{"gene":"PF3D7_API02600","run_date":"2026-09-08T15:24:04","timeline":{"discoveries":[{"year":1996,"finding":"PF3D7_API02600 (apicoplast ribosomal protein S11) is encoded on the 35 kb plastid-like DNA circle of P. falciparum, as part of a complete gene map identifying 17 ribosomal protein genes on this organellar genome. Transcription of these genes, including S11, is polycistronic.","method":"Complete gene mapping of the 35 kb apicoplast DNA circle by sequencing and annotation","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct genomic mapping by sequencing with functional annotation; single study but comprehensive coverage of the entire apicoplast genome","pmids":["8757284"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"finding":"Transcripts encoding PF3D7_API02600 (apicoplast ribosomal protein S11) are part of polycistronic apicoplast transcripts that undergo RNA processing involving tRNA excision at conserved sequence motifs; the locus is also represented in long antisense transcripts processed at the same sites as sense transcripts.","method":"RNA analysis including identification of processing sites, sequencing of apicoplast transcripts, and detection of antisense sequences","journal":"Protist","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, transcript-level observation with no direct functional manipulation of S11 protein; S11 is not individually distinguished from other ribosomal protein transcripts in the abstract","pmids":["27458998"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_API02600 (S11) is an apicoplast ribosomal small subunit protein encoded on the 35 kb plastid-like DNA circle of P. falciparum, expressed from polycistronic transcripts that are processed via tRNA excision at conserved motifs; beyond its membership in the apicoplast ribosome, no direct mechanistic studies of S11 protein function have been reported."},"narrative":{"mechanistic_narrative":"PF3D7_API02600 (S11) is one of 17 ribosomal protein genes encoded on the 35 kb plastid-like DNA circle of Plasmodium falciparum, identifying it as a component of the apicoplast small ribosomal subunit machinery [PMID:8757284]. Its coding sequence is transcribed as part of polycistronic apicoplast transcripts [PMID:8757284] that are subsequently matured through RNA processing involving tRNA excision at conserved sequence motifs, with the locus also represented in long antisense transcripts processed at the same sites as sense transcripts [PMID:27458998]. Beyond this genomic assignment and transcript-level characterization, no direct study of the S11 protein's function, its assembly into the ribosome, or its individual role has been reported in the available corpus; the gene is characterized only as a member of the apicoplast ribosomal protein complement.","teleology":[{"year":1996,"claim":"Establishing whether the apicoplast genome encodes its own translational machinery required mapping the organellar genes; the complete gene map placed S11 among 17 ribosomal protein genes on the 35 kb circle and showed these genes are transcribed polycistronically.","evidence":"complete gene mapping of the 35 kb apicoplast DNA circle by sequencing and annotation in P. falciparum","pmids":["8757284"],"confidence":"Medium","gaps":["does not demonstrate S11 protein expression or incorporation into a functional ribosome","no evidence for S11-specific function distinct from the shared ribosomal protein complement","polycistronic transcription shown at the genome level, not resolved to S11 individually"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"claim":"How the polycistronic apicoplast transcripts covering S11 are matured was addressed by mapping processing sites, showing tRNA excision at conserved motifs and the existence of antisense transcripts processed at the same positions.","evidence":"RNA analysis mapping processing sites, sequencing of apicoplast transcripts, and detection of antisense sequences in P. falciparum","pmids":["27458998"],"confidence":"Low","gaps":["transcript-level observation with no direct functional manipulation of the S11 protein; S11 is not individually distinguished from other ribosomal protein transcripts","functional consequence of antisense transcripts unknown","does not link processing to S11 protein abundance or ribosome assembly"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether the S11 protein itself has a distinct role in apicoplast ribosome assembly, translation, or parasite viability remains unaddressed.","evidence":"no direct functional study of the S11 protein in the corpus","pmids":[],"confidence":"Low","gaps":["no direct evidence of S11 protein expression or ribosome incorporation","no genetic knockout or knockdown of S11","no structural model of S11 within the apicoplast small subunit"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["apicoplast small ribosomal subunit"],"partners":[],"other_free_text":["Encoded on the 35 kb plastid-like DNA circle among 17 apicoplast ribosomal protein genes [#0]","Transcribed as part of polycistronic apicoplast transcripts [#0]","Transcript locus matured via tRNA excision at conserved motifs and represented in processed antisense transcripts [#1]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"8757284","id":"PMC_8757284","title":"Complete gene map of the plastid-like DNA of the malaria parasite Plasmodium falciparum.","date":"1996","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8757284","citation_count":447,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27458998","id":"PMC_27458998","title":"Transcripts in the Plasmodium Apicoplast Undergo Cleavage at tRNAs and Editing, and Include Antisense Sequences.","date":"2016","source":"Protist","url":"https://pubmed.ncbi.nlm.nih.gov/27458998","citation_count":16,"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":3652,"output_tokens":619,"usd":0.01012,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5227,"output_tokens":1517,"usd":0.03203,"stage2_stop_reason":"end_turn"},"total_usd":0.04215,"stage1_batch_id":"msgbatch_01S4WrhSkksYHeZXxqf3za3o","stage2_batch_id":"msgbatch_019VBBeuW6G52X8gZfsFDfb5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"PF3D7_API02600 (apicoplast ribosomal protein S11) is encoded on the 35 kb plastid-like DNA circle of P. falciparum, as part of a complete gene map identifying 17 ribosomal protein genes on this organellar genome. Transcription of these genes, including S11, is polycistronic.