data:geo:PXD023249"], "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:33673118", "parent_hash": "sha256:df6d58bf2fe413b8f2bc6467b4479cc4fd73f6974d43413174ea472a4cbd1fb1", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD023249 licence not read", "asset:data:geo:PXD023249 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": ["ducer, Pseudoalteromonas rubra strain S4059. Proteomic analyses (data are available via ProteomeXch", "Growing Bacteria and Sample Preparation for Proteomic Analyses The protein samples were prepared a", "(TFA) to a final concentration of 1%. Before mass spectrometry analysis, the peptides were desalted on SOLA", "reconstituted in 1% TFA, 2% Acetonitrile for Mass Spectrometry (MS, Merck, Darmstadt, Germany) analysis. Su"], "order_basis": "paper_text_order:372", "id": "assay:1"}]}