{"gene":"DNAAF2","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2008,"finding":"Ktu/PF13 (DNAAF2) is required for cytoplasmic pre-assembly of both outer and inner dynein arm complexes before intraflagellar transport loads them into the ciliary compartment; in the absence of Ktu/PF13, both outer and inner dynein arms are missing or defective in the axoneme, leading to loss of motility.","method":"Genetic analysis of medaka ktu mutant and Chlamydomonas pf13 mutant; biochemical and immunohistochemical studies in human PCD patient cells; identification of human loss-of-function mutations","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal genetic and biochemical evidence across three organisms (medaka, Chlamydomonas, human), multiple orthogonal methods (immunohistochemistry, biochemistry, genetics), replicated across labs","pmids":["19052621"],"is_preprint":false},{"year":2010,"finding":"PF13/KTU (DNAAF2) contains a PIH (protein interacting with HSP90) domain and is involved in preassembly of outer arm dynein and a specific subset of inner arm dyneins, but not all inner arm dyneins; a distinct PIH family member (MOT48) handles preassembly of a different subset of inner arm dyneins, demonstrating that multiple PIH proteins function in preassembly of different dynein subsets.","method":"Chlamydomonas mutant analysis (ida10/mot48); comparative genomic analysis; axonemal dynein subunit profiling","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function in Chlamydomonas with defined dynein subtype phenotype, replicated and extended by subsequent studies","pmids":["20603327"],"is_preprint":false},{"year":2012,"finding":"DNAAF2 (KTU/PF13) acts at a similar preassembly stage as DNAAF3 (PF22) and DNAAF1 (ODA7/LRRC50); altered abundance of dynein subunits in DNAAF3-null Chlamydomonas cytoplasm places these factors in a conserved, multistep cytoplasmic dynein preassembly pathway.","method":"Chlamydomonas PF22-null mutant analysis; quantification of dynein subunit levels in cytoplasm; epistatic comparison with PF13 and ODA7 mutants","journal":"Nature genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis by comparison of cytoplasmic dynein subunit abundance across multiple Chlamydomonas mutants in a single study","pmids":["22387996"],"is_preprint":false},{"year":2013,"finding":"DYX1C1 (DNAAF4) physically interacts with DNAAF2 (KTU) in the cytoplasm, placing them together in the cytoplasmic ODA and IDA preassembly pathway; DYX1C1's interactome is enriched for molecular chaperones.","method":"Co-immunoprecipitation of DYX1C1 with DNAAF2 in respiratory epithelial cells; interactome analysis enriched for chaperones","journal":"Nature genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP in a single study, but supported by consistent functional data across mouse, zebrafish, and human genetics","pmids":["23872636"],"is_preprint":false},{"year":2016,"finding":"PIH1D3 physically interacts and co-precipitates with cytoplasmic ODA/IDA assembly factors DNAAF2 and DNAAF4, and is required for preassembly of both outer and inner dynein arms, extending the DNAAF2-containing preassembly complex.","method":"Co-immunoprecipitation of PIH1D3 with DNAAF2 and DNAAF4; immunofluorescence and ultrastructural analysis in PIH1D3 loss-of-function patients","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP in patient-derived cells, supported by ultrastructural phenotype and replicated independently in a companion paper (PMID:28176794)","pmids":["28041644"],"is_preprint":false},{"year":2017,"finding":"DNAAF2 is part of a cytoplasmic HSP90 co-chaperone complex analogous to the R2TP complex (DNAAF2-DNAAF4-HSP90) that stabilizes and pre-assembles axonemal dynein arms before their import into cilia; PIH1D3 is part of a complementary R2TP-like HSP90 co-chaperone complex that affects assembly of a subset of inner arm dyneins.","method":"Genomic deletion and point mutation analysis in X-linked PCD patients; complex composition inferred from known DNAAF2-DNAAF4-HSP90 interaction data and PIH1D3 functional studies","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — biochemical complex characterization referenced from prior work; PIH1D3 role established by patient genetics and immunofluorescence in a single study","pmids":["28176794"],"is_preprint":false},{"year":2018,"finding":"During motile ciliogenesis, DNAAF2 belongs to an 'early' phase of preassembly protein expression (together with HEATR2 and SPAG1) that precedes other preassembly proteins and is independent of MCIDAS regulation; DNAAF2 co-localizes with HEATR2 and SPAG1 in perinuclear foci containing dynein arm proteins, and DNAAF2 interacts with SPAG1 as shown by immunoprecipitation and FRET.","method":"Monitoring of ciliogenesis in primary airway epithelial cells and MCIDAS-regulated iPSCs; immunoprecipitation; Förster resonance energy transfer (FRET); HEAT domain deletion analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (IP, FRET, live-cell imaging, domain deletion) in a single rigorous study establishing both interaction and subcellular localization with functional context","pmids":["29358401"],"is_preprint":false},{"year":2018,"finding":"C11orf70 (CFAP300) interacts with DNAAF2 in the cytoplasm and is involved in cytoplasmic assembly of both outer and inner dynein arms, extending the network of DNAAF2-interacting preassembly factors.","method":"Co-immunoprecipitation of C11orf70 with DNAAF2; immunofluorescence and transmission electron microscopy of C11orf70 loss-of-function cilia","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP experiment supported by consistent functional and ultrastructural evidence in patient cells","pmids":["29727693"],"is_preprint":false},{"year":2018,"finding":"Systematic zebrafish mutant analysis of all four PIH proteins (including ktu/DNAAF2) by cryo-electron tomography shows that KTU is required for assembly of specific axonemal dynein subtypes in spermatozoa; loss of ktu causes loss of particular dynein subtypes that correlates with abnormal sperm motility, and different organs show distinct dynein subtype compositions explaining differential ciliary motility phenotypes.","method":"Zebrafish ktu mutant; cryo-electron tomography of axonemal dynein structure in mutant spermatozoa; sperm motility analysis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-electron tomography with direct structural resolution of dynein subtypes in ktu loss-of-function zebrafish, combined with motility phenotype, replicated across all four PIH proteins","pmids":["29741156"],"is_preprint":false},{"year":2019,"finding":"In Chlamydomonas, PF13 (DNAAF2 ortholog) does not form an R2TP-like complex with RuvBL1/2 and RPAP3 (unlike MOT48), but WDR92 physically interacts with PF13 and other DNAAFs, suggesting PF13 participates in dynein preassembly through a distinct, WDR92-linked mechanism.","method":"Immunoprecipitation of WDR92 followed by mass spectrometry; co-immunoprecipitation assays in Chlamydomonas","journal":"Journal of molecular cell biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and mass spectrometry in Chlamydomonas, single lab, establishes both positive interaction (WDR92-PF13) and negative result (PF13 not in R2TP-like complex)","pmids":["30428028"],"is_preprint":false},{"year":2019,"finding":"Homozygous null Dnaaf2 mouse embryos fail to progress beyond organogenesis with left-right patterning defects and other abnormalities, demonstrating that DNAAF2 is an essential in vivo component of cilia function; this recapitulates human PCD.","method":"Characterization of novel null Dnaaf2 allele (from IMPC) on defined C57BL/6NJ background; embryonic phenotyping","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic knockout with defined developmental phenotype in mammalian model, single lab","pmids":["31107948"],"is_preprint":false},{"year":2020,"finding":"In Chlamydomonas, PF13 (DNAAF2 ortholog), MOT48, and TWI1 define partially overlapping but distinct steps in the ciliary dynein preassembly pathway; double mutants (twi1;pf13 and mot48;twi1) show greater dynein assembly and motility defects than single mutants, demonstrating that these PIH proteins have both common and unique functions in preassembly of different ciliary dyneins.","method":"Chlamydomonas double mutant analysis (twi1-1; pf13 and mot48-2; twi1-1); axonemal dynein subunit profiling; motility analysis","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis via double mutant analysis in Chlamydomonas with multiple orthogonal readouts (motility, dynein subunit levels), rigorous controls","pmids":["33141819"],"is_preprint":false},{"year":2021,"finding":"DNAAF2 (KTU) loss-of-function in human males causes complete loss of outer dynein arms (ODAs) in sperm flagella, while some respiratory cilia from the same individual can retain ODAs in the proximal compartment; the cytoplasmic dynein preassembly process governed by DNAAF2 is also critical in sperm, and mutant sperm show significantly reduced flagellar length.","method":"High-speed video microscopy and transmission electron microscopy of sperm from DNAAF2-mutant PCD patients; immunofluorescence comparison of dynein arm composition in sperm vs respiratory cilia","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct structural and functional analysis of patient sperm by TEM and immunofluorescence, single study with multiple orthogonal methods","pmids":["33635866"],"is_preprint":false},{"year":2022,"finding":"The DNAAF4 (DYX1C1) pathogenic variant G373E reduces DNAAF4 protein stability but does not affect its expression or its interaction with DNAAF2, as shown by Co-immunoprecipitation, confirming that the DNAAF4-DNAAF2 physical interaction is maintained even in the presence of this PCD-causing mutation.","method":"Co-immunoprecipitation of DNAAF4 with DNAAF2 after plasmid transfection; Western blot for protein stability; whole-exome sequencing","journal":"Frontiers in genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP experiment in transfected cells, single lab, limited mechanistic follow-up beyond protein stability assessment","pmids":["36583018"],"is_preprint":false}],"current_model":"DNAAF2 (KTU/PF13) is a PIH-domain-containing cytoplasmic protein that functions as part of an HSP90 co-chaperone-like complex (with DNAAF4/DYX1C1 and HSP90, analogous to R2TP) to pre-assemble outer and a specific subset of inner axonemal dynein arm complexes in the cytoplasm before they are loaded onto intraflagellar transport machinery and delivered into cilia and sperm flagella; it belongs to an 'early' ciliogenesis preassembly module together with HEATR2 and SPAG1 that localizes to perinuclear foci, interacts with SPAG1, and acts in partially overlapping but distinct steps from other PIH proteins (MOT48/PIH1D1 and TWI1/PIH1D2), with loss of DNAAF2 causing complete absence of both outer and inner dynein arms in the axoneme, ciliary and flagellar immotility, and primary ciliary dyskinesia with left-right body axis defects and male infertility."},"narrative":{"mechanistic_narrative":"DNAAF2 (KTU/PF13) is a cytoplasmic preassembly factor required to build axonemal dynein arm complexes before they are delivered into motile cilia and sperm flagella [PMID:19052621]. It carries a PIH (protein interacting with HSP90) domain and, with DNAAF4/DYX1C1 and HSP90, forms an R2TP-like co-chaperone complex that stabilizes and assembles outer and inner dynein arms in the cytoplasm [PMID:23872636, PMID:28176794]. Within this preassembly network DNAAF2 physically engages multiple partners — DNAAF4 [PMID:23872636, PMID:36583018], PIH1D3 [PMID:28041644], SPAG1 [PMID:29358401], CFAP300/C11orf70 [PMID:29727693], and WDR92 [PMID:30428028] — and operates in an 'early' module with HEATR2 and SPAG1 that localizes to dynein-containing perinuclear foci ahead of other preassembly proteins [PMID:29358401]. DNAAF2 acts in a multistep, conserved pathway alongside DNAAF1 and DNAAF3, and functions in partially overlapping but distinct steps from other PIH proteins (MOT48/PIH1D1 and TWI1), each handling specific dynein subtypes [PMID:22387996, PMID:33141819]. Loss of DNAAF2 causes absence of both outer and inner dynein arms, ciliary and flagellar immotility, primary ciliary dyskinesia with left-right patterning defects, and male infertility with shortened, dynein-deficient sperm flagella [PMID:19052621, PMID:29741156, PMID:31107948, PMID:33635866].","teleology":[{"year":2008,"claim":"Established that dynein arms are assembled in the cytoplasm before ciliary delivery and identified DNAAF2 as the factor required for this preassembly, defining a new class of ciliary disease genes acting outside the cilium.","evidence":"Genetic analysis of medaka ktu and Chlamydomonas pf13 mutants plus human PCD patient cells and loss-of-function mutations","pmids":["19052621"],"confidence":"High","gaps":["Did not resolve the biochemical composition of the preassembly complex","Mechanism of dynein stabilization not defined"]},{"year":2010,"claim":"Showed DNAAF2 is a PIH-domain protein handling only a subset of dyneins, revealing that distinct PIH proteins partition dynein preassembly into separable substrate classes.","evidence":"Chlamydomonas ida10/mot48 mutant analysis with axonemal dynein subunit profiling and comparative genomics","pmids":["20603327"],"confidence":"High","gaps":["Which specific dynein subunits DNAAF2 directly binds not identified","Biochemical basis of subset specificity unknown"]},{"year":2012,"claim":"Placed DNAAF2 within a conserved multistep cytoplasmic preassembly pathway alongside DNAAF1 and DNAAF3 via cytoplasmic dynein subunit abundance.","evidence":"Chlamydomonas PF22-null mutant analysis with quantification of cytoplasmic dynein subunit levels and epistatic comparison","pmids":["22387996"],"confidence":"Medium","gaps":["Step order among DNAAF1/2/3 not strictly defined","Direct physical interactions among the factors not tested here"]},{"year":2013,"claim":"Demonstrated a direct DNAAF2–DNAAF4 cytoplasmic interaction and a chaperone-enriched interactome, framing DNAAF2 within a co-chaperone assembly machine.","evidence":"Co-immunoprecipitation of DYX1C1/DNAAF4 with DNAAF2 in respiratory epithelial cells with interactome analysis","pmids":["23872636"],"confidence":"Medium","gaps":["Single Co-IP","Stoichiometry and assembled complex architecture not determined"]},{"year":2017,"claim":"Defined the DNAAF2–DNAAF4–HSP90 module as an R2TP-like HSP90 co-chaperone complex and distinguished it from a complementary PIH1D3 complex acting on inner-arm dyneins.","evidence":"Genomic deletion/point mutation analysis in X-linked PCD patients with complex composition inferred from prior interaction data and PIH1D3 functional studies","pmids":["28176794"],"confidence":"Medium","gaps":["R2TP-like architecture inferred rather than reconstituted","Division of labor between the two co-chaperone complexes not mechanistically resolved"]},{"year":2016,"claim":"Extended the DNAAF2 preassembly complex by showing PIH1D3 co-precipitates with DNAAF2 and DNAAF4 and is required for both outer and inner arm assembly.","evidence":"Co-immunoprecipitation of PIH1D3 with DNAAF2/DNAAF4 plus immunofluorescence and ultrastructure in patient cells","pmids":["28041644"],"confidence":"Medium","gaps":["Whether PIH1D3 and DNAAF2 occupy the same or separate complexes not resolved","Direct vs indirect binding not distinguished"]},{"year":2018,"claim":"Identified DNAAF2 as a member of an 'early', MCIDAS-independent preassembly module with HEATR2 and SPAG1, localizing to perinuclear dynein-containing foci, defining temporal and spatial organization of preassembly.","evidence":"Ciliogenesis monitoring in airway epithelial cells and iPSCs, IP, FRET, and HEAT-domain