{"gene":"PACRG","run_date":"2026-04-29T11:37:57","timeline":{"discoveries":[{"year":2005,"finding":"PACRG localizes along the full length of the axoneme in Trypanosoma brucei, and simultaneous RNAi knockdown of both T. brucei PACRG homologues causes flagellar paralysis and loss of outer doublet microtubules from the canonical 9+2 formation, establishing PACRG as required for functional stability of axonemal outer doublets in motile and sensory cilia/flagella.","method":"RNAi knockdown, GFP fusion localization, transmission electron microscopy","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 — clean KD with defined structural phenotype plus direct localization; replicated across two paralogs","pmids":["16278296"],"is_preprint":false},{"year":2007,"finding":"PACRG localizes to the inner junction between A- and B-tubules of outer doublet microtubules in Chlamydomonas axonemes, suggesting it is a structural component involved in inter-tubule linkage.","method":"Indirect immunofluorescence, immuno-electron microscopy, Sarkosyl extraction fractionation","journal":"Cell motility and the cytoskeleton","confidence":"High","confidence_rationale":"Tier 2 — direct localization by immunoEM with structural functional consequence; consistent with multiple other studies","pmids":["17654607"],"is_preprint":false},{"year":2007,"finding":"PACRG protein is regulated by the ubiquitin-proteasomal system, is present in Lewy bodies and glial cytoplasmic inclusions in Parkinson's disease and Multiple System Atrophy, and is expressed in astrocytes and pigmented noradrenergic neurons of the locus coeruleus.","method":"Immunohistochemistry, proteasome inhibition assays","journal":"Neurobiology of disease","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, proteasome inhibition plus immunohistochemistry; moderate evidence","pmids":["17590346"],"is_preprint":false},{"year":2008,"finding":"PACRG directly binds to microtubules and α/β-tubulin heterodimers with high affinity, bundles microtubules, and forms branched aggregates with unpolymerized tubulin dimers; the microtubule-binding region is highly conserved across organisms.","method":"Co-sedimentation assay, fluorescence microscopy, in vitro binding","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro reconstitution of tubulin binding; single lab","pmids":["18387367"],"is_preprint":false},{"year":2015,"finding":"MEIG1 and PACRG form a complex in the manchette of elongating spermatids; PACRG recruits MEIG1 to the manchette, MEIG1 stabilizes PACRG against proteasomal degradation, and the complex is required to transport cargo proteins such as SPAG16L to build the sperm flagella.","method":"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence in knockout mice, proteasome inhibition","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, KO mouse phenotype, multiple orthogonal methods; single lab but comprehensive","pmids":["25715396"],"is_preprint":false},{"year":2016,"finding":"PACRG and its interactors form a signaling complex anchored to axonemal doublet microtubules that includes interactions with radial spokes; this complex is part of a regulatory pathway involving the central apparatus, radial spokes, and specific inner dynein arm subforms to control dynein-driven microtubule sliding.","method":"In vitro microtubule sliding assay, biochemical fractionation, Chlamydomonas PACRG mutant analysis","journal":"Cytoskeleton (Hoboken, N.J.)","confidence":"Medium","confidence_rationale":"Tier 2 — in vitro functional assay with mutant axonemes; single lab","pmids":["27770595"],"is_preprint":false},{"year":2016,"finding":"In C. elegans, PACRG localizes to a subset of nonmotile cilia and influences gustatory plasticity via heterotrimeric G-protein signaling, and promotes longevity by acting upstream of the FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling.","method":"C. elegans genetics, behavioral assays, epistasis analysis, localization studies","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 — genetic epistasis with defined pathway placement; single lab","pmids":["27193298"],"is_preprint":false},{"year":2016,"finding":"MEIG1 adopts a unique fold with a large surface for protein interactions; four residues (W50, K57, F66, Y68) forming a contiguous hydrophobic patch are essential for PACRG binding and for stabilizing PACRG in bacteria.","method":"Site-directed mutagenesis, pull-down assays, structural characterization","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 — mutagenesis combined with binding assays defining interaction interface; single lab but multiple mutants","pmids":["26726850"],"is_preprint":false},{"year":2019,"finding":"PACRG and FAP20 together form the inner junction bridge between A- and B-tubules along the length of all nine ciliary doublet microtubules; loss of PACRG and/or FAP20 reduces assembly of inner-arm dynein IDA b and beak-MIP structures, impairs ciliary motility and microtubule sliding velocity, and addition of exogenous PACRG and/or FAP20 to isolated mutant axonemes restores sliding velocity.","method":"Cryo-electron tomography, Chlamydomonas pacrg mutants, in vitro microtubule sliding assay, rescue with exogenous protein","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1 — cryo-ET structural data, functional assay, reconstitution rescue; multiple orthogonal methods","pmids":["31116684"],"is_preprint":false},{"year":2020,"finding":"PACRG promotes TNF-induced NF-κB activation by stabilizing the linear ubiquitin chain assembly complex (LUBAC); upon TNF stimulation PACRG is recruited to the activated TNF receptor complex and interacts with LUBAC components (HOIP, HOIL-1L, SHARPIN); in SHARPIN-deficient cells PACRG functionally replaces SHARPIN, prevents LUBAC destabilization, restores HOIP-dependent linear ubiquitylation, and protects cells from TNF-induced apoptosis.","method":"Co-immunoprecipitation, NF-κB reporter assays, SHARPIN-deficient cell rescue, linear ubiquitylation assays, TNF receptor complex purification","journal":"Science signaling","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, genetic rescue, multiple