{"gene":"PF3D7_0507600","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2016,"finding":"CAF40 (PF3D7_0507600) was experimentally captured as an mRNA-associated protein in P. falciparum blood stages; it was detected in polysomal fractions, identifying it as a component of the CCR4-NOT complex that associates with mRNA during blood-stage development.","method":"mRNA interactome capture (oligo-dT pulldown) followed by mass spectrometry; polysome fractionation and proteomics","journal":"Genome biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct experimental capture of mRNA association by oligo-dT pulldown and polysome fractionation MS, single lab, single study","pmids":["27381095"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"CAF40 (PF3D7_0507600) was identified as an RNA-dependent protein (RDP) in P. falciparum by sucrose density gradient ultracentrifugation (R-DeeP), co-segregating with stress granule- and P-body-associated proteins (alongside CITH and CAF1), consistent with its membership in RNA-regulatory complexes.","method":"R-DeeP (sucrose density gradient ultracentrifugation) coupled with quantitative mass spectrometry","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — unbiased proteome-wide co-sedimentation assay, single lab, single method","pmids":["38355719"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2024,"finding":"CAF40 (PF3D7_0507600) co-immunoprecipitates with PfDOZI in both schizonts and gametocytes (day 5) of P. falciparum, placing it as a component of PB-like mRNPs (schizonts) and germ cell granule-like mRNPs (gametocytes) within the CCR4-NOT deadenylase complex.","method":"GFP-trap immunoprecipitation of PfDOZI::GFP followed by LC-MS/MS","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal-style IP with mass spectrometry in two life stages, single lab","pmids":["38702310"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"finding":"CAF40 (PF3D7_0507600) was identified as a binding partner of the CCR4-1 deadenylase in Plasmodium yoelii by immunoprecipitation, confirming its membership in the canonical CAF1/CCR4/NOT complex in Plasmodium.","method":"Co-immunoprecipitation of PyCCR4-1 followed by mass spectrometry (label-free quantification)","journal":"PLoS biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP/MS identifying complex membership, single lab","pmids":["34673764"],"is_preprint":false,"attribution":[{"species":"Plasmodium yoelii","strain":""}]},{"year":2025,"finding":"CAF40 (PF3D7_0507600) was identified as a proximity interactor of PfRNF1 (a RING finger E3 ubiquitin ligase) in P. falciparum immature gametocytes by BioID-based proteomics, placing it at the interface of RNA metabolism and the ubiquitin-proteasome system in gametocytes.","method":"BioID proximity labeling followed by mass spectrometry","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proximity labeling (BioID), single lab, single method; does not confirm direct physical interaction","pmids":["40564933"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"finding":"CAF40 (PF3D7_0507600) co-immunoprecipitates with the RNA-binding protein GD1 at day 6 of P. falciparum gametocytogenesis, suggesting formation of a repressive P-body-like structure at this stage; furthermore, changes in GD1 protein levels (deletion or overexpression) lead to downregulation of CAF40 protein levels, indicating that CAF40 abundance in gametocytes depends on GD1 homeostasis.","method":"Immunoprecipitation of GD1-HA-mScarlet followed by LC-MS/MS; quantitative proteomics of GD1 deletion and overexpression lines","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP/MS plus quantitative proteomics in loss-of-function and gain-of-function lines, single lab, two orthogonal methods","pmids":["41986327"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0507600 (CAF40) is a core subunit of the CCR4-NOT deadenylase complex in Plasmodium falciparum and P. yoelii; it associates with mRNA, co-immunoprecipitates with the CCR4-1 deadenylase, PfDOZI, and GD1, and partakes in P-body-like and germ cell granule-like mRNPs during gametocyte development, where its protein levels are regulated downstream of the RNA-binding protein GD1."