deletion","pmids":["29358401"],"confidence":"High","gaps":["Function of the perinuclear foci not mechanistically defined","Order of assembly events within the early module unresolved"]},{"year":2018,"claim":"Added CFAP300/C11orf70 as a cytoplasmic DNAAF2 interactor required for assembly of both dynein arm types, broadening the interaction network.","evidence":"Co-immunoprecipitation of C11orf70 with DNAAF2 plus immunofluorescence and TEM of patient cilia","pmids":["29727693"],"confidence":"Medium","gaps":["Single Co-IP","Position of CFAP300 in the assembly sequence not established"]},{"year":2018,"claim":"Used cryo-electron tomography to directly link DNAAF2 loss to absence of specific dynein subtypes and tissue-specific motility phenotypes, connecting molecular substrate specificity to organ-level outcomes.","evidence":"Zebrafish ktu mutant with cryo-ET of axonemal dynein and sperm motility analysis","pmids":["29741156"],"confidence":"High","gaps":["Direct DNAAF2 binding to the affected dynein subtypes not shown","How subtype specificity is encoded remains open"]},{"year":2019,"claim":"Showed the DNAAF2 ortholog does not form a canonical R2TP-like complex but interacts with WDR92, indicating a distinct preassembly mechanism for DNAAF2 versus MOT48.","evidence":"WDR92 immunoprecipitation/mass spectrometry and Co-IP in Chlamydomonas","pmids":["30428028"],"confidence":"Medium","gaps":["Functional role of WDR92–PF13 interaction not defined","Reconciliation with the human R2TP-like model unresolved"]},{"year":2019,"claim":"Demonstrated that DNAAF2 is essential in vivo in mammals, with null embryos failing organogenesis and showing left-right defects, validating it as a disease-relevant ciliary factor.","evidence":"Characterization of a null Dnaaf2 mouse allele with embryonic phenotyping","pmids":["31107948"],"confidence":"Medium","gaps":["Tissue-specific molecular consequences not dissected","Single lab"]},{"year":2020,"claim":"Genetic double-mutant epistasis defined DNAAF2, MOT48, and TWI1 as having both shared and unique steps, refining the substrate division among PIH preassembly factors.","evidence":"Chlamydomonas double-mutant analysis with dynein subunit profiling and motility readouts","pmids":["33141819"],"confidence":"High","gaps":["Molecular basis of the overlapping vs unique functions not identified","Direct substrate handoff not visualized"]},{"year":2021,"claim":"Showed DNAAF2 governs dynein preassembly in human sperm, with mutant flagella losing outer dynein arms and shortening, while respiratory cilia can retain proximal ODAs, revealing tissue-differential consequences.","evidence":"High-speed video microscopy, TEM, and immunofluorescence of sperm vs respiratory cilia from DNAAF2-mutant patients","pmids":["33635866"],"confidence":"Medium","gaps":["Basis for tissue-differential ODA retention not explained","Single study"]},{"year":2022,"claim":"Found a PCD-causing DNAAF4 variant destabilizes DNAAF4 protein without disrupting the DNAAF2–DNAAF4 interaction, pinpointing protein stability rather than complex assembly as a disease mechanism.","evidence":"Co-immunoprecipitation in transfected cells, Western blot stability assay, and whole-exome sequencing","pmids":["36583018"],"confidence":"Low","gaps":["Single Co-IP in transfected cells, not endogenous","Downstream consequence for dynein assembly not tested"]},{"year":null,"claim":"How DNAAF2 directly recognizes and chaperones specific dynein heavy/intermediate chains, and how it coordinates with HSP90, WDR92, and the other DNAAFs at the structural level, remains undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No reconstituted DNAAF2–dynein complex or structure","Mechanism of substrate selectivity unresolved","Reconciliation of R2TP-like vs WDR92-linked models open"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[3,5]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,6]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[3,5]}],"complexes":["R2TP-like HSP90 co-chaperone complex (DNAAF2-DNAAF4-HSP90)","cytoplasmic dynein arm preassembly complex"],"partners":["DNAAF4","PIH1D3","SPAG1","HEATR2","CFAP300","WDR92","HSP90"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NVR5","full_name":"Protein kintoun","aliases":["Dynein assembly factor 2, axonemal"],"length_aa":837,"mass_kda":91.1,"function":"Required for cytoplasmic pre-assembly of axonemal dyneins, thereby playing a central role in motility in cilia and flagella. Involved in pre-assembly of dynein arm complexes in the cytoplasm before intraflagellar transport loads them for the ciliary compartment","subcellular_location":"Cytoplasm; Dynein axonemal particle","url":"https://www.uniprot.org/uniprotkb/Q9NVR5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DNAAF2","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DNAAF2","total_profiled":1310},"omim":[{"mim_id":"618058","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 300; CFAP300","url":"https://www.omim.org/entry/618058"},{"mim_id":"612518","title":"CILIARY DYSKINESIA, PRIMARY, 10; CILD10","url":"https://www.omim.org/entry/612518"},{"mim_id":"612517","title":"DYNEIN, AXONEMAL, ASSEMBLY FACTOR 2; DNAAF2","url":"https://www.omim.org/entry/612517"},{"mim_id":"608706","title":"DYNEIN, AXONEMAL, ASSEMBLY FACTOR 4; DNAAF4","url":"https://www.omim.org/entry/608706"},{"mim_id":"300933","title":"DYNEIN, AXONEMAL, ASSEMBLY FACTOR 6; DNAAF6","url":"https://www.omim.org/entry/300933"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Basal body","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Nucleoli","reliability":"Additional"},{"location":"Golgi apparatus","reliability":"Additional"},{"location":"Primary cilium","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DNAAF2"},"hgnc":{"alias_symbol":["FLJ10563","KTU","pf13","CILD10"],"prev_symbol":["C14orf104"]},"alphafold":{"accession":"Q9NVR5","domains":[{"cath_id":"-","chopping":"69-103_120-205","consensus_level":"high","plddt":93.0803,"start":69,"end":205},{"cath_id":"2.60.40.790","chopping":"256-348","consensus_level":"high","plddt":89.3813,"start":256,"end":348},{"cath_id":"2.60.40.790","chopping":"526-636","consensus_level":"high","plddt":91.6686,"start":526,"end":636}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NVR5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NVR5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NVR5-F1-predicted_aligned_error_v6.png","plddt_mean":64.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DNAAF2","jax_strain_url":"https://www.jax.org/strain/search?query=DNAAF2"},"sequence":{"accession":"Q9NVR5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NVR5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NVR5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NVR5"}},"corpus_meta":[{"pmid":"19052621","id":"PMC_19052621","title":"Ktu/PF13 is required for cytoplasmic pre-assembly of axonemal dyneins.","date":"2008","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/19052621","citation_count":293,"is_preprint":false},{"pmid":"23872636","id":"PMC_23872636","title":"DYX1C1 is required for axonemal dynein assembly and ciliary motility.","date":"2013","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23872636","citation_count":222,"is_preprint":false},{"pmid":"22387996","id":"PMC_22387996","title":"Mutations in axonemal dynein assembly factor DNAAF3 cause primary ciliary dyskinesia.","date":"2012","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22387996","citation_count":212,"is_preprint":false},{"pmid":"8244002","id":"PMC_8244002","title":"Cloning of flagellar genes in Chlamydomonas reinhardtii by DNA insertional mutagenesis.","date":"1993","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8244002","citation_count":191,"is_preprint":false},{"pmid":"24335496","id":"PMC_24335496","title":"Molecular evidence for the localization of Plasmodium falciparum immature gametocytes in bone marrow.","date":"2013","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/24335496","citation_count":134,"is_preprint":false},{"pmid":"28176794","id":"PMC_28176794","title":"X-linked primary ciliary dyskinesia due to mutations in the cytoplasmic axonemal dynein assembly factor PIH1D3.