{"gene":"PF3D7_0519800","run_date":"2026-09-07T10:55:52","timeline":{"discoveries":[{"year":2012,"finding":"PF3D7_0519800 (EELM2) was detected as a nuclear protein in P. falciparum by high-accuracy mass spectrometry-based nuclear proteomics, with nuclear localization validated by transgenic cell line imaging.","method":"Organellar proteomics (mass spectrometry) combined with experimental validation using transgenic cell lines (fluorescence microscopy)","journal":"Genome biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct subcellular fractionation and mass spectrometry with validation in transgenic lines, single lab","pmids":["23181666"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"PF3D7_0519800 (PfEELM2) physically interacts with PfMORC (PF3D7_1468100), a chromatin-associated microrchidia protein, as part of a nuclear protein complex involved in epigenetic control of gene expression during asexual blood stage development.","method":"Multi-omic analyses including co-immunoprecipitation/protein interaction proteomics (PfMORC pull-down) identifying PfEELM2 as an interactor","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP/pulldown from one lab identifying EELM2 as a member of the PfMORC complex, no direct functional perturbation of EELM2 itself","pmids":["39412522"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0519800 (EELM2) is a nuclear protein in P. falciparum that physically associates with the chromatin-remodeling PfMORC complex, implicating it in epigenetic regulation of gene expression during asexual blood stage development, though its direct molecular function within the complex has not been experimentally defined."},"narrative":{"mechanistic_narrative":"PF3D7_0519800 (EELM2) is a nuclear protein of Plasmodium falciparum implicated in epigenetic control of gene expression during asexual blood stage development [PMID:23181666, PMID:39412522]. It was first identified as a genuine nuclear resident by mass spectrometry-based nuclear proteomics with localization confirmed in transgenic parasites [PMID:23181666], and was subsequently recovered as a physical interactor of the chromatin-associated microrchidia protein PfMORC (PF3D7_1468100) within a nuclear protein complex [PMID:39412522]. Beyond its nuclear localization and its membership in the PfMORC complex, no direct molecular function for EELM2 itself has been experimentally defined in the available corpus; its role is currently inferred only from complex association, and it has not been functionally perturbed.","teleology":[{"year":2012,"claim":"Establishing where EELM2 resides was the first step in assigning it any function; nuclear proteomics placed the protein in the nucleus, consistent with a role in nuclear/chromatin processes rather than cytoplasmic metabolism.","evidence":"Mass spectrometry-based nuclear organellar proteomics with validation by fluorescence imaging of transgenic cell lines","pmids":["23181666"],"confidence":"Medium","gaps":["Localization alone does not indicate molecular activity or DNA/chromatin binding","No interaction partners identified at this stage","Sub-nuclear distribution (heterochromatin vs euchromatin) not resolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"claim":"Connecting EELM2 to a defined machinery, co-immunoprecipitation showed it physically associates with the chromatin-remodeling PfMORC complex, providing the first mechanistic context by linking it to epigenetic regulation of asexual-stage gene expression.","evidence":"Multi-omic analysis including PfMORC pull-down/interaction proteomics identifying PfEELM2 as an interactor","pmids":["39412522"],"confidence":"Medium","gaps":["Single Co-IP/pulldown from one lab with no direct functional perturbation of EELM2 itself","Whether the interaction is direct or bridged by other complex members is unresolved","The specific contribution of EELM2 to PfMORC complex activity is undefined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The direct molecular function of EELM2 within the PfMORC complex — and whether it is required for the complex's chromatin/gene-regulatory activity — remains unestablished.","evidence":"No functional perturbation, structural, or biochemical activity data for EELM2 in the available corpus","pmids":[],"confidence":"Low","gaps":["No genetic knockout/knockdown of EELM2 to test its role","No biochemical or enzymatic activity assigned to EELM2","No structural model or definition of the EELM2 domain's contribution to the complex"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PfMORC complex"],"partners":["PFMORC (PF3D7_1468100)"],"other_free_text":["Nuclear protein of P. falciparum validated by nuclear proteomics and transgenic imaging [#0].","Physically associates with the chromatin-associated PfMORC complex implicated in epigenetic gene regulation during asexual blood stage development [#1].","No direct molecular function, enzymatic activity, or functional perturbation of EELM2 itself is established in the corpus; its role is inferred solely from complex membership."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"23181666","id":"PMC_23181666","title":"Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum.","date":"2012","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/23181666","citation_count":119,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39412522","id":"PMC_39412522","title":"A Plasmodium falciparum MORC protein complex modulates epigenetic control of gene expression through interaction with heterochromatin.","date":"2024","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/39412522","citation_count":12,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfEELM2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3901,"output_tokens":594,"usd":0.010306,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5171,"output_tokens":1532,"usd":0.032078,"stage2_stop_reason":"end_turn"},"total_usd":0.042384,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"PF3D7_0519800 (EELM2) was detected as a nuclear protein in P. falciparum by high-accuracy mass spectrometry-based nuclear proteomics, with nuclear localization validated by transgenic cell line imaging.