{"gene":"PF3D7_0828000","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2013,"finding":"Genetic deletion of ROM3 (PbROM3) in P. berghei demonstrated that ROM3 is dispensable for blood stage development but is essential for sporozoite production: ROM3-null parasites established oocysts normally in mosquitoes but failed to produce sporozoites, establishing ROM3 as the first apicomplexan rhomboid with a vital role in sporogony.","method":"Gene deletion (loss-of-function) with stage-specific phenotypic analysis in P. berghei","journal":"Molecular microbiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with defined cellular phenotype (sporogony failure), systematic analysis across all eight rhomboids in one study, replicated in context of broader family screen","pmids":["23490234"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2014,"finding":"ROM3 mRNA in P. berghei gametocytes is associated with the translational repressors DOZI and CITH, indicating that ROM3 transcript is stored in a translationally repressed state in female gametocytes for later use during post-fertilization development.","method":"RNA immunoprecipitation followed by microarray analysis (RIP-Chip) using DOZI and CITH as bait","journal":"Genome biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — RIP-Chip is a direct binding experiment but ROM3 is one of many hits and no functional follow-up specific to ROM3 was performed in this paper","pmids":["25418785"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"finding":"ROM3 transcript is among the female-enriched, translationally repressed mRNAs in P. berghei gametocytes; upon deletion of pbpp6, upregulation of mRNP complex subunits was associated with altered expression of these translationally repressed transcripts including rom3, corroborating its status as a stored, repressed transcript in female gametocytes.","method":"Comparative transcriptomic and proteomic analysis of wild-type vs. Δpbpp6 P. berghei gametocytes","journal":"PLoS pathogens","confidence":"Low","confidence_rationale":"Tier 3 / Weak — ROM3 mentioned as part of a class of translationally repressed transcripts in a study focused on PbPP6; no direct experiment on ROM3 itself","pmids":["40623036"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"finding":"SHIFTiKO inducible DiCre-based screen of P. falciparum rhomboid proteases confirmed that ROM3 is dispensable during asexual blood stage replication.","method":"Inducible frameshift knockout (SHIFTiKO / DiCre-lox) with pooled barcode-based phenotyping across asexual replication cycles","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean inducible KO with direct fitness measurement, but single study and ROM3 is one of several genes screened without detailed follow-up","pmids":["39739757"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"ROM3 (PF3D7_0828000) is a rhomboid-like intramembrane protease that is dispensable for asexual blood stage development in both P. berghei and P. falciparum, but is essential for sporozoite production during sporogony in P. berghei (ROM3-null oocysts form normally yet fail to generate sporozoites); its mRNA is stored in a translationally repressed state bound by DOZI/CITH in female gametocytes, suggesting its expression is post-transcriptionally regulated for deployment at a later life-cycle stage."},"narrative":{"mechanistic_narrative":"ROM3 (PF3D7_0828000) is a rhomboid-like intramembrane protease that functions not in the asexual blood stage but at the mosquito-transmission stage of the Plasmodium life cycle, where it is required for sporozoite formation [PMID:23490234]. In P. berghei, genetic deletion of ROM3 leaves blood-stage development and oocyst establishment intact, yet ROM3-null oocysts fail to generate sporozoites, marking ROM3 as an apicomplexan rhomboid with a vital role in sporogony [PMID:23490234]. Consistent with a life-cycle-stage-delayed function, ROM3 mRNA is stored in a translationally repressed state in female gametocytes, where it is bound by the translational repressors DOZI and CITH [PMID:25418785] and is counted among the female-enriched repressed transcripts whose regulation is perturbed upon loss of PbPP6 [PMID:40623036]. Its dispensability during asexual replication is conserved in P. falciparum, where an inducible knockout screen confirmed no fitness defect in blood-stage growth [PMID:39739757]. Beyond these genetic and RNA-association findings, the catalytic activity, membrane substrates, and molecular partners of ROM3 have not been characterized in the available corpus.","teleology":[{"year":2013,"claim":"Established whether ROM3 has a required cellular role and at which life-cycle stage, resolving the question of which apicomplexan rhomboid governs mosquito-stage development.","evidence":"Gene deletion with stage-specific phenotypic analysis across all rhomboids in P. berghei","pmids":["23490234"],"confidence":"High","gaps":["The proteolytic substrate cleaved by ROM3 during sporogony is unidentified","Catalytic activity of