{"gene":"PF3D7_0409900","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2025,"finding":"ALP5b (PF3D7_0409900 / PBANKA_1007500) was identified as a subunit of an atypical Plasmodium Arp2/3 complex by co-immunoprecipitation of GFP-tagged ARPC1 from activated male gametocytes; AlphaFold structural prediction indicates that ALP5b is structurally similar to human ARP2, and multimer predictions suggest it occupies the ARP2 position within the five-subunit complex.","method":"Co-immunoprecipitation (GFP-tag pulldown of ARPC1), AlphaFold structural prediction and DALI structural comparison","journal":"Nature microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP identifying ALP5b as a partner, supported by orthogonal structural prediction; single lab, no in vitro reconstitution or mutagenesis reported in abstract","pmids":["40514561"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"finding":"ALP5b (PF3D7_0409900) localizes to the nucleus of male gametocytes and interacts with ALP5a; deletion of ALP5b alone does not affect blood-stage growth, gametocyte development, or actin nucleation, but simultaneous deletion of both ALP5a and ALP5b is lethal to the parasite.","method":"Genetic knockout (single and double deletion), fluorescence localization, co-immunoprecipitation","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined viability phenotype plus direct localization experiment, single lab with multiple orthogonal methods","pmids":["41218080"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"finding":"Deletion of ALP5b (PF3D7_0409900) in P. berghei results in oocysts that are significantly smaller and fail to mature, with defective DNA segregation during male gametogenesis; genetic cross experiments revealed defects in male gamete integrity, establishing that ALP5b is required for proper DNA segregation and malaria transmission.","method":"Genetic knockout, oocyst size measurement, genetic crosses, fluorescence microscopy of male gametogenesis","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with specific cellular phenotype (DNA segregation defect) confirmed by genetic crosses, single lab","pmids":["41218080"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"finding":"The atypical Arp2/3 complex containing ALP5b (PF3D7_0409900/Arp2 homolog) localizes to endomitotic spindles (not the cytoplasm) and interacts with the kinetochore-associated protein AKiT7; disruption of Arp2/3 subunits causes kinetochore-spindle detachment, formation of subhaploid gametes, and transmission blockade, indicating ALP5b participates in nuclear actin polymerization at the mitotic spindle to ensure kinetochore-spindle attachment.","method":"Co-immunoprecipitation, fluorescence localization to spindles, genetic disruption with kinetochore-spindle association assay","journal":"Nature microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization tied to functional consequence (kinetochore detachment phenotype upon disruption), single lab with multiple orthogonal methods","pmids":["40514561","40828051"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"ALP5b (PF3D7_0409900) is a structural homolog of human ARP2 that forms part of an atypical five-subunit Arp2/3 complex in Plasmodium male gametocytes; this complex localizes to endomitotic spindles, interacts with the kinetochore-associated protein AKiT7, and is required for proper kinetochore-spindle attachment and DNA segregation during male gametogenesis, such that its loss causes defective oocyst maturation and blocks malaria transmission."},"narrative":{"mechanistic_narrative":"ALP5b (PF3D7_0409900) is a structural homolog of human ARP2 that serves as a subunit of an atypical five-subunit Arp2/3 complex operating in the nucleus of Plasmodium male gametocytes [PMID:40514561]. Identified in P. berghei by reciprocal co-immunoprecipitation of GFP-tagged ARPC1, ALP5b is predicted by AlphaFold and DALI to occupy the ARP2 position within the complex [PMID:40514561], and it directly interacts with its paralog ALP5a [PMID:41218080]. Rather than acting in the cytoplasm, this complex localizes to endomitotic spindles and associates with the kinetochore-associated protein AKiT7; disruption of Arp2/3 subunits causes kinetochore-spindle detachment and formation of subhaploid gametes, placing ALP5b in nuclear actin polymerization at the mitotic spindle to ensure proper kinetochore-spindle attachment [PMID:40514561, PMID:40828051]. Loss of ALP5b in P. berghei produces small, non-maturing oocysts, defective DNA segregation during male gametogenesis, and a block in malaria transmission [PMID:41218080]. ALP5b is genetically redundant with ALP5a for viability — single deletion is tolerated for blood-stage growth and gametocyte development, whereas simultaneous deletion of both paralogs is lethal [PMID:41218080]. All direct evidence derives from the P. berghei ortholog; no biochemical reconstitution or activity data for ALP5b itself has been