{"gene":"TG_318750","gene_symbol":"DPA","run_date":"2026-09-08T15:15:13","timeline":{"discoveries":[{"year":2008,"finding":"TgDPA encodes a 286 amino acid protein (~31 kDa) with a deoxyribose phosphate aldolase (DeoC) domain (~30% homology to E. coli DeoC); immunofluorescent analysis with a polyclonal antibody against recombinant TgDPA demonstrated that the protein is expressed specifically in bradyzoites both in vivo and in vitro, establishing it as a bradyzoite-specific marker.","method":"RT-PCR, quantitative PCR, recombinant protein expression, immunofluorescence assay","journal":"Experimental parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization by immunofluorescence and stage-specific expression confirmed by qPCR, single lab, no functional mechanism established","pmids":["18950626"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2010,"finding":"TgDPA physically interacts with actin depolymerizing factor (TgADF), as shown by yeast two-hybrid screening, co-immunoprecipitation, and GST pull-down assay; addition of GST-TgDPA to TgADF lowered the extent of actin polymerization and enhanced filamentous actin disassembly in vitro, indicating TgDPA enhances TgADF activity to promote actin filament dynamics in bradyzoites.","method":"Yeast two-hybrid, co-immunoprecipitation, GST pull-down, actin polymerization and disassembly kinetics assay","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal binding shown by Co-IP and GST pull-down, functional consequence measured by in vitro actin kinetics, single lab","pmids":["20433874"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2014,"finding":"Crystal structure of TgDPA revealed a TIM barrel fold with key catalytic residues absent compared to canonical deoxyribose-5-phosphate aldolase (DERA) family members; consistent with this, biochemical assays showed TgDPA is catalytically inactive on dR5P substrate. Despite lacking enzymatic activity, TgDPA is competent to bind polymerized actin in vitro, similar to TgALD1.","method":"X-ray crystallography, structural comparison, biochemical activity assays (dR5P substrate), in vitro actin binding assay","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with biochemical activity assays and actin binding assay; multiple orthogonal methods in a single rigorous study confirming catalytic inactivity and actin interaction","pmids":["25284756"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgDPA is a bradyzoite-specific, catalytically inactive aldolase-like protein (lacking key DERA active-site residues, unable to cleave dR5P) that instead functions as an actin-regulatory protein: it binds polymerized actin directly and interacts with the actin depolymerizing factor TgADF to enhance actin filament disassembly, thereby modulating actin dynamics in the bradyzoite stage."},"narrative":{"mechanistic_narrative":"TgDPA is a bradyzoite-specific protein of Toxoplasma gondii that has repurposed an aldolase scaffold into an actin-regulatory function [PMID:18950626, PMID:25284756]. Although it carries a deoxyribose phosphate aldolase (DeoC) domain and adopts a TIM barrel fold, it lacks the key catalytic residues of the canonical DERA family and is enzymatically inactive on the dR5P substrate [PMID:25284756]. Instead, TgDPA binds polymerized actin directly and physically interacts with the actin depolymerizing factor TgADF, enhancing TgADF activity to lower actin polymerization and promote filament disassembly in vitro [PMID:20433874, PMID:25284756]. Through this activity it modulates actin filament dynamics in the bradyzoite stage, where it is expressed specifically both in vivo and in vitro [PMID:18950626]. Beyond this actin-regulatory role, no additional mechanistic function has been characterized in the available corpus.","teleology":[{"year":2008,"claim":"Establishing when and where TgDPA is expressed was necessary to place the aldolase-domain protein in a biological context; stage-specific expression defined it as a bradyzoite marker.","evidence":"RT-PCR, qPCR, and immunofluorescence with an anti-recombinant TgDPA antibody in T. gondii","pmids":["18950626"],"confidence":"Medium","gaps":["No functional mechanism established","Catalytic competence of the DeoC domain untested","Single lab"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2010,"claim":"Whether TgDPA had a role beyond a putative metabolic enzyme was unknown; identifying TgADF as a binding partner and measuring functional consequences revealed an actin-regulatory role.","evidence":"Yeast two-hybrid, Co-IP, GST pull-down, and in vitro actin polymerization/disassembly kinetics assays in T. gondii","pmids":["20433874"],"confidence":"Medium","gaps":["In vivo consequence of the TgDPA-TgADF interaction not tested","Whether actin regulation depends on aldolase activity unresolved at this point","Single lab"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2014,"claim":"It