A Potential Role for the Gsdf-eEF1α Complex in Inhibiting Germ Cell Proliferation: A Protein-Interaction Analysis in Medaka (Oryzias latipes) From a Proteomics Perspective.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33293461", "kind": "science-record", "revision": 6, "content_hash": "sha256:c38349fda0aebe2ff6723c14167ac4bcd3f284f68bdee2c9a98b36251802edef", "created_at": "2026-11-01T15:41:18Z", "updated_at": "2026-11-01T21:24:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Potential Role for the Gsdf-eEF1α Complex in Inhibiting Germ Cell Proliferation: A Protein-Interaction Analysis in Medaka (Oryzias latipes) From a Proteomics Perspective.", "doi": "10.1074/mcp.RA120.002306", "pmid": "33293461", "authors": ["Xinting Zhang", "Yuyang Chang", "Wanying Zhai", "Feng Qian", "Yingqing Zhang", "Shumei Xu", "Haiyan Guo", "Siyu Wang", "Ruiqin Hu", "Xiaozhu Zhong", "Xiaomiao Zhao", "Liangbiao Chen", "Guijun Guan"], "journal": "Molecular & cellular proteomics : MCP", "year": 2021, "abstract": "Gonadal soma-derived factor (gsdf) has been demonstrated to be essential for testicular differentiation in medaka (Oryzias latipes). To understand the protein dynamics of Gsdf in spermatogenesis regulation, we used a His-tag \"pull-down\" assay coupled with shotgun LC-MS/MS to identify a group of potential interacting partners for Gsdf, which included cytoplasmic dynein light chain 2, eukaryotic polypeptide elongation factor 1 alpha (eEF1α), and actin filaments in the mature medaka testis. As for the interaction with transforming growth factor β-dynein being critical for spermatogonial division in Drosophila melanogaster, the physical interactions of Gsdf-dynein and Gsdf-eEF1α were identified through a yeast 2-hybrid screening of an adult testis cDNA library using Gsdf as bait, which were verified by a paired yeast 2-hybrid assay. Coimmunoprecipitation of Gsdf and eEF1α was defined in adult testes as supporting the requirement of a Gsdf and eEF1α interaction in testis development. Proteomics analysis (data are available via ProteomeXchange with identifier PXD022153) and ultrastructural observations showed that Gsdf deficiency activated eEF1α-mediated protein synthesis and ribosomal biogenesis, which in turn led to the differentiation of undifferentiated germ cells. Thus, our results provide a framework and new insight into the coordination of a Gsdf (transforming growth factor β) and eEF1α complex in the basic processes of germ cell proliferation, transcriptional and translational control of sexual RNA, which may be fundamentally conserved across the phyla during sexual differentiation.", "claims": [{"id": "claim-method", "statement": "Paired comparisons were performed using Student’s t test with probabilities of ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33293461", "locator": "sections[12] \"Experimental Replicates and Statistical Analysis\" paragraph 2", "quote": "Paired comparisons were performed using Student’s t test with probabilities of ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data set analyzed here has been deposited in ProteomeXchange with identifier PXD022153. All data are available in the associated supplementary data files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33293461", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The data set analyzed here has been deposited in ProteomeXchange with identifier PXD022153. All data are available in the associated supplementary data files."}], "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:33293461"], "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:PXD022153"], "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:PXD022153"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33293461", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1074/mcp.RA120.002306", "sha256": "sha256:2d8f8198fd3bec633069a6dc857080b70ab86208d1ff364cb696201da6e037d8", "bytes": 51613, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1074/mcp.RA120.002306", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7950199", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD022153", "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=PXD022153", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD022153", "version": null, "note": "The data set analyzed here has been deposited in ProteomeXchange with identifier PXD022153. All data are available in the associated supplementary data files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data set analyzed here has been deposited in ProteomeXchange with identifier PXD022153. All data are available in the associated supplementary data files.