characterized in the available corpus.","teleology":[{"year":2025,"claim":"Establishing that ALP5b is a bona fide component of a Plasmodium Arp2/3-like complex answered whether this actin-like protein has a defined molecular assembly and position within it.","evidence":"Reciprocal Co-IP of GFP-tagged ARPC1 from activated male gametocytes plus AlphaFold multimer and DALI structural prediction, in P. berghei","pmids":["40514561"],"confidence":"Medium","gaps":["No in vitro reconstitution or mutagenesis confirming the predicted ARP2 position","Structural placement rests on prediction, not experimental structure","Actin-nucleating activity of the complex not demonstrated for ALP5b"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"claim":"Localization and paralog-interaction studies defined where ALP5b acts and revealed genetic redundancy, answering whether ALP5b is individually essential.","evidence":"Single and double genetic knockouts, fluorescence localization, and Co-IP in P. berghei male gametocytes","pmids":["41218080"],"confidence":"Medium","gaps":["Molecular basis of ALP5a–ALP5b redundancy not resolved","Whether the two paralogs occupy the same complex or distinct complexes is unclear","Synthetic lethality mechanism unknown"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"claim":"Phenotyping ALP5b deletion connected the complex to a specific cellular process, showing ALP5b is required for DNA segregation and transmission.","evidence":"Genetic knockout with oocyst size measurement, genetic crosses, and microscopy of male gametogenesis in P. berghei","pmids":["41218080"],"confidence":"Medium","gaps":["Direct molecular link between ALP5b loss and DNA mis-segregation not defined","Whether the oocyst defect is cell-autonomous to the male lineage untested at molecular level"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2025,"claim":"Spindle localization and the AKiT7 interaction pinned the complex's function to kinetochore-spindle attachment, explaining the DNA segregation defect mechanistically.","evidence":"Co-IP, fluorescence localization to endomitotic spindles, and genetic disruption with kinetochore-spindle association assay in P. berghei","pmids":["40514561","40828051"],"confidence":"Medium","gaps":["Whether ALP5b specifically (vs other subunits) contacts AKiT7 not resolved","Nuclear actin polymerization at the spindle not directly visualized for ALP5b","Mechanism coupling actin dynamics to kinetochore attachment unknown"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":null,"claim":"Whether the ARP2-position assignment, actin-nucleating activity, and P. falciparum function of ALP5b hold biochemically remains open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No in vitro reconstitution of the ALP5b-containing complex","No experimental structure of ALP5b or its position in the complex","Function shown only in P. berghei; P. falciparum ALP5b not directly assayed"],"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Atypical five-subunit Plasmodium Arp2/3 complex (ALP5b occupies the ARP2 position) [#0, #3]"],"partners":["ARPC1 (CO-IP BAIT IDENTIFYING COMPLEX MEMBERSHIP) [#0]","ALP5A (PARALOG, DIRECT INTERACTOR; DOUBLE DELETION LETHAL) [#1]","AKIT7 (KINETOCHORE-ASSOCIATED PROTEIN, COMPLEX INTERACTOR) [#3]"],"other_free_text":["Structural homolog of human ARP2 by AlphaFold/DALI prediction [#0]","Individually dispensable for blood-stage growth and gametocyte development; required for oocyst maturation and malaria transmission [#1, #2]","All functional evidence derives from the P. berghei ortholog (PBANKA_1007500); P. falciparum ALP5b not directly assayed"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"41218080","id":"PMC_41218080","title":"Plasmodium actin-like proteins are essential for DNA segregation during male gametogenesis and malaria transmission.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/41218080","citation_count":2,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ALP5b"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"42629988","id":"PMC_42629988","title":"Plasmodium Actin-Like Proteins 3 and 5a Are Required for Subsequent Steps of Mosquito Infection.","date":"2026","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/42629988","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["actin-like protein"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40514561","id":"","title":"An atypical Arp2/3 complex is required for Plasmodium DNA segregation and malaria transmission.","date":"2025","source":"Nature microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/40514561","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ALP5b"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40828051","id":"","title":"Discovery of an Atypical Arp2/3 Complex in Malaria Parasites Sheds New Light on Nuclear Actin.","date":"2025","source":"Cytoskeleton (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/40828051","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["ALP5b"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5826,"output_tokens":1272,"usd":0.018279,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6129,"output_tokens":2542,"usd":0.047098,"stage2_stop_reason":"end_turn"},"total_usd":0.065377,"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\": 2025,\n      \"finding\": \"ALP5b (PF3D7_0409900 / PBANKA_1007500) was identified as a subunit of an atypical Plasmodium Arp2/3 complex by co-immunoprecipitation of GFP-tagged ARPC1 from activated male gametocytes; AlphaFold structural prediction indicates that ALP5b is structurally similar to human ARP2, and multimer predictions suggest it occupies the ARP2 position within the five-subunit complex.\",\n      \"method\": \"Co-immunoprecipitation (GFP-tag pulldown of ARPC1), AlphaFold structural prediction and DALI structural comparison\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP identifying ALP5b as a partner, supported by orthogonal structural prediction; single lab, no in vitro reconstitution or mutagenesis reported in abstract\",\n      \"pmids\": [\"40514561\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ALP5b (PF3D7_0409900) localizes to the nucleus of male gametocytes and interacts with ALP5a; deletion of ALP5b alone does not affect blood-stage growth, gametocyte development, or actin nucleation, but simultaneous deletion of both ALP5a and ALP5b is lethal to the parasite.\",\n      \"method\": \"Genetic knockout (single and double deletion), fluorescence localization, co-immunoprecipitation\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined viability phenotype plus direct localization experiment, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"41218080\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Deletion of ALP5b (PF3D7_0409900) in P. berghei results in oocysts that are significantly smaller and fail to mature, with defective DNA segregation during male gametogenesis; genetic cross experiments revealed defects in male gamete integrity, establishing that ALP5b is required for proper DNA segregation and malaria transmission.\",\n      \"method\": \"Genetic knockout, oocyst size measurement, genetic crosses, fluorescence microscopy of male gametogenesis\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with specific cellular phenotype (DNA segregation defect) confirmed by genetic crosses, single lab\",\n      \"pmids\": [\"41218080\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The atypical Arp2/3 complex containing ALP5b (PF3D7_0409900/Arp2 homolog) localizes to endomitotic spindles (not the cytoplasm) and interacts with the kinetochore-associated protein AKiT7; disruption of Arp2/3 subunits causes kinetochore-spindle detachment, formation of subhaploid gametes, and transmission blockade, indicating ALP5b participates in nuclear actin polymerization at the mitotic spindle to ensure kinetochore-spindle attachment.\",\n      \"method\": \"Co-immunoprecipitation, fluorescence localization to spindles, genetic disruption with kinetochore-spindle association assay\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization tied to functional consequence (kinetochore detachment phenotype upon disruption), single lab with multiple orthogonal methods\",\n      \"pmids\": [\"40514561\", \"40828051\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium berghei\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"ALP5b (PF3D7_0409900) is a structural homolog of human ARP2 that forms part of an atypical five-subunit Arp2/3 complex in Plasmodium male gametocytes; this complex localizes to endomitotic spindles, interacts with the kinetochore-associated protein AKiT7, and is required for proper kinetochore-spindle attachment and DNA segregation during male gametogenesis, such that its loss causes defective oocyst maturation and blocks malaria transmission.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ALP5b (PF3D7_0409900) is a structural homolog of human ARP2 that serves as a subunit of an atypical five-subunit Arp2/3 complex operating in the nucleus of Plasmodium male gametocytes [#0]. Identified in P. berghei by reciprocal co-immunoprecipitation of GFP-tagged ARPC1, ALP5b is predicted by AlphaFold and DALI to occupy the ARP2 position within the complex [#0], and it directly interacts with its paralog ALP5a [#1]. Rather than acting in the cytoplasm, this complex localizes to endomitotic spindles and associates with the kinetochore-associated protein AKiT7; disruption of Arp2/3 subunits causes kinetochore-spindle detachment and formation of subhaploid gametes, placing ALP5b in nuclear actin polymerization at the mitotic spindle to ensure proper kinetochore-spindle attachment [#3]. Loss of ALP5b in P. berghei produces small, non-maturing oocysts, defective DNA segregation during male gametogenesis, and a block in malaria transmission [#2]. ALP5b is genetically redundant with ALP5a for viability — single deletion is tolerated for blood-stage growth and gametocyte development, whereas simultaneous deletion of both paralogs is lethal [#1]. All direct evidence derives from the P. berghei ortholog; no biochemical reconstitution or activity data for ALP5b itself has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2025,\n      \"claim\": \"Establishing that ALP5b is a bona fide component of a Plasmodium Arp2/3-like complex answered whether this actin-like protein has a defined molecular assembly and position within it.