{"gene":"PF3D7_0409600","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2002,"finding":"PF3D7_0409600 (pfRPA1, the large subunit of P. falciparum replication protein A) was identified by affinity purification and mass spectrometry as a ~55 kDa factor and shown by gel retardation (EMSA) to be the major single-stranded DNA binding activity in parasite protein extracts. Its ssDNA-binding activity is expressed in a cell cycle-dependent manner, peaking in late trophozoites and schizonts, coinciding with the onset of chromosomal DNA replication. The protein lacks the N-terminal protein interaction domain present in higher-eukaryote RPA1 orthologues, making it a short-type RPA1. Its mRNA is detected ~20–24 h post-invasion.","method":"Affinity purification, mass spectrometry, gel retardation (EMSA), Northern/RT-PCR for transcript timing","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical identification by affinity purification + MS, functional ssDNA-binding confirmed by EMSA with cell-cycle correlation; single lab, multiple orthogonal methods","pmids":["11880371"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"Recombinant PF3D7_0409600 protein (designated PfRPA1L, the large subunit form) functionally substitutes for the bacterial single-stranded DNA binding protein (SSB) in initiating homologous pairing and Rad51-mediated strand exchange activity in vitro. Its stimulatory function in the Rad51-Rad54 strand exchange reaction is negatively regulated in a dose-dependent manner by PfRPA1S (the short-type RPA1 paralogue). Upon methyl methane sulfonate-induced DNA damage in live parasites, both PfRPA1L transcript and protein are upregulated alongside PfRad51, PfRad54, and PfRPA1S.","method":"In vitro DNA strand exchange assay with recombinant proteins, dose-response inhibition assay, comet assay for DNA damage induction, RT-PCR and western blot for transcript/protein upregulation","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — in vitro reconstitution of strand exchange with recombinant protein plus in vivo damage-response validation; single lab, multiple orthogonal methods","pmids":["23631919"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0409600 (the large subunit of P. falciparum replication protein A) is the principal single-stranded DNA binding protein in P. falciparum, expressed in a cell cycle-dependent manner peaking at late trophozoite/schizont stages; recombinant PF3D7_0409600 protein stimulates PfRad51-Rad54-mediated homologous strand exchange in vitro (acting analogously to bacterial SSB), while this activity is negatively regulated in a dose-dependent fashion by the parasite's short-type RPA1 paralogue, and both proteins are upregulated in response to DNA damage in vivo."},"narrative":{"mechanistic_narrative":"PF3D7_0409600 is the large subunit of P. falciparum replication protein A and constitutes the major single-stranded DNA binding activity in the parasite, an activity expressed in a cell cycle-dependent manner that peaks in late trophozoites and schizonts, coinciding with the onset of chromosomal DNA replication [PMID:11880371]. It is a short-type RPA1, lacking the N-terminal protein interaction domain found in higher-eukaryote RPA1 orthologues [PMID:11880371]. Functionally, recombinant PF3D7_0409600 substitutes for bacterial SSB to initiate homologous pairing and stimulate PfRad51-PfRad54-mediated strand exchange in vitro, a stimulatory function that is negatively regulated in a dose-dependent manner by the short-type RPA1 paralogue PfRPA1S; upon methyl methanesulfonate-induced DNA damage in live parasites, PF3D7_0409600 transcript and protein are upregulated alongside PfRad51, PfRad54, and PfRPA1S [PMID:23631919]. Beyond its ssDNA-binding and strand-exchange stimulatory roles, no further mechanistic detail for PF3D7_0409600 has been characterized in the available corpus.","teleology":[{"year":2002,"claim":"Whether P. falciparum possesses a dedicated single-stranded DNA binding protein and how its activity is timed relative to replication was unknown; this work identified PF3D7_0409600 as the parasite's principal ssDNA-binding factor and linked its activity to the replicative cell cycle.","evidence":"Affinity purification and mass spectrometry identifying a ~55 kDa factor, EMSA for ssDNA binding, and Northern/RT-PCR for cell-cycle transcript timing in P. falciparum extracts","pmids":["11880371"],"confidence":"Medium","gaps":["Direct role in replication fork progression not tested in vivo","Absence of the N-terminal interaction domain leaves partner recruitment mechanism unresolved","No structural characterization of the ssDNA-binding mode"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"claim":"Whether PF3D7_0409600 participates in homologous recombination and how its activity is controlled was unknown; reconstitution showed it stimulates Rad51-Rad54 strand exchange and is antagonized by its short-type paralogue, placing it in the parasite's DNA damage response.","evidence":"In vitro strand exchange assay with recombinant proteins, dose-response inhibition by PfRPA1S, comet assay for MMS-induced damage, and RT-PCR/western blot for damage-induced upregulation in live P. falciparum","pmids":["23631919"],"confidence":"Medium","gaps":["In vivo requirement for HR (e.g. genetic knockout/knockdown) not established","Molecular