{"gene":"PF3D7_0935900","run_date":"2026-09-08T12:51:27","timeline":{"discoveries":[{"year":2004,"finding":"REX1 is a ring-stage protein that localizes to Maurer's clefts in P. falciparum-infected erythrocytes. It contains predicted coiled-coil regions and a region with similarity to a domain in vesicle-tethering proteins, and persists in Maurer's clefts throughout erythrocyte infection.","method":"Immunofluorescence microscopy, sequence analysis, transcriptional profiling","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization by imaging with functional inference, single lab but foundational characterization paper","pmids":["15481109"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"finding":"REX1 export to Maurer's clefts occurs via a two-phase PEXEL-independent mechanism: a single hydrophobic stretch plus 10 additional amino acids mediates export across the parasitophorous vacuole membrane as a soluble protein, while a predicted coiled-coil sequence is required for final localization at the Maurer's clefts.","method":"Transgenic parasites expressing GFP-REX1 chimeras with truncations; biochemical fractionation","journal":"Traffic (Copenhagen, Denmark)","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple domain-deletion chimeras with biochemical characterization of solubility, single lab but two orthogonal methods (live imaging + fractionation)","pmids":["18489703"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"finding":"REX1 is required for normal Maurer's cleft architecture: REX1-GFP preferentially associates with edges of Maurer's clefts, vesicle-like structures, and stalk-like tethering extensions. Truncation or deletion of REX1 causes stacking of Maurer's cleft cisternae. Complementation of D10 parasites (which lack rex1) with full-length REX1-GFP restores the unstacked (3D7-type) Maurer's cleft phenotype.","method":"Transgenic parasite lines expressing REX1 truncations or deletion; electron microscopy; complementation assay in D10 parasites","journal":"Molecular microbiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function phenotype confirmed by electron microscopy and rescue/complementation experiment, replicated across multiple mutant lines","pmids":["18573183"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":2011,"finding":"REX1 is required for assembly of the P. falciparum virulence complex at the host erythrocyte surface. Truncation of the REX1 C-terminal domain compromises Maurer's cleft architecture and PfEMP1-mediated cytoadherence but permits some PfEMP1 trafficking to the RBC surface. Deletion of the REX1 coiled-coil region ablates PfEMP1 surface display, trapping PfEMP1 at Maurer's clefts. Complementation with REX1 partly restores PfEMP1-mediated CD36 binding. Complete REX1 deletion is associated with loss of KAHRP and defective KAHRP-GFP trafficking.","method":"Targeted mutagenesis (truncation and deletion) of REX1; immunofluorescence; cytoadherence assay to CD36; KAHRP-GFP trafficking assay; complementation","journal":"Molecular microbiology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple domain mutants with orthogonal functional readouts (cytoadherence, PfEMP1 surface display, KAHRP-GFP trafficking), complementation performed, single lab","pmids":["21696460"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":2015,"finding":"A repeat sequence domain of REX1 controls Maurer's cleft architecture and virulence protein trafficking. Inducible knockdown of REX1 causes stacking of Maurer's cleft cisternae. Loss of the repeat sequence domain results in formation of giant Maurer's cleft stacks that retain tether-like structures and the ability to dock onto the RBC membrane skeleton, but show deficient PfEMP1 export to the RBC surface and markedly reduced CD36 binding. REX1 is predicted to form a largely α-helical structure with a repetitive charge pattern in the repeat sequence domain.","method":"Inducible knockdown; transgenic parasites with REX1 domain deletions; immunofluorescence; electron microscopy; CD36 binding assay; structural prediction","journal":"Molecular microbiology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — inducible knockdown plus genetic dissection with multiple domain mutants and functional readouts (EM ultrastructure + cytoadherence), single lab","pmids":["26304012"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2016,"finding":"REX1 is ubiquitylated in P. falciparum-infected red blood cells, with ubiquitylation reaching a maximum level at the trophozoite stage.","method":"Tandem Ubiquitin-Binding Entities (TUBEs) pulldown coupled to mass spectrometry across ring, trophozoite, and schizont stages","journal":"Journal of proteomics","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, single MS-based method identifying ubiquitylation across stages; no writer/eraser identified","pmids":["26972027"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2009,"finding":"Synthetic