Genomic and proteomic characterization of a newly isolated Paenarthrobacter ilicis strain and its plasmid-mediated xanthan degradation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41369518", "kind": "science-record", "revision": 3, "content_hash": "sha256:7de74f9439f7dd4b36021ecba82d8ff161845f3ddf9be404d21bca9cb5f91517", "created_at": "2026-11-01T20:31:23Z", "updated_at": "2026-11-01T22:15:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Genomic and proteomic characterization of a newly isolated Paenarthrobacter ilicis strain and its plasmid-mediated xanthan degradation.", "doi": "10.1128/spectrum.01690-25", "pmid": "41369518", "authors": ["Michael Thomas", "Andreas Schlüter", "Jenny Fjodorova", "Christian Rückert", "Tobias Busche", "Karsten Niehaus"], "journal": "Microbiology spectrum", "year": 2026, "abstract": "Environmental soil samples enriched with xanthan gum led to the discovery and isolation of a novel strain of motile Paenarthrobacter ilicis in Bielefeld, Germany, which possesses a previously uncharacterized xanthan utilization gene region on its sole plasmid. This bacterium is the first member of the Paenarthrobacter genus to feature the ability to degrade xanthan. Growth experiments elucidated the optimal growth conditions with regard to pH (7.0) and temperature (28°C-30°C). The genome of Paenarthrobacter ilicis strain 6C consists of two replicons, namely a chromosome with 4,049,144 nucleotides (62.8% GC content) and a plasmid of 147,742 base pairs (61.8% GC content). This novel Paenarthrobacter ilicis strain carries 3,806 predicted coding regions, approximately half (51%) of which were verified with proteome analysis. Cultures grown with either glucose or xanthan as a carbon source were compared in relation to protein abundances at four growth stages and time points with regard to both intracellular and extracellular protein fractions. The proteome analysis (data are available via ProteomeXchange with identifier PXD063987) was undertaken using an LC-ESI-MS-MS shotgun proteomics approach, and the proteins were identified and quantified via label-free quantification using MaxQuant 2.6.6. This proteomics investigation exposed significant differences in protein abundances with regard to time and condition. Among the most highly enriched proteins seen when feeding exclusively on xanthan as a carbon source were enzymes encoded on a xanthan degradation plasmid (pPANIL_6C) with a xanthan utilization region coding for the PL8 xanthan lyase, GH38-, GH3-, GH9-family proteins, and several sugar transporters. These proteins constitute key components of a prospective xanthan degradation pathway.IMPORTANCEA novel Paenarthrobacter isolate was sequenced and characterized by proteome analysis to provide the first clear look at a novel genus in the realm of xanthan-degrading microorganisms. This research provides additional groundwork for the ongoing characterization of Paenarthrobacter, as well as widening the understanding of xanthan-degrading microorganisms. For the first time, a xanthan degradation region was identified on a plasmid 1 kb directly downstream from a mobilization gene (mobF), posing the question of whether this metabolic capacity can be shared through horizontal gene transfer. Overall, this research expands the current knowledge base regarding Paenarthrobacter biology, as well as microbial xanthan degradation and utilization.", "claims": [{"id": "claim-method", "statement": "The proteins in the ROI and “Rest of Genome” groups were compared and used in statistical tests (t-test and K-S test) to determine if the fold change behavior of the ROI group is significantly different from that of all other proteins.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41369518", "locator": "sections[33] \"Statistical evaluation\" paragraph 5", "quote": "The proteins in the ROI and “Rest of Genome” groups were compared and used in statistical tests (t-test and K-S test) to determine if the fold change behavior of the ROI group is significantly different from that of all other proteins."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The trimmed genomic data are available from SRA via BioProject PRJNA1182270. 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The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD063987 and https://dx.doi.org/10.6019/PXD063987 (53)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "At an OD600 of 1.0, 12 proteins were measured, and all of them were significantly overabundant in the xanthan condition (100%).", "kind": "quantitative", "target": {"value": 100.0, "unit": "per cent", "tolerance": null, "source": "At an OD600 of 1.0, 12 proteins were measured, and all of them were significantly overabundant in the xanthan condition (100%)."}, "evidence": [{"asset": "source:pmid:41369518", "locator": "sections[7] \"Differences in the Paenarthrobacter ilicis 6C proteome grown in medium with xanthan relative to glucose\" paragraph 8", "quote": "At an OD600 of 1.0, 12 proteins were measured, and all of them were significantly overabundant in the xanthan condition (100%)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "At an OD600 of 1.0, 12 proteins were measured, and all of them were significantly overabundant in the xanthan condition (100%).", "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:41369518"], "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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