{"gene":"PF3D7_0320700","run_date":"2026-09-07T10:55:51","timeline":{"discoveries":[{"year":2007,"finding":"PfSP21 (PF3D7_0320700), the catalytic subunit of the signal peptidase complex from P. falciparum, cleaves peptide substrates containing a signal peptidase cleavage site, demonstrating endopeptidase activity against signal peptides of secretory proteins.","method":"In vitro peptide cleavage assay","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro enzymatic activity demonstrated, but single lab and single method without mutagenesis or structural validation","pmids":["18054093"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"PfSP21 (PF3D7_0320700) is phosphorylated by protein kinase C, and this phosphorylation upregulates its signal peptidase enzymatic activity.","method":"In vitro kinase assay followed by peptide cleavage assay","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — biochemical assay establishing PTM and its functional consequence, but single lab with no mutagenesis confirmation of the phosphorylation site","pmids":["18054093"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"PfSP21 (PF3D7_0320700) localizes to the endoplasmic reticulum of P. falciparum, consistent with its role in co-translational signal peptide cleavage of secretory proteins.","method":"Immunofluorescence assay (IFA)","journal":"Molecular and biochemical parasitology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single localization method (IFA) without functional consequence directly tied to ER localization","pmids":["18054093"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"Knockdown of PfSP21 (PF3D7_0320700) by dsRNA inhibits intra-erythrocytic growth of P. falciparum in culture, correlated with decreased endogenous PfSP21 protein levels, establishing that PfSP21 is required for parasite growth.","method":"dsRNA-mediated knockdown with parasite growth assay and Western blot confirmation","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean loss-of-function with defined cellular phenotype and protein-level confirmation, but single lab and no rescue experiment","pmids":["18054093"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PfSP21 (PF3D7_0320700) is the catalytic subunit of the signal peptidase complex in P. falciparum, localized to the ER, where it cleaves N-terminal signal peptides from secretory preproteins; its enzymatic activity is upregulated by protein kinase C-mediated phosphorylation, and it is required for intra-erythrocytic parasite growth."},"narrative":{"mechanistic_narrative":"PfSP21 (PF3D7_0320700) is the catalytic subunit of the P. falciparum signal peptidase complex, an endopeptidase that cleaves N-terminal signal peptides from secretory preproteins, as shown by in vitro cleavage of substrates bearing a signal peptidase cleavage site [PMID:18054093]. Consistent with a role in co-translational processing of the secretory pathway, it localizes to the parasite endoplasmic reticulum [PMID:18054093]. Its catalytic activity is regulated by post-translational modification: protein kinase C phosphorylates PfSP21 and this phosphorylation upregulates its enzymatic activity [PMID:18054093]. dsRNA-mediated knockdown reduces endogenous PfSP21 levels and inhibits intra-erythrocytic growth, establishing that the protein is required for asexual blood-stage proliferation [PMID:18054093]. Beyond these findings from a single study, no further mechanistic detail — structural basis of catalysis, mapping of the phosphorylation site, or the identity of complex partners — has been characterized in the available corpus.","teleology":[{"year":2007,"claim":"Whether PF3D7_0320700 possesses intrinsic signal peptidase activity was unknown; demonstrating endopeptidase cleavage of signal-peptide substrates established it as the catalytic subunit of the parasite signal peptidase complex.","evidence":"In vitro peptide cleavage assay against a signal peptidase cleavage-site substrate","pmids":["18054093"],"confidence":"Medium","gaps":["No mutagenesis of catalytic residues to confirm the active site","No structural validation of the enzyme or its substrate binding","Identity of other signal peptidase complex subunits in P. falciparum not defined here"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"The question of how PfSP21 activity is regulated was addressed by showing that protein kinase C phosphorylates it and thereby upregulates its peptidase activity, linking a signalling kinase to control of secretory protein processing.","evidence":"In vitro kinase assay followed by peptide cleavage assay","pmids":["18054093"],"confidence":"Medium","gaps":["Phosphorylation site not mapped by mutagenesis","Physiological relevance of PKC regulation in vivo not established","Which parasite PKC acts on PfSP21 not identified"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"Subcellular context was unresolved; immunofluorescence placing PfSP21 in the endoplasmic reticulum supported a