Proteomic analysis of protein lysine 2-hydroxyisobutyrylation (Khib) in soybean leaves.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36631736", "kind": "science-record", "revision": 3, "content_hash": "sha256:1a8140652ea82ff4ca9e14068df3137b7cd368e93f2e3fd526605eae5c788916", "created_at": "2026-11-01T19:01:11Z", "updated_at": "2026-11-01T22:08:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Proteomic analysis of protein lysine 2-hydroxyisobutyrylation (Khib) in soybean leaves.", "doi": "10.1186/s12870-022-04033-6", "pmid": "36631736", "authors": ["Wei Zhao", "Ting-Hu Ren", "Yan-Zheng Zhou", "Sheng-Bo Liu", "Xin-Yang Huang", "Tang-Yuan Ning", "Geng Li"], "journal": "BMC plant biology", "year": 2023, "abstract": "BACKGROUND: Protein lysine 2-hydroxyisobutyrylation (Khib) is a novel post-translational modification (PTM) discovered in cells or tissues of animals, microorganisms and plants in recent years. Proteome-wide identification of Khib-modified proteins has been performed in several plant species, suggesting that Khib-modified proteins are involved in a variety of biological processes and metabolic pathways. However, the protein Khib modification in soybean, a globally important legume crop that provides the rich source of plant protein and oil, remains unclear.\nRESULTS: In this study, the Khib-modified proteins in soybean leaves were identified for the first time using affinity enrichment and high-resolution mass spectrometry-based proteomic techniques, and a systematic bioinformatics analysis of these Khib-modified proteins was performed. Our results showed that a total of 4251 Khib sites in 1532 proteins were identified as overlapping in three replicates (the raw mass spectrometry data are available via ProteomeXchange with the identifier of PXD03650). These Khib-modified proteins are involved in a wide range of cellular processes, particularly enriched in biosynthesis, central carbon metabolism and photosynthesis, and are widely distributed in subcellular locations, mainly in chloroplasts, cytoplasm and nucleus. In addition, a total of 12 sequence motifs were extracted from all identified Khib peptides, and a basic amino acid residue (K), an acidic amino acid residue (E) and three aliphatic amino acid residues with small side chains (G/A/V) were found to be more preferred around the Khib site. Furthermore, 16 highly-connected clusters of Khib proteins were retrieved from the global PPI network, which suggest that Khib modifications tend to occur in proteins associated with specific functional clusters.\nCONCLUSIONS: These findings suggest that Khib modification is an abundant and conserved PTM in soybean and that this modification may play an important role in regulating physiological processes in soybean leaves. The Khib proteomic data obtained in this study will help to further elucidate the regulatory mechanisms of Khib modification in soybean in the future.", "claims": [{"id": "claim-method", "statement": "GO term or KEGG pathway enrichment analysis were carried out with the DAVID tool [41], and annotation terms with a corrected p-value < 0.05 by Fisher’s exact test were considered significantly enriched.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36631736", "locator": "sections[15] \"Functional annotation of Khib-modified peptides and proteins\" paragraph 2", "quote": "GO term or KEGG pathway enrichment analysis were carried out with the DAVID tool [41], and annotation terms with a corrected p-value < 0.05 by Fisher’s exact test were considered significantly enriched."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data of MS spectrometry were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier of PXD036505 (http://www.ebi.ac.uk/pride/archive/projects/PXD036505).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36631736", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "The raw data of MS spectrometry were deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier of PXD036505 (http://www.ebi.ac.uk/pride/archive/projects/PXD036505)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Our results showed that a total of 4251 Khib sites in 1532 proteins were identified as overlapping in three replicates (the raw mass spectrometry data are available via ProteomeXchange with the identifier of PXD03650).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36631736", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Our results showed that a total of 4251 Khib sites in 1532 proteins were identified as overlapping in three replicates (the raw mass spectrometry data are available via ProteomeXchange with the identifier of PXD03650)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Our results showed that a total of 4251 Khib sites in 1532 proteins were identified as overlapping in three replicates (the raw mass spectrometry data are available via ProteomeXchange with the identifier of PXD03650).", "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:36631736"], "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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