{"gene":"PF3D7_0410400","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2018,"finding":"RRP4 (PfRrp4) localizes to the cytoplasm of P. falciparum asexual-stage parasites, as determined by indirect immunofluorescence using antibodies raised against recombinant protein.","method":"Indirect immunofluorescence (IFA) with anti-recombinant-protein antibody","journal":"The Journal of eukaryotic microbiology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiment, single lab, single method; replicated across multiple time points in asexual stage","pmids":["29664138"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"Recombinant RRP4 (PfRrp4) showed no processing activity toward either single-stranded RNA (ssRNA) or double-stranded RNA (dsRNA) in an in vitro ribonuclease assay, indicating it lacks catalytic RNA-degrading activity.","method":"In vitro exoribonuclease assay with recombinant protein","journal":"The Journal of eukaryotic microbiology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — direct in vitro biochemical assay establishing a negative catalytic result; single lab, single method","pmids":["29664138"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"finding":"RRP4 (PfRrp4) co-localizes with PfRrp6 at the nuclear periphery in P. falciparum, as shown by co-immunofluorescence assay (Co-IFA) in a dual-tagged CRISPR-Cas9 transgenic line (PfRrp6-Ty1::HA-PfRrp4), establishing that RRP4 is a component of the RNA exosome core complex in vivo.","method":"Co-immunofluorescence assay (Co-IFA) with epitope-tagged transgenic parasites generated by CRISPR-Cas9; Western blot validation of tagging","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal epitope tagging with Co-IFA and Western blot confirmation, single lab, two orthogonal methods","pmids":["32487761"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":2020,"finding":"RRP4 (PfRrp4) was used as a marker for the RNA exosome core complex and shown by RNA immunoprecipitation sequencing (RIP-seq) to associate with RUF6 ncRNA loci, consistent with its role as a structural subunit of the exosome core.","method":"RNA immunoprecipitation followed by sequencing (RIP-seq) using Ty1-HA-tagged PfRrp4","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP-seq with epitope-tagged protein, single lab; provides genome-wide occupancy data but functional consequence attributed to PfRrp6, not directly to RRP4","pmids":["32487761"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]}],"current_model":"In P. falciparum, RRP4 (PF3D7_0410400) is a non-catalytic structural subunit of the RNA exosome core complex that localizes to the nuclear periphery (and cytoplasm), lacks intrinsic ribonuclease activity against ssRNA or dsRNA in vitro, and physically associates with the catalytic subunit PfRrp6 in vivo."},"narrative":{"mechanistic_narrative":"RRP4 (PF3D7_0410400) is a non-catalytic structural subunit of the RNA exosome core complex in Plasmodium falciparum [PMID:32487761]. Recombinant PfRrp4 exhibits no exoribonuclease activity against either single- or double-stranded RNA in vitro, marking it as a scaffolding rather than a catalytic component of the exosome [PMID:29664138]. In asexual-stage parasites the protein localizes to the cytoplasm by immunofluorescence [PMID:29664138], and in dual-tagged transgenic lines it co-localizes with the catalytic subunit PfRrp6 at the nuclear periphery, establishing its physical incorporation into the exosome core in vivo [PMID:32487761]. Used as a marker for the core complex, PfRrp4 associates with RUF6 non-coding RNA loci by RIP-seq, placing the exosome at these loci, though the functional consequence at these sites was attributed to PfRrp6 rather than to RRP4 itself [PMID:32487761]. Beyond its membership in the exosome core and this genomic occupancy, no independent regulatory or enzymatic function of RRP4 has been characterized in the available corpus.","teleology":[{"year":2018,"claim":"Whether PfRrp4 itself carries RNA-degrading activity was unknown; establishing that it does not clarified that the subunit is structural rather than catalytic within the exosome.","evidence":"In vitro exoribonuclease assay on recombinant protein against ssRNA and dsRNA substrates","pmids":["29664138"],"confidence":"Medium","gaps":["A negative in vitro result does not exclude activity requiring cofactors or assembly into the full complex","Does not define which structural role RRP4 plays in the core"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"claim":"The subcellular distribution of RRP4 was undefined; immunofluorescence localized it to the parasite cytoplasm during asexual stages, providing the first spatial context.","evidence":"Indirect immunofluorescence with anti-recombinant-protein antibody across asexual time points","pmids":["29664138"],"confidence":"Medium","gaps":["Single-antibody, single-lab localization not reconciled with later nuclear-periphery signal","Does not address localization in sexual or other stages"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"claim":"Whether RRP4 assembles with the catalytic exosome subunit in vivo was unresolved; reciprocal epitope tagging showed co-localization with PfRrp6 at the nuclear periphery, establishing RRP4 as a bona fide component of the exosome core complex.","evidence":"Co-immunofluorescence in a dual-tagged CRISPR-Cas9 line (PfRrp6-Ty1::HA-PfRrp4) with Western blot validation","pmids":["32487761"],"confidence":"Medium","gaps":["Co-IFA shows co-localization but not direct physical interaction (no reciprocal Co-IP