ROM3 has not been demonstrated biochemically","The subcellular localization within the oocyst/sporoblast is not defined"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2014,"claim":"Explained how a protein required only at a later mosquito stage is regulated, showing ROM3 mRNA is post-transcriptionally stored rather than expressed on demand.","evidence":"RIP-Chip using DOZI and CITH as bait in P. berghei gametocytes","pmids":["25418785"],"confidence":"Medium","gaps":["ROM3 was one of many transcripts recovered; no ROM3-specific functional follow-up","Timing and trigger of ROM3 translational de-repression not determined","Direct link between repressed storage and the sporogony phenotype not shown"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"claim":"Confirmed the dispensability of ROM3 during asexual blood-stage replication in a second species, generalizing the P. berghei finding to P. falciparum.","evidence":"SHIFTiKO inducible DiCre frameshift knockout with pooled barcode phenotyping in P. falciparum","pmids":["39739757"],"confidence":"Medium","gaps":["Single screen without ROM3-specific follow-up","Does not test mosquito-stage function in P. falciparum","No assessment of gametocyte or transmission phenotype"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Corroborated ROM3's status as a stored, translationally repressed female-gametocyte transcript by linking its regulation to mRNP complex control.","evidence":"Comparative transcriptomic/proteomic analysis of wild-type vs Δpbpp6 P. berghei gametocytes","pmids":["40623036"],"confidence":"Low","gaps":["ROM3 mentioned only as part of a repressed-transcript class in a PbPP6-focused study; no direct ROM3 experiment","Does not establish a mechanistic role for PbPP6 in ROM3 regulation","No protein-level measurement of ROM3 across the transition"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"The molecular mechanism of ROM3 — its catalytic activity, membrane substrate(s), and how its intramembrane proteolysis drives sporozoite formation — remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No substrate identified for ROM3","No demonstration of intramembrane protease activity","No structural or localization data for the protein"],"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["DOZI (MRNA-BINDING TRANSLATIONAL REPRESSOR; BINDS ROM3 TRANSCRIPT)","CITH (TRANSLATIONAL REPRESSOR; BINDS ROM3 TRANSCRIPT)"],"other_free_text":["ROM3 is dispensable for asexual blood-stage development in both P. berghei [#0] and P. falciparum [#3].","ROM3 is essential for sporozoite production during sporogony in P. berghei; null oocysts form normally but fail to generate sporozoites [#0].","ROM3 mRNA is stored in a DOZI/CITH-associated, translationally repressed state in female P. berghei gametocytes [#1, #2].","No catalytic activity, substrate, or subcellular localization of ROM3 has been characterized in the available corpus."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"23490234","id":"PMC_23490234","title":"Loss-of-function analyses defines vital and redundant functions of the Plasmodium rhomboid protease family.","date":"2013","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/23490234","citation_count":41,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27448565","id":"PMC_27448565","title":"A novel validated assay to support the discovery of new anti-malarial gametocytocidal agents.","date":"2016","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/27448565","citation_count":4,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40623036","id":"","title":"Loss of serine/threonine protein phosphatase 6 severely impairs sexual stage development in malaria parasite Plasmodium berghei.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/40623036","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35994647","id":"","title":"Malaria parasite evades mosquito immunity by glutaminyl cyclase-mediated posttranslational protein modification.","date":"2022","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/35994647","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"39739757","id":"","title":"A scaleable inducible knockout system for studying essential gene function in the malaria parasite.","date":"2025","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/39739757","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"38270586","id":"","title":"A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture.","date":"2024","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/38270586","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28599096","id":"","title":"Proteases as antimalarial targets: strategies for genetic, chemical, and therapeutic validation.","date":"2017","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/28599096","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"27911910","id":"","title":"Molecular Markers of Radiation Induced Attenuation in Intrahepatic Plasmodium falciparum Parasites.