basis of PfRPA1S dose-dependent inhibition not defined","Physical interaction between PF3D7_0409600 and Rad51/Rad54 not directly demonstrated"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"How PF3D7_0409600 is recruited to sites of replication and repair in the absence of the canonical N-terminal interaction domain, and its genetic essentiality in the parasite, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No genetic loss-of-function data for PF3D7_0409600","No defined protein interactome or complex architecture","No structural model of the ssDNA-bound or Rad51-stimulating state"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Replication protein A (large subunit)"],"partners":["PFRPA1S (SHORT-TYPE RPA1 PARALOGUE; NEGATIVE REGULATOR)","PFRAD51","PFRAD54"],"other_free_text":["Short-type RPA1 lacking the N-terminal protein interaction domain present in higher-eukaryote RPA1 orthologues [#0]","ssDNA-binding activity peaks in late trophozoites/schizonts, coinciding with chromosomal DNA replication onset; mRNA detected ~20-24 h post-invasion [#0]","Transcript and protein upregulated upon MMS-induced DNA damage in vivo [#1]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"11880371","id":"PMC_11880371","title":"Plasmodium falciparum possesses a cell cycle-regulated short type replication protein A large subunit encoded by an unusual transcript.","date":"2002","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11880371","citation_count":54,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRPA1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"23631919","id":"PMC_23631919","title":"Opposing roles for two molecular forms of replication protein A in Rad51-Rad54-mediated DNA recombination in Plasmodium falciparum.","date":"2013","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/23631919","citation_count":27,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfRPA1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25184562","id":"PMC_25184562","title":"DNA repair mechanisms and their biological roles in the malaria parasite Plasmodium falciparum.","date":"2014","source":"Microbiology and molecular biology reviews : MMBR","url":"https://pubmed.ncbi.nlm.nih.gov/25184562","citation_count":91,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29587837","id":"PMC_29587837","title":"Checks and balances? DNA replication and the cell cycle in Plasmodium.","date":"2018","source":"Parasites & vectors","url":"https://pubmed.ncbi.nlm.nih.gov/29587837","citation_count":84,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28936205","id":"PMC_28936205","title":"Homologous Recombination in Protozoan Parasites and Recombinase Inhibitors.","date":"2017","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/28936205","citation_count":22,"is_preprint":false,"source_species":["Pf"],"role":"citation_expansion","match_terms":["fwd_cite"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5131,"output_tokens":911,"usd":0.014529,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5619,"output_tokens":1900,"usd":0.037797,"stage2_stop_reason":"end_turn"},"total_usd":0.052326,"stage1_batch_id":"msgbatch_01DbiymDmubkPpYvdbAu5a7V","stage2_batch_id":"msgbatch_012TbrWvMRH129T7PQ4SmvrJ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2002,\n      \"finding\": \"PF3D7_0409600 (pfRPA1, the large subunit of P. falciparum replication protein A) was identified by affinity purification and mass spectrometry as a ~55 kDa factor and shown by gel retardation (EMSA) to be the major single-stranded DNA binding activity in parasite protein extracts. Its ssDNA-binding activity is expressed in a cell cycle-dependent manner, peaking in late trophozoites and schizonts, coinciding with the onset of chromosomal DNA replication. The protein lacks the N-terminal protein interaction domain present in higher-eukaryote RPA1 orthologues, making it a short-type RPA1. Its mRNA is detected ~20–24 h post-invasion.\",\n      \"method\": \"Affinity purification, mass spectrometry, gel retardation (EMSA), Northern/RT-PCR for transcript timing\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical identification by affinity purification + MS, functional ssDNA-binding confirmed by EMSA with cell-cycle correlation; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"11880371\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Recombinant PF3D7_0409600 protein (designated PfRPA1L, the large subunit form) functionally substitutes for the bacterial single-stranded DNA binding protein (SSB) in initiating homologous pairing and Rad51-mediated strand exchange activity in vitro. Its stimulatory function in the Rad51-Rad54 strand exchange reaction is negatively regulated in a dose-dependent manner by PfRPA1S (the short-type RPA1 paralogue). Upon methyl methane sulfonate-induced DNA damage in live parasites, both PfRPA1L transcript and protein are upregulated alongside PfRad51, PfRad54, and PfRPA1S.