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/28176794","citation_count":120,"is_preprint":false},{"pmid":"28041644","id":"PMC_28041644","title":"Mutations in PIH1D3 Cause X-Linked Primary Ciliary Dyskinesia with Outer and Inner Dynein Arm Defects.","date":"2016","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28041644","citation_count":112,"is_preprint":false},{"pmid":"17492602","id":"PMC_17492602","title":"Features of apoptosis in Plasmodium falciparum erythrocytic stage through a putative role of PfMCA1 metacaspase-like protein.","date":"2007","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/17492602","citation_count":91,"is_preprint":false},{"pmid":"25404021","id":"PMC_25404021","title":"Mutations in Plasmodium falciparum K13 propeller gene from Bangladesh (2009-2013).","date":"2014","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/25404021","citation_count":79,"is_preprint":false},{"pmid":"29358401","id":"PMC_29358401","title":"Establishment of the early cilia preassembly protein complex during motile ciliogenesis.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/29358401","citation_count":67,"is_preprint":false},{"pmid":"33635866","id":"PMC_33635866","title":"Defects in the cytoplasmic assembly of axonemal dynein arms cause morphological abnormalities and dysmotility in sperm cells leading to male infertility.","date":"2021","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33635866","citation_count":67,"is_preprint":false},{"pmid":"20603327","id":"PMC_20603327","title":"Discrete PIH proteins function in the cytoplasmic preassembly of different subsets of axonemal dyneins.","date":"2010","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/20603327","citation_count":61,"is_preprint":false},{"pmid":"29741156","id":"PMC_29741156","title":"Systematic studies of all PIH proteins in zebrafish reveal their distinct roles in axonemal dynein assembly.","date":"2018","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/29741156","citation_count":54,"is_preprint":false},{"pmid":"29727693","id":"PMC_29727693","title":"Mutations in C11orf70 Cause Primary Ciliary Dyskinesia with Randomization of Left/Right Body Asymmetry Due to Defects of Outer and Inner Dynein Arms.","date":"2018","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29727693","citation_count":53,"is_preprint":false},{"pmid":"22154137","id":"PMC_22154137","title":"Ciliary motility: the components and cytoplasmic preassembly mechanisms of the axonemal dyneins.","date":"2011","source":"Differentiation; research in biological diversity","url":"https://pubmed.ncbi.nlm.nih.gov/22154137","citation_count":51,"is_preprint":false},{"pmid":"22388867","id":"PMC_22388867","title":"Hydrophobin genes of the entomopathogenic fungus, Metarhizium brunneum, are differentially expressed and corresponding mutants are decreased in virulence.","date":"2012","source":"Current genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22388867","citation_count":49,"is_preprint":false},{"pmid":"32188438","id":"PMC_32188438","title":"Deletion of genomic islands in the Pseudomonas putida KT2440 genome can create an optimal chassis for synthetic biology applications.","date":"2020","source":"Microbial cell factories","url":"https://pubmed.ncbi.nlm.nih.gov/32188438","citation_count":38,"is_preprint":false},{"pmid":"3299002","id":"PMC_3299002","title":"The use of operon fusions in studies of the heat-shock response: effects of altered sigma 32 on heat-shock promoter function in Escherichia coli.","date":"1987","source":"Molecular & general genetics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/3299002","citation_count":38,"is_preprint":false},{"pmid":"19492356","id":"PMC_19492356","title":"The motile cilium in development and disease: emerging new insights.","date":"2009","source":"BioEssays : news and reviews in molecular, cellular and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/19492356","citation_count":36,"is_preprint":false},{"pmid":"34331347","id":"PMC_34331347","title":"Genome-wide association studies of preweaning growth and in vivo carcass composition traits in Esme sheep.","date":"2021","source":"Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie","url":"https://pubmed.ncbi.nlm.nih.gov/34331347","citation_count":36,"is_preprint":false},{"pmid":"21298021","id":"PMC_21298021","title":"Allelic diversity of the Plasmodium falciparum erythrocyte membrane protein 1 entails variant-specific red cell surface epitopes.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21298021","citation_count":35,"is_preprint":false},{"pmid":"34582907","id":"PMC_34582907","title":"A promoter engineering-based strategy enhances polyhydroxyalkanoate production in Pseudomonas putida KT2440.","date":"2021","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/34582907","citation_count":34,"is_preprint":false},{"pmid":"28765600","id":"PMC_28765600","title":"Combinatorial metabolic engineering of Pseudomonas putida KT2440 for efficient mineralization of 1,2,3-trichloropropane.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28765600","citation_count":31,"is_preprint":false},{"pmid":"20439955","id":"PMC_20439955","title":"Association of microsatellite variations of Plasmodium falciparum Na+/H+ exchanger (Pfnhe-1) gene with reduced in vitro susceptibility to quinine: lack of confirmation in clinical isolates from Africa.","date":"2010","source":"The American journal of tropical medicine and hygiene","url":"https://pubmed.ncbi.nlm.nih.gov/20439955","citation_count":31,"is_preprint":false},{"pmid":"25326042","id":"PMC_25326042","title":"Comparative analysis of IgG responses to Plasmodium falciparum MSP1p19 and PF13-DBL1α1 using ELISA and a magnetic bead-based duplex assay (MAGPIX®-Luminex) in a Senegalese meso-endemic community.","date":"2014","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/25326042","citation_count":27,"is_preprint":false},{"pmid":"30428028","id":"PMC_30428028","title":"Chlamydomonas WDR92 in association with R2TP-like complex and multiple DNAAFs to regulate ciliary dynein preassembly.","date":"2019","source":"Journal of molecular cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/30428028","citation_count":27,"is_preprint":false},{"pmid":"17452636","id":"PMC_17452636","title":"Characterization of a UBC13 kinase in Plasmodium falciparum.","date":"2007","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/17452636","citation_count":25,"is_preprint":false},{"pmid":"23259643","id":"PMC_23259643","title":"Expression of a type B RIFIN in Plasmodium falciparum merozoites and gametes.","date":"2012","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/23259643","citation_count":24,"is_preprint":false},{"pmid":"20509952","id":"PMC_20509952","title":"Identification of a major rif transcript common to gametocytes and sporozoites of Plasmodium falciparum.","date":"2010","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/20509952","citation_count":24,"is_preprint":false},{"pmid":"20582613","id":"PMC_20582613","title":"SAM domain-dependent activity of PfTKL3, an essential tyrosine kinase-like kinase of the human malaria parasite Plasmodium falciparum.","date":"2010","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/20582613","citation_count":24,"is_preprint":false},{"pmid":"22615315","id":"PMC_22615315","title":"In vitro-reduced susceptibility to artemether in P. falciparum and its association with polymorphisms on transporter genes.","date":"2012","source":"The Journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/22615315","citation_count":23,"is_preprint":false},{"pmid":"19442305","id":"PMC_19442305","title":"The