{"gene":"PF3D7_0903400","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2022,"finding":"PF3D7_0903400 (DDX60) was detected as a biotinylated proximity-labelling hit of the male development 1 (Md1) protein in P. falciparum gametocytes, placing DDX60 in the neighbourhood of cytoplasmic RNP granule-like structures that include translational repressors, CCR4–NOT complex members, and other dead-box RNA helicases. This establishes DDX60's membership in an Md1-associated cytoplasmic ribonucleoprotein complex, but no direct enzymatic activity or independent functional role for DDX60 was demonstrated in this study.","method":"TurboID proximity labelling followed by mass spectrometry (Md1-TurboID strain vs. untagged WT control)","journal":"Nature","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single proximity-labelling experiment; DDX60 is one of many hits with no direct functional follow-up for DDX60 itself","pmids":["36477538"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0903400 (DDX60) is a putative ATP-dependent RNA helicase in P. falciparum that has been catalogued among the parasite's DEAD/H-box helicases involved in RNA metabolism, detected as a proximity-labelling hit near the male-fate determinant Md1 in cytoplasmic RNP granule-like structures, and found to be transcriptionally downregulated in a KIC5 mutant context; however, no direct enzymatic activity, substrate, structure, or independent loss-of-function phenotype has been experimentally established for DDX60 itself."},"narrative":{"mechanistic_narrative":"PF3D7_0903400 (DDX60) is a putative ATP-dependent RNA helicase of P. falciparum whose only experimental characterization places it within an Md1-associated cytoplasmic ribonucleoprotein complex in gametocytes, where proximity labelling of the male development 1 (Md1) protein recovered DDX60 alongside translational repressors, CCR4–NOT complex members, and other DEAD-box RNA helicases in RNP granule-like structures [PMID:36477538]. Beyond this membership in an Md1-proximal RNP environment [PMID:36477538], no direct enzymatic activity, substrate, structure, or independent loss-of-function phenotype has been characterized for DDX60 in the available corpus.","teleology":[{"year":2022,"claim":"To place DDX60 in a cellular context, proximity labelling asked which proteins neighbour the male-fate determinant Md1, and recovered DDX60 as a hit, establishing that it resides within an Md1-associated cytoplasmic RNP complex rather than acting in isolation.","evidence":"TurboID proximity labelling followed by mass spectrometry in a P. falciparum Md1-TurboID gametocyte strain versus untagged wild-type control","pmids":["36477538"],"confidence":"Low","gaps":["Single proximity-labelling experiment with no direct functional follow-up for DDX60 itself; membership is inferred from spatial proximity, not a validated interaction","No ATP-dependent helicase or RNA-binding activity demonstrated for DDX60","No independent loss-of-function phenotype for DDX60 established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether DDX60 has intrinsic RNA helicase activity, a defined RNA substrate, and a distinct role in gametocyte RNP granule function or male development remains unknown.","evidence":"No direct enzymatic, structural, or genetic characterization of DDX60 is present in the corpus","pmids":[],"confidence":"Low","gaps":["No biochemical reconstitution of ATP-dependent helicase activity","No substrate or interaction partner directly validated","No knockdown/knockout phenotype for DDX60 reported"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Md1-associated cytoplasmic ribonucleoprotein complex [#0]"],"partners":["MD1 (PROXIMITY-LABELLING NEIGHBOUR) [#0]"],"other_free_text":["Detected in proximity to translational repressors, CCR4–NOT complex members, and other DEAD-box RNA helicases in gametocyte RNP granule-like structures [#0]","Annotated as a putative ATP-dependent RNA helicase; no direct enzymatic activity has been demonstrated for DDX60 itself in the corpus"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"26525978","id":"PMC_26525978","title":"A bioinformatic survey of RNA-binding proteins in Plasmodium.","date":"2015","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/26525978","citation_count":62,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"4971014","id":"PMC_4971014","title":"DNA, RNA , and protein synthesis in erythrocytic forms of Plasmodium knowlesi.","date":"1968","source":"The American journal of tropical medicine and hygiene","url":"https://pubmed.ncbi.nlm.nih.gov/4971014","citation_count":56,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39630601","id":"","title":"Cytoadhesion of Plasmodium falciparum-Infected Red Blood Cells Changes the Expression of Cytokine-, Histone- and Antiviral Protein-Encoding Genes in Brain Endothelial Cells.","date":"2024","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/39630601","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["DDX60"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36624300","id":"","title":"Protein KIC5 is a novel regulator of artemisinin stress response in the malaria parasite Plasmodium falciparum.","date":"2023","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/36624300","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["DDX60"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"36477538","id":"","title":"A transcriptional switch controls sex determination in Plasmodium falciparum.","date":"2022","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/36477538","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["DDX60"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35464842","id":"","title":"Identification of Co-Existing Mutations and Gene Expression Trends Associated With K13-Mediated Artemisinin Resistance in Plasmodium falciparum.