Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29078019", "kind": "science-record", "revision": 8, "content_hash": "sha256:211141c083e01001a3a322de3d529b061e6ce74b329a6a65440f40f509ec5cef", "created_at": "2026-11-01T15:40:29Z", "updated_at": "2026-11-01T22:43:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis.", "doi": "10.1111/tpj.13752", "pmid": "29078019", "authors": ["Kim Osman", "Jianhua Yang", "Elisabeth Roitinger", "Christophe Lambing", "Stefan Heckmann", "Elaine Howell", "Maria Cuacos", "Richard Imre", "Gerhard Dürnberger", "Karl Mechtler", "Susan Armstrong", "F Christopher H Franklin"], "journal": "The Plant journal : for cell and molecular biology", "year": 2018, "abstract": "During meiosis, the formation of crossovers (COs) generates genetic variation and provides physical links that are essential for accurate chromosome segregation. COs occur in the context of a proteinaceous chromosome axis. The transcriptomes and proteomes of anthers and meiocytes comprise several thousand genes and proteins, but because of the level of complexity relatively few have been functionally characterized. Our understanding of the physical and functional interactions between meiotic proteins is also limited. Here we use affinity proteomics to analyse the proteins that are associated with the meiotic chromosome axis protein, ASY1, in Brassica oleracea anthers and meiocytes. We show that during prophase I ASY1 and its interacting partner, ASY3, are extensively phosphorylated, and we precisely assign phosphorylation sites. We identify 589 proteins that co-immunoprecipitate with ASY1. These correspond to 492 Arabidopsis orthologues, over 90% of which form a coherent protein-protein interaction (PPI) network containing known and candidate meiotic proteins, including proteins more usually associated with other cellular processes such as DNA replication and proteolysis. Mutant analysis confirms that affinity proteomics is a viable strategy for revealing previously unknown meiotic proteins, and we show how the PPI network can be used to prioritise candidates for analysis. Finally, we identify another axis-associated protein with a role in meiotic recombination. Data are available via ProteomeXchange with identifier PXD006042.", "claims": [{"id": "claim-method", "statement": "Fertility in WT and mutant plants was compared using single‐factor anova. Chi‐square (χ2) tests were carried out using graphpad prism 7 (https://graphpad.com) using Yate's correction.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29078019", "locator": "sections[22] \"Statistical procedures\" paragraph 2", "quote": "Fertility in WT and mutant plants was compared using single‐factor anova. Chi‐square (χ2) tests were carried out using graphpad prism 7 (https://graphpad.com) using Yate's correction."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD006042.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29078019", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD006042."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:29078019"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD006042"], "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": ["data:geo:PXD006042"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29078019", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1111/tpj.13752", "sha256": "sha256:d428bd00785a744657c08f61a0d6e8d161af46dd5b3424c2b4893bb300d71e0d", "bytes": 81525, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1111/tpj.13752", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5767750", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD006042", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD006042", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD006042", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD006042.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD006042.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Affinity proteomics targeting the meiotic chromosome axis protein, ASY1, from Brassica oleracea.", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29078019:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d8de522bab3df72ecc0ff3a25289fa15b07d51c7f898bef48d63ba8205361fa", "bytes": 2448, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#tpj13752-tbl-0001", "version": null, "note": "Phosphorylation sites identified in BoASY1 and BoASY3", "structure": {"pmcid": "PMC5767750", "section_index": 9, "section_title": "BoASY1 and BoASY3 are phosphorylated at multiple sites", "row_count": 31, "column_count": 5}, "table": {"label": "Table 1", "caption": "Phosphorylation sites identified in BoASY1 and BoASY3", "rows": [["Protein", "Site", "Phosphopeptide(s)", "Tissue", "ptmRS: Best site