{"gene":"PF3D7_0204800","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2022,"finding":"The E415G mutation in PF3D7_0204800 (PfEXO, the 3'-5' exonuclease) was introduced into P. falciparum by CRISPR-Cas9 gene editing; transgenic parasites carrying E415G showed no increase in piperaquine IC90 or PPQ survival, establishing that this single point mutation alone does not confer piperaquine resistance, though it may modestly affect parasite fitness.","method":"CRISPR-Cas9 gene editing to introduce E415G mutation; drug sensitivity assays (IC90, PPQ survival assay, bimodal dose-response), ring-stage survival assay, growth assays","journal":"Malaria journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean allelic-exchange transgenic line with multiple orthogonal drug-sensitivity readouts in a single lab","pmids":["35459163"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"B5"}]},{"year":2025,"finding":"PF3D7_0204800 (designated PfExomit2) localizes to the mitochondrion of P. falciparum, as shown by immunofluorescence with antibodies against the recombinant protein and chromatin immunoprecipitation. Recombinant PfExomit2 functions as a bipolar exonuclease on dsDNA with 3'-5' exonuclease activity on ssDNA. PfExomit2 interacts with the mitochondrial mismatch repair protein PfMutS (pull-down assay) and with the DSBR protein PfRad51 (pull-down assay), suggesting it participates in both MMR and DSBR pathways in the mitochondrion.","method":"Immunofluorescence localization with anti-recombinant-protein antibodies; chromatin immunoprecipitation; in vitro exonuclease assay with recombinant protein on defined DNA substrates; pull-down assays with PfMutS and PfRad51","journal":"The FEBS journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (IFA, ChIP, in vitro enzymatic assay, pull-downs) in a single lab establishing localization, activity, and interactions","pmids":["41243319"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0204800 (PfExomit2) is a mitochondrion-localized 3'-5' exonuclease in P. falciparum that exhibits bipolar dsDNA exonuclease activity and 3'-5' ssDNA exonuclease activity in vitro, interacts with the mismatch repair protein PfMutS and the double-strand break repair protein PfRad51, implicating it in mitochondrial MMR and DSBR pathways; a single point mutation (E415G) in the protein does not itself confer piperaquine resistance."},"narrative":{"mechanistic_narrative":"PF3D7_0204800 (PfExomit2) is a mitochondrion-localized 3'-5' exonuclease of Plasmodium falciparum implicated in mitochondrial DNA repair [PMID:41243319]. Recombinant PfExomit2 acts as a bipolar exonuclease on double-stranded DNA and displays 3'-5' exonuclease activity on single-stranded DNA in vitro, and it physically interacts with the mismatch repair protein PfMutS and the double-strand break repair protein PfRad51, placing it within mitochondrial mismatch repair (MMR) and double-strand break repair (DSBR) pathways [PMID:41243319]. Introduction of the single E415G point mutation by CRISPR-Cas9 does not increase piperaquine IC90 or survival, establishing that this substitution alone does not confer piperaquine resistance [PMID:35459163]. Beyond its localization, in vitro activity, and these two interaction partners, no further mechanistic detail about PfExomit2 has been characterized in the available corpus.","teleology":[{"year":2022,"claim":"To test whether an exonuclease point mutation drives clinical antimalarial resistance, the field asked whether E415G in PF3D7_0204800 is causal for piperaquine resistance rather than merely associated.","evidence":"CRISPR-Cas9 allelic exchange to introduce E415G in P. falciparum B5, with IC90, PPQ survival, ring-stage survival, and growth assays","pmids":["35459163"],"confidence":"Medium","gaps":["Does not exclude a contributory role of E415G in a resistance background with other mutations","Effect on parasite fitness only modestly assessed","Does not address the protein's normal enzymatic function"],"attribution":[{"species":"Plasmodium falciparum","strain":"B5"}]},{"year":2025,"claim":"To define the cellular and biochemical role of the protein, work established where PfExomit2 localizes, what enzymatic activity it possesses, and which repair-pathway proteins it partners with.","evidence":"Immunofluorescence and ChIP for mitochondrial localization, in vitro exonuclease assays on defined dsDNA/ssDNA substrates with recombinant protein, and pull-down assays with PfMutS and PfRad51","pmids":["41243319"],"confidence":"Medium","gaps":["Pull-down interactions with PfMutS and PfRad51 lack reciprocal/orthogonal validation and structural mapping","Functional consequence of the exonuclease activity for mitochondrial genome integrity not demonstrated in vivo","No genetic knockout/knockdown phenotype to confirm a role in MMR or DSBR"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether PfExomit2 exonuclease activity is functionally required for mitochondrial DNA repair in vivo, and how its interactions with PfMutS and PfRad51 coordinate MMR versus DSBR, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No