peptides from conserved regions of REX1 bind specifically and saturably to red blood cell proteins. Three REX1-derived high-activity binding peptides (HABPs) were identified; their binding was sensitive to enzymatic treatment of RBCs, indicating dependence on specific RBC surface receptors.","method":"Solid-phase peptide synthesis; RBC binding assays with saturation and enzyme-treatment controls; circular dichroism","journal":"Vaccine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — peptide binding assay, single lab, no identification of specific RBC receptor partner","pmids":["19755146"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"REX1 was identified as a potential interaction partner of the Maurer's cleft membrane protein SEMP1 by co-immunoprecipitation, with co-localization at Maurer's clefts confirmed.","method":"Co-immunoprecipitation (Co-IP); immunofluorescence co-localization","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP from one lab; REX1 identified as interactor of SEMP1 but not the primary subject of the study; no functional dissection of the REX1–SEMP1 interaction","pmids":["25062022"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2021,"finding":"PfMC-2TM tightly co-localizes with REX1 at Maurer's clefts from as early as 4 hours post-invasion, establishing REX1 as a marker of nascent Maurer's clefts at the earliest stages of erythrocyte infection.","method":"Immunofluorescence co-localization with anti-REX1 antibodies in synchronized P. falciparum 3D7 cultures","journal":"Pathogens (Basel, Switzerland)","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-localization only, single lab, REX1 used as a reference marker rather than as the primary experimental subject","pmids":["33916455"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]}],"current_model":"REX1 (PF3D7_0935900) is a PEXEL-negative P. falciparum Maurer's cleft protein that is exported as a soluble protein via a hydrophobic stretch plus 10 flanking amino acids, then anchored to Maurer's clefts through its coiled-coil domain; it is required for maintaining the unstacked disc morphology of Maurer's cleft cisternae (through a repeat sequence domain), for forward trafficking of PfEMP1 to the red blood cell surface, and for assembly of the virulence complex including KAHRP, with REX1 itself subject to ubiquitylation that peaks at the trophozoite stage."},"narrative":{"mechanistic_narrative":"REX1 (PF3D7_0935900) is a PEXEL-negative Maurer's cleft protein of P. falciparum-infected erythrocytes that establishes and maintains the architecture of these parasite-induced membrane compartments and enables trafficking of virulence proteins to the host red blood cell surface [PMID:15481109, PMID:18573183, PMID:21696460]. It is exported from the parasite as a soluble protein across the parasitophorous vacuole membrane through a single hydrophobic stretch plus 10 flanking residues, and is then anchored at the Maurer's clefts via a predicted coiled-coil sequence [PMID:18489703]. At the clefts REX1 preferentially associates with cisternal edges, vesicle-like structures, and stalk-like tethers, and is required to maintain the unstacked disc morphology of the cisternae: truncation, coiled-coil deletion, or inducible knockdown causes stacking of the cisternae, a defect reversed by complementation with full-length REX1 [PMID:18573183, PMID:26304012]. A repeat sequence domain within REX1 governs this architectural control and downstream PfEMP1 export [PMID:26304012]. Loss of REX1 function compromises forward trafficking of PfEMP1 to the erythrocyte surface and CD36-dependent cytoadherence, traps PfEMP1 at the clefts, and disrupts KAHRP trafficking, identifying REX1 as an assembly factor for the host-cell virulence complex [PMID:21696460]. REX1 is itself ubiquitylated, with modification peaking at the trophozoite stage [PMID:26972027].","teleology":[{"year":2004,"claim":"Establishing where and when REX1 acts was the first requirement; imaging placed it at Maurer's clefts from the ring stage onward, defining it as a stable resident of the exported membrane system rather than a transient factor.","evidence":"Immunofluorescence, sequence analysis, and transcriptional profiling in P. falciparum","pmids":["15481109"],"confidence":"Medium","gaps":["Functional role not tested","Coiled-coil and vesicle-tethering similarities were sequence predictions only"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2008,"claim":"How a PEXEL-negative protein reaches the clefts was unknown; dissection of export chimeras showed a two-phase route in which a hydrophobic stretch plus 10 residues drives soluble export across the PVM and a coiled-coil dictates final cleft localization, defining distinct export and anchoring signals.","evidence":"GFP-REX1 truncation chimeras with live imaging and biochemical fractionation in transgenic P. falciparum","pmids":["18489703"],"confidence":"High","gaps":["The