\",\n      \"method\": \"In vitro DNA strand exchange assay with recombinant proteins, dose-response inhibition assay, comet assay for DNA damage induction, RT-PCR and western blot for transcript/protein upregulation\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro reconstitution of strand exchange with recombinant protein plus in vivo damage-response validation; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"23631919\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0409600 (the large subunit of P. falciparum replication protein A) is the principal single-stranded DNA binding protein in P. falciparum, expressed in a cell cycle-dependent manner peaking at late trophozoite/schizont stages; recombinant PF3D7_0409600 protein stimulates PfRad51-Rad54-mediated homologous strand exchange in vitro (acting analogously to bacterial SSB), while this activity is negatively regulated in a dose-dependent fashion by the parasite's short-type RPA1 paralogue, and both proteins are upregulated in response to DNA damage in vivo.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0409600 is the large subunit of P. falciparum replication protein A and constitutes the major single-stranded DNA binding activity in the parasite, an activity expressed in a cell cycle-dependent manner that peaks in late trophozoites and schizonts, coinciding with the onset of chromosomal DNA replication [#0]. It is a short-type RPA1, lacking the N-terminal protein interaction domain found in higher-eukaryote RPA1 orthologues [#0]. Functionally, recombinant PF3D7_0409600 substitutes for bacterial SSB to initiate homologous pairing and stimulate PfRad51-PfRad54-mediated strand exchange in vitro, a stimulatory function that is negatively regulated in a dose-dependent manner by the short-type RPA1 paralogue PfRPA1S; upon methyl methanesulfonate-induced DNA damage in live parasites, PF3D7_0409600 transcript and protein are upregulated alongside PfRad51, PfRad54, and PfRPA1S [#1]. Beyond its ssDNA-binding and strand-exchange stimulatory roles, no further mechanistic detail for PF3D7_0409600 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Whether P. falciparum possesses a dedicated single-stranded DNA binding protein and how its activity is timed relative to replication was unknown; this work identified PF3D7_0409600 as the parasite's principal ssDNA-binding factor and linked its activity to the replicative cell cycle.\",\n      \"evidence\": \"Affinity purification and mass spectrometry identifying a ~55 kDa factor, EMSA for ssDNA binding, and Northern/RT-PCR for cell-cycle transcript timing in P. falciparum extracts\",\n      \"pmids\": [\"11880371\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct role in replication fork progression not tested in vivo\",\n        \"Absence of the N-terminal interaction domain leaves partner recruitment mechanism unresolved\",\n        \"No structural characterization of the ssDNA-binding mode\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Whether PF3D7_0409600 participates in homologous recombination and how its activity is controlled was unknown; reconstitution showed it stimulates Rad51-Rad54 strand exchange and is antagonized by its short-type paralogue, placing it in the parasite's DNA damage response.\",\n      \"evidence\": \"In vitro strand exchange assay with recombinant proteins, dose-response inhibition by PfRPA1S, comet assay for MMS-induced damage, and RT-PCR/western blot for damage-induced upregulation in live P. falciparum\",\n      \"pmids\": [\"23631919\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"In vivo requirement for HR (e.g. genetic knockout/knockdown) not established\",\n        \"Molecular basis of PfRPA1S dose-dependent inhibition not defined\",\n        \"Physical interaction between PF3D7_0409600 and Rad51/Rad54 not directly demonstrated\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PF3D7_0409600 is recruited to sites of replication and repair in the absence of the canonical N-terminal interaction domain, and its genetic essentiality in the parasite, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No genetic loss-of-function data for PF3D7_0409600\",\n        \"No defined protein interactome or complex architecture\",\n        \"No structural model of the ssDNA-bound or Rad51-stimulating state\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003697\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0003684\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006260\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0035825\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0006281\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [\n      \"Replication protein A (large subunit)\"\n    ],\n    \"partners\": [\n      \"PfRPA1S (short-type RPA1 paralogue; negative regulator)\",\n      \"PfRad51\",\n      \"PfRad54\"\n    ],\n    \"other_free_text\": [\n      \"Short-type RPA1 lacking the N-terminal protein interaction domain present in higher-eukaryote RPA1 orthologues [#0]\",\n      \"ssDNA-binding activity peaks in late trophozoites/schizonts, coinciding with chromosomal DNA replication onset; mRNA detected ~20-24 h post-invasion [#0]\",\n      \"Transcript and protein upregulated upon MMS-induced DNA damage in vivo [#1]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0409600","name":null,"product":"replication protein A1, large subunit","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1007200","name":null,"product":"replication protein A1, large subunit, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0307700","name":null,"product":"replication protein A1, large subunit, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPA1","evaluation":null}