loss-of-function phenotype linking the enzyme to mitochondrial genome maintenance","Mechanism of substrate handoff between PfExomit2 and its repair partners unknown"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFMUTS","PFRAD51"],"other_free_text":["E415G point mutation introduced by CRISPR-Cas9 does not confer piperaquine resistance [#0]","Recombinant PfExomit2 shows bipolar exonuclease activity on dsDNA and 3'-5' exonuclease activity on ssDNA in vitro [#1]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"15926203","id":"PMC_15926203","title":"The plastidic DNA replication enzyme complex of Plasmodium falciparum.","date":"2005","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15926203","citation_count":68,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["3'-5' exonuclease"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24670267","id":"PMC_24670267","title":"Generation of rodent malaria parasites with a high mutation rate by destructing proofreading activity of DNA polymerase δ.","date":"2014","source":"DNA research : an international journal for rapid publication of reports on genes and genomes","url":"https://pubmed.ncbi.nlm.nih.gov/24670267","citation_count":13,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["3'-5' exonuclease"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"31386260","id":"PMC_31386260","title":"Plasmodium falciparum Apn1 homolog is a mitochondrial base excision repair protein with restricted enzymatic functions.","date":"2019","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/31386260","citation_count":11,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["3'-5' exonuclease"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"33743509","id":"PMC_33743509","title":"Plasmodium Ape1 is a multifunctional enzyme in mitochondrial base excision repair and is required for efficient transition from liver to blood stage infection.","date":"2021","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/33743509","citation_count":9,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["3'-5' exonuclease"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35459163","id":"PMC_35459163","title":"A single point mutation in the Plasmodium falciparum 3'-5' exonuclease does not alter piperaquine susceptibility.","date":"2022","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/35459163","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["3'-5' exonuclease"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26911594","id":"PMC_26911594","title":"Biochemical and functional characterization of Plasmodium falciparum DNA polymerase δ.","date":"2016","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/26911594","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["3'-5' exonuclease"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"41243319","id":"PMC_41243319","title":"Plasmodium mitochondrial exodeoxyribonucleases, Exomit1 and Exomit2, are conserved within alveolates with Exomit1 essential for the establishment of blood-stage infection.","date":"2025","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/41243319","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["3'-5' exonuclease"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7167,"output_tokens":861,"usd":0.017208,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5455,"output_tokens":1634,"usd":0.034063,"stage2_stop_reason":"end_turn"},"total_usd":0.051271,"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\": 2022,\n      \"finding\": \"The E415G mutation in PF3D7_0204800 (PfEXO, the 3'-5' exonuclease) was introduced into P. falciparum by CRISPR-Cas9 gene editing; transgenic parasites carrying E415G showed no increase in piperaquine IC90 or PPQ survival, establishing that this single point mutation alone does not confer piperaquine resistance, though it may modestly affect parasite fitness.\",\n      \"method\": \"CRISPR-Cas9 gene editing to introduce E415G mutation; drug sensitivity assays (IC90, PPQ survival assay, bimodal dose-response), ring-stage survival assay, growth assays\",\n      \"journal\": \"Malaria journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean allelic-exchange transgenic line with multiple orthogonal drug-sensitivity readouts in a single lab\",\n      \"pmids\": [\"35459163\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"B5\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PF3D7_0204800 (designated PfExomit2) localizes to the mitochondrion of P. falciparum, as shown by immunofluorescence with antibodies against the recombinant protein and chromatin immunoprecipitation. Recombinant PfExomit2 functions as a bipolar exonuclease on dsDNA with 3'-5' exonuclease activity on ssDNA. PfExomit2 interacts with the mitochondrial mismatch repair protein PfMutS (pull-down assay) and with the DSBR protein PfRad51 (pull-down assay), suggesting it participates in both MMR and DSBR pathways in the mitochondrion.