{"gene":"PF3D7_API02300","run_date":"2026-09-08T15:24:04","timeline":{"discoveries":[{"year":1996,"finding":"RPS5 (PF3D7_API02300) is encoded on the 35 kb plastid-like (apicoplast) DNA circle of P. falciparum, as part of a set of 17 ribosomal protein genes identified in the complete gene map of this organellar genome; transcription of this locus is polycistronic.","method":"Complete gene mapping and sequence analysis of the 35 kb apicoplast DNA circle","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — comprehensive gene mapping with sequence identification across the entire apicoplast genome, single study but genome-scale with direct experimental mapping","pmids":["8757284"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"finding":"Polycistronic transcripts from the apicoplast genome of P. falciparum (which include RPS5/PF3D7_API02300-containing operons) undergo RNA processing via excision of tRNA molecules at sites associated with a conserved sequence motif; antisense transcripts covering these loci are also processed at the same sites.","method":"RNA transcript analysis, identification of processing sites, RT-PCR and sequencing of apicoplast transcripts","journal":"Protist","confidence":"Low","confidence_rationale":"Tier 3 / Weak — transcript-level analysis applies broadly to apicoplast polycistronic units including the RPS5 locus, but RPS5 is not individually distinguished from other ribosomal protein genes in the abstract","pmids":["27458998"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"RPS5 (PF3D7_API02300) is an apicoplast small subunit ribosomal protein encoded on the P. falciparum 35 kb apicoplast genome within a polycistronic transcription unit that undergoes tRNA-mediated RNA processing; beyond its membership in the apicoplast ribosome, no direct functional or structural mechanistic data have been established for this protein."},"narrative":{"mechanistic_narrative":"RPS5 (PF3D7_API02300) is a small-subunit ribosomal protein gene encoded on the 35 kb plastid-like (apicoplast) DNA circle of Plasmodium falciparum, identified as one of a set of 17 ribosomal protein genes in the complete gene map of this organellar genome, and transcribed from a polycistronic locus [PMID:8757284]. The polycistronic transcripts that include the RPS5-containing operon undergo RNA processing through excision of tRNA molecules at sites associated with a conserved sequence motif, with antisense transcripts across the same loci processed at identical positions [PMID:27458998]. Beyond its membership in the apicoplast ribosome and this transcript-level processing context, no direct functional or structural mechanistic data have been established for RPS5 in the available corpus; the protein is not individually distinguished from other apicoplast ribosomal protein genes in the processing analysis [PMID:27458998].","teleology":[{"year":1996,"claim":"Before this work it was unknown which ribosomal protein genes the apicoplast genome carries; complete mapping placed RPS5 on the 35 kb DNA circle, establishing it as an organelle-encoded component of the apicoplast translational machinery.","evidence":"Complete gene mapping and sequence analysis of the 35 kb apicoplast DNA circle in P. falciparum","pmids":["8757284"],"confidence":"Medium","gaps":["No evidence that the RPS5 gene product is expressed as a protein or assembled into a ribosome","No functional or structural characterization of RPS5 individually","Polycistronic organization inferred at the genome level, not resolved for the RPS5 transcript specifically"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"claim":"It was unclear how the apicoplast polycistronic transcripts are matured; transcript analysis showed that tRNA excision at a conserved motif processes the operons containing RPS5, defining the RNA-processing context of the locus.","evidence":"RNA transcript analysis with RT-PCR and sequencing of apicoplast transcripts, identifying processing sites in P. falciparum","pmids":["27458998"],"confidence":"Low","gaps":["RPS5 is not individually distinguished from other ribosomal protein genes in this transcript-level analysis","Does not establish RPS5 protein levels, translation, or ribosome assembly","The enzyme(s) mediating tRNA excision at these sites are not identified"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether RPS5 protein is expressed, incorporated into the apicoplast small ribosomal subunit, and required for organelle translation or parasite viability remains uncharacterized in the available corpus.","evidence":"","pmids":[],"confidence":"Low","gaps":["No direct evidence of RPS5 protein expression or ribosome incorporation","No genetic knockout, knockdown, or essentiality data for RPS5","No structural model or interaction partners defined for the RPS5 protein"],"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 (apicoplast) DNA circle of P. falciparum as one of 17 ribosomal protein genes [#0]","Transcribed from a polycistronic locus whose transcripts are matured by tRNA excision at a conserved sequence motif [#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":3654,"output_tokens":619,"usd":0.010124,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5225,"output_tokens":1581,"usd":0.032825,"stage2_stop_reason":"end_turn"},"total_usd":0.042949,"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\": \"RPS5 (PF3D7_API02300) is encoded on the 35 kb plastid-like (apicoplast) DNA circle of P. falciparum, as part of a set of 17 ribosomal protein genes identified in the complete gene map of this organellar genome; transcription of this locus is polycistronic.