functional assays; single lab but comprehensive and mechanistically complete","pmids":["32019898"],"is_preprint":false},{"year":2021,"finding":"Crystal structure of human PACRG in complex with MEIG1 reveals a helical repeat fold for PACRG with a loop mediating MEIG1 interaction; PACRG simultaneously binds to axonemal doublet microtubules and recruits free tubulin to catalyze formation of the inner junction, as supported by single-molecule fluorescence microscopy and Chlamydomonas doublet microtubule structural data.","method":"X-ray crystallography, single-molecule fluorescence microscopy, cryo-EM structural comparison","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus single-molecule functional microscopy; mechanistically comprehensive","pmids":["33529594"],"is_preprint":false},{"year":2021,"finding":"Pull-down of PACRG from HEK293T cell lysates followed by LC-MS/MS identified 74 potential interaction partners; GO enrichment analysis indicated that the highest proportion of partners have transcription regulator and transcription factor activity, suggesting a role in transcription regulation.","method":"His6 pull-down, LC-MS/MS, GO enrichment analysis","journal":"Molecules (Basel, Switzerland)","confidence":"Low","confidence_rationale":"Tier 3 — single pull-down MS; no functional validation of interactions","pmids":["33923444"],"is_preprint":false},{"year":2023,"finding":"DNALI1 interacts with PACRG and stabilizes it via co-immunoprecipitation in the manchette; DNALI1-deficient mice show mislocalization of MEIG1, PACRG, and SPAG16L from the manchette, establishing DNALI1 as required for formation of the MEIG1/PACRG complex within the manchette during sperm flagellum assembly.","method":"Co-immunoprecipitation, pull-down assays, conditional KO mouse, immunofluorescence","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP plus KO mouse with defined localization phenotype; mechanistically placed","pmids":["37083624"],"is_preprint":false},{"year":2025,"finding":"DNAH10 bridges the interaction between UCHL3 and PACRG; UCHL3 binds PACRG and stabilizes it via deubiquitination, and DNAH10 enhances this UCHL3-PACRG complex interaction to facilitate intra-manchette transport during spermiogenesis.","method":"Co-immunoprecipitation, pull-down, localization studies in DNAH10-deficient mice","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP and KO mouse with defined phenotype; single lab","pmids":["41058558"],"is_preprint":false},{"year":2025,"finding":"PACRG and FAP20 synergistically stabilize B-tubule dynamics in a cell-free reconstitution system: together they localize to B-tubules in high-density patches, decrease B-tubule depolymerization velocity, increase rescue frequency, and cryo-tomography of in vitro reconstructed doublets reveals reduced B-tubule curvature fluctuations promoting a more rigid conformation.","method":"Cell-free reconstitution, TIRF microscopy, cryo-electron tomography","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with cryo-ET structural validation; preprint but rigorous multimodal approach","pmids":["bio_10.1101_2025.03.12.642377"],"is_preprint":true},{"year":2012,"finding":"PACRG localizes to cilia and is expressed throughout vertebrate embryogenesis in ciliated tissues; loss-of-function by morpholino in Xenopus produces left-right axis defects, neural tube closure defects, and gastrulation defects, with cytoplasmic localization around the nucleus also observed.","method":"Morpholino knockdown, immunofluorescence, GFP fusion live imaging, scanning electron microscopy, in situ hybridization","journal":"Cilia","confidence":"Medium","confidence_rationale":"Tier 2 — KD with defined ciliary phenotype plus direct localization; single lab vertebrate model","pmids":["23351225"],"is_preprint":false}],"current_model":"PACRG is a conserved axonemal inner-junction protein that, together with FAP20, bridges the A- and B-tubules of doublet microtubules to stabilize B-tubule dynamics and support assembly of inner dynein arms; in the manchette of elongating spermatids it forms a complex with MEIG1 (which it recruits and which in turn stabilizes PACRG against proteasomal degradation) and DNALI1 to transport cargo proteins such as SPAG16L for sperm flagellum assembly; outside the cilium, PACRG promotes TNF-induced canonical NF-κB signaling by stabilizing the LUBAC complex and can functionally substitute for SHARPIN to restore linear ubiquitylation."},"narrative":{"teleology":[{"year":2005,"claim":"The fundamental question of whether PACRG has a structural role in cilia was answered when knockdown in Trypanosoma brucei demonstrated that PACRG is required for outer doublet microtubule integrity and flagellar motility, establishing it as a core axonemal component.","evidence":"RNAi knockdown of both PACRG homologues in T. brucei with GFP localization and TEM","pmids":["16278296"],"confidence":"High","gaps":["Precise position within the doublet was unknown","Mechanism of structural contribution unresolved","Mammalian relevance not yet established"]},{"year":2007,"claim":"The question of where exactly PACRG sits within the doublet was resolved by immuno-electron microscopy placing it at the inner junction between A- and B-tubules, defining its structural niche.","evidence":"Immuno-EM and Sarkosyl fractionation of Chlamydomonas axonemes","pmids":["17654607"],"confidence":"High","gaps":["Binding partners at the inner junction not identified","Whether PACRG directly contacts tubulin was untested"]},{"year":2008,"claim":"Whether PACRG directly engages tubulin was answered by in vitro reconstitution showing high-affinity binding to α/β-tubulin heterodimers and microtubule bundling activity, establishing PACRG as a bona fide tubulin-binding protein.","evidence":"Co-sedimentation and fluorescence microscopy with purified tubulin","pmids":["18387367"],"confidence":"Medium","gaps":["In vivo relevance of bundling activity unclear","Binding domain not mapped","No structural data on the PACRG-tubulin interface"]},{"year":2012,"claim":"Whether PACRG functions in vertebrate cilia was established when morpholino knockdown