cleft-side receptor or partner engaged by the coiled-coil not identified","Machinery mediating PVM translocation not defined"],"attribution":[]},{"year":2008,"claim":"Whether REX1 has a structural role was resolved by loss-of-function and rescue: deletion or truncation stacks the cleft cisternae and complementation of REX1-deficient D10 parasites restores unstacked morphology, establishing REX1 as necessary for normal cleft architecture.","evidence":"REX1 truncation/deletion lines, electron microscopy, and complementation in D10 P. falciparum","pmids":["18573183"],"confidence":"High","gaps":["Molecular basis by which REX1 prevents cisternal stacking not defined","Whether REX1 acts alone or through partners at cleft edges unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":2011,"claim":"Linking cleft architecture to virulence, domain mutagenesis showed REX1 is required to assemble the surface virulence complex: coiled-coil deletion traps PfEMP1 at the clefts and ablates surface display, while full deletion also disrupts KAHRP, and complementation partly restores CD36 binding.","evidence":"REX1 truncation/deletion mutants, cytoadherence to CD36, PfEMP1 surface assays, KAHRP-GFP trafficking, and complementation in P. falciparum 3D7","pmids":["21696460"],"confidence":"High","gaps":["Direct interaction of REX1 with PfEMP1 or KAHRP not demonstrated","Mechanism connecting cleft morphology to cargo export unresolved"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":2015,"claim":"Mapping the architectural function to a specific region, inducible knockdown and domain deletion identified a repeat sequence domain that controls cisternal morphology and PfEMP1 export while leaving tethers and membrane docking intact, separating docking from cargo delivery.","evidence":"Inducible knockdown, REX1 domain-deletion lines, electron microscopy, CD36 binding, and structural prediction in P. falciparum","pmids":["26304012"],"confidence":"High","gaps":["How the charged repeat pattern enforces the unstacked geometry not experimentally established","No high-resolution structure"],"attribution":[]},{"year":2016,"claim":"A regulatory layer was uncovered by showing REX1 is ubiquitylated with a trophozoite-stage maximum, raising the possibility of stage-dependent control of REX1 function.","evidence":"TUBEs ubiquitin pulldown with mass spectrometry across ring, trophozoite, and schizont stages in P. falciparum","pmids":["26972027"],"confidence":"Medium","gaps":["No E3 ligase (writer) or deubiquitinase (eraser) identified","Functional consequence of REX1 ubiquitylation untested","Modified residues not mapped"],"attribution":[]},{"year":2021,"claim":"Interaction and marker studies placed REX1 in the cleft protein network, identifying it as an interaction partner of SEMP1, a co-localizing partner of PfMC-2TM, and an early marker of nascent clefts from ~4 hours post-invasion.","evidence":"Co-immunoprecipitation with SEMP1 and immunofluorescence co-localization with SEMP1 and PfMC-2TM in P. falciparum 3D7","pmids":["25062022","33916455"],"confidence":"Low","gaps":["SEMP1 interaction rests on a single Co-IP without reciprocal validation or functional dissection","Co-localization does not establish direct binding for PfMC-2TM","Biological role of these associations for REX1 function untested"],"attribution":[{"species":"Plasmodium falciparum","strain":"3D7"}]},{"year":null,"claim":"The direct molecular partners through which REX1 anchors to the clefts, enforces unstacked cisternal geometry, and drives PfEMP1/KAHRP export remain undefined, as does the functional role of its trophozoite-peak ubiquitylation.","evidence":"","pmids":[],"confidence":"Low","gaps":["No direct REX1-PfEMP1 or REX1-KAHRP binding demonstrated","No structure of REX1 or its repeat domain","Ubiquitin writer/eraser and functional effect unknown"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["SEMP1 (CO-IP INTERACTOR, SINGLE CO-IP, UNVALIDATED) [#7]","PFMC-2TM (CO-LOCALIZING MAURER'S CLEFT PROTEIN) [#8]","PFEMP1 (TRAFFICKING-DEPENDENT, NO DIRECT BINDING SHOWN) [#3]","KAHRP (TRAFFICKING-DEPENDENT, NO DIRECT BINDING SHOWN) [#3]"],"other_free_text":["PEXEL-negative exported protein; soluble export across the PVM via a hydrophobic stretch plus 10 flanking residues [#1]","Coiled-coil sequence required for Maurer's cleft anchoring [#1]","Repeat sequence domain (predicted largely alpha-helical with repetitive charge pattern) controls unstacked cisternal architecture and PfEMP1 export [#4]","Required to maintain unstacked Maurer's cleft cisternal morphology; loss causes cisternal stacking [#2, #4]","Required for CD36-dependent cytoadherence and surface display of PfEMP1 [#3, #4]","Ubiquitylated in infected RBCs, peaking at trophozoite stage; no writer/eraser identified [#5]","REX1-derived peptides bind RBC proteins in an enzyme-sensitive manner; no receptor identified (Low