{"gene":"PF3D7_1427800","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2018,"finding":"Recombinant PfRrp41 (PF3D7_1427800) exhibited catalytic activity for single-stranded RNA (ssRNA) in vitro, establishing it as a catalytic subunit of the P. falciparum RNA exosome-like complex.","method":"In vitro ribonuclease activity assay using recombinant protein","journal":"The Journal of eukaryotic microbiology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro enzymatic activity demonstrated with recombinant protein, but single lab, single method, no mutagenesis confirmation","pmids":["29664138"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"PfRrp41 (PF3D7_1427800) localizes to the cytoplasm of P. falciparum asexual-stage parasites, as determined by indirect immunofluorescence.","method":"Indirect immunofluorescence assay (IFA) with Western blot confirmation of protein expression","journal":"The Journal of eukaryotic microbiology","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, indirect immunofluorescence localization without direct functional consequence linked to localization","pmids":["29664138"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_1427800 (RRP41) is a cytoplasmic, catalytically active subunit of the P. falciparum RNA exosome-like complex that degrades single-stranded RNA in vitro and is expressed throughout the asexual stage of the parasite."},"narrative":{"mechanistic_narrative":"PF3D7_1427800 (RRP41) is a catalytically active subunit of the P. falciparum RNA exosome-like complex that degrades single-stranded RNA. Recombinant PfRrp41 exhibits ribonuclease activity against ssRNA in vitro, establishing it as a catalytic component of the parasite exosome-like machinery [PMID:29664138], and the protein localizes to the cytoplasm of asexual-stage parasites [PMID:29664138]. Beyond this in vitro activity and localization, no further mechanistic detail — including substrate specificity in vivo, complex partners, or functional consequences of its ribonuclease activity — has been characterized in the available corpus.","teleology":[{"year":2018,"claim":"Whether PF3D7_1427800 is itself an active nuclease or merely a structural exosome subunit was unknown; demonstrating intrinsic ribonuclease activity established it as a catalytic component of the parasite RNA exosome-like complex.","evidence":"In vitro ribonuclease activity assay with recombinant PfRrp41 against ssRNA substrate","pmids":["29664138"],"confidence":"Medium","gaps":["Activity shown by a single lab with a single method and no catalytic-site mutagenesis to confirm the activity is intrinsic to RRP41","Substrate specificity and in vivo RNA targets not defined","Contribution to an assembled exosome complex not tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"The subcellular compartment in which PF3D7_1427800 operates was unknown; immunofluorescence placed the protein in the cytoplasm of asexual-stage parasites, indicating a cytoplasmic site of exosome-like RNA turnover.","evidence":"Indirect immunofluorescence assay with Western blot confirmation of expression in asexual-stage P. falciparum","pmids":["29664138"],"confidence":"Medium","gaps":["Localization by indirect IFA in a single lab, not linked to a functional consequence","No data on nuclear versus cytoplasmic exosome distribution or stage-specific relocalization","Complex assembly state at the localized site not determined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The identity of the in vivo RNA substrates, the composition of the RRP41-containing exosome-like complex, and the biological role of its ribonuclease activity in parasite biology remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No interacting exosome subunits or complex partners identified for PF3D7_1427800 in the corpus","No genetic or knockdown data linking RRP41 activity to a parasite phenotype","No structural model or catalytic-residue mapping"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["RNA exosome-like complex (P. falciparum)"],"partners":[],"other_free_text":["Expressed throughout the asexual stage of P. falciparum [#1].","Corpus establishes PF3D7_1427800 as a catalytic ssRNA-degrading subunit of the exosome-like complex; no specific partner subunits of this complex are identified for RRP41 in the available evidence."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"29664138","id":"PMC_29664138","title":"Characterization of the Catalytic Subunits of the RNA Exosome-like Complex in Plasmodium falciparum.","date":"2018","source":"The Journal of eukaryotic microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/29664138","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRRP41"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19200392","id":"","title":"Analysis of small nucleolar RNAs reveals unique genetic features in malaria parasites.","date":"2009","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/19200392","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RRP41"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4372,"output_tokens":531,"usd":0.01054,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5083,"output_tokens":1550,"usd":0.032082,"stage2_stop_reason":"end_turn"},"total_usd":0.042622,"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\": 2018,\n      \"finding\": \"Recombinant PfRrp41 (PF3D7_1427800) exhibited catalytic activity for single-stranded RNA (ssRNA) in vitro, establishing it as a catalytic subunit of the P. falciparum RNA exosome-like complex.