{"gene":"PF3D7_1114100","run_date":"2026-09-08T12:51:28","timeline":{"discoveries":[{"year":2006,"finding":"ROM1 (PfROM1) is a rhomboid intramembrane protease with distinct substrate specificity: it cleaves AMA1 (the only PfROM able to do so) and shares specificity with rhomboid proteases from other organisms, but differs from PfROM4. In a heterologous cleavage assay, PfROM1 was able to cleave diverse adhesins including TRAP, CTRP, MTRAP, EBA-175, BAEBL, JESEBL, MAEBL, AMA1, Rh1, Rh2a, Rh2b, and Rh4, but not PTRAMP, with cleavage dependent on the adhesin transmembrane domains. Swapping TMDs between BAEBL and AMA1 switched the relative substrate preferences of PfROM1 and PfROM4, demonstrating that specificity is encoded in the adhesin transmembrane domain.","method":"Heterologous cell-based cleavage assay; transmembrane domain swap mutagenesis","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro/heterologous enzymatic assay with mutagenesis (TMD swaps), multiple substrates tested, comprehensive analysis in a single rigorous study","pmids":["17040128"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"finding":"ROM1 (PfROM1) localizes to a novel, previously unidentified secretory organelle in P. falciparum merozoites, termed the 'mononeme' — a single, thread-like structure on one side of the merozoite, in close proximity to subpellicular microtubules, distinct from micronemes, rhoptries, and dense granules. Upon merozoite release from schizonts, PfROM1 relocates from this lateral asymmetric position to the apical and posterior poles.","method":"Immunoconfocal microscopy with organelle marker co-staining","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization by immunoconfocal microscopy with multiple co-markers, single lab, no functional consequence directly linked to the mononeme localization","pmids":["18048320"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2009,"finding":"P. berghei ROM1 (PbROM1) localizes to the surface of sporozoites after salivary gland invasion and to the apical end of blood-stage merozoites. Genetic deletion of PbROM1 is not lethal but results in attenuation: PbROM1-null parasites are cleared by the host immune system and fail to cause lethal infection, indicating a non-essential but important role in invasive stages. Wild-type P. berghei is lethal to mice, whereas animals infected with PbROM1 null mutants clear the infection and develop long-lasting protective immunity.","method":"Gene deletion (null mutant generation); immunofluorescence localization; in vivo mouse infection assay","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic KO with defined in vivo phenotype and localization, single lab, two complementary methods","pmids":["19148267"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2011,"finding":"P. yoelii ROM1 (PyROM1) is required for proper formation of the parasitophorous vacuole (PV) during hepatic stage development. PyROM1-deficient sporozoites enter hepatocytes at normal rates and display normal gliding motility and cell traversal, but within the first 12 hours post-invasion, ~50% of pyrom1(-) parasites exhibit morphologically aberrant PVs (confirmed by UIS4 immunofluorescence and transmission electron microscopy), leading to developmental failure. PyROM1 is dispensable for mosquito-stage development (normal oocyst and salivary gland sporozoite counts). ROM1 steady-state mRNA is upregulated ~20-fold in salivary gland sporozoites relative to blood stages.","method":"Gene deletion (pyrom1(-) parasites); immunofluorescence microscopy (UIS4 PVM marker); transmission electron microscopy; quantitative lifecycle stage analysis","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with specific phenotypic readout (PV morphology), multiple orthogonal methods (IFA + TEM + quantitative lifecycle analysis), single lab but rigorous","pmids":["21909259"],"is_preprint":false,"attribution":[{"species":"Plasmodium yoelii","strain":""}]},{"year":2013,"finding":"In P. berghei, ROM1 gene deletion is viable (ROM1 is dispensable for blood-stage development). ROM1-null parasites show a delay in blood-stage patency following liver infection but, in contrast to a prior study (PMID:19148267), blood-stage parasites have similar growth and virulence to wild-type. ROM1 is thus non-essential for asexual blood-stage replication in this model.","method":"Systematic gene deletion analysis across all eight P. berghei rhomboid-like proteins; blood-stage and mosquito-stage phenotypic assays","journal":"Molecular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic deletion panel with defined phenotypic readouts, but result partially contradicts PMID:19148267 (different outcome in blood stage virulence); single lab","pmids":["23490234"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"ROM1 (PF3D7_1114100) is a rhomboid intramembrane serine protease with substrate specificity distinct from PfROM4: it cleaves invasion adhesins (including AMA1, EBA-175, TRAP, and others) via their transmembrane domains as demonstrated in heterologous assays; in P. falciparum merozoites it localizes to a novel organelle termed the mononeme; in rodent malaria models (P. yoelii, P. berghei), genetic deletion reveals a non-essential but functionally important role — specifically, ROM1 is required for proper parasitophorous vacuole formation during hepatic-stage development and contributes to blood-stage patency after liver infection, while being dispensable for mosquito-stage development."