\",\n      \"method\": \"Organellar proteomics (mass spectrometry) combined with experimental validation using transgenic cell lines (fluorescence microscopy)\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct subcellular fractionation and mass spectrometry with validation in transgenic lines, single lab\",\n      \"pmids\": [\"23181666\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PF3D7_0519800 (PfEELM2) physically interacts with PfMORC (PF3D7_1468100), a chromatin-associated microrchidia protein, as part of a nuclear protein complex involved in epigenetic control of gene expression during asexual blood stage development.\",\n      \"method\": \"Multi-omic analyses including co-immunoprecipitation/protein interaction proteomics (PfMORC pull-down) identifying PfEELM2 as an interactor\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP/pulldown from one lab identifying EELM2 as a member of the PfMORC complex, no direct functional perturbation of EELM2 itself\",\n      \"pmids\": [\"39412522\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0519800 (EELM2) is a nuclear protein in P. falciparum that physically associates with the chromatin-remodeling PfMORC complex, implicating it in epigenetic regulation of gene expression during asexual blood stage development, though its direct molecular function within the complex has not been experimentally defined.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0519800 (EELM2) is a nuclear protein of Plasmodium falciparum implicated in epigenetic control of gene expression during asexual blood stage development [#0, #1]. It was first identified as a genuine nuclear resident by mass spectrometry-based nuclear proteomics with localization confirmed in transgenic parasites [#0], and was subsequently recovered as a physical interactor of the chromatin-associated microrchidia protein PfMORC (PF3D7_1468100) within a nuclear protein complex [#1]. Beyond its nuclear localization and its membership in the PfMORC complex, no direct molecular function for EELM2 itself has been experimentally defined in the available corpus; its role is currently inferred only from complex association, and it has not been functionally perturbed.\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Establishing where EELM2 resides was the first step in assigning it any function; nuclear proteomics placed the protein in the nucleus, consistent with a role in nuclear/chromatin processes rather than cytoplasmic metabolism.\",\n      \"evidence\": \"Mass spectrometry-based nuclear organellar proteomics with validation by fluorescence imaging of transgenic cell lines\",\n      \"pmids\": [\"23181666\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Localization alone does not indicate molecular activity or DNA/chromatin binding\",\n        \"No interaction partners identified at this stage\",\n        \"Sub-nuclear distribution (heterochromatin vs euchromatin) not resolved\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connecting EELM2 to a defined machinery, co-immunoprecipitation showed it physically associates with the chromatin-remodeling PfMORC complex, providing the first mechanistic context by linking it to epigenetic regulation of asexual-stage gene expression.\",\n      \"evidence\": \"Multi-omic analysis including PfMORC pull-down/interaction proteomics identifying PfEELM2 as an interactor\",\n      \"pmids\": [\"39412522\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single Co-IP/pulldown from one lab with no direct functional perturbation of EELM2 itself\",\n        \"Whether the interaction is direct or bridged by other complex members is unresolved\",\n        \"The specific contribution of EELM2 to PfMORC complex activity is undefined\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular function of EELM2 within the PfMORC complex — and whether it is required for the complex's chromatin/gene-regulatory activity — remains unestablished.\",\n      \"evidence\": \"No functional perturbation, structural, or biochemical activity data for EELM2 in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No genetic knockout/knockdown of EELM2 to test its role\",\n        \"No biochemical or enzymatic activity assigned to EELM2\",\n        \"No structural model or definition of the EELM2 domain's contribution to the complex\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006325\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [\n      \"PfMORC complex\"\n    ],\n    \"partners\": [\n      \"PfMORC (PF3D7_1468100)\"\n    ],\n    \"other_free_text\": [\n      \"Nuclear protein of P. falciparum validated by nuclear proteomics and transgenic imaging [#0].\",\n      \"Physically associates with the chromatin-associated PfMORC complex implicated in epigenetic gene regulation during asexual blood stage development [#1].\",\n      \"No direct molecular function, enzymatic activity, or functional perturbation of EELM2 itself is established in the corpus; its role is inferred solely from complex membership.\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0519800","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 1 of 2 cited papers name other catalogue genes (PF3D7_0420300, PF3D7_0613800, PF3D7_1007700). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0519800","name":null,"product":"EELM2 domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1234600","name":null,"product":"EELM2 domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1013300","name":null,"product":"EELM2 domain-containing protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}