\",\n      \"method\": \"In vitro ribonuclease activity assay using recombinant protein\",\n      \"journal\": \"The Journal of eukaryotic microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro enzymatic activity demonstrated with recombinant protein, but single lab, single method, no mutagenesis confirmation\",\n      \"pmids\": [\"29664138\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PfRrp41 (PF3D7_1427800) localizes to the cytoplasm of P. falciparum asexual-stage parasites, as determined by indirect immunofluorescence.\",\n      \"method\": \"Indirect immunofluorescence assay (IFA) with Western blot confirmation of protein expression\",\n      \"journal\": \"The Journal of eukaryotic microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, indirect immunofluorescence localization without direct functional consequence linked to localization\",\n      \"pmids\": [\"29664138\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1427800 (RRP41) is a cytoplasmic, catalytically active subunit of the P. falciparum RNA exosome-like complex that degrades single-stranded RNA in vitro and is expressed throughout the asexual stage of the parasite.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1427800 (RRP41) is a catalytically active subunit of the P. falciparum RNA exosome-like complex that degrades single-stranded RNA. Recombinant PfRrp41 exhibits ribonuclease activity against ssRNA in vitro, establishing it as a catalytic component of the parasite exosome-like machinery [#0], and the protein localizes to the cytoplasm of asexual-stage parasites [#1]. Beyond this in vitro activity and localization, no further mechanistic detail — including substrate specificity in vivo, complex partners, or functional consequences of its ribonuclease activity — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Whether PF3D7_1427800 is itself an active nuclease or merely a structural exosome subunit was unknown; demonstrating intrinsic ribonuclease activity established it as a catalytic component of the parasite RNA exosome-like complex.\",\n      \"evidence\": \"In vitro ribonuclease activity assay with recombinant PfRrp41 against ssRNA substrate\",\n      \"pmids\": [\n        \"29664138\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Activity shown by a single lab with a single method and no catalytic-site mutagenesis to confirm the activity is intrinsic to RRP41\",\n        \"Substrate specificity and in vivo RNA targets not defined\",\n        \"Contribution to an assembled exosome complex not tested\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The subcellular compartment in which PF3D7_1427800 operates was unknown; immunofluorescence placed the protein in the cytoplasm of asexual-stage parasites, indicating a cytoplasmic site of exosome-like RNA turnover.\",\n      \"evidence\": \"Indirect immunofluorescence assay with Western blot confirmation of expression in asexual-stage P. falciparum\",\n      \"pmids\": [\n        \"29664138\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Localization by indirect IFA in a single lab, not linked to a functional consequence\",\n        \"No data on nuclear versus cytoplasmic exosome distribution or stage-specific relocalization\",\n        \"Complex assembly state at the localized site not determined\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The identity of the in vivo RNA substrates, the composition of the RRP41-containing exosome-like complex, and the biological role of its ribonuclease activity in parasite biology remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No interacting exosome subunits or complex partners identified for PF3D7_1427800 in the corpus\",\n        \"No genetic or knockdown data linking RRP41 activity to a parasite phenotype\",\n        \"No structural model or catalytic-residue mapping\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0000175\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      },\n      {\n        \"term_id\": \"GO:0004540\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0005737\",\n        \"supporting_discovery_ids\": [\n          1\n        ]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0006401\",\n        \"supporting_discovery_ids\": [\n          0\n        ]\n      }\n    ],\n    \"complexes\": [\n      \"RNA exosome-like complex (P. falciparum)\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Expressed throughout the asexual stage of P. falciparum [#1].\",\n      \"Corpus establishes PF3D7_1427800 as a catalytic ssRNA-degrading subunit of the exosome-like complex; no specific partner subunits of this complex are identified for RRP41 in the available evidence.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1427800","name":null,"product":"exosome complex component RRP41","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1016800","name":null,"product":"exosome complex component RRP41, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1330900","name":null,"product":"exosome complex component RRP41, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RRP41","evaluation":null}