diamidine DB75 targets the nucleus of Plasmodium falciparum.","date":"2009","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/19442305","citation_count":22,"is_preprint":false},{"pmid":"1553969","id":"PMC_1553969","title":"Multicenter study of change in dialysis therapy-maintenance hemodialysis to continuous ambulatory peritoneal dialysis.","date":"1992","source":"American journal of kidney diseases : the official journal of the National Kidney Foundation","url":"https://pubmed.ncbi.nlm.nih.gov/1553969","citation_count":22,"is_preprint":false},{"pmid":"21669011","id":"PMC_21669011","title":"Polymorphism of Plasmodium falciparum Na(+)/H(+) exchanger is indicative of a low in vitro quinine susceptibility in isolates from Viet Nam.","date":"2011","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/21669011","citation_count":20,"is_preprint":false},{"pmid":"26773071","id":"PMC_26773071","title":"Bioaffinity Mass Spectrometry Screening.","date":"2016","source":"Journal of biomolecular screening","url":"https://pubmed.ncbi.nlm.nih.gov/26773071","citation_count":19,"is_preprint":false},{"pmid":"35395277","id":"PMC_35395277","title":"Enhanced production of polyhydroxyalkanoates in Pseudomonas putida KT2440 by a combination of genome streamlining and promoter engineering.","date":"2022","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/35395277","citation_count":19,"is_preprint":false},{"pmid":"29149898","id":"PMC_29149898","title":"Detection of Plasmodium falciparum male and female gametocytes and determination of parasite sex ratio in human endemic populations by novel, cheap and robust RTqPCR assays.","date":"2017","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/29149898","citation_count":19,"is_preprint":false},{"pmid":"34269931","id":"PMC_34269931","title":"Screening and characterization of hypothetical proteins of Plasmodium falciparum as novel vaccine candidates in the fight against malaria using reverse vaccinology.","date":"2021","source":"Journal, genetic engineering & biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/34269931","citation_count":19,"is_preprint":false},{"pmid":"33141819","id":"PMC_33141819","title":"Mutations in PIH proteins MOT48, TWI1 and PF13 define common and unique steps for preassembly of each, different ciliary dynein.","date":"2020","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33141819","citation_count":16,"is_preprint":false},{"pmid":"7542875","id":"PMC_7542875","title":"Cytochrome P450 genes expressed in porcine ovaries: identification of novel forms, evidence for gene conversion, and evolutionary relationships.","date":"1995","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/7542875","citation_count":14,"is_preprint":false},{"pmid":"34753648","id":"PMC_34753648","title":"Development of a novel promoter engineering-based strategy for creating an efficient para-nitrophenol-mineralizing bacterium.","date":"2021","source":"Journal of hazardous materials","url":"https://pubmed.ncbi.nlm.nih.gov/34753648","citation_count":13,"is_preprint":false},{"pmid":"20493843","id":"PMC_20493843","title":"Plasmodium falciparum: nitric oxide modulates heme speciation in isolated food vacuoles.","date":"2010","source":"Experimental parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/20493843","citation_count":13,"is_preprint":false},{"pmid":"31422234","id":"PMC_31422234","title":"Assessment of predatory bacteria and prey interactions using culture-based methods and EMA-qPCR.","date":"2019","source":"Microbiological research","url":"https://pubmed.ncbi.nlm.nih.gov/31422234","citation_count":12,"is_preprint":false},{"pmid":"31107948","id":"PMC_31107948","title":"A null allele of Dnaaf2 displays embryonic lethality and mimics human ciliary dyskinesia.","date":"2019","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31107948","citation_count":10,"is_preprint":false},{"pmid":"32638265","id":"PMC_32638265","title":"Novel compound heterozygous DNAAF2 mutations cause primary ciliary dyskinesia in a Han Chinese family.","date":"2020","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32638265","citation_count":10,"is_preprint":false},{"pmid":"37678685","id":"PMC_37678685","title":"Metabolic engineering of genome-streamlined strain Pseudomonas putida KTU-U27 for medium-chain-length polyhydroxyalkanoate production from xylose and cellobiose.","date":"2023","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/37678685","citation_count":10,"is_preprint":false},{"pmid":"38471353","id":"PMC_38471353","title":"Unveiling potential repurposed drug candidates for Plasmodium falciparum through in silico evaluation: A synergy of structure-based approaches, structure prediction, and molecular dynamics simulations.","date":"2024","source":"Computational biology and chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/38471353","citation_count":9,"is_preprint":false},{"pmid":"35239159","id":"PMC_35239159","title":"Novel Gene Variants Associated with Primary Ciliary Dyskinesia.","date":"2022","source":"Indian journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/35239159","citation_count":8,"is_preprint":false},{"pmid":"39004944","id":"PMC_39004944","title":"Genetics of 67 patients of suspected primary ciliary dyskinesia from India.","date":"2024","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39004944","citation_count":7,"is_preprint":false},{"pmid":"35456843","id":"PMC_35456843","title":"Interaction of Bdellovibrio bacteriovorus with Gram-Negative and Gram-Positive Bacteria in Dual Species and Polymicrobial Communities.","date":"2022","source":"Microorganisms","url":"https://pubmed.ncbi.nlm.nih.gov/35456843","citation_count":7,"is_preprint":false},{"pmid":"37001652","id":"PMC_37001652","title":"Creating an efficient 1,2-dichloroethane-mineralizing bacterium by a combination of pathway engineering and promoter engineering.","date":"2023","source":"The Science of the total environment","url":"https://pubmed.ncbi.nlm.nih.gov/37001652","citation_count":7,"is_preprint":false},{"pmid":"23274650","id":"PMC_23274650","title":"Co-expression network with protein-protein interaction and transcription regulation in malaria parasite Plasmodium falciparum.","date":"2012","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/23274650","citation_count":7,"is_preprint":false},{"pmid":"23208889","id":"PMC_23208889","title":"Plasmodium falciparum Na+/H+ exchanger (pfnhe-1) genetic polymorphism in Indian Ocean malaria-endemic areas.","date":"2012","source":"The American journal of tropical medicine and hygiene","url":"https://pubmed.ncbi.nlm.nih.gov/23208889","citation_count":6,"is_preprint":false},{"pmid":"36583018","id":"PMC_36583018","title":"Homozygous mutation in DNAAF4 causes primary ciliary dyskinesia in a Chinese family.