Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25728785", "kind": "science-record", "revision": 3, "content_hash": "sha256:113279141ac18c7eec0594ed592fa09b1a5e9aacb0434b1238c6fb77b92f1c84", "created_at": "2026-11-01T15:40:07Z", "updated_at": "2026-11-01T18:47:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots.", "doi": "10.1002/pmic.201400530", "pmid": "25728785", "authors": ["Hongtao Zhang", "Michael J Deery", "Lucy Gannon", "Stephen J Powers", "Kathryn S Lilley", "Frederica L Theodoulou"], "journal": "Proteomics", "year": 2015, "abstract": "According to the Arg/N-end rule pathway, proteins with basic N-termini are targeted for degradation by the Arabidopsis thaliana E3 ligase, PROTEOLYSIS6 (PRT6). Proteins can also become PRT6 substrates following post-translational arginylation by arginyltransferases ATE1 and 2. Here, we undertook a quantitative proteomics study of Arg/N-end rule mutants, ate1/2 and prt6, to investigate the impact of this pathway on the root proteome. Tandem mass tag labelling identified a small number of proteins with increased abundance in the mutants, some of which represent downstream targets of transcription factors known to be N-end rule substrates. Isolation of N-terminal peptides using terminal amine isotope labelling of samples (TAILS) combined with triple dimethyl labelling identified 1465 unique N-termini. Stabilising residues were over-represented among the free neo-N-termini, but destabilising residues were not markedly enriched in N-end rule mutants. The majority of free neo-N-termini were revealed following cleavage of organellar targeting signals, thus compartmentation may account in part for the presence of destabilising residues in the wild-type N-terminome. Our data suggest that PRT6 does not have a marked impact on the global proteome of Arabidopsis roots and is likely involved in the controlled degradation of relatively few regulatory proteins. All MS data have been deposited in the ProteomeXchange with identifier PXD001719 (http://proteomecentral.proteomexchange.org/dataset/PXD001719).", "claims": [{"id": "claim-data-access", "statement": "All MS data have been deposited in the ProteomeXchange with identifier PXD001719 (http://proteomecentral.proteomexchange.org/dataset/PXD001719).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25728785", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All MS data have been deposited in the ProteomeXchange with identifier PXD001719 (http://proteomecentral.proteomexchange.org/dataset/PXD001719)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "TMT labelling quantified 3765 Arabidopsis root proteins, with 17 proteins consistently up-regulated in both experiments, supporting the headline conclusion that PRT6 does not have a marked impact on the global root proteome; the specific statistical treatment is not stated in the listed main-text sections, the protein dataset is provided in Supporting Information Table 1, and the MS data are deposited in ProteomeXchange under PXD001719.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25728785", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our data suggest that PRT6 does not have a marked impact on the global proteome of Arabidopsis roots and is likely involved in the controlled degradation of relatively few regulatory proteins."}, {"asset": "source:pmid:25728785", "locator": "sections[11] \"3.2 Identification of proteins differentially regulated in N-end rule mutants by TMT labelling\" paragraph 2", "quote": "A total of 3300 proteins were quantified in experiment 1 and 2863 in experiment 2, with an overlap of 2408 (Fig. 2B), however, the vast majority of these proteins did not change in abundance in the mutants (Fig. 2C)."}, {"asset": "source:pmid:25728785", "locator": "sections[11] \"3.2 Identification of proteins differentially regulated in N-end rule mutants by TMT labelling\" paragraph 4", "quote": "Seventeen up-regulated proteins were identified in both experiments, four of which were previously shown to be up-regulated at the transcriptional level in both prt6 and ate1/2 [13]."}, {"asset": "source:pmid:25728785", "locator": "sections[11] \"3.2 Identification of proteins differentially regulated in N-end rule mutants by TMT labelling\" paragraph 2", "quote": "The full dataset is presented in Supporting Information Table 1."}, {"asset": "source:pmid:25728785", "locator": "sections[11] \"3.2 Identification of proteins differentially regulated in N-end rule mutants by TMT labelling\" paragraph 3", "quote": "Plots depict log (2) transformed ratios of abundance of 3765 proteins ranked from low to high."}, {"asset": "source:pmid:25728785", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All MS data have been deposited in the ProteomeXchange with identifier PXD001719 (http://proteomecentral.proteomexchange.org/dataset/PXD001719)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "TMT labelling quantified 3765 Arabidopsis root proteins, with 17 proteins consistently up-regulated in both experiments, supporting the headline conclusion that PRT6 does not have a marked impact on the global root proteome; the specific statistical treatment is not stated in the listed main-text sections, the protein dataset is provided in Supporting Information Table 1, and the MS data are deposited in ProteomeXchange under PXD001719.", "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:25728785"], "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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