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35464842","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["DDX60"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8090,"output_tokens":493,"usd":0.015832,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5022,"output_tokens":1190,"usd":0.02743,"stage2_stop_reason":"end_turn"},"total_usd":0.043262,"stage1_batch_id":"msgbatch_01SRp5hyRc82zNjddxyCCXGk","stage2_batch_id":"msgbatch_01K3BTmBazRo3pRrMvyaPMTY","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"PF3D7_0903400 (DDX60) was detected as a biotinylated proximity-labelling hit of the male development 1 (Md1) protein in P. falciparum gametocytes, placing DDX60 in the neighbourhood of cytoplasmic RNP granule-like structures that include translational repressors, CCR4–NOT complex members, and other dead-box RNA helicases. This establishes DDX60's membership in an Md1-associated cytoplasmic ribonucleoprotein complex, but no direct enzymatic activity or independent functional role for DDX60 was demonstrated in this study.\",\n      \"method\": \"TurboID proximity labelling followed by mass spectrometry (Md1-TurboID strain vs. untagged WT control)\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single proximity-labelling experiment; DDX60 is one of many hits with no direct functional follow-up for DDX60 itself\",\n      \"pmids\": [\"36477538\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0903400 (DDX60) is a putative ATP-dependent RNA helicase in P. falciparum that has been catalogued among the parasite's DEAD/H-box helicases involved in RNA metabolism, detected as a proximity-labelling hit near the male-fate determinant Md1 in cytoplasmic RNP granule-like structures, and found to be transcriptionally downregulated in a KIC5 mutant context; however, no direct enzymatic activity, substrate, structure, or independent loss-of-function phenotype has been experimentally established for DDX60 itself.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0903400 (DDX60) is a putative ATP-dependent RNA helicase of P. falciparum whose only experimental characterization places it within an Md1-associated cytoplasmic ribonucleoprotein complex in gametocytes, where proximity labelling of the male development 1 (Md1) protein recovered DDX60 alongside translational repressors, CCR4–NOT complex members, and other DEAD-box RNA helicases in RNP granule-like structures [#0]. Beyond this membership in an Md1-proximal RNP environment [#0], no direct enzymatic activity, substrate, structure, or independent loss-of-function phenotype has been characterized for DDX60 in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"To place DDX60 in a cellular context, proximity labelling asked which proteins neighbour the male-fate determinant Md1, and recovered DDX60 as a hit, establishing that it resides within an Md1-associated cytoplasmic RNP complex rather than acting in isolation.\",\n      \"evidence\": \"TurboID proximity labelling followed by mass spectrometry in a P. falciparum Md1-TurboID gametocyte strain versus untagged wild-type control\",\n      \"pmids\": [\"36477538\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single proximity-labelling experiment with no direct functional follow-up for DDX60 itself; membership is inferred from spatial proximity, not a validated interaction\",\n        \"No ATP-dependent helicase or RNA-binding activity demonstrated for DDX60\",\n        \"No independent loss-of-function phenotype for DDX60 established\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether DDX60 has intrinsic RNA helicase activity, a defined RNA substrate, and a distinct role in gametocyte RNP granule function or male development remains unknown.\",\n      \"evidence\": \"No direct enzymatic, structural, or genetic characterization of DDX60 is present in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No biochemical reconstitution of ATP-dependent helicase activity\",\n        \"No substrate or interaction partner directly validated\",\n        \"No knockdown/knockout phenotype for DDX60 reported\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0036464\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [\"Md1-associated cytoplasmic ribonucleoprotein complex [#0]\"],\n    \"partners\": [\"Md1 (proximity-labelling neighbour) [#0]\"],\n    \"other_free_text\": [\n      \"Detected in proximity to translational repressors, CCR4–NOT complex members, and other DEAD-box RNA helicases in gametocyte RNP granule-like structures [#0]\",\n      \"Annotated as a putative ATP-dependent RNA helicase; no direct enzymatic activity has been demonstrated for DDX60 itself in the corpus\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0903400","name":null,"product":"ATP-dependent RNA helicase DDX60, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0418000","name":null,"product":"ATP-dependent RNA helicase DDX60, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0701100","name":null,"product":"ATP-dependent RNA helicase DDX60, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"DDX60","evaluation":null}