in Xenopus produced left-right asymmetry defects and neural tube closure defects, linking PACRG to developmental ciliopathy phenotypes.","evidence":"Morpholino knockdown in Xenopus with phenotypic scoring and localization","pmids":["23351225"],"confidence":"Medium","gaps":["Morpholino approach lacks genetic knockout confirmation","Downstream signaling pathways not defined","No mammalian loss-of-function model at this point"]},{"year":2015,"claim":"The question of how PACRG participates in spermatogenesis was answered by demonstrating that PACRG and MEIG1 form a manchette complex that transports SPAG16L cargo for flagellum assembly, with reciprocal stabilization between the partners.","evidence":"Yeast two-hybrid, reciprocal co-IP, and knockout mouse analysis with proteasome inhibition","pmids":["25715396"],"confidence":"High","gaps":["Motor driving manchette transport not identified","Full cargo repertoire unknown","Whether other axonemal proteins require this complex was untested"]},{"year":2016,"claim":"Three studies collectively expanded PACRG's functional scope: it was placed within a radial spoke–inner dynein arm regulatory cascade in Chlamydomonas, mapped to a MEIG1 hydrophobic binding interface by mutagenesis, and shown to influence G-protein signaling and longevity in C. elegans nonmotile cilia.","evidence":"Chlamydomonas mutant sliding assays; site-directed mutagenesis with pull-downs; C. elegans epistasis and behavioral assays","pmids":["27770595","26726850","27193298"],"confidence":"Medium","gaps":["C. elegans signaling role not confirmed in mammals","Structural basis of radial spoke interaction unknown","How PACRG couples to G-protein signaling unresolved"]},{"year":2019,"claim":"A central structural question—how the inner junction is built—was resolved by cryo-electron tomography showing that PACRG and FAP20 together constitute the inner junction bridge along all nine doublets, and that their absence specifically impairs inner dynein arm b assembly and ciliary motility.","evidence":"Cryo-ET of Chlamydomonas pacrg mutants, in vitro sliding assay with rescue by exogenous protein","pmids":["31116684"],"confidence":"High","gaps":["Atomic-resolution structure of PACRG in situ not yet available","Mechanism of inner dynein arm recruitment by PACRG/FAP20 unknown"]},{"year":2020,"claim":"An unexpected non-ciliary function was uncovered: PACRG stabilizes the LUBAC ubiquitin ligase complex and promotes TNF-induced NF-κB signaling, functionally substituting for SHARPIN in SHARPIN-deficient cells to restore linear ubiquitylation and suppress apoptosis.","evidence":"Reciprocal co-IP, NF-κB reporter assays, SHARPIN-deficient cell rescue, TNF receptor complex purification","pmids":["32019898"],"confidence":"High","gaps":["Whether PACRG and SHARPIN act redundantly in vivo unknown","How ciliary versus NF-κB functions are partitioned in different tissues unresolved","Structural basis of PACRG–LUBAC interaction not determined"]},{"year":2021,"claim":"The atomic structure of human PACRG–MEIG1 revealed a helical repeat fold and showed that PACRG simultaneously binds doublet microtubules and recruits free tubulin to catalyze inner junction formation, providing the first high-resolution mechanistic model for inner junction biogenesis.","evidence":"X-ray crystallography and single-molecule fluorescence microscopy","pmids":["33529594"],"confidence":"High","gaps":["Full in situ atomic model of PACRG within the doublet not achieved","Whether tubulin recruitment is rate-limiting for inner junction assembly unknown"]},{"year":2023,"claim":"The manchette transport machinery was further defined when DNALI1 was shown to interact with and stabilize PACRG, and its loss caused mislocalization of the entire MEIG1/PACRG/SPAG16L complex, establishing DNALI1 as an upstream organizer.","evidence":"Reciprocal co-IP, conditional knockout mouse, immunofluorescence","pmids":["37083624"],"confidence":"High","gaps":["Motor protein driving the DNALI1–PACRG complex along manchette microtubules not identified","Whether DNALI1 functions as an inner arm dynein light chain in this context is unclear"]},{"year":2025,"claim":"Regulation of PACRG protein levels during spermiogenesis was further elaborated by showing that UCHL3 deubiquitinates and stabilizes PACRG, with DNAH10 bridging the UCHL3–PACRG interaction to facilitate intra-manchette transport.","evidence":"Co-IP, pull-down, localization in DNAH10-deficient mice","pmids":["41058558"],"confidence":"Medium","gaps":["Specific ubiquitin linkage type cleaved by UCHL3 on PACRG not defined","Whether DNAH10 motor activity is required for transport unknown","Single lab finding"]},{"year":null,"claim":"Key unresolved questions include how PACRG's ciliary and NF-κB signaling functions are differentially regulated across tissues, whether PACRG loss causes ciliopathy in mammals, and the complete cargo repertoire transported by the MEIG1–PACRG–DNALI1 manchette complex.","evidence":"","pmids":[],"confidence":"Low","gaps":["No mammalian PACRG knockout phenotype fully characterized","Tissue-specific regulation of ciliary versus NF-κB roles unknown","Complete manchette transport cargo inventory not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[1,3,8,10,14]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,8,10]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[9]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1,5,6,8,15]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[3,4,10,12]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,8,10,14]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[9]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[9]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[4,12,13]}],"complexes":["PACRG-FAP20 inner junction complex","MEIG1-PACRG manchette complex","LUBAC"],"partners":["FAP20","MEIG1","DNALI1","HOIP","HOIL1","SHARPIN","UCHL3","DNAH10"],"other_free_text":[]},"mechanistic_narrative":"PACRG is a conserved axonemal inner-junction protein that, together with FAP20, bridges the A- and B-tubules of ciliary doublet microtubules to stabilize B-tubule dynamics, support