},"narrative":{"mechanistic_narrative":"ROM1 (PF3D7_1114100) is a rhomboid intramembrane serine protease of Plasmodium that participates in the parasite's invasive life-cycle stages through transmembrane-domain cleavage of adhesins and through a stage-specific role in intracellular development [PMID:17040128, PMID:21909259]. In a heterologous cleavage assay ROM1 displays a broad substrate range distinct from PfROM4 — it is the only PfROM able to cleave AMA1 and also cleaves TRAP, CTRP, MTRAP, EBA-175, BAEBL, JESEBL, MAEBL, Rh1, Rh2a, Rh2b and Rh4 but not PTRAMP, with cleavage determined by the substrate transmembrane domain, since swapping TMDs between BAEBL and AMA1 switches the relative preferences of ROM1 and PfROM4 [PMID:17040128]. In P. falciparum merozoites ROM1 localizes to a distinct thread-like secretory organelle, the mononeme, and redistributes to the apical and posterior poles upon merozoite release [PMID:18048320]. Genetic dissection in rodent malaria models establishes that ROM1 is non-essential yet functionally important: in P. yoelii it is required for proper parasitophorous vacuole formation during hepatic-stage development, with ~50% of null parasites forming aberrant PVs and failing to develop, while remaining dispensable for mosquito-stage development [PMID:21909259]; in P. berghei ROM1 deletion is viable, attenuates the infection and delays blood-stage patency after liver infection [PMID:19148267, PMID:23490234]. Reports diverge on blood-stage virulence of P. berghei ROM1-null parasites: one study found immune clearance and loss of lethality [PMID:19148267], whereas a systematic deletion panel found growth and virulence similar to wild-type [PMID:23490234].","teleology":[{"year":2006,"claim":"Whether ROM1 had defined enzymatic substrates and how it differed from other parasite rhomboids was unknown; this work established ROM1 as an intramembrane protease with a broad, TMD-encoded substrate specificity distinct from PfROM4.","evidence":"Heterologous cell-based cleavage assay with a panel of adhesins plus transmembrane-domain swap mutagenesis, in P. falciparum sequences","pmids":["17040128"],"confidence":"High","gaps":["Cleavage shown in a heterologous system, not demonstrated on endogenous substrates in the parasite","Which of these substrates ROM1 processes physiologically in vivo is not established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2007,"claim":"The subcellular location of ROM1 was unknown; imaging placed it in a previously unidentified secretory organelle, the mononeme, and revealed dynamic redistribution during merozoite release.","evidence":"Immunoconfocal microscopy with organelle marker co-staining in P. falciparum merozoites","pmids":["18048320"],"confidence":"Medium","gaps":["No functional consequence directly linked to mononeme localization","Single lab; mechanism of trafficking to and from the mononeme unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2009,"claim":"Whether ROM1 is required for parasite viability and virulence was untested; deletion in P. berghei showed it is non-essential but that its loss attenuates infection and enables immune clearance.","evidence":"Gene deletion, immunofluorescence localization, and in vivo mouse infection in P. berghei","pmids":["19148267"],"confidence":"Medium","gaps":["Molecular basis of attenuation not defined","Blood-stage virulence phenotype later contradicted by a systematic deletion study"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2011,"claim":"The specific life-cycle process ROM1 supports was unclear; this work localized its essential contribution to hepatic-stage parasitophorous vacuole formation rather than to invasion or motility.","evidence":"pyrom1(-) gene deletion with UIS4 IFA, transmission electron microscopy, and quantitative lifecycle staging in P. yoelii","pmids":["21909259"],"confidence":"High","gaps":["The molecular substrate whose cleavage underlies PV formation is not identified","Why only ~50% of null parasites form aberrant PVs is unexplained"],"attribution":[{"species":"Plasmodium yoelii","strain":""}]},{"year":2013,"claim":"Given conflicting reports on blood-stage requirement, a systematic deletion panel clarified that ROM1 is dispensable for asexual blood-stage replication and mainly delays patency after liver infection.","evidence":"Systematic gene deletion across all eight P. berghei rhomboid-like proteins with blood- and mosquito-stage phenotyping","pmids":["23490234"],"confidence":"Medium","gaps":["Blood-stage virulence outcome contradicts PMID 19148267","Underlying cause of delayed patency not mechanistically defined"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"The endogenous substrate(s) ROM1 cleaves in vivo — and how those cleavage events connect its mononeme localization to hepatic parasitophorous vacuole formation — remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No demonstrated endogenous substrate in intact parasites","Link between protease activity and PV formation phenotype not