\",\n      \"method\": \"Complete gene mapping and sequence analysis of the 35 kb apicoplast DNA circle\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — comprehensive gene mapping with sequence identification across the entire apicoplast genome, single study but genome-scale with direct experimental mapping\",\n      \"pmids\": [\"8757284\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Polycistronic transcripts from the apicoplast genome of P. falciparum (which include RPS5/PF3D7_API02300-containing operons) undergo RNA processing via excision of tRNA molecules at sites associated with a conserved sequence motif; antisense transcripts covering these loci are also processed at the same sites.\",\n      \"method\": \"RNA transcript analysis, identification of processing sites, RT-PCR and sequencing of apicoplast transcripts\",\n      \"journal\": \"Protist\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — transcript-level analysis applies broadly to apicoplast polycistronic units including the RPS5 locus, but RPS5 is not individually distinguished from other ribosomal protein genes in the abstract\",\n      \"pmids\": [\"27458998\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"RPS5 (PF3D7_API02300) is an apicoplast small subunit ribosomal protein encoded on the P. falciparum 35 kb apicoplast genome within a polycistronic transcription unit that undergoes tRNA-mediated RNA processing; beyond its membership in the apicoplast ribosome, no direct functional or structural mechanistic data have been established for this protein.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RPS5 (PF3D7_API02300) is a small-subunit ribosomal protein gene encoded on the 35 kb plastid-like (apicoplast) DNA circle of Plasmodium falciparum, identified as one of a set of 17 ribosomal protein genes in the complete gene map of this organellar genome, and transcribed from a polycistronic locus [#0]. The polycistronic transcripts that include the RPS5-containing operon undergo RNA processing through excision of tRNA molecules at sites associated with a conserved sequence motif, with antisense transcripts across the same loci processed at identical positions [#1]. Beyond its membership in the apicoplast ribosome and this transcript-level processing context, no direct functional or structural mechanistic data have been established for RPS5 in the available corpus; the protein is not individually distinguished from other apicoplast ribosomal protein genes in the processing analysis [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Before this work it was unknown which ribosomal protein genes the apicoplast genome carries; complete mapping placed RPS5 on the 35 kb DNA circle, establishing it as an organelle-encoded component of the apicoplast translational machinery.\",\n      \"evidence\": \"Complete gene mapping and sequence analysis of the 35 kb apicoplast DNA circle in P. falciparum\",\n      \"pmids\": [\n        \"8757284\"\n      ],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No evidence that the RPS5 gene product is expressed as a protein or assembled into a ribosome\",\n        \"No functional or structural characterization of RPS5 individually\",\n        \"Polycistronic organization inferred at the genome level, not resolved for the RPS5 transcript specifically\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"It was unclear how the apicoplast polycistronic transcripts are matured; transcript analysis showed that tRNA excision at a conserved motif processes the operons containing RPS5, defining the RNA-processing context of the locus.\",\n      \"evidence\": \"RNA transcript analysis with RT-PCR and sequencing of apicoplast transcripts, identifying processing sites in P. falciparum\",\n      \"pmids\": [\n        \"27458998\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"RPS5 is not individually distinguished from other ribosomal protein genes in this transcript-level analysis\",\n        \"Does not establish RPS5 protein levels, translation, or ribosome assembly\",\n        \"The enzyme(s) mediating tRNA excision at these sites are not identified\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether RPS5 protein is expressed, incorporated into the apicoplast small ribosomal subunit, and required for organelle translation or parasite viability remains uncharacterized in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct evidence of RPS5 protein expression or ribosome incorporation\",\n        \"No genetic knockout, knockdown, or essentiality data for RPS5\",\n        \"No structural model or interaction partners defined for the RPS5 protein\"\n      ],\n      \"attribution\": [\n        {\n          \"species\": \"Plasmodium falciparum\",\n          \"strain\": \"\"\n        }\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0003735\",\n        \"supporting_discovery_ids\": [0]\n      }\n    ],\n    \"localization\": [\n      {\n        \"term_id\": \"GO:0020011\",\n        \"supporting_discovery_ids\": [0]\n      }\n    ],\n    \"pathway\": [\n      {\n        \"term_id\": \"GO:0006412\",\n        \"supporting_discovery_ids\": [0]\n      }\n    ],\n    \"complexes\": [\n      \"apicoplast small ribosomal subunit\"\n    ],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Encoded on the 35 kb plastid-like (apicoplast) DNA circle of P. falciparum as one of 17 ribosomal protein genes [#0]\",\n      \"Transcribed from a polycistronic locus whose transcripts are matured by tRNA excision at a conserved sequence motif [#1]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_API02300","name":null,"product":"apicoplast ribosomal protein S5","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"RPS5","evaluation":null}