role in co-translational signal peptide cleavage of secretory proteins.","evidence":"Immunofluorescence assay in P. falciparum","pmids":["18054093"],"confidence":"Low","gaps":["Single localization method (IFA) without orthogonal confirmation","ER localization not directly tied to a functional consequence","Membrane topology within the ER not resolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"Whether PfSP21 is required for the parasite was tested by dsRNA knockdown, which reduced protein levels and inhibited intra-erythrocytic growth, establishing the gene as necessary for asexual blood-stage proliferation.","evidence":"dsRNA-mediated knockdown with growth assay and Western blot confirmation","pmids":["18054093"],"confidence":"Medium","gaps":["No rescue experiment to confirm on-target specificity","Growth defect not mechanistically linked to loss of signal peptidase activity","Single lab and single method"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"The molecular architecture of the P. falciparum signal peptidase complex, the mapping of PfSP21 catalytic and phosphorylation residues, and the specific substrate repertoire whose processing underlies the growth requirement remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No identification of partner subunits of the complex","No structure or catalytic-site mutagenesis","Substrate spectrum in vivo undefined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Signal peptidase complex"],"partners":[],"other_free_text":["Catalytic subunit of the P. falciparum signal peptidase complex [#0]","Enzymatic activity upregulated by protein kinase C-mediated phosphorylation [#1]","Required for intra-erythrocytic (asexual blood-stage) parasite growth [#3]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"18054093","id":"PMC_18054093","title":"Plasmodium falciparum signal peptidase is regulated by phosphorylation and required for intra-erythrocytic growth.","date":"2007","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/18054093","citation_count":19,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3370,"output_tokens":991,"usd":0.012488,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5690,"output_tokens":2055,"usd":0.039912,"stage2_stop_reason":"end_turn"},"total_usd":0.0524,"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\": 2007,\n      \"finding\": \"PfSP21 (PF3D7_0320700), the catalytic subunit of the signal peptidase complex from P. falciparum, cleaves peptide substrates containing a signal peptidase cleavage site, demonstrating endopeptidase activity against signal peptides of secretory proteins.\",\n      \"method\": \"In vitro peptide cleavage assay\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro enzymatic activity demonstrated, but single lab and single method without mutagenesis or structural validation\",\n      \"pmids\": [\"18054093\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PfSP21 (PF3D7_0320700) is phosphorylated by protein kinase C, and this phosphorylation upregulates its signal peptidase enzymatic activity.\",\n      \"method\": \"In vitro kinase assay followed by peptide cleavage assay\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — biochemical assay establishing PTM and its functional consequence, but single lab with no mutagenesis confirmation of the phosphorylation site\",\n      \"pmids\": [\"18054093\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PfSP21 (PF3D7_0320700) localizes to the endoplasmic reticulum of P. falciparum, consistent with its role in co-translational signal peptide cleavage of secretory proteins.\",\n      \"method\": \"Immunofluorescence assay (IFA)\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single localization method (IFA) without functional consequence directly tied to ER localization\",\n      \"pmids\": [\"18054093\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Knockdown of PfSP21 (PF3D7_0320700) by dsRNA inhibits intra-erythrocytic growth of P. falciparum in culture, correlated with decreased endogenous PfSP21 protein levels, establishing that PfSP21 is required for parasite growth.\",\n      \"method\": \"dsRNA-mediated knockdown with parasite growth assay and Western blot confirmation\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean loss-of-function with defined cellular phenotype and protein-level confirmation, but single lab and no rescue experiment\",\n      \"pmids\": [\"18054093\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PfSP21 (PF3D7_0320700) is the catalytic subunit of the signal peptidase complex in P. falciparum, localized to the ER, where it cleaves N-terminal signal peptides from secretory preproteins; its enzymatic activity is upregulated by protein kinase C-mediated phosphorylation, and it is required for intra-erythrocytic parasite growth.