established","Species divergence in blood-stage virulence phenotype unreconciled"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":["Cleaves adhesins including AMA1, TRAP, CTRP, MTRAP, EBA-175, BAEBL, JESEBL, MAEBL, Rh1, Rh2a, Rh2b and Rh4, but not PTRAMP, in a heterologous assay; specificity encoded in the substrate transmembrane domain [#0]","Substrate specificity distinct from PfROM4 [#0]","Localizes to the mononeme in P. falciparum merozoites and redistributes to apical/posterior poles at release [#1]","Non-essential but functionally important; required for hepatic-stage parasitophorous vacuole formation in P. yoelii [#3]","Deletion in P. berghei attenuates infection and delays blood-stage patency; blood-stage virulence phenotype reported divergently across studies [#2, #4]","ROM1 mRNA upregulated ~20-fold in salivary gland sporozoites relative to blood stages [#3]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"17040128","id":"PMC_17040128","title":"Two Plasmodium rhomboid proteases preferentially cleave different adhesins implicated in all invasive stages of malaria.","date":"2006","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/17040128","citation_count":180,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfROM1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"17000879","id":"PMC_17000879","title":"Intramembrane proteolysis mediates shedding of a key adhesin during erythrocyte invasion by the malaria parasite.","date":"2006","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17000879","citation_count":150,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18048320","id":"PMC_18048320","title":"Mononeme: a new secretory organelle in Plasmodium falciparum merozoites identified by localization of rhomboid-1 protease.","date":"2007","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/18048320","citation_count":50,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfROM1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"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":["ROM1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19148267","id":"PMC_19148267","title":"Distinct roles of Plasmodium rhomboid 1 in parasite development and malaria pathogenesis.","date":"2009","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/19148267","citation_count":34,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PbROM1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21909259","id":"PMC_21909259","title":"Plasmodium protease ROM1 is important for proper formation of the parasitophorous vacuole.","date":"2011","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/21909259","citation_count":27,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ROM1","PyROM1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28690071","id":"PMC_28690071","title":"Plasmodium vivax rhomboid-like protease 1 gene diversity in Thailand.","date":"2017","source":"Experimental parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/28690071","citation_count":1,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PvROM1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6409,"output_tokens":1846,"usd":0.023459,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6969,"output_tokens":2732,"usd":0.051573,"stage2_stop_reason":"end_turn"},"total_usd":0.075032,"stage1_batch_id":"msgbatch_01DisAaTypwmC8QwdMBuePHo","stage2_batch_id":"msgbatch_0184zxZTqxiEfdYYfPMfkqjb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"ROM1 (PfROM1) is a rhomboid intramembrane protease with distinct substrate specificity: it cleaves AMA1 (the only PfROM able to do so) and shares specificity with rhomboid proteases from other organisms, but differs from PfROM4. In a heterologous cleavage assay, PfROM1 was able to cleave diverse adhesins including TRAP, CTRP, MTRAP, EBA-175, BAEBL, JESEBL, MAEBL, AMA1, Rh1, Rh2a, Rh2b, and Rh4, but not PTRAMP, with cleavage dependent on the adhesin transmembrane domains. Swapping TMDs between BAEBL and AMA1 switched the relative substrate preferences of PfROM1 and PfROM4, demonstrating that specificity is encoded in the adhesin transmembrane domain.\",\n      \"method\": \"Heterologous cell-based cleavage assay; transmembrane domain swap mutagenesis\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro/heterologous enzymatic assay with mutagenesis (TMD swaps), multiple substrates tested, comprehensive analysis in a single rigorous study\",\n      \"pmids\": [\"17040128\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"ROM1 (PfROM1) localizes to a novel, previously unidentified secretory organelle in P. falciparum merozoites, termed the 'mononeme' — a single, thread-like structure on one side of the merozoite, in close proximity to subpellicular microtubules, distinct from micronemes, rhoptries, and dense granules. Upon merozoite release from schizonts, PfROM1 relocates from this lateral asymmetric position to the apical and posterior poles.