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "A potential role of Gsdf-eEF1 complex in inhibiting germ cell proliferation: A protein interaction analysis in medaka (Oryzias latipes) from a proteomics perspective", "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:33293461:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5324a80fd31cefd7014e27b7d836f4a786c2b281198ee7093ea0ae138749f85c", "bytes": 479, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[6]/table-wrap[1]#tbl1", "version": null, "note": "Genotyping analysis of hybrid progenies (Tg gsdf+/−XY♂ mating gsdf−/− XX ♀)", "structure": {"pmcid": "PMC7950199", "section_index": 6, "section_title": "Generation of Transgenic Intersex Medaka", "row_count": 5, "column_count": 6}, "table": {"label": "Table 1", "caption": "Genotyping analysis of hybrid progenies (Tg gsdf+/−XY♂ mating gsdf−/− XX ♀)", "rows": [["Offsprings", "Heterozygotes (Ht, gsdf+/−)", "Homozygotes (Hm, gsdf−/−)", "Ht:Hm"], ["Tg+", "Tg-", "Tg+", "Tg-"], ["XX", "7♂", "10♀", "8♀", "5♀", "17:13"], ["XY", "5♂", "9♂", "11⚥", "6♀", "14:17"], ["XX:XY", "7:5", "10:9", "8:11", "5:6", "31:30"]], "row_count": 5, "column_count": 6, "numeric_cells": 15, "header_rows": 2, "locator": "section[6]/table-wrap[1]#tbl1"}}], "gaps": ["asset:data:geo:PXD022153 not downloaded", "asset:data:geo:PXD022153 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}, {"id": "method-2", "family": null, "specific": null, "label": "Student’s t test for paired comparisons", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Paired comparisons were performed using Student’s t test with probabilities of ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["PXD022153"], "resolved_accessions": ["PXD022153"], "statements": ["The data set analyzed here has been deposited in ProteomeXchange with identifier PXD022153. All data are available in the associated supplementary data files."], "basis": "The paper names PXD022153 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:33293461", "data:geo:PXD022153", "asset:table:pmid:33293461:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD022153"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:24:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 42466, "completion_tokens": 971, "cached_tokens": 784}}, "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:33293461", "type": "paper", "label": "pmid:33293461"}, {"id": "source:pmid:33293461", "type": "manuscript", "label": "PMID 33293461 full text"}, {"id": "data:geo:PXD022153", "type": "dataset", "label": "GEO PXD022153"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33293461", "type": "paper", "label": "pmid:33293461"}, {"id": "source:pmid:33293461", "type": "manuscript", "label": "PMID 33293461 full text"}, {"id": "data:geo:PXD022153", "type": "dataset", "label": "GEO PXD022153"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33293461", "type": "extraction", "used": ["source:pmid:33293461"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD022153", "type": "accession_resolution", "used": ["data:geo:PXD022153"], "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:33293461", "parent_hash": "sha256:9a5ab5c6e901bb75966b1dc56e4f47292b135f07e2153b02a084ca90b8a27472", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD022153 licence not read", "asset:data:geo:PXD022153 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": 0.99, "evidence": ["Analysis in Medaka (Oryzias latipes) From a Proteomics Perspective.", "and eEF1α interaction in testis development. Proteomics analysis (data are available via ProteomeXch", "of ∗p < 0.05, ∗∗p < 0.01, and ∗∗∗p < 0.001. Proteomic Analysis of Normal and gsdf KO Gonads The pr", "s-tag \"pull-down\" assay coupled with shotgun LC-MS/MS to identify a group of potential interacting"], "order_basis": "paper_text_order:105", "id": "assay:1"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["yeast 2-hybrid screening of an adult testis cDNA library using Gsdf as bait, which were verified by a"], "order_basis": "paper_text_order:883", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["cation, RNA metabolisms, vitellogenesis, and apoptosis through these upregulated and downregulated"], "order_basis": "paper_text_order:7288", "id": "assay:3"}, {"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": ["ples, which correspond to the heavy chain of mouse IgG and recombinant Gsdf, respectively. Only"], "order_basis": "paper_text_order:8357", "id": "assay:4"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["pathway enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}