confidence) [#6]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"15481109","id":"PMC_15481109","title":"A novel Plasmodium falciparum ring stage protein, REX, is located in Maurer's clefts.","date":"2004","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/15481109","citation_count":78,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18489703","id":"PMC_18489703","title":"Targeting of the ring exported protein 1 to the Maurer's clefts is mediated by a two-phase process.","date":"2008","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/18489703","citation_count":66,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1","ring-exported protein 1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"18573183","id":"PMC_18573183","title":"Targeted mutagenesis of the ring-exported protein-1 of Plasmodium falciparum disrupts the architecture of Maurer's cleft organelles.","date":"2008","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/18573183","citation_count":60,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1","ring-exported protein 1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21696460","id":"PMC_21696460","title":"Genetic ablation of a Maurer's cleft protein prevents assembly of the Plasmodium falciparum virulence complex.","date":"2011","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/21696460","citation_count":34,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1","ring-exported protein 1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"28719294","id":"PMC_28719294","title":"Molecular Markers for Sensitive Detection of Plasmodium falciparum Asexual Stage Parasites and their Application in a Malaria Clinical Trial.","date":"2017","source":"The American journal of tropical medicine and hygiene","url":"https://pubmed.ncbi.nlm.nih.gov/28719294","citation_count":24,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1","ring-exported protein 1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26972027","id":"PMC_26972027","title":"New insights into host-parasite ubiquitin proteome dynamics in P. falciparum infected red blood cells using a TUBEs-MS approach.","date":"2016","source":"Journal of proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/26972027","citation_count":21,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26304012","id":"PMC_26304012","title":"A repeat sequence domain of the ring-exported protein-1 of Plasmodium falciparum controls export machinery architecture and virulence protein trafficking.","date":"2015","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/26304012","citation_count":20,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1","ring-exported protein 1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25062022","id":"PMC_25062022","title":"Characterization of the small exported Plasmodium falciparum membrane protein SEMP1.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25062022","citation_count":20,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19755146","id":"PMC_19755146","title":"Synthetic peptides from conserved regions of the Plasmodium falciparum early transcribed membrane and ring exported proteins bind specifically to red blood cell proteins.","date":"2009","source":"Vaccine","url":"https://pubmed.ncbi.nlm.nih.gov/19755146","citation_count":8,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"33916455","id":"PMC_33916455","title":"Trafficking and Association of Plasmodium falciparum MC-2TM with the Maurer's Clefts.","date":"2021","source":"Pathogens (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/33916455","citation_count":4,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"19263081","id":"PMC_19263081","title":"REX1 and Pf62: are they one and the same?","date":"2009","source":"Parasitology research","url":"https://pubmed.ncbi.nlm.nih.gov/19263081","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["REX1"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7780,"output_tokens":2584,"usd":0.03105,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8030,"output_tokens":3288,"usd":0.061175,"stage2_stop_reason":"end_turn"},"total_usd":0.092225,"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\": 2004,\n      \"finding\": \"REX1 is a ring-stage protein that localizes to Maurer's clefts in P. falciparum-infected erythrocytes. It contains predicted coiled-coil regions and a region with similarity to a domain in vesicle-tethering proteins, and persists in Maurer's clefts throughout erythrocyte infection.\",\n      \"method\": \"Immunofluorescence microscopy, sequence analysis, transcriptional profiling\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization by imaging with functional inference, single lab but foundational characterization paper\",\n      \"pmids\": [\"15481109\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"REX1 export to Maurer's clefts occurs via a two-phase PEXEL-independent mechanism: a single hydrophobic stretch plus 10 additional amino acids mediates export across the parasitophorous vacuole membrane as a soluble protein, while a predicted coiled-coil sequence is required for final localization at the Maurer's clefts.