Phosphorylation of plastoglobular proteins in Arabidopsis thaliana.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26962209", "kind": "science-record", "revision": 7, "content_hash": "sha256:825c04576d9e03f3a8abdf85704825a64360843d1e41b20cbdd2ef87bc4b760e", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T21:58:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Phosphorylation of plastoglobular proteins in Arabidopsis thaliana.", "doi": "10.1093/jxb/erw091", "pmid": "26962209", "authors": ["Jens N Lohscheider", "Giulia Friso", "Klaas J van Wijk"], "journal": "Journal of experimental botany", "year": 2016, "abstract": "Plastoglobules (PGs) are plastid lipid-protein particles with a small specialized proteome and metabolome. Among the 30 core PG proteins are six proteins of the ancient ABC1 atypical kinase (ABC1K) family and their locations in an Arabidopsis mRNA-based co-expression network suggested central regulatory roles. To identify candidate ABC1K targets and a possible ABC1K hierarchical phosphorylation network within the chloroplast PG proteome, we searched Arabidopsis phosphoproteomics data from publicly available sources. Evaluation of underlying spectra and/or associated information was challenging for a variety of reasons, but supported pSer sites and a few pThr sites in nine PG proteins, including five FIBRILLINS. PG phosphorylation motifs are discussed in the context of possible responsible kinases. The challenges of collection and evaluation of published Arabidopsis phosphorylation data are discussed, illustrating the importance of deposition of all mass spectrometry data in well-organized repositories such as PRIDE and ProteomeXchange. This study provides a starting point for experimental testing of phosho-sites in PG proteins and also suggests that phosphoproteomics studies specifically designed toward the PG proteome and its ABC1K are needed to understand phosphorylation networks in these specialized particles.", "claims": [{"id": "claim-method", "statement": "In our recent meta-analysis and application of motif-x and MMFPH prediction algorithms, we identified several motif families for pS and pT sites, which could be divided into more specific types (van Wijk et al., 2014).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26962209", "locator": "sections[8] \"p-Site motifs and candidate plastid kinases\" paragraph 2", "quote": "In our recent meta-analysis and application of motif-x and MMFPH prediction algorithms, we identified several motif families for pS and pT sites, which could be divided into more specific types (van Wijk et al., 2014)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Spectral data were downloaded from PhosphAt 4.0, PRIDE (http://www.ebi.ac.uk/pride/archive/) or provided by the authors (upon request) of the corresponding publications (Supplementary Table S1 at JXB online).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26962209", "locator": "sections[3] \"Collection and evaluation of p-proteomics data\" paragraph 2", "quote": "Spectral data were downloaded from PhosphAt 4.0, PRIDE (http://www.ebi.ac.uk/pride/archive/) or provided by the authors (upon request) of the corresponding publications (Supplementary Table S1 at JXB online)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:26962209"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:26962209", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1093/jxb/erw091", "sha256": "sha256:e76bb8cd9856858769cebdd42fc808efa8b7cf07a29c5b9019f9c7aafa56f485", "bytes": 50531, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1093/jxb/erw091", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4915526", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:26962209:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:abbd4323e43732135401ba71c10273a1f0cb9e7dd0a8a1b4312a2b22c9abe836", "bytes": 3126, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#T1", "version": null, "note": "PG-localized and related FIBRILLIN proteins that show reported and (mostly) confirmed p-peptides", "structure": {"pmcid": "PMC4915526", "section_index": 6, "section_title": "Assembly and evaluation of the PG p-proteome", "row_count": 24, "column_count": 9}, "table": {"label": "Table 1.", "caption": "PG-localized and related FIBRILLIN proteins that show reported and (mostly) confirmed p-peptides", "rows": [["Protein i.d.a", "Protein name", "Locationb", "Abundance rank in isolated PGc", "Module in coexpresion networkd", "Reported p-peptidese", "p-Site residue number (low confidence p-sites)f", "Protein length (predicted N-term (exp. N-term))g", "Motif subtype (based on van Wijk et al. 2014)"], ["AT4G0402", "FBN1A", "Core PG", "1", "Not in network", "VFApSpSpSpTVpSVADK", "S74, S75, S76, T77, S79", "318; A56 (S41, A56, T57)", "SxpS, pSxS"], ["AT4G0402", "FBN1A", "Core PG", "1", "Not in network", "ApTDIDDEWGQDGVER", "T57", "318; A56 (S41, A56, T57)", "TD"], ["AT4G2224", "FBN1B", "Core PG", "3", "Not in network", "ApTDTGEIGSALLAAEEAIEDVEETERLKR", "T61", "310; A60 (A60)", "TD"], ["AT4G2224", "FBN1B", "Core PG", "3", "Not in