},"narrative":{"mechanistic_narrative":"PF3D7_0507600 (CAF40) is an mRNA-associated component of the CCR4-NOT deadenylase machinery in Plasmodium, functioning within RNA-regulatory ribonucleoprotein complexes across the parasite life cycle [PMID:27381095, PMID:34673764]. It was first captured as an mRNA-binding protein present in polysomal fractions of P. falciparum blood stages [PMID:27381095], and in P. yoelii it co-immunoprecipitates with the CCR4-1 deadenylase, establishing its membership in the canonical CAF1/CCR4/NOT complex [PMID:34673764]. In P. falciparum it behaves as an RNA-dependent protein that co-sediments with stress granule- and P-body-associated factors including CITH and CAF1 [PMID:38355719], and it co-immunoprecipitates with PfDOZI in both schizonts and gametocytes, marking it as a constituent of P-body-like mRNPs in schizonts and germ cell granule-like mRNPs in gametocytes [PMID:38702310]. During gametocytogenesis, CAF40 associates with the RNA-binding protein GD1 within a repressive P-body-like structure, and its protein abundance depends on GD1 homeostasis, being downregulated when GD1 is deleted or overexpressed [PMID:41986327]. Beyond these complex-membership and abundance-regulation findings, no dedicated biochemical characterization of CAF40's own molecular activity has been established in the available corpus.","teleology":[{"year":2016,"claim":"Establishing whether CAF40 physically engages mRNA in the parasite addressed whether it participates in post-transcriptional regulation rather than being merely inferred by homology.","evidence":"oligo-dT mRNA interactome capture plus polysome fractionation and MS in P. falciparum blood stages","pmids":["27381095"],"confidence":"Medium","gaps":["Does not distinguish direct RNA binding from association via complex partners","No functional consequence of mRNA association demonstrated","Single study, single lab"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"claim":"Co-IP of the CCR4-1 deadenylase in a rodent malaria model tested whether CAF40 is a bona fide subunit of the deadenylase complex in Plasmodium.","evidence":"Co-immunoprecipitation of PyCCR4-1 with label-free quantification MS in P. yoelii","pmids":["34673764"],"confidence":"Medium","gaps":["Direct binary interaction between CAF40 and CCR4-1 not resolved","Functional contribution of CAF40 to deadenylase activity not tested","Shown in P. yoelii, not P. falciparum"],"attribution":[{"species":"Plasmodium yoelii","strain":""}]},{"year":2024,"claim":"Unbiased co-sedimentation and reciprocal-style IP defined the RNP context of CAF40 across life stages, linking it to P-body-like and germ cell granule-like mRNPs.","evidence":"R-DeeP sucrose-gradient co-sedimentation MS and GFP-trap IP of PfDOZI::GFP in P. falciparum schizonts and gametocytes","pmids":["38355719","38702310"],"confidence":"Medium","gaps":["Whether CAF40 is required for mRNP assembly is untested","No target mRNAs of CAF40 identified","Stoichiometry within these granules unknown"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Proximity labeling placed CAF40 near an E3 ubiquitin ligase in immature gametocytes, raising a potential interface between RNA metabolism and the ubiquitin-proteasome system.","evidence":"BioID proximity labeling with MS in P. falciparum immature gametocytes","pmids":["40564933"],"confidence":"Low","gaps":["BioID does not confirm direct physical interaction with PfRNF1","Functional significance of the proximity unknown","Single method, single lab"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2026,"claim":"Combining IP with loss- and gain-of-function proteomics showed that CAF40 partners with GD1 in gametocytes and that its abundance is controlled by GD1 homeostasis, linking CAF40 levels to an RNA-binding regulator.","evidence":"IP of GD1-HA-mScarlet with LC-MS/MS plus quantitative proteomics of GD1 deletion and overexpression lines in P. falciparum","pmids":["41986327"],"confidence":"Medium","gaps":["Mechanism by which GD1 controls CAF40 abundance not defined","Whether the GD1-CAF40 interaction is direct is unresolved","Functional consequence of altered CAF40 levels not tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The intrinsic molecular activity of CAF40, its direct RNA targets, and its specific functional contribution to deadenylation and translational repression remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No CAF40-specific loss-of-function phenotype reported","No structural or biochemical characterization of CAF40's own activity","No identified mRNA substrates regulated via CAF40"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["CCR4-NOT deadenylase complex (CAF1/CCR4/NOT)","P-body-like mRNP","germ cell granule-like mRNP"],"partners":["CCR4-1 DEADENYLASE (P. YOELII)","PFDOZI","GD1","CITH (CO-SEDIMENTATION)","CAF1 (CO-SEDIMENTATION)","PFRNF1 (PROXIMITY INTERACTOR)"],"other_free_text":["CAF40 protein abundance in gametocytes depends on GD1 homeostasis, decreasing with both GD1 deletion and overexpression [#5]","The corpus establishes CAF40 primarily through complex membership and co-association; no CAF40-specific enzymatic activity or loss-of-function phenotype is characterized."