\",\n      \"method\": \"Transgenic parasites expressing GFP-REX1 chimeras with truncations; biochemical fractionation\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple domain-deletion chimeras with biochemical characterization of solubility, single lab but two orthogonal methods (live imaging + fractionation)\",\n      \"pmids\": [\"18489703\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"REX1 is required for normal Maurer's cleft architecture: REX1-GFP preferentially associates with edges of Maurer's clefts, vesicle-like structures, and stalk-like tethering extensions. Truncation or deletion of REX1 causes stacking of Maurer's cleft cisternae. Complementation of D10 parasites (which lack rex1) with full-length REX1-GFP restores the unstacked (3D7-type) Maurer's cleft phenotype.\",\n      \"method\": \"Transgenic parasite lines expressing REX1 truncations or deletion; electron microscopy; complementation assay in D10 parasites\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function phenotype confirmed by electron microscopy and rescue/complementation experiment, replicated across multiple mutant lines\",\n      \"pmids\": [\"18573183\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"REX1 is required for assembly of the P. falciparum virulence complex at the host erythrocyte surface. Truncation of the REX1 C-terminal domain compromises Maurer's cleft architecture and PfEMP1-mediated cytoadherence but permits some PfEMP1 trafficking to the RBC surface. Deletion of the REX1 coiled-coil region ablates PfEMP1 surface display, trapping PfEMP1 at Maurer's clefts. Complementation with REX1 partly restores PfEMP1-mediated CD36 binding. Complete REX1 deletion is associated with loss of KAHRP and defective KAHRP-GFP trafficking.\",\n      \"method\": \"Targeted mutagenesis (truncation and deletion) of REX1; immunofluorescence; cytoadherence assay to CD36; KAHRP-GFP trafficking assay; complementation\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple domain mutants with orthogonal functional readouts (cytoadherence, PfEMP1 surface display, KAHRP-GFP trafficking), complementation performed, single lab\",\n      \"pmids\": [\"21696460\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"A repeat sequence domain of REX1 controls Maurer's cleft architecture and virulence protein trafficking. Inducible knockdown of REX1 causes stacking of Maurer's cleft cisternae. Loss of the repeat sequence domain results in formation of giant Maurer's cleft stacks that retain tether-like structures and the ability to dock onto the RBC membrane skeleton, but show deficient PfEMP1 export to the RBC surface and markedly reduced CD36 binding. REX1 is predicted to form a largely α-helical structure with a repetitive charge pattern in the repeat sequence domain.\",\n      \"method\": \"Inducible knockdown; transgenic parasites with REX1 domain deletions; immunofluorescence; electron microscopy; CD36 binding assay; structural prediction\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — inducible knockdown plus genetic dissection with multiple domain mutants and functional readouts (EM ultrastructure + cytoadherence), single lab\",\n      \"pmids\": [\"26304012\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"REX1 is ubiquitylated in P. falciparum-infected red blood cells, with ubiquitylation reaching a maximum level at the trophozoite stage.\",\n      \"method\": \"Tandem Ubiquitin-Binding Entities (TUBEs) pulldown coupled to mass spectrometry across ring, trophozoite, and schizont stages\",\n      \"journal\": \"Journal of proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single MS-based method identifying ubiquitylation across stages; no writer/eraser identified\",\n      \"pmids\": [\"26972027\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Synthetic peptides from conserved regions of REX1 bind specifically and saturably to red blood cell proteins. Three REX1-derived high-activity binding peptides (HABPs) were identified; their binding was sensitive to enzymatic treatment of RBCs, indicating dependence on specific RBC surface receptors.\",\n      \"method\": \"Solid-phase peptide synthesis; RBC binding assays with saturation and enzyme-treatment controls; circular dichroism\",\n      \"journal\": \"Vaccine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — peptide binding assay, single lab, no identification of specific RBC receptor partner\",\n      \"pmids\": [\"19755146\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"REX1 was identified as a potential interaction partner of the Maurer's cleft membrane protein SEMP1 by co-immunoprecipitation, with co-localization at Maurer's clefts confirmed.