inner dynein arm assembly, and enable ciliary motility [PMID:16278296, PMID:17654607, PMID:31116684]. Structurally, PACRG adopts a helical repeat fold, binds both assembled doublet microtubules and free tubulin heterodimers, and catalyzes inner junction formation; its crystal structure with MEIG1 reveals a loop-mediated interaction interface essential for PACRG stability [PMID:33529594, PMID:18387367]. In elongating spermatids, PACRG forms a manchette-associated complex with MEIG1 and DNALI1 that transports cargo proteins such as SPAG16L for sperm flagellum assembly, with MEIG1 stabilizing PACRG against proteasomal degradation and UCHL3/DNAH10 further regulating PACRG levels through deubiquitination [PMID:25715396, PMID:37083624, PMID:41058558]. Outside its ciliary roles, PACRG promotes TNF-induced canonical NF-κB signaling by stabilizing the LUBAC complex, interacting with HOIP, HOIL-1L, and SHARPIN, and functionally substituting for SHARPIN to restore linear ubiquitylation and protect cells from TNF-induced apoptosis [PMID:32019898]."},"prefetch_data":{"uniprot":{"accession":"Q96M98","full_name":"Parkin coregulated gene protein","aliases":["Molecular chaperone/chaperonin-binding protein","PARK2 coregulated gene protein"],"length_aa":296,"mass_kda":33.3,"function":"Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating (PubMed:36191189). Suppresses cell death induced by accumulation of unfolded Pael receptor (Pael-R, a substrate of Parkin) (PubMed:14532270). Facilitates the formation of inclusions consisting of Pael-R, molecular chaperones, protein degradation molecules and itself when proteasome is inhibited (PubMed:14532270). May play an important role in the formation of Lewy bodies and protection of dopaminergic neurons against Parkinson disease (PubMed:14532270)","subcellular_location":"Cytoplasm, cytoskeleton, cilium axoneme; Cytoplasm, cytoskeleton, flagellum axoneme","url":"https://www.uniprot.org/uniprotkb/Q96M98/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PACRG","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PACRG","total_profiled":1310},"omim":[{"mim_id":"614174","title":"MEIOSIS/SPERMIOGENESIS-ASSOCIATED PROTEIN 1; MEIG1","url":"https://www.omim.org/entry/614174"},{"mim_id":"609590","title":"QKI, KH DOMAIN-CONTAINING RNA-BINDING PROTEIN; QKI","url":"https://www.omim.org/entry/609590"},{"mim_id":"608427","title":"PARKIN COREGULATED GENE; PACRG","url":"https://www.omim.org/entry/608427"},{"mim_id":"607572","title":"LEPROSY, SUSCEPTIBILITY TO, 2; LPRS2","url":"https://www.omim.org/entry/607572"},{"mim_id":"606420","title":"ENGULFMENT AND CELL MOTILITY GENE 1; ELMO1","url":"https://www.omim.org/entry/606420"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mid piece","reliability":"Supported"},{"location":"Principal piece","reliability":"Supported"},{"location":"End piece","reliability":"Supported"},{"location":"Mitochondria","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"fallopian tube","ntpm":28.6},{"tissue":"testis","ntpm":23.4}],"url":"https://www.proteinatlas.org/search/PACRG"},"hgnc":{"alias_symbol":["PARK2CRG","FLJ32724","Glup","HAK005771","BUG21","pf12"],"prev_symbol":[]},"alphafold":{"accession":"Q96M98","domains":[{"cath_id":"1.25.40","chopping":"70-202_257-285","consensus_level":"medium","plddt":95.1838,"start":70,"end":285}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96M98","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96M98-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96M98-F1-predicted_aligned_error_v6.png","plddt_mean":76.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PACRG","jax_strain_url":"https://www.jax.org/strain/search?query=PACRG"},"sequence":{"accession":"Q96M98","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96M98.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96M98/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96M98"}},"corpus_meta":[{"pmid":"14737177","id":"PMC_14737177","title":"Susceptibility to leprosy is associated with PARK2 and PACRG.","date":"2004","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/14737177","citation_count":352,"is_preprint":false},{"pmid":"16278296","id":"PMC_16278296","title":"The Parkin co-regulated gene product, PACRG, is an evolutionarily conserved axonemal protein that functions in outer-doublet microtubule morphogenesis.","date":"2005","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/16278296","citation_count":83,"is_preprint":false},{"pmid":"16734611","id":"PMC_16734611","title":"PARK2/PACRG polymorphisms and susceptibility to typhoid and paratyphoid fever.","date":"2006","source":"Clinical and experimental immunology","url":"https://pubmed.ncbi.nlm.nih.gov/16734611","citation_count":69,"is_preprint":false},{"pmid":"30181372","id":"PMC_30181372","title":"Bifunctional Enzyme SpoT Is Involved in Biofilm Formation of Helicobacter pylori with Multidrug Resistance by Upregulating Efflux Pump Hp1174 (gluP).","date":"2018","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/30181372","citation_count":63,"is_preprint":false},{"pmid":"25715396","id":"PMC_25715396","title":"A MEIG1/PACRG complex in the manchette is essential for building the sperm flagella.","date":"2015","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/25715396","citation_count":50,"is_preprint":false},{"pmid":"14743368","id":"PMC_14743368","title":"It's a double knock-out! The quaking mouse is a spontaneous deletion of parkin and parkin co-regulated gene (PACRG).","date":"2004","source":"Movement disorders : official journal of the Movement Disorder Society","url":"https://pubmed.ncbi.nlm.nih.gov/14743368","citation_count":48,"is_preprint":false},{"pmid":"31116684","id":"PMC_31116684","title":"PACRG and FAP20 form the inner junction of axonemal doublet microtubules and regulate ciliary motility.","date":"2019","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/31116684","citation_count":43,"is_preprint":false},{"pmid":"17068781","id":"PMC_17068781","title":"Deletion of the parkin and PACRG gene promoter in early-onset