Association of Proteomics Changes with Al-Sensitive Root Zones in Switchgrass.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29565292", "kind": "science-record", "revision": 7, "content_hash": "sha256:cd3ce04fbec440d4ff897a7f4ec9f9917c33c31c64bf13d7e8c33c9011137bb9", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T21:59:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Association of Proteomics Changes with Al-Sensitive Root Zones in Switchgrass.", "doi": "10.3390/proteomes6020015", "pmid": "29565292", "authors": ["Mahesh Rangu", "Zhujia Ye", "Sarabjit Bhatti", "Suping Zhou", "Yong Yang", "Tara Fish", "Theodore W Thannhauser"], "journal": "Proteomes", "year": 2018, "abstract": "In this paper, we report on aluminum (Al)-induced root proteomic changes in switchgrass. After growth in a hydroponic culture system supplemented with 400 μM of Al, plants began to show signs of physiological stress such as a reduction in photosynthetic rate. At this time, the basal 2-cm long root tips were harvested and divided into two segments, each of 1-cm in length, for protein extraction. Al-induced changes in proteomes were identified using tandem mass tags mass spectrometry (TMT-MS)-based quantitative proteomics analysis. A total of 216 proteins (approximately 3.6% of total proteins) showed significant differences between non-Al treated control and treated groups with significant fold change (twice the standard deviation; FDR adjusted p-value < 0.05). The apical root tip tissues expressed more dramatic proteome changes (164 significantly changed proteins; 3.9% of total proteins quantified) compared to the elongation/maturation zones (52 significantly changed proteins, 1.1% of total proteins quantified). Significantly changed proteins from the apical 1-cm root apex tissues were clustered into 25 biological pathways; proteins involved in the cell cycle (rotamase FKBP 1 isoforms, and CDC48 protein) were all at a reduced abundance level compared to the non-treated control group. In the root elongation/maturation zone tissues, the identified proteins were placed into 18 pathways, among which proteins involved in secondary metabolism (lignin biosynthesis) were identified. Several STRING protein interaction networks were developed for these Al-induced significantly changed proteins. This study has identified a large number of Al-responsive proteins, including transcription factors, which will be used for exploring new Al tolerance genes and mechanisms. Data are available via ProteomeXchange with identifiers PXD008882 and PXD009125.", "claims": [{"id": "claim-method", "statement": "Then, a t-test (general linear model procedure) of all constituent peptides was performed to obtain a raw p value, and the p values of all proteins were subjected to false discovery rate (FDR) corrections. These two tests give the statistical significance of every protein between the Al-treated and control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29565292", "locator": "sections[7] \"2.5. Protein Identification and Quantification, and Statistical Analysis\" paragraph 2", "quote": "Then, a t-test (general linear model procedure) of all constituent peptides was performed to obtain a raw p value, and the p values of all proteins were subjected to false discovery rate (FDR) corrections. These two tests give the statistical significance of every protein between the Al-treated and control samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD009125 and PXD008882 under project title “Association of proteomics changes with Al-sensitive root zones in switchgrass” (http://www.ebi.ac.uk/pride).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29565292", "locator": "sections[6] \"2.4. 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