\",\n      \"method\": \"Immunoconfocal microscopy with organelle marker co-staining\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization by immunoconfocal microscopy with multiple co-markers, single lab, no functional consequence directly linked to the mononeme localization\",\n      \"pmids\": [\"18048320\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"P. berghei ROM1 (PbROM1) localizes to the surface of sporozoites after salivary gland invasion and to the apical end of blood-stage merozoites. Genetic deletion of PbROM1 is not lethal but results in attenuation: PbROM1-null parasites are cleared by the host immune system and fail to cause lethal infection, indicating a non-essential but important role in invasive stages. Wild-type P. berghei is lethal to mice, whereas animals infected with PbROM1 null mutants clear the infection and develop long-lasting protective immunity.\",\n      \"method\": \"Gene deletion (null mutant generation); immunofluorescence localization; in vivo mouse infection assay\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic KO with defined in vivo phenotype and localization, single lab, two complementary methods\",\n      \"pmids\": [\"19148267\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"P. yoelii ROM1 (PyROM1) is required for proper formation of the parasitophorous vacuole (PV) during hepatic stage development. PyROM1-deficient sporozoites enter hepatocytes at normal rates and display normal gliding motility and cell traversal, but within the first 12 hours post-invasion, ~50% of pyrom1(-) parasites exhibit morphologically aberrant PVs (confirmed by UIS4 immunofluorescence and transmission electron microscopy), leading to developmental failure. PyROM1 is dispensable for mosquito-stage development (normal oocyst and salivary gland sporozoite counts). ROM1 steady-state mRNA is upregulated ~20-fold in salivary gland sporozoites relative to blood stages.\",\n      \"method\": \"Gene deletion (pyrom1(-) parasites); immunofluorescence microscopy (UIS4 PVM marker); transmission electron microscopy; quantitative lifecycle stage analysis\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with specific phenotypic readout (PV morphology), multiple orthogonal methods (IFA + TEM + quantitative lifecycle analysis), single lab but rigorous\",\n      \"pmids\": [\"21909259\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium yoelii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"In P. berghei, ROM1 gene deletion is viable (ROM1 is dispensable for blood-stage development). ROM1-null parasites show a delay in blood-stage patency following liver infection but, in contrast to a prior study (PMID:19148267), blood-stage parasites have similar growth and virulence to wild-type. ROM1 is thus non-essential for asexual blood-stage replication in this model.\",\n      \"method\": \"Systematic gene deletion analysis across all eight P. berghei rhomboid-like proteins; blood-stage and mosquito-stage phenotypic assays\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic deletion panel with defined phenotypic readouts, but result partially contradicts PMID:19148267 (different outcome in blood stage virulence); single lab\",\n      \"pmids\": [\"23490234\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"ROM1 (PF3D7_1114100) is a rhomboid intramembrane serine protease with substrate specificity distinct from PfROM4: it cleaves invasion adhesins (including AMA1, EBA-175, TRAP, and others) via their transmembrane domains as demonstrated in heterologous assays; in P. falciparum merozoites it localizes to a novel organelle termed the mononeme; in rodent malaria models (P. yoelii, P. berghei), genetic deletion reveals a non-essential but functionally important role — specifically, ROM1 is required for proper parasitophorous vacuole formation during hepatic-stage development and contributes to blood-stage patency after liver infection, while being dispensable for mosquito-stage development.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ROM1 (PF3D7_1114100) is a rhomboid intramembrane serine protease of Plasmodium that participates in the parasite's invasive life-cycle stages through transmembrane-domain cleavage of adhesins and through a stage-specific role in intracellular development [#0, #3]. In a heterologous cleavage assay ROM1 displays a broad substrate range distinct from PfROM4 — it is the only PfROM able to cleave AMA1 and also cleaves TRAP, CTRP, MTRAP, EBA-175, BAEBL, JESEBL, MAEBL, Rh1, Rh2a, Rh2b and Rh4 but not PTRAMP, with cleavage determined by the substrate transmembrane domain, since swapping TMDs between BAEBL and AMA1 switches the relative preferences of ROM1 and PfROM4 [#0]. In P. falciparum merozoites ROM1 localizes to a distinct thread-like secretory organelle, the mononeme, and redistributes to the apical and posterior poles upon merozoite release [#1]. Genetic dissection in rodent malaria models establishes that ROM1 is non-essential yet functionally important: in P. yoelii it is required for proper parasitophorous vacuole formation during hepatic-stage development, with ~50% of null parasites forming aberrant PVs and failing to develop, while remaining dispensable for mosquito-stage development [#3]; in P. berghei ROM1 deletion is viable, attenuates the infection and delays blood-stage patency after liver infection [#2, #4]. Reports diverge on blood-stage virulence of P. berghei ROM1-null parasites: one study found immune clearance and loss of lethality [#2], whereas a systematic deletion panel found growth and virulence similar to wild-type [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Whether ROM1 had defined enzymatic substrates and how it differed from other parasite rhomboids was unknown; this work established ROM1 as an intramembrane protease with a broad, TMD-encoded substrate specificity distinct from PfROM4.