parkinsonism.","date":"2007","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/17068781","citation_count":36,"is_preprint":false},{"pmid":"17654607","id":"PMC_17654607","title":"Axonemal localization of Chlamydomonas PACRG, a homologue of the human Parkin-coregulated gene 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the manchette and is required for proper sperm flagellum assembly in mice.","date":"2023","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/37083624","citation_count":13,"is_preprint":false},{"pmid":"15925106","id":"PMC_15925106","title":"Genetic analysis of parkin co-regulated gene (PACRG) in patients with early-onset parkinsonism.","date":"2005","source":"Neuroscience letters","url":"https://pubmed.ncbi.nlm.nih.gov/15925106","citation_count":12,"is_preprint":false},{"pmid":"23351225","id":"PMC_23351225","title":"Ciliary and non-ciliary expression and function of PACRG during vertebrate development.","date":"2012","source":"Cilia","url":"https://pubmed.ncbi.nlm.nih.gov/23351225","citation_count":12,"is_preprint":false},{"pmid":"32747620","id":"PMC_32747620","title":"Associations of PRKN-PACRG SNPs and G × G and G × E interactions with the risk of hyperlipidaemia.","date":"2020","source":"Scientific 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genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21816242","citation_count":5,"is_preprint":false},{"pmid":"33923444","id":"PMC_33923444","title":"Functional Expression, Purification and Identification of Interaction Partners of PACRG.","date":"2021","source":"Molecules (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/33923444","citation_count":4,"is_preprint":false},{"pmid":"36444670","id":"PMC_36444670","title":"Molecular dynamics study reveals key disruptors of MEIG1-PACRG interaction.","date":"2022","source":"Proteins","url":"https://pubmed.ncbi.nlm.nih.gov/36444670","citation_count":3,"is_preprint":false},{"pmid":"41058558","id":"PMC_41058558","title":"DNAH10 interacts with UCHL3-PACRG complex to coordinate sperm head and flagella development during spermiogenesis.","date":"2025","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/41058558","citation_count":0,"is_preprint":false},{"pmid":"39763986","id":"PMC_39763986","title":"In silico discovery of potential inhibitors targeting the MEIG1-PACRG complex for male contraceptive development.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39763986","citation_count":0,"is_preprint":false},{"pmid":"40265567","id":"PMC_40265567","title":"In Silico Discovery of Potential Inhibitors Targeting the MEIG1-PACRG Complex for Male Contraceptive Development.","date":"2025","source":"Proteins","url":"https://pubmed.ncbi.nlm.nih.gov/40265567","citation_count":0,"is_preprint":false},{"pmid":"28965374","id":"PMC_28965374","title":"[Construction of a GFP-fused mouse PACRG baculovirus recombinant vector and expression of the fusion protein in Sf9 inset cells].","date":"2016","source":"Zhonghua nan ke xue = National journal of andrology","url":"https://pubmed.ncbi.nlm.nih.gov/28965374","citation_count":0,"is_preprint":false},{"pmid":"39845515","id":"PMC_39845515","title":"PACRG is Expressed on the Left Side of the Brain Vesicle in the Ascidian Halocynthia Larva.","date":"2024","source":"Development & reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/39845515","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.12.642377","title":"Cell-free Reconstitution Reveals Synergistic Stabilization of Microtubule Doublets by PACRG and FAP20","date":"2025-03-12","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.12.642377","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":18376,"output_tokens":3556,"usd":0.054234},"stage2":{"model":"claude-opus-4-6","input_tokens":6988,"output_tokens":3030,"usd":0.166035},"total_usd":0.220269,"stage1_batch_id":"msgbatch_012ZiiCUBfB62NCTQd4Bk1Jo","stage2_batch_id":"msgbatch_01Xuqq9aUHoQouS7UVGZNStZ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"PACRG localizes along the full length of the axoneme in Trypanosoma brucei, and simultaneous RNAi knockdown of both T. brucei PACRG homologues causes flagellar paralysis and loss of outer doublet microtubules from the canonical 9+2 formation, establishing PACRG as required for functional stability of axonemal outer doublets in motile and sensory cilia/flagella.\",\n      \"method\": \"RNAi knockdown, GFP fusion localization, transmission electron microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KD with defined structural phenotype plus direct localization; replicated across two paralogs\",\n      \"pmids\": [\"16278296\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PACRG localizes to the inner junction between A- and B-tubules of outer doublet microtubules in Chlamydomonas axonemes, suggesting it is a structural component involved in inter-tubule linkage.\",\n      \"method\": \"Indirect immunofluorescence, immuno-electron microscopy, Sarkosyl extraction fractionation\",\n      \"journal\": \"Cell motility and the cytoskeleton\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct localization by immunoEM with structural functional consequence; consistent with multiple other studies\",\n      \"pmids\": [\"17654607\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PACRG protein is regulated by the ubiquitin-proteasomal system, is present in Lewy bodies and glial cytoplasmic inclusions in Parkinson's disease and Multiple System Atrophy, and is expressed in astrocytes and pigmented noradrenergic neurons of the locus coeruleus.\",\n      \"method\": \"Immunohistochemistry, proteasome inhibition assays\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, proteasome inhibition plus immunohistochemistry; moderate evidence\",\n      \"pmids\": [\"17590346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PACRG directly binds to microtubules and α/β-tubulin heterodimers with high affinity, bundles microtubules, and forms branched aggregates with unpolymerized tubulin dimers; the microtubule-binding region is highly conserved across organisms.