was unclear whether TgDPA retained aldolase activity or acted purely as an actin-binding scaffold; structural and biochemical analysis showed it is catalytically dead yet binds actin, reconciling the aldolase fold with the actin-regulatory function.","evidence":"X-ray crystallography, structural comparison to DERA, dR5P biochemical activity assays, and in vitro actin binding in T. gondii","pmids":["25284756"],"confidence":"High","gaps":["Structural basis of the actin/TgADF interaction not resolved","In vivo requirement of TgDPA for bradyzoite actin dynamics untested"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"The physiological role of TgDPA-mediated actin regulation in bradyzoite biology, and whether it is required for cyst formation or persistence, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No genetic knockout/knockdown phenotype in the corpus","No in vivo functional consequence established","Structural model of the actin-binding interface lacking"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["TGADF (ACTIN DEPOLYMERIZING FACTOR)","POLYMERIZED ACTIN"],"other_free_text":["Bradyzoite-specific marker in Toxoplasma gondii [#0]","TIM barrel fold with DeoC/DERA-family aldolase domain but catalytically inactive on dR5P due to absent key active-site residues [#2]","Enhances TgADF-mediated actin filament disassembly in vitro [#1]"]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"18950626","id":"PMC_18950626","title":"Toxoplasma gondii: Identification and characterization of bradyzoite-specific deoxyribose phosphate aldolase-like gene (TgDPA).","date":"2008","source":"Experimental parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18950626","citation_count":22,"is_preprint":false},{"pmid":"25284756","id":"PMC_25284756","title":"Structural and functional divergence of the aldolase fold in Toxoplasma gondii.","date":"2014","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/25284756","citation_count":11,"is_preprint":false},{"pmid":"20433874","id":"PMC_20433874","title":"Toxoplasma gondii deoxyribose phosphate aldolase-like protein (TgDPA) interacts with actin depolymerizing factor (TgADF) to enhance the actin filament dynamics in the bradyzoite stage.","date":"2010","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/20433874","citation_count":6,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3835,"output_tokens":976,"usd":0.013073,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5835,"output_tokens":1774,"usd":0.036762,"stage2_stop_reason":"end_turn"},"total_usd":0.049835,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"TgDPA encodes a 286 amino acid protein (~31 kDa) with a deoxyribose phosphate aldolase (DeoC) domain (~30% homology to E. coli DeoC); immunofluorescent analysis with a polyclonal antibody against recombinant TgDPA demonstrated that the protein is expressed specifically in bradyzoites both in vivo and in vitro, establishing it as a bradyzoite-specific marker.\",\n      \"method\": \"RT-PCR, quantitative PCR, recombinant protein expression, immunofluorescence assay\",\n      \"journal\": \"Experimental parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization by immunofluorescence and stage-specific expression confirmed by qPCR, single lab, no functional mechanism established\",\n      \"pmids\": [\"18950626\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"TgDPA physically interacts with actin depolymerizing factor (TgADF), as shown by yeast two-hybrid screening, co-immunoprecipitation, and GST pull-down assay; addition of GST-TgDPA to TgADF lowered the extent of actin polymerization and enhanced filamentous actin disassembly in vitro, indicating TgDPA enhances TgADF activity to promote actin filament dynamics in bradyzoites.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, GST pull-down, actin polymerization and disassembly kinetics assay\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding shown by Co-IP and GST pull-down, functional consequence measured by in vitro actin kinetics, single lab\",\n      \"pmids\": [\"20433874\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal structure of TgDPA revealed a TIM barrel fold with key catalytic residues absent compared to canonical deoxyribose-5-phosphate aldolase (DERA) family members; consistent with this, biochemical assays showed TgDPA is catalytically inactive on dR5P substrate. Despite lacking enzymatic activity, TgDPA is competent to bind polymerized actin in vitro, similar to TgALD1.