\",\n      \"method\": \"Co-immunoprecipitation (Co-IP); immunofluorescence co-localization\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP from one lab; REX1 identified as interactor of SEMP1 but not the primary subject of the study; no functional dissection of the REX1–SEMP1 interaction\",\n      \"pmids\": [\"25062022\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PfMC-2TM tightly co-localizes with REX1 at Maurer's clefts from as early as 4 hours post-invasion, establishing REX1 as a marker of nascent Maurer's clefts at the earliest stages of erythrocyte infection.\",\n      \"method\": \"Immunofluorescence co-localization with anti-REX1 antibodies in synchronized P. falciparum 3D7 cultures\",\n      \"journal\": \"Pathogens (Basel, Switzerland)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-localization only, single lab, REX1 used as a reference marker rather than as the primary experimental subject\",\n      \"pmids\": [\"33916455\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    }\n  ],\n  \"current_model\": \"REX1 (PF3D7_0935900) is a PEXEL-negative P. falciparum Maurer's cleft protein that is exported as a soluble protein via a hydrophobic stretch plus 10 flanking amino acids, then anchored to Maurer's clefts through its coiled-coil domain; it is required for maintaining the unstacked disc morphology of Maurer's cleft cisternae (through a repeat sequence domain), for forward trafficking of PfEMP1 to the red blood cell surface, and for assembly of the virulence complex including KAHRP, with REX1 itself subject to ubiquitylation that peaks at the trophozoite stage.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"REX1 (PF3D7_0935900) is a PEXEL-negative Maurer's cleft protein of P. falciparum-infected erythrocytes that establishes and maintains the architecture of these parasite-induced membrane compartments and enables trafficking of virulence proteins to the host red blood cell surface [#0, #2, #3]. It is exported from the parasite as a soluble protein across the parasitophorous vacuole membrane through a single hydrophobic stretch plus 10 flanking residues, and is then anchored at the Maurer's clefts via a predicted coiled-coil sequence [#1]. At the clefts REX1 preferentially associates with cisternal edges, vesicle-like structures, and stalk-like tethers, and is required to maintain the unstacked disc morphology of the cisternae: truncation, coiled-coil deletion, or inducible knockdown causes stacking of the cisternae, a defect reversed by complementation with full-length REX1 [#2, #4]. A repeat sequence domain within REX1 governs this architectural control and downstream PfEMP1 export [#4]. Loss of REX1 function compromises forward trafficking of PfEMP1 to the erythrocyte surface and CD36-dependent cytoadherence, traps PfEMP1 at the clefts, and disrupts KAHRP trafficking, identifying REX1 as an assembly factor for the host-cell virulence complex [#3]. REX1 is itself ubiquitylated, with modification peaking at the trophozoite stage [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing where and when REX1 acts was the first requirement; imaging placed it at Maurer's clefts from the ring stage onward, defining it as a stable resident of the exported membrane system rather than a transient factor.\",\n      \"evidence\": \"Immunofluorescence, sequence analysis, and transcriptional profiling in P. falciparum\",\n      \"pmids\": [\"15481109\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role not tested\", \"Coiled-coil and vesicle-tethering similarities were sequence predictions only\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"How a PEXEL-negative protein reaches the clefts was unknown; dissection of export chimeras showed a two-phase route in which a hydrophobic stretch plus 10 residues drives soluble export across the PVM and a coiled-coil dictates final cleft localization, defining distinct export and anchoring signals.\",\n      \"evidence\": \"GFP-REX1 truncation chimeras with live imaging and biochemical fractionation in transgenic P. falciparum\",\n      \"pmids\": [\"18489703\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The cleft-side receptor or partner engaged by the coiled-coil not identified\", \"Machinery mediating PVM translocation not defined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Whether REX1 has a structural role was resolved by loss-of-function and rescue: deletion or truncation stacks the cleft cisternae and complementation of REX1-deficient D10 parasites restores unstacked morphology, establishing REX1 as necessary for normal cleft architecture.\",\n      \"evidence\": \"REX1 truncation/deletion lines, electron microscopy, and complementation in D10 P. falciparum\",\n      \"pmids\": [\"18573183\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis by which REX1 prevents cisternal stacking not defined\", \"Whether REX1 acts alone or through partners at cleft edges unresolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Linking cleft architecture to virulence, domain mutagenesis showed REX1 is required to assemble the surface virulence complex: coiled-coil deletion traps PfEMP1 at the clefts and ablates surface display, while full deletion also disrupts KAHRP, and complementation partly restores CD36 binding.