\",\n      \"method\": \"Co-sedimentation assay, fluorescence microscopy, in vitro binding\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro reconstitution of tubulin binding; single lab\",\n      \"pmids\": [\"18387367\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"MEIG1 and PACRG form a complex in the manchette of elongating spermatids; PACRG recruits MEIG1 to the manchette, MEIG1 stabilizes PACRG against proteasomal degradation, and the complex is required to transport cargo proteins such as SPAG16L to build the sperm flagella.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence in knockout mice, proteasome inhibition\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, KO mouse phenotype, multiple orthogonal methods; single lab but comprehensive\",\n      \"pmids\": [\"25715396\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PACRG and its interactors form a signaling complex anchored to axonemal doublet microtubules that includes interactions with radial spokes; this complex is part of a regulatory pathway involving the central apparatus, radial spokes, and specific inner dynein arm subforms to control dynein-driven microtubule sliding.\",\n      \"method\": \"In vitro microtubule sliding assay, biochemical fractionation, Chlamydomonas PACRG mutant analysis\",\n      \"journal\": \"Cytoskeleton (Hoboken, N.J.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vitro functional assay with mutant axonemes; single lab\",\n      \"pmids\": [\"27770595\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In C. elegans, PACRG localizes to a subset of nonmotile cilia and influences gustatory plasticity via heterotrimeric G-protein signaling, and promotes longevity by acting upstream of the FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling.\",\n      \"method\": \"C. elegans genetics, behavioral assays, epistasis analysis, localization studies\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with defined pathway placement; single lab\",\n      \"pmids\": [\"27193298\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"MEIG1 adopts a unique fold with a large surface for protein interactions; four residues (W50, K57, F66, Y68) forming a contiguous hydrophobic patch are essential for PACRG binding and for stabilizing PACRG in bacteria.\",\n      \"method\": \"Site-directed mutagenesis, pull-down assays, structural characterization\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — mutagenesis combined with binding assays defining interaction interface; single lab but multiple mutants\",\n      \"pmids\": [\"26726850\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PACRG and FAP20 together form the inner junction bridge between A- and B-tubules along the length of all nine ciliary doublet microtubules; loss of PACRG and/or FAP20 reduces assembly of inner-arm dynein IDA b and beak-MIP structures, impairs ciliary motility and microtubule sliding velocity, and addition of exogenous PACRG and/or FAP20 to isolated mutant axonemes restores sliding velocity.\",\n      \"method\": \"Cryo-electron tomography, Chlamydomonas pacrg mutants, in vitro microtubule sliding assay, rescue with exogenous protein\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-ET structural data, functional assay, reconstitution rescue; multiple orthogonal methods\",\n      \"pmids\": [\"31116684\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PACRG promotes TNF-induced NF-κB activation by stabilizing the linear ubiquitin chain assembly complex (LUBAC); upon TNF stimulation PACRG is recruited to the activated TNF receptor complex and interacts with LUBAC components (HOIP, HOIL-1L, SHARPIN); in SHARPIN-deficient cells PACRG functionally replaces SHARPIN, prevents LUBAC destabilization, restores HOIP-dependent linear ubiquitylation, and protects cells from TNF-induced apoptosis.\",\n      \"method\": \"Co-immunoprecipitation, NF-κB reporter assays, SHARPIN-deficient cell rescue, linear ubiquitylation assays, TNF receptor complex purification\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, genetic rescue, multiple functional assays; single lab but comprehensive and mechanistically complete\",\n      \"pmids\": [\"32019898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Crystal structure of human PACRG in complex with MEIG1 reveals a helical repeat fold for PACRG with a loop mediating MEIG1 interaction; PACRG simultaneously binds to axonemal doublet microtubules and recruits free tubulin to catalyze formation of the inner junction, as supported by single-molecule fluorescence microscopy and Chlamydomonas doublet microtubule structural data.\",\n      \"method\": \"X-ray crystallography, single-molecule fluorescence microscopy, cryo-EM structural comparison\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus single-molecule functional microscopy; mechanistically comprehensive\",\n      \"pmids\": [\"33529594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Pull-down of PACRG from HEK293T cell lysates followed by LC-MS/MS identified 74 potential interaction partners; GO enrichment analysis indicated that the highest proportion of partners have transcription regulator and transcription factor activity, suggesting a role in transcription regulation.\",\n      \"method\": \"His6 pull-down, LC-MS/MS, GO enrichment analysis\",\n      \"journal\": \"Molecules (Basel, Switzerland)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single pull-down MS; no functional validation of interactions\",\n      \"pmids\": [\"33923444\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DNALI1 interacts with PACRG and stabilizes it via co-immunoprecipitation in the manchette; DNALI1-deficient mice show mislocalization of MEIG1, PACRG, and SPAG16L from the manchette, establishing DNALI1 as required for formation of the MEIG1/PACRG complex within the manchette during sperm flagellum assembly.\",\n      \"method\": \"Co-immunoprecipitation, pull-down assays, conditional KO mouse, immunofluorescence\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP plus KO mouse with defined localization phenotype; mechanistically placed\",\n      \"pmids\": [\"37083624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DNAH10 bridges the interaction between UCHL3 and PACRG; UCHL3 binds PACRG and stabilizes it via deubiquitination, and DNAH10 enhances this UCHL3-PACRG complex interaction to facilitate intra-manchette transport during spermiogenesis.