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PfSP21 (PF3D7_0320700) is the catalytic subunit of the P. falciparum signal peptidase complex, an endopeptidase that cleaves N-terminal signal peptides from secretory preproteins, as shown by in vitro cleavage of substrates bearing a signal peptidase cleavage site [#0]. Consistent with a role in co-translational processing of the secretory pathway, it localizes to the parasite endoplasmic reticulum [#2]. Its catalytic activity is regulated by post-translational modification: protein kinase C phosphorylates PfSP21 and this phosphorylation upregulates its enzymatic activity [#1]. dsRNA-mediated knockdown reduces endogenous PfSP21 levels and inhibits intra-erythrocytic growth, establishing that the protein is required for asexual blood-stage proliferation [#3]. Beyond these findings from a single study, no further mechanistic detail — structural basis of catalysis, mapping of the phosphorylation site, or the identity of complex partners — has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Whether PF3D7_0320700 possesses intrinsic signal peptidase activity was unknown; demonstrating endopeptidase cleavage of signal-peptide substrates established it as the catalytic subunit of the parasite signal peptidase complex.\",\n      \"evidence\": \"In vitro peptide cleavage assay against a signal peptidase cleavage-site substrate\",\n      \"pmids\": [\"18054093\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No mutagenesis of catalytic residues to confirm the active site\",\n        \"No structural validation of the enzyme or its substrate binding\",\n        \"Identity of other signal peptidase complex subunits in P. falciparum not defined here\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"The question of how PfSP21 activity is regulated was addressed by showing that protein kinase C phosphorylates it and thereby upregulates its peptidase activity, linking a signalling kinase to control of secretory protein processing.\",\n      \"evidence\": \"In vitro kinase assay followed by peptide cleavage assay\",\n      \"pmids\": [\"18054093\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Phosphorylation site not mapped by mutagenesis\",\n        \"Physiological relevance of PKC regulation in vivo not established\",\n        \"Which parasite PKC acts on PfSP21 not identified\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Subcellular context was unresolved; immunofluorescence placing PfSP21 in the endoplasmic reticulum supported a role in co-translational signal peptide cleavage of secretory proteins.\",\n      \"evidence\": \"Immunofluorescence assay in P. falciparum\",\n      \"pmids\": [\"18054093\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single localization method (IFA) without orthogonal confirmation\",\n        \"ER localization not directly tied to a functional consequence\",\n        \"Membrane topology within the ER not resolved\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Whether PfSP21 is required for the parasite was tested by dsRNA knockdown, which reduced protein levels and inhibited intra-erythrocytic growth, establishing the gene as necessary for asexual blood-stage proliferation.\",\n      \"evidence\": \"dsRNA-mediated knockdown with growth assay and Western blot confirmation\",\n      \"pmids\": [\"18054093\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No rescue experiment to confirm on-target specificity\",\n        \"Growth defect not mechanistically linked to loss of signal peptidase activity\",\n        \"Single lab and single method\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular architecture of the P. falciparum signal peptidase complex, the mapping of PfSP21 catalytic and phosphorylation residues, and the specific substrate repertoire whose processing underlies the growth requirement remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No identification of partner subunits of the complex\",\n        \"No structure or catalytic-site mutagenesis\",\n        \"Substrate spectrum in vivo undefined\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004252\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0004252\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006465\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0045047\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"Signal peptidase complex\"],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Catalytic subunit of the P. falciparum signal peptidase complex [#0]\",\n      \"Enzymatic activity upregulated by protein kinase C-mediated phosphorylation [#1]\",\n      \"Required for intra-erythrocytic (asexual blood-stage) parasite growth [#3]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0320700","name":null,"product":"signal peptidase complex subunit 2","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1217800","name":null,"product":"signal peptidase complex subunit 2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0820100","name":null,"product":"signal peptidase complex subunit 2, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}