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36583018","citation_count":3,"is_preprint":false},{"pmid":"34252604","id":"PMC_34252604","title":"A transcriptome-wide association study to detect novel genes for volumetric bone mineral density.","date":"2021","source":"Bone","url":"https://pubmed.ncbi.nlm.nih.gov/34252604","citation_count":3,"is_preprint":false},{"pmid":"27489776","id":"PMC_27489776","title":"A cross strain Plasmodium falciparum microarray optimized for the transcriptome analysis of Plasmodium falciparum patient derived isolates.","date":"2016","source":"Genomics data","url":"https://pubmed.ncbi.nlm.nih.gov/27489776","citation_count":3,"is_preprint":false},{"pmid":"29627593","id":"PMC_29627593","title":"Quantification of receptor activation by oxytocin and vasopressin in endocytosis-coupled bioluminescence reduction assay using nanoKAZ.","date":"2018","source":"Analytical biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29627593","citation_count":2,"is_preprint":false},{"pmid":"40372413","id":"PMC_40372413","title":"Systems Metabolic Engineering of Genome-Reduced Pseudomonas putida for Efficient Production of Polyhydroxyalkanoate from p-Coumaric Acid.","date":"2025","source":"Journal of agricultural and food chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40372413","citation_count":2,"is_preprint":false},{"pmid":"39884036","id":"PMC_39884036","title":"Creating a multifunctional degrader for co-mineralization of p-nitrophenol and 1,2-dichloroethane and its application in wastewater bioremediation.","date":"2025","source":"Journal of hazardous materials","url":"https://pubmed.ncbi.nlm.nih.gov/39884036","citation_count":2,"is_preprint":false},{"pmid":"1528199","id":"PMC_1528199","title":"Identification of invasive Yersinia species using oligonucleotide probes.","date":"1992","source":"Molecular and cellular probes","url":"https://pubmed.ncbi.nlm.nih.gov/1528199","citation_count":2,"is_preprint":false},{"pmid":"38939125","id":"PMC_38939125","title":"Evaluation of the antiviral activity of new dermaseptin analogs against Zika virus.","date":"2024","source":"Biochemistry and biophysics reports","url":"https://pubmed.ncbi.nlm.nih.gov/38939125","citation_count":1,"is_preprint":false},{"pmid":"40386398","id":"PMC_40386398","title":"Smoothened Inhibitor, PF-04449913 Inhibits the Development of Myelofibrosis in a JAK2V617F Transgenic Mouse Model by Reducing TGF-β and MAPK Signaling Pathways.","date":"2025","source":"Research square","url":"https://pubmed.ncbi.nlm.nih.gov/40386398","citation_count":1,"is_preprint":false},{"pmid":"40584616","id":"PMC_40584616","title":"Clinical features and genetic spectrum of children with primary ciliary dyskinesia in central China: a referral center retrospective analysis.","date":"2025","source":"Frontiers in pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/40584616","citation_count":0,"is_preprint":false},{"pmid":"41267578","id":"PMC_41267578","title":"Prevalence and Nationality Distribution of Known and Novel Genetic Variants in Children With Primary Ciliary Dyskinesia in the State of Qatar.","date":"2025","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41267578","citation_count":0,"is_preprint":false},{"pmid":"30266219","id":"PMC_30266219","title":"Reading disability due to an ocular motor disorder: A case of an adolescent girl with a previous diagnosis of dyslexia.","date":"2018","source":"Brain & development","url":"https://pubmed.ncbi.nlm.nih.gov/30266219","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":34589,"output_tokens":3850,"usd":0.080758,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11455,"output_tokens":4214,"usd":0.081312,"stage2_stop_reason":"end_turn"},"total_usd":0.16207,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2008,\n      \"finding\": \"Ktu/PF13 (DNAAF2) is required for cytoplasmic pre-assembly of both outer and inner dynein arm complexes before intraflagellar transport loads them into the ciliary compartment; in the absence of Ktu/PF13, both outer and inner dynein arms are missing or defective in the axoneme, leading to loss of motility.\",\n      \"method\": \"Genetic analysis of medaka ktu mutant and Chlamydomonas pf13 mutant; biochemical and immunohistochemical studies in human PCD patient cells; identification of human loss-of-function mutations\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal genetic and biochemical evidence across three organisms (medaka, Chlamydomonas, human), multiple orthogonal methods (immunohistochemistry, biochemistry, genetics), replicated across labs\",\n      \"pmids\": [\"19052621\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PF13/KTU (DNAAF2) contains a PIH (protein interacting with HSP90) domain and is involved in preassembly of outer arm dynein and a specific subset of inner arm dyneins, but not all inner arm dyneins; a distinct PIH family member (MOT48) handles preassembly of a different subset of inner arm dyneins, demonstrating that multiple PIH proteins function in preassembly of different dynein subsets.\",\n      \"method\": \"Chlamydomonas mutant analysis (ida10/mot48); comparative genomic analysis; axonemal dynein subunit profiling\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function in Chlamydomonas with defined dynein subtype phenotype, replicated and extended by subsequent studies\",\n      \"pmids\": [\"20603327\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"DNAAF2 (KTU/PF13) acts at a similar preassembly stage as DNAAF3 (PF22) and DNAAF1 (ODA7/LRRC50); altered abundance of dynein subunits in DNAAF3-null Chlamydomonas cytoplasm places these factors in a conserved, multistep cytoplasmic dynein preassembly pathway.\",\n      \"method\": \"Chlamydomonas PF22-null mutant analysis; quantification of dynein subunit levels in cytoplasm; epistatic comparison with PF13 and ODA7 mutants\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis by comparison of cytoplasmic dynein subunit abundance across multiple Chlamydomonas mutants in a single study\",\n      \"pmids\": [\"22387996\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DYX1C1 (DNAAF4) physically interacts with DNAAF2 (KTU) in the cytoplasm, placing them together in the cytoplasmic ODA and IDA preassembly pathway; DYX1C1's interactome is enriched for molecular chaperones.\",\n      \"method\": \"Co-immunoprecipitation of DYX1C1 with DNAAF2 in respiratory epithelial cells; interactome analysis enriched for chaperones\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP in a single study, but supported by consistent functional data across mouse, zebrafish, and human genetics\",\n      \"pmids\": [\"23872636\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PIH1D3 physically interacts and co-precipitates with cytoplasmic ODA/IDA assembly factors DNAAF2 and DNAAF4, and is required for preassembly of both outer and inner dynein arms, extending the DNAAF2-containing preassembly complex.\",\n      \"method\": \"Co-immunoprecipitation of PIH1D3 with DNAAF2 and DNAAF4; immunofluorescence and ultrastructural analysis in PIH1D3 loss-of-function patients\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP in patient-derived cells, supported by ultrastructural phenotype and replicated independently in a companion paper (PMID:28176794)\",\n      \"pmids\": [\"28041644\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"DNAAF2 is part of a cytoplasmic HSP90 co-chaperone complex analogous to the R2TP complex (DNAAF2-DNAAF4-HSP90) that stabilizes and pre-assembles axonemal dynein arms before their import into cilia; PIH1D3 is part of a complementary R2TP-like HSP90 co-chaperone complex that affects assembly of a subset of inner arm dyneins.\",\n      \"method\": \"Genomic deletion and point mutation analysis in X-linked PCD patients; complex composition inferred from known DNAAF2-DNAAF4-HSP90 interaction data and PIH1D3 functional studies\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — biochemical complex characterization referenced from prior work; PIH1D3 role established by patient genetics and immunofluorescence in a single study\",\n      \"pmids\": [\"28176794\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"During motile ciliogenesis, DNAAF2 belongs to an 'early' phase of preassembly protein expression (together with HEATR2 and SPAG1) that precedes other preassembly proteins and is independent of MCIDAS regulation; DNAAF2 co-localizes with HEATR2 and SPAG1 in perinuclear foci containing dynein arm proteins, and DNAAF2 interacts with SPAG1 as shown by immunoprecipitation and FRET.\",\n      \"method\": \"Monitoring of ciliogenesis in primary airway epithelial cells and MCIDAS-regulated iPSCs; immunoprecipitation; Förster resonance energy transfer (FRET); HEAT domain deletion analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (IP, FRET, live-cell imaging, domain deletion) in a single rigorous study establishing both interaction and subcellular localization with functional context\",\n      \"pmids\": [\"29358401\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"C11orf70 (CFAP300) interacts with DNAAF2 in the cytoplasm and is involved in cytoplasmic assembly of both outer and inner dynein arms, extending the network of DNAAF2-interacting preassembly factors.