\",\n      \"evidence\": \"REX1 truncation/deletion mutants, cytoadherence to CD36, PfEMP1 surface assays, KAHRP-GFP trafficking, and complementation in P. falciparum 3D7\",\n      \"pmids\": [\"21696460\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct interaction of REX1 with PfEMP1 or KAHRP not demonstrated\", \"Mechanism connecting cleft morphology to cargo export unresolved\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Mapping the architectural function to a specific region, inducible knockdown and domain deletion identified a repeat sequence domain that controls cisternal morphology and PfEMP1 export while leaving tethers and membrane docking intact, separating docking from cargo delivery.\",\n      \"evidence\": \"Inducible knockdown, REX1 domain-deletion lines, electron microscopy, CD36 binding, and structural prediction in P. falciparum\",\n      \"pmids\": [\"26304012\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the charged repeat pattern enforces the unstacked geometry not experimentally established\", \"No high-resolution structure\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"A regulatory layer was uncovered by showing REX1 is ubiquitylated with a trophozoite-stage maximum, raising the possibility of stage-dependent control of REX1 function.\",\n      \"evidence\": \"TUBEs ubiquitin pulldown with mass spectrometry across ring, trophozoite, and schizont stages in P. falciparum\",\n      \"pmids\": [\"26972027\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No E3 ligase (writer) or deubiquitinase (eraser) identified\", \"Functional consequence of REX1 ubiquitylation untested\", \"Modified residues not mapped\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Interaction and marker studies placed REX1 in the cleft protein network, identifying it as an interaction partner of SEMP1, a co-localizing partner of PfMC-2TM, and an early marker of nascent clefts from ~4 hours post-invasion.\",\n      \"evidence\": \"Co-immunoprecipitation with SEMP1 and immunofluorescence co-localization with SEMP1 and PfMC-2TM in P. falciparum 3D7\",\n      \"pmids\": [\"25062022\", \"33916455\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"SEMP1 interaction rests on a single Co-IP without reciprocal validation or functional dissection\", \"Co-localization does not establish direct binding for PfMC-2TM\", \"Biological role of these associations for REX1 function untested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"3D7\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular partners through which REX1 anchors to the clefts, enforces unstacked cisternal geometry, and drives PfEMP1/KAHRP export remain undefined, as does the functional role of its trophozoite-peak ubiquitylation.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct REX1-PfEMP1 or REX1-KAHRP binding demonstrated\", \"No structure of REX1 or its repeat domain\", \"Ubiquitin writer/eraser and functional effect unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0020030\", \"supporting_discovery_ids\": [0, 1, 2, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0046718\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"SEMP1 (Co-IP interactor, single Co-IP, unvalidated) [#7]\",\n      \"PfMC-2TM (co-localizing Maurer's cleft protein) [#8]\",\n      \"PfEMP1 (trafficking-dependent, no direct binding shown) [#3]\",\n      \"KAHRP (trafficking-dependent, no direct binding shown) [#3]\"\n    ],\n    \"other_free_text\": [\n      \"PEXEL-negative exported protein; soluble export across the PVM via a hydrophobic stretch plus 10 flanking residues [#1]\",\n      \"Coiled-coil sequence required for Maurer's cleft anchoring [#1]\",\n      \"Repeat sequence domain (predicted largely alpha-helical with repetitive charge pattern) controls unstacked cisternal architecture and PfEMP1 export [#4]\",\n      \"Required to maintain unstacked Maurer's cleft cisternal morphology; loss causes cisternal stacking [#2, #4]\",\n      \"Required for CD36-dependent cytoadherence and surface display of PfEMP1 [#3, #4]\",\n      \"Ubiquitylated in infected RBCs, peaking at trophozoite stage; no writer/eraser identified [#5]\",\n      \"REX1-derived peptides bind RBC proteins in an enzyme-sensitive manner; no receptor identified (Low confidence) [#6]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0935900","name":null,"product":"ring-exported protein 1","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0734500","name":null,"product":"Plasmodium exported protein, unknown function","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"REX1","evaluation":null}