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"30703164","id":"PMC_30703164","title":"Plasmodium male gametocyte development and transmission are critically regulated by the two putative deadenylases of the CAF1/CCR4/NOT complex.","date":"2019","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/30703164","citation_count":30,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41986327","id":"","title":"GID/CTLH E3 ligase complex control cell fate programs for sexual development of Plasmodium falciparum.","date":"2026","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41986327","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF40"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40564933","id":"","title":"The Plasmodium falciparum RING Finger Protein PfRNF1 Forms an Interaction Network with Regulators of Sexual Development.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40564933","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF40"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38355719","id":"","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":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF40"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38702310","id":"","title":"The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38702310","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF40"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"34673764","id":"","title":"The Plasmodium NOT1-G paralogue is an essential regulator of sexual stage maturation and parasite transmission.","date":"2021","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/34673764","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF40"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31795940","id":"","title":"Hierarchical transcriptional control regulates Plasmodium falciparum sexual differentiation.","date":"2019","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/31795940","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF40"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29561870","id":"","title":"Multispecies reconstructions uncover widespread conservation, and lineage-specific elaborations in eukaryotic mRNA metabolism.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29561870","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF40"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27381095","id":"","title":"The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum.","date":"2016","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/27381095","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["CAF40"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12613,"output_tokens":1670,"usd":0.031445,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6656,"output_tokens":2599,"usd":0.049127,"stage2_stop_reason":"end_turn"},"total_usd":0.080572,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"CAF40 (PF3D7_0507600) was experimentally captured as an mRNA-associated protein in P. falciparum blood stages; it was detected in polysomal fractions, identifying it as a component of the CCR4-NOT complex that associates with mRNA during blood-stage development.\",\n      \"method\": \"mRNA interactome capture (oligo-dT pulldown) followed by mass spectrometry; polysome fractionation and proteomics\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct experimental capture of mRNA association by oligo-dT pulldown and polysome fractionation MS, single lab, single study\",\n      \"pmids\": [\"27381095\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CAF40 (PF3D7_0507600) was identified as an RNA-dependent protein (RDP) in P. falciparum by sucrose density gradient ultracentrifugation (R-DeeP), co-segregating with stress granule- and P-body-associated proteins (alongside CITH and CAF1), consistent with its membership in RNA-regulatory complexes.\",\n      \"method\": \"R-DeeP (sucrose density gradient ultracentrifugation) coupled with quantitative mass spectrometry\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — unbiased proteome-wide co-sedimentation assay, single lab, single method\",\n      \"pmids\": [\"38355719\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CAF40 (PF3D7_0507600) co-immunoprecipitates with PfDOZI in both schizonts and gametocytes (day 5) of P. falciparum, placing it as a component of PB-like mRNPs (schizonts) and germ cell granule-like mRNPs (gametocytes) within the CCR4-NOT deadenylase complex.