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/27911910","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"35073987","id":"","title":"Eimeria proteins: order amidst disorder.","date":"2022","source":"Parasites & vectors","url":"https://pubmed.ncbi.nlm.nih.gov/35073987","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":true,"competing_organism_match":"Eimeria","competing_organism_only":true},{"pmid":"34832610","id":"","title":"In Silico Survey and Characterization of Babesia microti Functional and Non-Functional Proteases.","date":"2021","source":"Pathogens (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/34832610","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":true,"competing_organism_match":"Babesia","competing_organism_only":true},{"pmid":"25418785","id":"","title":"Genome-wide RIP-Chip analysis of translational repressor-bound mRNAs in the Plasmodium gametocyte.","date":"2014","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/25418785","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM3"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13310,"output_tokens":1161,"usd":0.028673,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5973,"output_tokens":2155,"usd":0.04187,"stage2_stop_reason":"end_turn"},"total_usd":0.070543,"stage1_batch_id":"msgbatch_01SRp5hyRc82zNjddxyCCXGk","stage2_batch_id":"msgbatch_01K3BTmBazRo3pRrMvyaPMTY","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"Genetic deletion of ROM3 (PbROM3) in P. berghei demonstrated that ROM3 is dispensable for blood stage development but is essential for sporozoite production: ROM3-null parasites established oocysts normally in mosquitoes but failed to produce sporozoites, establishing ROM3 as the first apicomplexan rhomboid with a vital role in sporogony.\",\n      \"method\": \"Gene deletion (loss-of-function) with stage-specific phenotypic analysis in P. berghei\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined cellular phenotype (sporogony failure), systematic analysis across all eight rhomboids in one study, replicated in context of broader family screen\",\n      \"pmids\": [\"23490234\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ROM3 mRNA in P. berghei gametocytes is associated with the translational repressors DOZI and CITH, indicating that ROM3 transcript is stored in a translationally repressed state in female gametocytes for later use during post-fertilization development.\",\n      \"method\": \"RNA immunoprecipitation followed by microarray analysis (RIP-Chip) using DOZI and CITH as bait\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — RIP-Chip is a direct binding experiment but ROM3 is one of many hits and no functional follow-up specific to ROM3 was performed in this paper\",\n      \"pmids\": [\"25418785\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ROM3 transcript is among the female-enriched, translationally repressed mRNAs in P. berghei gametocytes; upon deletion of pbpp6, upregulation of mRNP complex subunits was associated with altered expression of these translationally repressed transcripts including rom3, corroborating its status as a stored, repressed transcript in female gametocytes.\",\n      \"method\": \"Comparative transcriptomic and proteomic analysis of wild-type vs. Δpbpp6 P. berghei gametocytes\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — ROM3 mentioned as part of a class of translationally repressed transcripts in a study focused on PbPP6; no direct experiment on ROM3 itself\",\n      \"pmids\": [\"40623036\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SHIFTiKO inducible DiCre-based screen of P. falciparum rhomboid proteases confirmed that ROM3 is dispensable during asexual blood stage replication.\",\n      \"method\": \"Inducible frameshift knockout (SHIFTiKO / DiCre-lox) with pooled barcode-based phenotyping across asexual replication cycles\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean inducible KO with direct fitness measurement, but single study and ROM3 is one of several genes screened without detailed follow-up\",\n      \"pmids\": [\"39739757\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"ROM3 (PF3D7_0828000) is a rhomboid-like intramembrane protease that is dispensable for asexual blood stage development in both P. berghei and P. falciparum, but is essential for sporozoite production during sporogony in P. berghei (ROM3-null oocysts form normally yet fail to generate sporozoites); its mRNA is stored in a translationally repressed state bound by DOZI/CITH in female gametocytes, suggesting its expression is post-transcriptionally regulated for deployment at a later life-cycle stage.