\",\n      \"method\": \"Co-immunoprecipitation of C11orf70 with DNAAF2; immunofluorescence and transmission electron microscopy of C11orf70 loss-of-function cilia\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP experiment supported by consistent functional and ultrastructural evidence in patient cells\",\n      \"pmids\": [\"29727693\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Systematic zebrafish mutant analysis of all four PIH proteins (including ktu/DNAAF2) by cryo-electron tomography shows that KTU is required for assembly of specific axonemal dynein subtypes in spermatozoa; loss of ktu causes loss of particular dynein subtypes that correlates with abnormal sperm motility, and different organs show distinct dynein subtype compositions explaining differential ciliary motility phenotypes.\",\n      \"method\": \"Zebrafish ktu mutant; cryo-electron tomography of axonemal dynein structure in mutant spermatozoa; sperm motility analysis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-electron tomography with direct structural resolution of dynein subtypes in ktu loss-of-function zebrafish, combined with motility phenotype, replicated across all four PIH proteins\",\n      \"pmids\": [\"29741156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In Chlamydomonas, PF13 (DNAAF2 ortholog) does not form an R2TP-like complex with RuvBL1/2 and RPAP3 (unlike MOT48), but WDR92 physically interacts with PF13 and other DNAAFs, suggesting PF13 participates in dynein preassembly through a distinct, WDR92-linked mechanism.\",\n      \"method\": \"Immunoprecipitation of WDR92 followed by mass spectrometry; co-immunoprecipitation assays in Chlamydomonas\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and mass spectrometry in Chlamydomonas, single lab, establishes both positive interaction (WDR92-PF13) and negative result (PF13 not in R2TP-like complex)\",\n      \"pmids\": [\"30428028\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Homozygous null Dnaaf2 mouse embryos fail to progress beyond organogenesis with left-right patterning defects and other abnormalities, demonstrating that DNAAF2 is an essential in vivo component of cilia function; this recapitulates human PCD.\",\n      \"method\": \"Characterization of novel null Dnaaf2 allele (from IMPC) on defined C57BL/6NJ background; embryonic phenotyping\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic knockout with defined developmental phenotype in mammalian model, single lab\",\n      \"pmids\": [\"31107948\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In Chlamydomonas, PF13 (DNAAF2 ortholog), MOT48, and TWI1 define partially overlapping but distinct steps in the ciliary dynein preassembly pathway; double mutants (twi1;pf13 and mot48;twi1) show greater dynein assembly and motility defects than single mutants, demonstrating that these PIH proteins have both common and unique functions in preassembly of different ciliary dyneins.\",\n      \"method\": \"Chlamydomonas double mutant analysis (twi1-1; pf13 and mot48-2; twi1-1); axonemal dynein subunit profiling; motility analysis\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis via double mutant analysis in Chlamydomonas with multiple orthogonal readouts (motility, dynein subunit levels), rigorous controls\",\n      \"pmids\": [\"33141819\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DNAAF2 (KTU) loss-of-function in human males causes complete loss of outer dynein arms (ODAs) in sperm flagella, while some respiratory cilia from the same individual can retain ODAs in the proximal compartment; the cytoplasmic dynein preassembly process governed by DNAAF2 is also critical in sperm, and mutant sperm show significantly reduced flagellar length.\",\n      \"method\": \"High-speed video microscopy and transmission electron microscopy of sperm from DNAAF2-mutant PCD patients; immunofluorescence comparison of dynein arm composition in sperm vs respiratory cilia\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct structural and functional analysis of patient sperm by TEM and immunofluorescence, single study with multiple orthogonal methods\",\n      \"pmids\": [\"33635866\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The DNAAF4 (DYX1C1) pathogenic variant G373E reduces DNAAF4 protein stability but does not affect its expression or its interaction with DNAAF2, as shown by Co-immunoprecipitation, confirming that the DNAAF4-DNAAF2 physical interaction is maintained even in the presence of this PCD-causing mutation.\",\n      \"method\": \"Co-immunoprecipitation of DNAAF4 with DNAAF2 after plasmid transfection; Western blot for protein stability; whole-exome sequencing\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP experiment in transfected cells, single lab, limited mechanistic follow-up beyond protein stability assessment\",\n      \"pmids\": [\"36583018\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DNAAF2 (KTU/PF13) is a PIH-domain-containing cytoplasmic protein that functions as part of an HSP90 co-chaperone-like complex (with DNAAF4/DYX1C1 and HSP90, analogous to R2TP) to pre-assemble outer and a specific subset of inner axonemal dynein arm complexes in the cytoplasm before they are loaded onto intraflagellar transport machinery and delivered into cilia and sperm flagella; it belongs to an 'early' ciliogenesis preassembly module together with HEATR2 and SPAG1 that localizes to perinuclear foci, interacts with SPAG1, and acts in partially overlapping but distinct steps from other PIH proteins (MOT48/PIH1D1 and TWI1/PIH1D2), with loss of DNAAF2 causing complete absence of both outer and inner dynein arms in the axoneme, ciliary and flagellar immotility, and primary ciliary dyskinesia with left-right body axis defects and male infertility.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DNAAF2 (KTU/PF13) is a cytoplasmic preassembly factor required to build axonemal dynein arm complexes before they are delivered into motile cilia and sperm flagella [#0]. It carries a PIH (protein interacting with HSP90) domain and, with DNAAF4/DYX1C1 and HSP90, forms an R2TP-like co-chaperone complex that stabilizes and assembles outer and inner dynein arms in the cytoplasm [#3, #5]. Within this preassembly network DNAAF2 physically engages multiple partners — DNAAF4 [#3, #13], PIH1D3 [#4], SPAG1 [#6], CFAP300/C11orf70 [#7], and WDR92 [#9] — and operates in an 'early' module with HEATR2 and SPAG1 that localizes to dynein-containing perinuclear foci ahead of other preassembly proteins [#6]. DNAAF2 acts in a multistep, conserved pathway alongside DNAAF1 and DNAAF3, and functions in partially overlapping but distinct steps from other PIH proteins (MOT48/PIH1D1 and TWI1), each handling specific dynein subtypes [#2, #11]. Loss of DNAAF2 causes absence of both outer and inner dynein arms, ciliary and flagellar immotility, primary ciliary dyskinesia with left-right patterning defects, and male infertility with shortened, dynein-deficient sperm flagella [#0, #8, #10, #12].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established that dynein arms are assembled in the cytoplasm before ciliary delivery and identified DNAAF2 as the factor required for this preassembly, defining a new class of ciliary disease genes acting outside the cilium.