\",\n      \"method\": \"Co-immunoprecipitation, pull-down, localization studies in DNAH10-deficient mice\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP and KO mouse with defined phenotype; single lab\",\n      \"pmids\": [\"41058558\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PACRG and FAP20 synergistically stabilize B-tubule dynamics in a cell-free reconstitution system: together they localize to B-tubules in high-density patches, decrease B-tubule depolymerization velocity, increase rescue frequency, and cryo-tomography of in vitro reconstructed doublets reveals reduced B-tubule curvature fluctuations promoting a more rigid conformation.\",\n      \"method\": \"Cell-free reconstitution, TIRF microscopy, cryo-electron tomography\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with cryo-ET structural validation; preprint but rigorous multimodal approach\",\n      \"pmids\": [\"bio_10.1101_2025.03.12.642377\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PACRG localizes to cilia and is expressed throughout vertebrate embryogenesis in ciliated tissues; loss-of-function by morpholino in Xenopus produces left-right axis defects, neural tube closure defects, and gastrulation defects, with cytoplasmic localization around the nucleus also observed.\",\n      \"method\": \"Morpholino knockdown, immunofluorescence, GFP fusion live imaging, scanning electron microscopy, in situ hybridization\",\n      \"journal\": \"Cilia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD with defined ciliary phenotype plus direct localization; single lab vertebrate model\",\n      \"pmids\": [\"23351225\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PACRG is a conserved axonemal inner-junction protein that, together with FAP20, bridges the A- and B-tubules of doublet microtubules to stabilize B-tubule dynamics and support assembly of inner dynein arms; in the manchette of elongating spermatids it forms a complex with MEIG1 (which it recruits and which in turn stabilizes PACRG against proteasomal degradation) and DNALI1 to transport cargo proteins such as SPAG16L for sperm flagellum assembly; outside the cilium, PACRG promotes TNF-induced canonical NF-κB signaling by stabilizing the LUBAC complex and can functionally substitute for SHARPIN to restore linear ubiquitylation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PACRG is a conserved axonemal inner-junction protein that, together with FAP20, bridges the A- and B-tubules of ciliary doublet microtubules to stabilize B-tubule dynamics, support inner dynein arm assembly, and enable ciliary motility [PMID:16278296, PMID:17654607, PMID:31116684]. Structurally, PACRG adopts a helical repeat fold, binds both assembled doublet microtubules and free tubulin heterodimers, and catalyzes inner junction formation; its crystal structure with MEIG1 reveals a loop-mediated interaction interface essential for PACRG stability [PMID:33529594, PMID:18387367]. In elongating spermatids, PACRG forms a manchette-associated complex with MEIG1 and DNALI1 that transports cargo proteins such as SPAG16L for sperm flagellum assembly, with MEIG1 stabilizing PACRG against proteasomal degradation and UCHL3/DNAH10 further regulating PACRG levels through deubiquitination [PMID:25715396, PMID:37083624, PMID:41058558]. Outside its ciliary roles, PACRG promotes TNF-induced canonical NF-κB signaling by stabilizing the LUBAC complex, interacting with HOIP, HOIL-1L, and SHARPIN, and functionally substituting for SHARPIN to restore linear ubiquitylation and protect cells from TNF-induced apoptosis [PMID:32019898].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"The fundamental question of whether PACRG has a structural role in cilia was answered when knockdown in Trypanosoma brucei demonstrated that PACRG is required for outer doublet microtubule integrity and flagellar motility, establishing it as a core axonemal component.\",\n      \"evidence\": \"RNAi knockdown of both PACRG homologues in T. brucei with GFP localization and TEM\",\n      \"pmids\": [\"16278296\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise position within the doublet was unknown\", \"Mechanism of structural contribution unresolved\", \"Mammalian relevance not yet established\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"The question of where exactly PACRG sits within the doublet was resolved by immuno-electron microscopy placing it at the inner junction between A- and B-tubules, defining its structural niche.\",\n      \"evidence\": \"Immuno-EM and Sarkosyl fractionation of Chlamydomonas axonemes\",\n      \"pmids\": [\"17654607\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Binding partners at the inner junction not identified\", \"Whether PACRG directly contacts tubulin was untested\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Whether PACRG directly engages tubulin was answered by in vitro reconstitution showing high-affinity binding to α/β-tubulin heterodimers and microtubule bundling activity, establishing PACRG as a bona fide tubulin-binding protein.\",\n      \"evidence\": \"Co-sedimentation and fluorescence microscopy with purified tubulin\",\n      \"pmids\": [\"18387367\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo relevance of bundling activity unclear\", \"Binding domain not mapped\", \"No structural data on the PACRG-tubulin interface\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Whether PACRG functions in vertebrate cilia was established when morpholino knockdown in Xenopus produced left-right asymmetry defects and neural tube closure defects, linking PACRG to developmental ciliopathy phenotypes.