\",\n      \"method\": \"Immunofluorescence localization with anti-recombinant-protein antibodies; chromatin immunoprecipitation; in vitro exonuclease assay with recombinant protein on defined DNA substrates; pull-down assays with PfMutS and PfRad51\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (IFA, ChIP, in vitro enzymatic assay, pull-downs) in a single lab establishing localization, activity, and interactions\",\n      \"pmids\": [\"41243319\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0204800 (PfExomit2) is a mitochondrion-localized 3'-5' exonuclease in P. falciparum that exhibits bipolar dsDNA exonuclease activity and 3'-5' ssDNA exonuclease activity in vitro, interacts with the mismatch repair protein PfMutS and the double-strand break repair protein PfRad51, implicating it in mitochondrial MMR and DSBR pathways; a single point mutation (E415G) in the protein does not itself confer piperaquine resistance.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0204800 (PfExomit2) is a mitochondrion-localized 3'-5' exonuclease of Plasmodium falciparum implicated in mitochondrial DNA repair [#1]. Recombinant PfExomit2 acts as a bipolar exonuclease on double-stranded DNA and displays 3'-5' exonuclease activity on single-stranded DNA in vitro, and it physically interacts with the mismatch repair protein PfMutS and the double-strand break repair protein PfRad51, placing it within mitochondrial mismatch repair (MMR) and double-strand break repair (DSBR) pathways [#1]. Introduction of the single E415G point mutation by CRISPR-Cas9 does not increase piperaquine IC90 or survival, establishing that this substitution alone does not confer piperaquine resistance [#0]. Beyond its localization, in vitro activity, and these two interaction partners, no further mechanistic detail about PfExomit2 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"To test whether an exonuclease point mutation drives clinical antimalarial resistance, the field asked whether E415G in PF3D7_0204800 is causal for piperaquine resistance rather than merely associated.\",\n      \"evidence\": \"CRISPR-Cas9 allelic exchange to introduce E415G in P. falciparum B5, with IC90, PPQ survival, ring-stage survival, and growth assays\",\n      \"pmids\": [\"35459163\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Does not exclude a contributory role of E415G in a resistance background with other mutations\",\n        \"Effect on parasite fitness only modestly assessed\",\n        \"Does not address the protein's normal enzymatic function\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"B5\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To define the cellular and biochemical role of the protein, work established where PfExomit2 localizes, what enzymatic activity it possesses, and which repair-pathway proteins it partners with.\",\n      \"evidence\": \"Immunofluorescence and ChIP for mitochondrial localization, in vitro exonuclease assays on defined dsDNA/ssDNA substrates with recombinant protein, and pull-down assays with PfMutS and PfRad51\",\n      \"pmids\": [\"41243319\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Pull-down interactions with PfMutS and PfRad51 lack reciprocal/orthogonal validation and structural mapping\",\n        \"Functional consequence of the exonuclease activity for mitochondrial genome integrity not demonstrated in vivo\",\n        \"No genetic knockout/knockdown phenotype to confirm a role in MMR or DSBR\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PfExomit2 exonuclease activity is functionally required for mitochondrial DNA repair in vivo, and how its interactions with PfMutS and PfRad51 coordinate MMR versus DSBR, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No loss-of-function phenotype linking the enzyme to mitochondrial genome maintenance\",\n        \"Mechanism of substrate handoff between PfExomit2 and its repair partners unknown\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008408\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0008296\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006298\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0006302\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PfMutS\",\n      \"PfRad51\"\n    ],\n    \"other_free_text\": [\n      \"E415G point mutation introduced by CRISPR-Cas9 does not confer piperaquine resistance [#0]\",\n      \"Recombinant PfExomit2 shows bipolar exonuclease activity on dsDNA and 3'-5' exonuclease activity on ssDNA in vitro [#1]\"\n    ]\n  }\n}","audit_flag":{"gene":"PF3D7_0204800","tier":"IDENTITY_CHECK","verdict":"identity unverified","subtype":"names_other_cards","uniprot_band":"","rules_fired":"R12","issue":"No cited paper names this card; 2 of 2 cited papers name other catalogue genes (PF3D7_1362500, PF3D7_1107400). The summary may describe one of those genes."},"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0204800","name":null,"product":"3'-5' exonuclease, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0302600","name":null,"product":"3'-5' exonuclease, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0416100","name":null,"product":"3'-5' exonuclease, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}