\",\n      \"evidence\": \"Heterologous cell-based cleavage assay with a panel of adhesins plus transmembrane-domain swap mutagenesis, in P. falciparum sequences\",\n      \"pmids\": [\"17040128\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cleavage shown in a heterologous system, not demonstrated on endogenous substrates in the parasite\", \"Which of these substrates ROM1 processes physiologically in vivo is not established\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"The subcellular location of ROM1 was unknown; imaging placed it in a previously unidentified secretory organelle, the mononeme, and revealed dynamic redistribution during merozoite release.\",\n      \"evidence\": \"Immunoconfocal microscopy with organelle marker co-staining in P. falciparum merozoites\",\n      \"pmids\": [\"18048320\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional consequence directly linked to mononeme localization\", \"Single lab; mechanism of trafficking to and from the mononeme unresolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Whether ROM1 is required for parasite viability and virulence was untested; deletion in P. berghei showed it is non-essential but that its loss attenuates infection and enables immune clearance.\",\n      \"evidence\": \"Gene deletion, immunofluorescence localization, and in vivo mouse infection in P. berghei\",\n      \"pmids\": [\"19148267\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of attenuation not defined\", \"Blood-stage virulence phenotype later contradicted by a systematic deletion study\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"The specific life-cycle process ROM1 supports was unclear; this work localized its essential contribution to hepatic-stage parasitophorous vacuole formation rather than to invasion or motility.\",\n      \"evidence\": \"pyrom1(-) gene deletion with UIS4 IFA, transmission electron microscopy, and quantitative lifecycle staging in P. yoelii\",\n      \"pmids\": [\"21909259\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The molecular substrate whose cleavage underlies PV formation is not identified\", \"Why only ~50% of null parasites form aberrant PVs is unexplained\"],\n      \"attribution\": [{\"species\": \"Plasmodium yoelii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Given conflicting reports on blood-stage requirement, a systematic deletion panel clarified that ROM1 is dispensable for asexual blood-stage replication and mainly delays patency after liver infection.\",\n      \"evidence\": \"Systematic gene deletion across all eight P. berghei rhomboid-like proteins with blood- and mosquito-stage phenotyping\",\n      \"pmids\": [\"23490234\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Blood-stage virulence outcome contradicts PMID 19148267\", \"Underlying cause of delayed patency not mechanistically defined\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The endogenous substrate(s) ROM1 cleaves in vivo — and how those cleavage events connect its mononeme localization to hepatic parasitophorous vacuole formation — remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No demonstrated endogenous substrate in intact parasites\", \"Link between protease activity and PV formation phenotype not established\", \"Species divergence in blood-stage virulence phenotype unreconciled\"],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004252\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0004175\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0016020\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0020009\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0044409\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": [\n      \"Cleaves adhesins including AMA1, TRAP, CTRP, MTRAP, EBA-175, BAEBL, JESEBL, MAEBL, Rh1, Rh2a, Rh2b and Rh4, but not PTRAMP, in a heterologous assay; specificity encoded in the substrate transmembrane domain [#0]\",\n      \"Substrate specificity distinct from PfROM4 [#0]\",\n      \"Localizes to the mononeme in P. falciparum merozoites and redistributes to apical/posterior poles at release [#1]\",\n      \"Non-essential but functionally important; required for hepatic-stage parasitophorous vacuole formation in P. yoelii [#3]\",\n      \"Deletion in P. berghei attenuates infection and delays blood-stage patency; blood-stage virulence phenotype reported divergently across studies [#2, #4]\",\n      \"ROM1 mRNA upregulated ~20-fold in salivary gland sporozoites relative to blood stages [#3]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1114100","name":null,"product":"rhomboid protease ROM1","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0933500","name":null,"product":"rhomboid protease ROM1","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0911700","name":null,"product":"rhomboid protease ROM1, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"ROM1","evaluation":null}