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ROM3 (PF3D7_0828000) is a rhomboid-like intramembrane protease that functions not in the asexual blood stage but at the mosquito-transmission stage of the Plasmodium life cycle, where it is required for sporozoite formation [#0]. In P. berghei, genetic deletion of ROM3 leaves blood-stage development and oocyst establishment intact, yet ROM3-null oocysts fail to generate sporozoites, marking ROM3 as an apicomplexan rhomboid with a vital role in sporogony [#0]. Consistent with a life-cycle-stage-delayed function, ROM3 mRNA is stored in a translationally repressed state in female gametocytes, where it is bound by the translational repressors DOZI and CITH [#1] and is counted among the female-enriched repressed transcripts whose regulation is perturbed upon loss of PbPP6 [#2]. Its dispensability during asexual replication is conserved in P. falciparum, where an inducible knockout screen confirmed no fitness defect in blood-stage growth [#3]. Beyond these genetic and RNA-association findings, the catalytic activity, membrane substrates, and molecular partners of ROM3 have not been characterized in the available corpus.\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established whether ROM3 has a required cellular role and at which life-cycle stage, resolving the question of which apicomplexan rhomboid governs mosquito-stage development.\",\n      \"evidence\": \"Gene deletion with stage-specific phenotypic analysis across all rhomboids in P. berghei\",\n      \"pmids\": [\"23490234\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The proteolytic substrate cleaved by ROM3 during sporogony is unidentified\",\n        \"Catalytic activity of ROM3 has not been demonstrated biochemically\",\n        \"The subcellular localization within the oocyst/sporoblast is not defined\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Explained how a protein required only at a later mosquito stage is regulated, showing ROM3 mRNA is post-transcriptionally stored rather than expressed on demand.\",\n      \"evidence\": \"RIP-Chip using DOZI and CITH as bait in P. berghei gametocytes\",\n      \"pmids\": [\"25418785\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"ROM3 was one of many transcripts recovered; no ROM3-specific functional follow-up\",\n        \"Timing and trigger of ROM3 translational de-repression not determined\",\n        \"Direct link between repressed storage and the sporogony phenotype not shown\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Confirmed the dispensability of ROM3 during asexual blood-stage replication in a second species, generalizing the P. berghei finding to P. falciparum.\",\n      \"evidence\": \"SHIFTiKO inducible DiCre frameshift knockout with pooled barcode phenotyping in P. falciparum\",\n      \"pmids\": [\"39739757\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single screen without ROM3-specific follow-up\",\n        \"Does not test mosquito-stage function in P. falciparum\",\n        \"No assessment of gametocyte or transmission phenotype\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Corroborated ROM3's status as a stored, translationally repressed female-gametocyte transcript by linking its regulation to mRNP complex control.\",\n      \"evidence\": \"Comparative transcriptomic/proteomic analysis of wild-type vs Δpbpp6 P. berghei gametocytes\",\n      \"pmids\": [\"40623036\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"ROM3 mentioned only as part of a repressed-transcript class in a PbPP6-focused study; no direct ROM3 experiment\",\n        \"Does not establish a mechanistic role for PbPP6 in ROM3 regulation\",\n        \"No protein-level measurement of ROM3 across the transition\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular mechanism of ROM3 — its catalytic activity, membrane substrate(s), and how its intramembrane proteolysis drives sporozoite formation — remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No substrate identified for ROM3\",\n        \"No demonstration of intramembrane protease activity\",\n        \"No structural or localization data for the protein\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004252\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0060287\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DOZI (mRNA-binding translational repressor; binds ROM3 transcript)\", \"CITH (translational repressor; binds ROM3 transcript)\"],\n    \"other_free_text\": [\n      \"ROM3 is dispensable for asexual blood-stage development in both P. berghei [#0] and P. falciparum [#3].\",\n      \"ROM3 is essential for sporozoite production during sporogony in P. berghei; null oocysts form normally but fail to generate sporozoites [#0].\",\n      \"ROM3 mRNA is stored in a DOZI/CITH-associated, translationally repressed state in female P. berghei gametocytes [#1, #2].\",\n      \"No catalytic activity, substrate, or subcellular localization of ROM3 has been characterized in the available corpus.\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0828000","name":null,"product":"rhomboid protease ROM3","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0702700","name":null,"product":"rhomboid protease ROM3","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1322100","name":null,"product":"rhomboid protease ROM3, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"ROM3","evaluation":null}