\",\n      \"method\": \"GFP-trap immunoprecipitation of PfDOZI::GFP followed by LC-MS/MS\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal-style IP with mass spectrometry in two life stages, single lab\",\n      \"pmids\": [\"38702310\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CAF40 (PF3D7_0507600) was identified as a binding partner of the CCR4-1 deadenylase in Plasmodium yoelii by immunoprecipitation, confirming its membership in the canonical CAF1/CCR4/NOT complex in Plasmodium.\",\n      \"method\": \"Co-immunoprecipitation of PyCCR4-1 followed by mass spectrometry (label-free quantification)\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP/MS identifying complex membership, single lab\",\n      \"pmids\": [\"34673764\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium yoelii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CAF40 (PF3D7_0507600) was identified as a proximity interactor of PfRNF1 (a RING finger E3 ubiquitin ligase) in P. falciparum immature gametocytes by BioID-based proteomics, placing it at the interface of RNA metabolism and the ubiquitin-proteasome system in gametocytes.\",\n      \"method\": \"BioID proximity labeling followed by mass spectrometry\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proximity labeling (BioID), single lab, single method; does not confirm direct physical interaction\",\n      \"pmids\": [\"40564933\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CAF40 (PF3D7_0507600) co-immunoprecipitates with the RNA-binding protein GD1 at day 6 of P. falciparum gametocytogenesis, suggesting formation of a repressive P-body-like structure at this stage; furthermore, changes in GD1 protein levels (deletion or overexpression) lead to downregulation of CAF40 protein levels, indicating that CAF40 abundance in gametocytes depends on GD1 homeostasis.\",\n      \"method\": \"Immunoprecipitation of GD1-HA-mScarlet followed by LC-MS/MS; quantitative proteomics of GD1 deletion and overexpression lines\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP/MS plus quantitative proteomics in loss-of-function and gain-of-function lines, single lab, two orthogonal methods\",\n      \"pmids\": [\"41986327\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0507600 (CAF40) is a core subunit of the CCR4-NOT deadenylase complex in Plasmodium falciparum and P. yoelii; it associates with mRNA, co-immunoprecipitates with the CCR4-1 deadenylase, PfDOZI, and GD1, and partakes in P-body-like and germ cell granule-like mRNPs during gametocyte development, where its protein levels are regulated downstream of the RNA-binding protein GD1.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0507600 (CAF40) is an mRNA-associated component of the CCR4-NOT deadenylase machinery in Plasmodium, functioning within RNA-regulatory ribonucleoprotein complexes across the parasite life cycle [#0, #3]. It was first captured as an mRNA-binding protein present in polysomal fractions of P. falciparum blood stages [#0], and in P. yoelii it co-immunoprecipitates with the CCR4-1 deadenylase, establishing its membership in the canonical CAF1/CCR4/NOT complex [#3]. In P. falciparum it behaves as an RNA-dependent protein that co-sediments with stress granule- and P-body-associated factors including CITH and CAF1 [#1], and it co-immunoprecipitates with PfDOZI in both schizonts and gametocytes, marking it as a constituent of P-body-like mRNPs in schizonts and germ cell granule-like mRNPs in gametocytes [#2]. During gametocytogenesis, CAF40 associates with the RNA-binding protein GD1 within a repressive P-body-like structure, and its protein abundance depends on GD1 homeostasis, being downregulated when GD1 is deleted or overexpressed [#5]. Beyond these complex-membership and abundance-regulation findings, no dedicated biochemical characterization of CAF40's own molecular activity has been established in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Establishing whether CAF40 physically engages mRNA in the parasite addressed whether it participates in post-transcriptional regulation rather than being merely inferred by homology.