{"gene":"PF3D7_0823200","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2024,"finding":"PF3D7_0823200, initially identified as an RNA-dependent protein (RDP) by sucrose density gradient ultracentrifugation and mass spectrometry (R-DeeP), was functionally characterized and validated as a bona fide RNA-binding protein. Using enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq), PF3D7_0823200 was shown to interact with various Plasmodium non-coding transcripts, including var gene transcripts and ap2 transcription factor transcripts.","method":"R-DeeP (sucrose density gradient ultracentrifugation + quantitative mass spectrometry), computational validation, eCLIP-seq","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal methods (R-DeeP proteome-wide screen + eCLIP-seq) in a single study; functional characterization and RNA-target identification directly demonstrated for PF3D7_0823200, but single lab","pmids":["38355719"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0823200 is a validated RNA-binding protein in P. falciparum that binds to non-coding transcripts including var gene and ap2 transcription factor transcripts, as demonstrated by eCLIP-seq, but its precise molecular function and mechanism of action remain uncharacterized beyond RNA binding."},"narrative":{"mechanistic_narrative":"PF3D7_0823200 is a validated RNA-binding protein of Plasmodium falciparum, initially flagged as an RNA-dependent protein in a proteome-wide R-DeeP screen and confirmed by eCLIP-seq to bind Plasmodium transcripts [PMID:38355719]. Its RNA targets include non-coding var gene transcripts and ap2 transcription factor transcripts, linking it to loci associated with antigenic variation and transcriptional regulation [PMID:38355719]. Beyond this demonstration of RNA binding and target identity, its precise molecular function, mechanism of action, and downstream regulatory consequences have not been characterized in the available corpus.","teleology":[{"year":2024,"claim":"It was unknown whether PF3D7_0823200 was a genuine RNA-binding protein or merely co-sedimented with RNA-containing complexes; orthogonal biochemical and crosslinking approaches established it as a bona fide RNA-binder with defined transcript targets.","evidence":"R-DeeP proteome-wide screen (sucrose gradient + quantitative MS) followed by eCLIP-seq in P. falciparum","pmids":["38355719"],"confidence":"Medium","gaps":["The molecular activity conferred by RNA binding (stabilization, decay, translation, localization) is unresolved.","The RNA-binding domain/region mediating target contact is not mapped.","Findings derive from a single lab without independent replication."],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The functional consequence of PF3D7_0823200 binding to var and ap2 non-coding transcripts — whether it regulates antigenic variation, transcription factor expression, or transcript fate — remains to be determined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No loss-of-function phenotype linking PF3D7_0823200 to var or ap2 regulation has been established.","No protein partners or complex context are defined.","No structural or mechanistic model of RNA engagement exists."],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["eCLIP-seq RNA targets include var gene non-coding transcripts and ap2 transcription factor transcripts [#0]","Identified as an RNA-dependent protein in R-DeeP proteome-wide screen [#0]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"24609083","id":"PMC_24609083","title":"Circular RNA is expressed across the eukaryotic tree of life.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24609083","citation_count":617,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17901154","id":"PMC_17901154","title":"Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis.","date":"2007","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/17901154","citation_count":81,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"20197405","id":"PMC_20197405","title":"The Puf-family RNA-binding protein PfPuf2 regulates sexual development and sex differentiation in the malaria parasite Plasmodium falciparum.","date":"2010","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/20197405","citation_count":78,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA-binding protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21625527","id":"PMC_21625527","title":"Transition of Plasmodium sporozoites into liver stage-like forms is regulated by the RNA binding protein Pumilio.","date":"2011","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/21625527","citation_count":70,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA-binding protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"12409450","id":"PMC_12409450","title":"The malaria parasite Plasmodium falciparum encodes members of the Puf RNA-binding protein family with conserved RNA binding activity.","date":"2002","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/12409450","citation_count":67,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA-binding protein","RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23637595","id":"PMC_23637595","title":"Puf mediates translation repression of transmission-blocking vaccine candidates in malaria parasites.","date":"2013","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/23637595","citation_count":62,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA-binding protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23356439","id":"PMC_23356439","title":"Perturbations of Plasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility.","date":"2013","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/23356439","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":"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":61,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22167473","id":"PMC_22167473","title":"PfAlbas constitute a new eukaryotic DNA/RNA-binding protein family in malaria parasites.","date":"2011","source":"Nucleic acids 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RNA","url":"https://pubmed.ncbi.nlm.nih.gov/27230797","citation_count":54,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26883588","id":"PMC_26883588","title":"A Plasmodium yoelii Mei2-Like RNA Binding Protein Is Essential for Completion of Liver Stage Schizogony.","date":"2016","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/26883588","citation_count":28,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA-binding protein","RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38355719","id":"PMC_38355719","title":"Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38355719","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RNA"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9265,"output_tokens":430,"usd":0.017122,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":4903,"output_tokens":1029,"usd":0.02512,"stage2_stop_reason":"end_turn"},"total_usd":0.042242,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2024,\n      \"finding\": \"PF3D7_0823200, initially identified as an RNA-dependent protein (RDP) by sucrose density gradient ultracentrifugation and mass spectrometry (R-DeeP), was functionally characterized and validated as a bona fide RNA-binding protein. Using enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq), PF3D7_0823200 was shown to interact with various Plasmodium non-coding transcripts, including var gene transcripts and ap2 transcription factor transcripts.\",\n      \"method\": \"R-DeeP (sucrose density gradient ultracentrifugation + quantitative mass spectrometry), computational validation, eCLIP-seq\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal methods (R-DeeP proteome-wide screen + eCLIP-seq) in a single study; functional characterization and RNA-target identification directly demonstrated for PF3D7_0823200, but single lab\",\n      \"pmids\": [\"38355719\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0823200 is a validated RNA-binding protein in P. falciparum that binds to non-coding transcripts including var gene and ap2 transcription factor transcripts, as demonstrated by eCLIP-seq, but its precise molecular function and mechanism of action remain uncharacterized beyond RNA binding.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0823200 is a validated RNA-binding protein of Plasmodium falciparum, initially flagged as an RNA-dependent protein in a proteome-wide R-DeeP screen and confirmed by eCLIP-seq to bind Plasmodium transcripts [#0]. Its RNA targets include non-coding var gene transcripts and ap2 transcription factor transcripts, linking it to loci associated with antigenic variation and transcriptional regulation [#0]. Beyond this demonstration of RNA binding and target identity, its precise molecular function, mechanism of action, and downstream regulatory consequences have not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2024,\n      \"claim\": \"It was unknown whether PF3D7_0823200 was a genuine RNA-binding protein or merely co-sedimented with RNA-containing complexes; orthogonal biochemical and crosslinking approaches established it as a bona fide RNA-binder with defined transcript targets.\",\n      \"evidence\": \"R-DeeP proteome-wide screen (sucrose gradient + quantitative MS) followed by eCLIP-seq in P. falciparum\",\n      \"pmids\": [\"38355719\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The molecular activity conferred by RNA binding (stabilization, decay, translation, localization) is unresolved.\",\n        \"The RNA-binding domain/region mediating target contact is not mapped.\",\n        \"Findings derive from a single lab without independent replication.\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The functional consequence of PF3D7_0823200 binding to var and ap2 non-coding transcripts — whether it regulates antigenic variation, transcription factor expression, or transcript fate — remains to be determined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No loss-of-function phenotype linking PF3D7_0823200 to var or ap2 regulation has been established.\",\n        \"No protein partners or complex context are defined.\",\n        \"No structural or mechanistic model of RNA engagement exists.\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"eCLIP-seq RNA targets include var gene non-coding transcripts and ap2 transcription factor transcripts [#0]\",\n      \"Identified as an RNA-dependent protein in R-DeeP proteome-wide screen [#0]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0823200","name":null,"product":"RNA-binding protein","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0707400","name":null,"product":"RNA-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1317200","name":null,"product":"RNA-binding protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}