\",\n      \"evidence\": \"Morpholino knockdown in Xenopus with phenotypic scoring and localization\",\n      \"pmids\": [\"23351225\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Morpholino approach lacks genetic knockout confirmation\", \"Downstream signaling pathways not defined\", \"No mammalian loss-of-function model at this point\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"The question of how PACRG participates in spermatogenesis was answered by demonstrating that PACRG and MEIG1 form a manchette complex that transports SPAG16L cargo for flagellum assembly, with reciprocal stabilization between the partners.\",\n      \"evidence\": \"Yeast two-hybrid, reciprocal co-IP, and knockout mouse analysis with proteasome inhibition\",\n      \"pmids\": [\"25715396\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Motor driving manchette transport not identified\", \"Full cargo repertoire unknown\", \"Whether other axonemal proteins require this complex was untested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Three studies collectively expanded PACRG's functional scope: it was placed within a radial spoke–inner dynein arm regulatory cascade in Chlamydomonas, mapped to a MEIG1 hydrophobic binding interface by mutagenesis, and shown to influence G-protein signaling and longevity in C. elegans nonmotile cilia.\",\n      \"evidence\": \"Chlamydomonas mutant sliding assays; site-directed mutagenesis with pull-downs; C. elegans epistasis and behavioral assays\",\n      \"pmids\": [\"27770595\", \"26726850\", \"27193298\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"C. elegans signaling role not confirmed in mammals\", \"Structural basis of radial spoke interaction unknown\", \"How PACRG couples to G-protein signaling unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"A central structural question—how the inner junction is built—was resolved by cryo-electron tomography showing that PACRG and FAP20 together constitute the inner junction bridge along all nine doublets, and that their absence specifically impairs inner dynein arm b assembly and ciliary motility.\",\n      \"evidence\": \"Cryo-ET of Chlamydomonas pacrg mutants, in vitro sliding assay with rescue by exogenous protein\",\n      \"pmids\": [\"31116684\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-resolution structure of PACRG in situ not yet available\", \"Mechanism of inner dynein arm recruitment by PACRG/FAP20 unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"An unexpected non-ciliary function was uncovered: PACRG stabilizes the LUBAC ubiquitin ligase complex and promotes TNF-induced NF-κB signaling, functionally substituting for SHARPIN in SHARPIN-deficient cells to restore linear ubiquitylation and suppress apoptosis.\",\n      \"evidence\": \"Reciprocal co-IP, NF-κB reporter assays, SHARPIN-deficient cell rescue, TNF receptor complex purification\",\n      \"pmids\": [\"32019898\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether PACRG and SHARPIN act redundantly in vivo unknown\", \"How ciliary versus NF-κB functions are partitioned in different tissues unresolved\", \"Structural basis of PACRG–LUBAC interaction not determined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"The atomic structure of human PACRG–MEIG1 revealed a helical repeat fold and showed that PACRG simultaneously binds doublet microtubules and recruits free tubulin to catalyze inner junction formation, providing the first high-resolution mechanistic model for inner junction biogenesis.\",\n      \"evidence\": \"X-ray crystallography and single-molecule fluorescence microscopy\",\n      \"pmids\": [\"33529594\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full in situ atomic model of PACRG within the doublet not achieved\", \"Whether tubulin recruitment is rate-limiting for inner junction assembly unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The manchette transport machinery was further defined when DNALI1 was shown to interact with and stabilize PACRG, and its loss caused mislocalization of the entire MEIG1/PACRG/SPAG16L complex, establishing DNALI1 as an upstream organizer.\",\n      \"evidence\": \"Reciprocal co-IP, conditional knockout mouse, immunofluorescence\",\n      \"pmids\": [\"37083624\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Motor protein driving the DNALI1–PACRG complex along manchette microtubules not identified\", \"Whether DNALI1 functions as an inner arm dynein light chain in this context is unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Regulation of PACRG protein levels during spermiogenesis was further elaborated by showing that UCHL3 deubiquitinates and stabilizes PACRG, with DNAH10 bridging the UCHL3–PACRG interaction to facilitate intra-manchette transport.\",\n      \"evidence\": \"Co-IP, pull-down, localization in DNAH10-deficient mice\",\n      \"pmids\": [\"41058558\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific ubiquitin linkage type cleaved by UCHL3 on PACRG not defined\", \"Whether DNAH10 motor activity is required for transport unknown\", \"Single lab finding\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include how PACRG's ciliary and NF-κB signaling functions are differentially regulated across tissues, whether PACRG loss causes ciliopathy in mammals, and the complete cargo repertoire transported by the MEIG1–PACRG–DNALI1 manchette complex.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mammalian PACRG knockout phenotype fully characterized\", \"Tissue-specific regulation of ciliary versus NF-κB roles unknown\", \"Complete manchette transport cargo inventory not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [1, 3, 8, 10, 14]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 8, 10]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1, 5, 6, 8, 15]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [3, 4, 10, 12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 8, 10, 14]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [4, 12, 13]}\n    ],\n    \"complexes\": [\n      \"PACRG-FAP20 inner junction complex\",\n      \"MEIG1-PACRG manchette complex\",\n      \"LUBAC\"\n    ],\n    \"partners\": [\n      \"FAP20\",\n      \"MEIG1\",\n      \"DNALI1\",\n      \"HOIP\",\n      \"HOIL1\",\n      \"SHARPIN\",\n      \"UCHL3\",\n      \"DNAH10\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}