shown)","Nuclear-periphery signal contrasts with the earlier cytoplasmic localization","Stoichiometry and full subunit composition of the complex not defined"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":2020,"claim":"The genomic targets of the exosome core were unknown; using tagged PfRrp4 as a marker, RIP-seq placed the complex at RUF6 ncRNA loci, linking the exosome to non-coding RNA regulation.","evidence":"RNA immunoprecipitation sequencing with Ty1-HA-tagged PfRrp4","pmids":["32487761"],"confidence":"Medium","gaps":["Functional consequence at these loci was attributed to PfRrp6, not directly to RRP4","Does not establish whether RRP4 contributes to target selection or is merely a passive scaffold"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":null,"claim":"It remains unknown whether RRP4 has any function beyond passive incorporation into the exosome core, including its precise structural role, full interactome, and contribution to RNA processing.","evidence":"","pmids":[],"confidence":"Low","gaps":["No genetic knockdown/knockout phenotype for RRP4 reported","No structural model of the P. falciparum exosome core","Direct physical interaction and stoichiometry with other subunits unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["RNA exosome core complex"],"partners":["PFRRP6 (CATALYTIC EXOSOME SUBUNIT)"],"other_free_text":["Recombinant PfRrp4 has no detectable exoribonuclease activity against ssRNA or dsRNA in vitro, consistent with a non-catalytic structural role [#1].","PfRrp4 associates with RUF6 non-coding RNA loci by RIP-seq, but the functional outcome at these loci was attributed to PfRrp6 rather than RRP4 [#3].","Cytoplasmic localization was reported in 2018 [#0], while co-localization with PfRrp6 at the nuclear periphery was reported in 2020 [#2]."]}},"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":["PfRRP4"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32487761","id":"","title":"Rrp6 Regulates Heterochromatic Gene Silencing via ncRNA RUF6 Decay in Malaria Parasites.","date":"2020","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/32487761","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RRP4"],"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":["RRP4"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"22126454","id":"","title":"Identification and analysis of the RNA degrading complexes and machinery of Giardia lamblia using an in silico approach.","date":"2011","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/22126454","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["RRP4"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7492,"output_tokens":1112,"usd":0.019578,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5898,"output_tokens":2256,"usd":0.042945,"stage2_stop_reason":"end_turn"},"total_usd":0.062523,"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\": 2018,\n      \"finding\": \"RRP4 (PfRrp4) localizes to the cytoplasm of P. falciparum asexual-stage parasites, as determined by indirect immunofluorescence using antibodies raised against recombinant protein.\",\n      \"method\": \"Indirect immunofluorescence (IFA) with anti-recombinant-protein antibody\",\n      \"journal\": \"The Journal of eukaryotic microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiment, single lab, single method; replicated across multiple time points in asexual stage\",\n      \"pmids\": [\"29664138\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Recombinant RRP4 (PfRrp4) showed no processing activity toward either single-stranded RNA (ssRNA) or double-stranded RNA (dsRNA) in an in vitro ribonuclease assay, indicating it lacks catalytic RNA-degrading activity.\",\n      \"method\": \"In vitro exoribonuclease assay with recombinant protein\",\n      \"journal\": \"The Journal of eukaryotic microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — direct in vitro biochemical assay establishing a negative catalytic result; single lab, single method\",\n      \"pmids\": [\"29664138\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RRP4 (PfRrp4) co-localizes with PfRrp6 at the nuclear periphery in P. falciparum, as shown by co-immunofluorescence assay (Co-IFA) in a dual-tagged CRISPR-Cas9 transgenic line (PfRrp6-Ty1::HA-PfRrp4), establishing that RRP4 is a component of the RNA exosome core complex in vivo.\",\n      \"method\": \"Co-immunofluorescence assay (Co-IFA) with epitope-tagged transgenic parasites generated by CRISPR-Cas9; Western blot validation of tagging\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal epitope tagging with Co-IFA and Western blot confirmation, single lab, two orthogonal methods\",\n      \"pmids\": [\"32487761\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RRP4 (PfRrp4) was used as a marker for the RNA exosome core complex and shown by RNA immunoprecipitation sequencing (RIP-seq) to associate with RUF6 ncRNA loci, consistent with its role as a structural subunit of the exosome core.\",\n      \"method\": \"RNA immunoprecipitation followed by sequencing (RIP-seq) using Ty1-HA-tagged PfRrp4\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP-seq with epitope-tagged protein, single lab; provides genome-wide occupancy data but functional consequence attributed to PfRrp6, not directly to RRP4\",\n      \"pmids\": [\"32487761\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    }\n  ],\n  \"current_model\": \"In P. falciparum, RRP4 (PF3D7_0410400) is a non-catalytic structural subunit of the RNA exosome core complex that localizes to the nuclear periphery (and cytoplasm), lacks intrinsic ribonuclease activity against ssRNA or dsRNA in vitro, and physically associates with the catalytic subunit PfRrp6 in vivo.