\",\n      \"evidence\": \"Reciprocal Co-IP of GFP-tagged ARPC1 from activated male gametocytes plus AlphaFold multimer and DALI structural prediction, in P. berghei\",\n      \"pmids\": [\"40514561\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No in vitro reconstitution or mutagenesis confirming the predicted ARP2 position\", \"Structural placement rests on prediction, not experimental structure\", \"Actin-nucleating activity of the complex not demonstrated for ALP5b\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Localization and paralog-interaction studies defined where ALP5b acts and revealed genetic redundancy, answering whether ALP5b is individually essential.\",\n      \"evidence\": \"Single and double genetic knockouts, fluorescence localization, and Co-IP in P. berghei male gametocytes\",\n      \"pmids\": [\"41218080\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Molecular basis of ALP5a–ALP5b redundancy not resolved\", \"Whether the two paralogs occupy the same complex or distinct complexes is unclear\", \"Synthetic lethality mechanism unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Phenotyping ALP5b deletion connected the complex to a specific cellular process, showing ALP5b is required for DNA segregation and transmission.\",\n      \"evidence\": \"Genetic knockout with oocyst size measurement, genetic crosses, and microscopy of male gametogenesis in P. berghei\",\n      \"pmids\": [\"41218080\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Direct molecular link between ALP5b loss and DNA mis-segregation not defined\", \"Whether the oocyst defect is cell-autonomous to the male lineage untested at molecular level\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Spindle localization and the AKiT7 interaction pinned the complex's function to kinetochore-spindle attachment, explaining the DNA segregation defect mechanistically.\",\n      \"evidence\": \"Co-IP, fluorescence localization to endomitotic spindles, and genetic disruption with kinetochore-spindle association assay in P. berghei\",\n      \"pmids\": [\"40514561\", \"40828051\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Whether ALP5b specifically (vs other subunits) contacts AKiT7 not resolved\", \"Nuclear actin polymerization at the spindle not directly visualized for ALP5b\", \"Mechanism coupling actin dynamics to kinetochore attachment unknown\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether the ARP2-position assignment, actin-nucleating activity, and P. falciparum function of ALP5b hold biochemically remains open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No in vitro reconstitution of the ALP5b-containing complex\", \"No experimental structure of ALP5b or its position in the complex\", \"Function shown only in P. berghei; P. falciparum ALP5b not directly assayed\"],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005200\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0051015\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005819\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0007059\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0007140\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0008608\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\n      \"Atypical five-subunit Plasmodium Arp2/3 complex (ALP5b occupies the ARP2 position) [#0, #3]\"\n    ],\n    \"partners\": [\n      \"ARPC1 (co-IP bait identifying complex membership) [#0]\",\n      \"ALP5a (paralog, direct interactor; double deletion lethal) [#1]\",\n      \"AKiT7 (kinetochore-associated protein, complex interactor) [#3]\"\n    ],\n    \"other_free_text\": [\n      \"Structural homolog of human ARP2 by AlphaFold/DALI prediction [#0]\",\n      \"Individually dispensable for blood-stage growth and gametocyte development; required for oocyst maturation and malaria transmission [#1, #2]\",\n      \"All functional evidence derives from the P. berghei ortholog (PBANKA_1007500); P. falciparum ALP5b not directly assayed\"\n    ]\n  }\n}\n```","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0409900","name":null,"product":"actin-like protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1007500","name":null,"product":"actin-like protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0308000","name":null,"product":"actin-like protein, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"ALP5b","evaluation":null}