\",\n      \"evidence\": \"oligo-dT mRNA interactome capture plus polysome fractionation and MS in P. falciparum blood stages\",\n      \"pmids\": [\"27381095\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not distinguish direct RNA binding from association via complex partners\", \"No functional consequence of mRNA association demonstrated\", \"Single study, single lab\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Co-IP of the CCR4-1 deadenylase in a rodent malaria model tested whether CAF40 is a bona fide subunit of the deadenylase complex in Plasmodium.\",\n      \"evidence\": \"Co-immunoprecipitation of PyCCR4-1 with label-free quantification MS in P. yoelii\",\n      \"pmids\": [\"34673764\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binary interaction between CAF40 and CCR4-1 not resolved\", \"Functional contribution of CAF40 to deadenylase activity not tested\", \"Shown in P. yoelii, not P. falciparum\"],\n      \"attribution\": [{\"species\": \"Plasmodium yoelii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Unbiased co-sedimentation and reciprocal-style IP defined the RNP context of CAF40 across life stages, linking it to P-body-like and germ cell granule-like mRNPs.\",\n      \"evidence\": \"R-DeeP sucrose-gradient co-sedimentation MS and GFP-trap IP of PfDOZI::GFP in P. falciparum schizonts and gametocytes\",\n      \"pmids\": [\"38355719\", \"38702310\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether CAF40 is required for mRNP assembly is untested\", \"No target mRNAs of CAF40 identified\", \"Stoichiometry within these granules unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Proximity labeling placed CAF40 near an E3 ubiquitin ligase in immature gametocytes, raising a potential interface between RNA metabolism and the ubiquitin-proteasome system.\",\n      \"evidence\": \"BioID proximity labeling with MS in P. falciparum immature gametocytes\",\n      \"pmids\": [\"40564933\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"BioID does not confirm direct physical interaction with PfRNF1\", \"Functional significance of the proximity unknown\", \"Single method, single lab\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Combining IP with loss- and gain-of-function proteomics showed that CAF40 partners with GD1 in gametocytes and that its abundance is controlled by GD1 homeostasis, linking CAF40 levels to an RNA-binding regulator.\",\n      \"evidence\": \"IP of GD1-HA-mScarlet with LC-MS/MS plus quantitative proteomics of GD1 deletion and overexpression lines in P. falciparum\",\n      \"pmids\": [\"41986327\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which GD1 controls CAF40 abundance not defined\", \"Whether the GD1-CAF40 interaction is direct is unresolved\", \"Functional consequence of altered CAF40 levels not tested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intrinsic molecular activity of CAF40, its direct RNA targets, and its specific functional contribution to deadenylation and translational repression remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No CAF40-specific loss-of-function phenotype reported\", \"No structural or biochemical characterization of CAF40's own activity\", \"No identified mRNA substrates regulated via CAF40\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0000932\", \"supporting_discovery_ids\": [2, 5]},\n      {\"term_id\": \"GO:0010494\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0000289\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0017148\", \"supporting_discovery_ids\": [2, 5]}\n    ],\n    \"complexes\": [\n      \"CCR4-NOT deadenylase complex (CAF1/CCR4/NOT)\",\n      \"P-body-like mRNP\",\n      \"germ cell granule-like mRNP\"\n    ],\n    \"partners\": [\n      \"CCR4-1 deadenylase (P. yoelii)\",\n      \"PfDOZI\",\n      \"GD1\",\n      \"CITH (co-sedimentation)\",\n      \"CAF1 (co-sedimentation)\",\n      \"PfRNF1 (proximity interactor)\"\n    ],\n    \"other_free_text\": [\n      \"CAF40 protein abundance in gametocytes depends on GD1 homeostasis, decreasing with both GD1 deletion and overexpression [#5]\",\n      \"The corpus establishes CAF40 primarily through complex membership and co-association; no CAF40-specific enzymatic activity or loss-of-function phenotype is characterized.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0507600","name":null,"product":"protein CAF40, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1107200","name":null,"product":"protein CAF40, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1026000","name":null,"product":"protein CAF40, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"CAF40","evaluation":null}