probabilities"], ["BoASY1", "S17", "EAEITEQD(S)LLLTR", "A", "S9(Phospho), 100.00"], ["S253 and S260", "STGPN(S)VHDEQP(S)DSDSEISQTK", "M", "S6 (Phosho), 97.33; S13 (Phosho), 99.82"], ["S260", "STGPNSVHDEQP(S)DSDSEISQTK", "A and M", "S13(Phospho), 99.99"], ["S260 and S262", "STGPNSVHDEQP(S)D(S)DSEISQTK", "S13(Phospho), 100.00; S15(Phospho), 100.00"], ["S262", "STGPNSVHDEQPSD(S)DSEISQTK", "S15(Phospho), 99.85"], ["S262 and S264", "STGPNSVHDEQPSD(S)D(S)EISQTK (with S264)", "S15(Phospho), 82.82; S17(Phospho), 90.01"], ["T294", "ETQFLVAAVEKQEDDDGEVDEDN(T)QDPVESQQQLER", "A and M", "T24(Phospho), 100.00"], ["QEDDDGEVDEDN(T)QDPVESQQQLER", "T13(Phospho), 100.00"], ["S300", "QEDDDGEVDEDNTQDPVE(S)QQQLER", "A and M", "S19(Phospho), 100.00"], ["QEDDDGEVDEDN(T)QDPVE(S)QQQLER (with T294)", "T13(Phospho), 100.00; S19(Phospho), 100.00"], ["S442 or S443", "MVQEGYVED(S)SNRR or MVQEGYVEDS(S)NRR", "A", "S10(Phospho), 50.00; S11(Phospho), 50.00"], ["T493", "TNGQDAKL(T)PDVSTR", "A and M", "T9(Phospho), 100.00"], ["L(T)PDVSTR", "T2(Phospho), 100.00"], ["S504", "GGIH(S)IGSDLTR", "", "S5(Phospho), 98.97"], ["S504 and S507", "GGIH(S)IG(S)DLTR", "A and M", "S5(Phospho), 100.00; S8(Phospho), 99.88"], ["S507", "GGIHSIG(S)DLTR", "", "S8(Phospho), 100.00"], ["S526", "SAMHQNGSVL(S)EQTISK", "M", "S11(Phospho), 99.98"], ["T536", "ANN(T)PMSSNAQPVASR", "A and M", "T4(Phospho), 100.00"], ["S539", "ANNTPM(S)SNAQPVASR", "A and M", "S7 (Phospho), 99.39"], ["S547 or S550", "ANNTPMSSNAQPVA(S)RESFAVK or", "M", "S15(Phospho), 50.00; S18(Phospho), 50.00"], ["ANNTPMSSNAQPVASRE(S)FAVK"], ["S568 and S569", "ICTDAGTD(S)(S)QASQDRR", "A and M", "S9 (Phospho), 99.89; S10 (Phospho), 91.24"], ["S569", "ICTDAGTDS(S)QASQDR", "A and M", "S10(Phospho), 96.10"], ["S572", "ICTDAGTDSSQA(S)QDRR", "A and M", "S13(Phospho), 98.72"], ["BoASY3", "S15", "SFGSNFHPS(S)QPR", "M", "S10(Phospho), 94.53"], ["S156", "GNEMDK(S)PER", "A and M", "S7(Phospho), 100.00"], ["S205", "A(S)PEYNEDVNSETPEVVK", "M", "S2(Phospho), 99.67"], ["T231 or S232", "LNQDK(T)SNDDPLTK or LNQDKT(S)NDDPLTK", "M", "T6(Phospho), 50.00; S7(Phospho), 50.00"], ["S251 or S253", "HHSDTIETD(S)E(S)PEVATR", "M", "S10(Phospho), 49.72; S12(Phospho), 49.72"], ["S432 and S441", "EK(S)VEPENDFQ(S)PTFGYK", "A", "S3(Phospho), 100.00; S12(Phospho), 92.49"]], "row_count": 31, "column_count": 5, "numeric_cells": 57, "header_rows": 1, "locator": "section[9]/table-wrap[1]#tpj13752-tbl-0001"}}], "gaps": ["asset:data:geo:PXD006042 not downloaded", "asset:data:geo:PXD006042 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Fertility in WT and mutant plants was compared using single‐factor anova. Chi‐square (χ2) tests were carried out using graphpad prism 7 (https://graphpad.com) using Yate's correction."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-3", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": "R1", "reachable": true, "accessions": ["PXD006042"], "resolved_accessions": ["PXD006042"], "statements": ["Data are available via ProteomeXchange with identifier PXD006042."], "basis": "The paper names PXD006042 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:29078019", "data:geo:PXD006042", "asset:table:pmid:29078019:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006042"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:10:26Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 66400, "completion_tokens": 1348, "cached_tokens": 648}}, "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:29078019", "type": "paper", "label": "pmid:29078019"}, {"id": "source:pmid:29078019", "type": "manuscript", "label": "PMID 29078019 full text"}, {"id": "data:geo:PXD006042", "type": "dataset", "label": "GEO PXD006042"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29078019", "type": "paper", "label": "pmid:29078019"}, {"id": "source:pmid:29078019", "type": "manuscript", "label": "PMID 29078019 full text"}, {"id": "data:geo:PXD006042", "type": "dataset", "label": "GEO PXD006042"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29078019", "type": "extraction", "used": ["source:pmid:29078019"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006042", "type": "accession_resolution", "used": ["data:geo:PXD006042"], "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:29078019", "parent_hash": "sha256:ec3d20f2a886d0d6ef143cf8b1381c994cb3350316c4c7eebd7f6f1c09d31beb", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:PXD006042 licence not read", "asset:data:geo:PXD006042 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Fertility in WT and mutant plants was compared using single‐factor anova. Chi‐square (χ2) tests were carried out using graphpad prism 7 (https://graphpad.com) using Yate's correction."], "order_basis": "analysis_only", "id": "assay:1"}]}