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RRP4 (PF3D7_0410400) is a non-catalytic structural subunit of the RNA exosome core complex in Plasmodium falciparum [#2]. Recombinant PfRrp4 exhibits no exoribonuclease activity against either single- or double-stranded RNA in vitro, marking it as a scaffolding rather than a catalytic component of the exosome [#1]. In asexual-stage parasites the protein localizes to the cytoplasm by immunofluorescence [#0], and in dual-tagged transgenic lines it co-localizes with the catalytic subunit PfRrp6 at the nuclear periphery, establishing its physical incorporation into the exosome core in vivo [#2]. Used as a marker for the core complex, PfRrp4 associates with RUF6 non-coding RNA loci by RIP-seq, placing the exosome at these loci, though the functional consequence at these sites was attributed to PfRrp6 rather than to RRP4 itself [#3]. Beyond its membership in the exosome core and this genomic occupancy, no independent regulatory or enzymatic function of RRP4 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Whether PfRrp4 itself carries RNA-degrading activity was unknown; establishing that it does not clarified that the subunit is structural rather than catalytic within the exosome.\",\n      \"evidence\": \"In vitro exoribonuclease assay on recombinant protein against ssRNA and dsRNA substrates\",\n      \"pmids\": [\"29664138\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"A negative in vitro result does not exclude activity requiring cofactors or assembly into the full complex\",\n        \"Does not define which structural role RRP4 plays in the core\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The subcellular distribution of RRP4 was undefined; immunofluorescence localized it to the parasite cytoplasm during asexual stages, providing the first spatial context.\",\n      \"evidence\": \"Indirect immunofluorescence with anti-recombinant-protein antibody across asexual time points\",\n      \"pmids\": [\"29664138\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-antibody, single-lab localization not reconciled with later nuclear-periphery signal\",\n        \"Does not address localization in sexual or other stages\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Whether RRP4 assembles with the catalytic exosome subunit in vivo was unresolved; reciprocal epitope tagging showed co-localization with PfRrp6 at the nuclear periphery, establishing RRP4 as a bona fide component of the exosome core complex.\",\n      \"evidence\": \"Co-immunofluorescence in a dual-tagged CRISPR-Cas9 line (PfRrp6-Ty1::HA-PfRrp4) with Western blot validation\",\n      \"pmids\": [\"32487761\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Co-IFA shows co-localization but not direct physical interaction (no reciprocal Co-IP shown)\",\n        \"Nuclear-periphery signal contrasts with the earlier cytoplasmic localization\",\n        \"Stoichiometry and full subunit composition of the complex not defined\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"The genomic targets of the exosome core were unknown; using tagged PfRrp4 as a marker, RIP-seq placed the complex at RUF6 ncRNA loci, linking the exosome to non-coding RNA regulation.\",\n      \"evidence\": \"RNA immunoprecipitation sequencing with Ty1-HA-tagged PfRrp4\",\n      \"pmids\": [\"32487761\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence at these loci was attributed to PfRrp6, not directly to RRP4\",\n        \"Does not establish whether RRP4 contributes to target selection or is merely a passive scaffold\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether RRP4 has any function beyond passive incorporation into the exosome core, including its precise structural role, full interactome, and contribution to RNA processing.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No genetic knockdown/knockout phenotype for RRP4 reported\",\n        \"No structural model of the P. falciparum exosome core\",\n        \"Direct physical interaction and stoichiometry with other subunits unresolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0004532\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005737\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0034399\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0071028\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\n      \"RNA exosome core complex\"\n    ],\n    \"partners\": [\n      \"PfRrp6 (catalytic exosome subunit)\"\n    ],\n    \"other_free_text\": [\n      \"Recombinant PfRrp4 has no detectable exoribonuclease activity against ssRNA or dsRNA in vitro, consistent with a non-catalytic structural role [#1].\",\n      \"PfRrp4 associates with RUF6 non-coding RNA loci by RIP-seq, but the functional outcome at these loci was attributed to PfRrp6 rather than RRP4 [#3].\",\n      \"Cytoplasmic localization was reported in 2018 [#0], while co-localization with PfRrp6 at the nuclear periphery was reported in 2020 [#2].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0410400","name":null,"product":"exosome complex component RRP4","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1007800","name":null,"product":"exosome complex component RRP4, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0308500","name":null,"product":"exosome complex component RRP4, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RRP4","evaluation":null}