\",\n      \"method\": \"X-ray crystallography, structural comparison, biochemical activity assays (dR5P substrate), in vitro actin binding assay\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with biochemical activity assays and actin binding assay; multiple orthogonal methods in a single rigorous study confirming catalytic inactivity and actin interaction\",\n      \"pmids\": [\"25284756\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"TgDPA is a bradyzoite-specific, catalytically inactive aldolase-like protein (lacking key DERA active-site residues, unable to cleave dR5P) that instead functions as an actin-regulatory protein: it binds polymerized actin directly and interacts with the actin depolymerizing factor TgADF to enhance actin filament disassembly, thereby modulating actin dynamics in the bradyzoite stage.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TgDPA is a bradyzoite-specific protein of Toxoplasma gondii that has repurposed an aldolase scaffold into an actin-regulatory function [#0, #2]. Although it carries a deoxyribose phosphate aldolase (DeoC) domain and adopts a TIM barrel fold, it lacks the key catalytic residues of the canonical DERA family and is enzymatically inactive on the dR5P substrate [#2]. Instead, TgDPA binds polymerized actin directly and physically interacts with the actin depolymerizing factor TgADF, enhancing TgADF activity to lower actin polymerization and promote filament disassembly in vitro [#1, #2]. Through this activity it modulates actin filament dynamics in the bradyzoite stage, where it is expressed specifically both in vivo and in vitro [#0]. Beyond this actin-regulatory role, no additional mechanistic function has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Establishing when and where TgDPA is expressed was necessary to place the aldolase-domain protein in a biological context; stage-specific expression defined it as a bradyzoite marker.\",\n      \"evidence\": \"RT-PCR, qPCR, and immunofluorescence with an anti-recombinant TgDPA antibody in T. gondii\",\n      \"pmids\": [\"18950626\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional mechanism established\", \"Catalytic competence of the DeoC domain untested\", \"Single lab\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Whether TgDPA had a role beyond a putative metabolic enzyme was unknown; identifying TgADF as a binding partner and measuring functional consequences revealed an actin-regulatory role.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, GST pull-down, and in vitro actin polymerization/disassembly kinetics assays in T. gondii\",\n      \"pmids\": [\"20433874\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo consequence of the TgDPA-TgADF interaction not tested\", \"Whether actin regulation depends on aldolase activity unresolved at this point\", \"Single lab\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"It was unclear whether TgDPA retained aldolase activity or acted purely as an actin-binding scaffold; structural and biochemical analysis showed it is catalytically dead yet binds actin, reconciling the aldolase fold with the actin-regulatory function.\",\n      \"evidence\": \"X-ray crystallography, structural comparison to DERA, dR5P biochemical activity assays, and in vitro actin binding in T. gondii\",\n      \"pmids\": [\"25284756\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the actin/TgADF interaction not resolved\", \"In vivo requirement of TgDPA for bradyzoite actin dynamics untested\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The physiological role of TgDPA-mediated actin regulation in bradyzoite biology, and whether it is required for cyst formation or persistence, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No genetic knockout/knockdown phenotype in the corpus\", \"No in vivo functional consequence established\", \"Structural model of the actin-binding interface lacking\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0051015\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0030042\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0030036\", \"supporting_discovery_ids\": [1, 2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TgADF (actin depolymerizing factor)\", \"polymerized actin\"],\n    \"other_free_text\": [\n      \"Bradyzoite-specific marker in Toxoplasma gondii [#0]\",\n      \"TIM barrel fold with DeoC/DERA-family aldolase domain but catalytically inactive on dR5P due to absent key active-site residues [#2]\",\n      \"Enhances TgADF-mediated actin filament disassembly in vitro [#1]\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_318750","name":"DPA","product":"deoxyribose-phosphate aldolase","uniprot_acc":"A0A125YRB4","chromosome":"TGME49_chrIV","start_pos":1109115},{"strain":"GT1","gene_id":"TGGT1_318750","name":null,"product":"deoxyribose-phosphate aldolase","uniprot_acc":null,"chromosome":"TGGT1_chrIV","start_pos":1051713},{"strain":"RH88","gene_id":"TGRH88_007790","name":null,"product":"deoxyribose-phosphate aldolase","uniprot_acc":null,"chromosome":"CM023085","start_pos":1132024},{"strain":"VEG","gene_id":"TGVEG_318750","name":null,"product":"deoxyribose-phosphate aldolase","uniprot_acc":"B9PVB4","chromosome":"TGVEG_chrIV","start_pos":1119607}]}