\",\n      \"evidence\": \"Genetic analysis of medaka ktu and Chlamydomonas pf13 mutants plus human PCD patient cells and loss-of-function mutations\",\n      \"pmids\": [\"19052621\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the biochemical composition of the preassembly complex\", \"Mechanism of dynein stabilization not defined\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Showed DNAAF2 is a PIH-domain protein handling only a subset of dyneins, revealing that distinct PIH proteins partition dynein preassembly into separable substrate classes.\",\n      \"evidence\": \"Chlamydomonas ida10/mot48 mutant analysis with axonemal dynein subunit profiling and comparative genomics\",\n      \"pmids\": [\"20603327\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which specific dynein subunits DNAAF2 directly binds not identified\", \"Biochemical basis of subset specificity unknown\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Placed DNAAF2 within a conserved multistep cytoplasmic preassembly pathway alongside DNAAF1 and DNAAF3 via cytoplasmic dynein subunit abundance.\",\n      \"evidence\": \"Chlamydomonas PF22-null mutant analysis with quantification of cytoplasmic dynein subunit levels and epistatic comparison\",\n      \"pmids\": [\"22387996\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Step order among DNAAF1/2/3 not strictly defined\", \"Direct physical interactions among the factors not tested here\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Demonstrated a direct DNAAF2–DNAAF4 cytoplasmic interaction and a chaperone-enriched interactome, framing DNAAF2 within a co-chaperone assembly machine.\",\n      \"evidence\": \"Co-immunoprecipitation of DYX1C1/DNAAF4 with DNAAF2 in respiratory epithelial cells with interactome analysis\",\n      \"pmids\": [\"23872636\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single Co-IP\", \"Stoichiometry and assembled complex architecture not determined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined the DNAAF2–DNAAF4–HSP90 module as an R2TP-like HSP90 co-chaperone complex and distinguished it from a complementary PIH1D3 complex acting on inner-arm dyneins.\",\n      \"evidence\": \"Genomic deletion/point mutation analysis in X-linked PCD patients with complex composition inferred from prior interaction data and PIH1D3 functional studies\",\n      \"pmids\": [\"28176794\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"R2TP-like architecture inferred rather than reconstituted\", \"Division of labor between the two co-chaperone complexes not mechanistically resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Extended the DNAAF2 preassembly complex by showing PIH1D3 co-precipitates with DNAAF2 and DNAAF4 and is required for both outer and inner arm assembly.\",\n      \"evidence\": \"Co-immunoprecipitation of PIH1D3 with DNAAF2/DNAAF4 plus immunofluorescence and ultrastructure in patient cells\",\n      \"pmids\": [\"28041644\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PIH1D3 and DNAAF2 occupy the same or separate complexes not resolved\", \"Direct vs indirect binding not distinguished\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified DNAAF2 as a member of an 'early', MCIDAS-independent preassembly module with HEATR2 and SPAG1, localizing to perinuclear dynein-containing foci, defining temporal and spatial organization of preassembly.\",\n      \"evidence\": \"Ciliogenesis monitoring in airway epithelial cells and iPSCs, IP, FRET, and HEAT-domain deletion\",\n      \"pmids\": [\"29358401\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Function of the perinuclear foci not mechanistically defined\", \"Order of assembly events within the early module unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Added CFAP300/C11orf70 as a cytoplasmic DNAAF2 interactor required for assembly of both dynein arm types, broadening the interaction network.\",\n      \"evidence\": \"Co-immunoprecipitation of C11orf70 with DNAAF2 plus immunofluorescence and TEM of patient cilia\",\n      \"pmids\": [\"29727693\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single Co-IP\", \"Position of CFAP300 in the assembly sequence not established\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Used cryo-electron tomography to directly link DNAAF2 loss to absence of specific dynein subtypes and tissue-specific motility phenotypes, connecting molecular substrate specificity to organ-level outcomes.\",\n      \"evidence\": \"Zebrafish ktu mutant with cryo-ET of axonemal dynein and sperm motility analysis\",\n      \"pmids\": [\"29741156\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct DNAAF2 binding to the affected dynein subtypes not shown\", \"How subtype specificity is encoded remains open\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed the DNAAF2 ortholog does not form a canonical R2TP-like complex but interacts with WDR92, indicating a distinct preassembly mechanism for DNAAF2 versus MOT48.\",\n      \"evidence\": \"WDR92 immunoprecipitation/mass spectrometry and Co-IP in Chlamydomonas\",\n      \"pmids\": [\"30428028\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role of WDR92–PF13 interaction not defined\", \"Reconciliation with the human R2TP-like model unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrated that DNAAF2 is essential in vivo in mammals, with null embryos failing organogenesis and showing left-right defects, validating it as a disease-relevant ciliary factor.\",\n      \"evidence\": \"Characterization of a null Dnaaf2 mouse allele with embryonic phenotyping\",\n      \"pmids\": [\"31107948\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Tissue-specific molecular consequences not dissected\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Genetic double-mutant epistasis defined DNAAF2, MOT48, and TWI1 as having both shared and unique steps, refining the substrate division among PIH preassembly factors.\",\n      \"evidence\": \"Chlamydomonas double-mutant analysis with dynein subunit profiling and motility readouts\",\n      \"pmids\": [\"33141819\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of the overlapping vs unique functions not identified\", \"Direct substrate handoff not visualized\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed DNAAF2 governs dynein preassembly in human sperm, with mutant flagella losing outer dynein arms and shortening, while respiratory cilia can retain proximal ODAs, revealing tissue-differential consequences.\",\n      \"evidence\": \"High-speed video microscopy, TEM, and immunofluorescence of sperm vs respiratory cilia from DNAAF2-mutant patients\",\n      \"pmids\": [\"33635866\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Basis for tissue-differential ODA retention not explained\", \"Single study\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Found a PCD-causing DNAAF4 variant destabilizes DNAAF4 protein without disrupting the DNAAF2–DNAAF4 interaction, pinpointing protein stability rather than complex assembly as a disease mechanism.\",\n      \"evidence\": \"Co-immunoprecipitation in transfected cells, Western blot stability assay, and whole-exome sequencing\",\n      \"pmids\": [\"36583018\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP in transfected cells, not endogenous\", \"Downstream consequence for dynein assembly not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DNAAF2 directly recognizes and chaperones specific dynein heavy/intermediate chains, and how it coordinates with HSP90, WDR92, and the other DNAAFs at the structural level, remains undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No reconstituted DNAAF2–dynein complex or structure\", \"Mechanism of substrate selectivity unresolved\", \"Reconciliation of R2TP-like vs WDR92-linked models open\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"complexes\": [\"R2TP-like HSP90 co-chaperone complex (DNAAF2-DNAAF4-HSP90)\", \"cytoplasmic dynein arm preassembly complex\"],\n    \"partners\": [\"DNAAF4\", \"PIH1D3\", \"SPAG1\", \"HEATR2\", \"CFAP300\", \"WDR92\", \"HSP90\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}