\",\n      \"method\": \"Complete gene mapping of the 35 kb apicoplast DNA circle by sequencing and annotation\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct genomic mapping by sequencing with functional annotation; single study but comprehensive coverage of the entire apicoplast genome\",\n      \"pmids\": [\"8757284\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Transcripts encoding PF3D7_API02600 (apicoplast ribosomal protein S11) are part of polycistronic apicoplast transcripts that undergo RNA processing involving tRNA excision at conserved sequence motifs; the locus is also represented in long antisense transcripts processed at the same sites as sense transcripts.\",\n      \"method\": \"RNA analysis including identification of processing sites, sequencing of apicoplast transcripts, and detection of antisense sequences\",\n      \"journal\": \"Protist\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, transcript-level observation with no direct functional manipulation of S11 protein; S11 is not individually distinguished from other ribosomal protein transcripts in the abstract\",\n      \"pmids\": [\"27458998\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_API02600 (S11) is an apicoplast ribosomal small subunit protein encoded on the 35 kb plastid-like DNA circle of P. falciparum, expressed from polycistronic transcripts that are processed via tRNA excision at conserved motifs; beyond its membership in the apicoplast ribosome, no direct mechanistic studies of S11 protein function have been reported.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_API02600 (S11) is one of 17 ribosomal protein genes encoded on the 35 kb plastid-like DNA circle of Plasmodium falciparum, identifying it as a component of the apicoplast small ribosomal subunit machinery [#0]. Its coding sequence is transcribed as part of polycistronic apicoplast transcripts [#0] that are subsequently matured through RNA processing involving tRNA excision at conserved sequence motifs, with the locus also represented in long antisense transcripts processed at the same sites as sense transcripts [#1]. Beyond this genomic assignment and transcript-level characterization, no direct study of the S11 protein's function, its assembly into the ribosome, or its individual role has been reported in the available corpus; the gene is characterized only as a member of the apicoplast ribosomal protein complement.\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing whether the apicoplast genome encodes its own translational machinery required mapping the organellar genes; the complete gene map placed S11 among 17 ribosomal protein genes on the 35 kb circle and showed these genes are transcribed polycistronically.\",\n      \"evidence\": \"complete gene mapping of the 35 kb apicoplast DNA circle by sequencing and annotation in P. falciparum\",\n      \"pmids\": [\"8757284\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"does not demonstrate S11 protein expression or incorporation into a functional ribosome\",\n        \"no evidence for S11-specific function distinct from the shared ribosomal protein complement\",\n        \"polycistronic transcription shown at the genome level, not resolved to S11 individually\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"How the polycistronic apicoplast transcripts covering S11 are matured was addressed by mapping processing sites, showing tRNA excision at conserved motifs and the existence of antisense transcripts processed at the same positions.\",\n      \"evidence\": \"RNA analysis mapping processing sites, sequencing of apicoplast transcripts, and detection of antisense sequences in P. falciparum\",\n      \"pmids\": [\"27458998\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"transcript-level observation with no direct functional manipulation of the S11 protein; S11 is not individually distinguished from other ribosomal protein transcripts\",\n        \"functional consequence of antisense transcripts unknown\",\n        \"does not link processing to S11 protein abundance or ribosome assembly\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether the S11 protein itself has a distinct role in apicoplast ribosome assembly, translation, or parasite viability remains unaddressed.\",\n      \"evidence\": \"no direct functional study of the S11 protein in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"no direct evidence of S11 protein expression or ribosome incorporation\",\n        \"no genetic knockout or knockdown of S11\",\n        \"no structural model of S11 within the apicoplast small subunit\"\n      ],\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003735\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0009536\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006412\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\n      \"apicoplast small ribosomal subunit\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Encoded on the 35 kb plastid-like DNA circle among 17 apicoplast ribosomal protein genes [#0]\",\n      \"Transcribed as part of polycistronic apicoplast transcripts [#0]\",\n      \"Transcript locus matured via tRNA excision at conserved motifs and represented in processed antisense transcripts [#1]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_API02600","name":null,"product":"apicoplast ribosomal protein S11","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"","evaluation":null}