network", "FAGPLGpTNSISTNAK", "T188", "310; A60 (A60)", "—"], ["AT2G3549", "FBN2", "Core PG", "4", "III (ABC1K9)", "pSGPELEESGTR", "S105", "376; S54 (S54)", "SG, SxP"], ["AT2G3549", "FBN2", "Core PG", "4", "III (ABC1K9)", "SGPELEESGpTR", "T114", "376; S54 (S54)", "—"], ["AT3G2340", "FBN4", "Core PG", "2", "III (ABC1K9)", "LLSVVpSGLNR", "S96", "284; S73 (A54, S57, S58)", "SG"], ["AT3G2340", "FBN4", "Core PG", "2", "III (ABC1K9)", "GLVApSVDDLER", "S105", "284; S73 (A54, S57, S58)", "—"], ["AT3G2340", "FBN4", "Core PG", "2", "III (ABC1K9)", "LLYSSAFpSSR", "S148", "284; S73 (A54, S57, S58)", "—"], ["AT3G2340", "FBN4", "Core PG", "2", "III (ABC1K9)", "pSLGGSRPGLPTGR", "S151", "284; S73 (A54, S57, S58)", "xSx, RS"], ["AT3G2340", "FBN4", "Core PG", "2", "III (ABC1K9)", "SLGGpSRPGLPTGR", "S155", "284; S73 (A54, S57, S58)", "GS"], ["AT2G4213", "FBN7B", "Core PG", "13", "IV", "IETPSSTVVETIEYDpS (C-terminus)", "S299", "299; A49 (A49, V51)", "DS"], ["AT1G3222", "FLAVIN REDUCATASE RELATED 1", "Core PG", "14", "Connected to UBIE1", "SCVKCTYAEAGLpSSASWpSAPIDIVADVK", "(S46), S51", "296; A58 (T39)", "SxP, SxpS"], ["AT1G3222", "FLAVIN REDUCATASE RELATED 1", "Core PG", "14", "Connected to UBIE1", "SCVKCTYAEAGLSpSASWpSAPIDIVADVK", "(S47), S51", "296; A58 (T39)", "SxP, SxpS, pSxS"], ["AT2G3446", "FLAVIN REDUCATASE RELATED 2", "Core PG", "21", "II (ABC1K1, 3 ,6)", "pSYKDLFASVK", "S269", "280; A52 (M35)", "SxxD/E"], ["AT1G0669", "NAD(P)-ALDO/KETO REDUCTASE", "Core PG", "20", "II (ABC1K1, 3 ,6)", "LGGpSDLKVTK", "(S54)", "377; A32 (A32, V33)", "GS, xSDx"], ["AT4G1320", "UNKOWN 1", "Core PG", "15", "III (ABC1K9)", "TIMVDVEESSSSpSDED", "S182", "185; C57", "SDx[D/E]"], ["AT4G3277", "VTE1 (cTP)", "Core PG", "10", "Not connected", "SISRVpSApSIpSpTPNSETDK (part of cTP)", "S47, S49 (S51, T52)", "488; V99 (S49)", "pSxS, SxpS, TP"], ["AT5G4265", "AOS", "Recruited to PG", "Not in network", "ASGpSETPDLTVATR", "S36", "518; A33 (S34)", "SxpS, GS"], ["AT5G4265", "AOS", "Recruited to PG", "Not in network", "ApSGSETPDLTVATR", "S34", "518; A33 (S34)", "pSxS, SG"], ["AT3G4514", "LOX2", "Recruited to PG", "Not in network", "EFYEpSPEK", "(S787)", "896; R56 (C50)", "SP"], ["AT3G2607", "FBN3A", "Thylakoid", "Not in network", "GATApSPDDQLR", "S92", "242; V51", "SP"], ["AT4G0003", "FBN9", "Plastid", "Not in network", "SSITTDDSLSApTWR", "(T87)", "212; C26", "—"]], "row_count": 24, "column_count": 9, "numeric_cells": 94, "header_rows": 1, "locator": "section[6]/table-wrap[1]#T1"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "BLAST"}}, {"id": "method-2", "family": "sequence_alignment", "specific": "msa", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "ClustalW"}}, {"id": "method-3", "family": null, "specific": null, "label": "motif-x and MMFPH prediction algorithms", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In our recent meta-analysis and application of motif-x and MMFPH prediction algorithms, we identified several motif families for pS and pT sites, which could be divided into more specific types (van Wijk et al., 2014)."}}], "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": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: blast."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["Spectral data were downloaded from PhosphAt 4.0, PRIDE (http://www.ebi.ac.uk/pride/archive/) or provided by the authors (upon request) of the corresponding publications (Supplementary Table S1 at JXB online)."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["sequence_align", "alignment_identity"], "assets": ["source:pmid:26962209", "asset:table:pmid:26962209:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": null, "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 0, "usage": {}}, "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:26962209", "type": "paper", "label": "pmid:26962209"}, {"id": "source:pmid:26962209", "type": "manuscript", "label": "PMID 26962209 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26962209", "type": "paper", "label": "pmid:26962209"}, {"id": "source:pmid:26962209", "type": "manuscript", "label": "PMID 26962209 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26962209", "type": "extraction", "used": ["source:pmid:26962209"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:26962209", "parent_hash": "sha256:f17e0f9c09b248de51701bb696546c78ea0045fe1ae0cc36050f5c9c5004bb3d", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "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": 0.93, "evidence": ["strating the importance of deposition of all mass spectrometry data in well-organized repositories such as"], "order_basis": "paper_text_order:986", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["y, sequences from human (Homo sapiens, Hsa), mouse (Mus musculus, Mmu), zebra fish (Danio rerio"], "order_basis": "paper_text_order:3311", "id": "assay:2"}, {"role": "analysis", "definition_id": "sequence_alignment", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["sequence_align", "alignment_identity"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["BLAST"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}