{"gene":"PACRG","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2005,"finding":"PACRG localizes along the full length of the axoneme in Trypanosoma brucei (GFP fusion); RNAi knockdown of both T. brucei PACRG homologues simultaneously caused flagellar paralysis, slow growth, defective organelle segregation, and structural loss of outer doublet microtubules from the canonical 9+2 formation, establishing PACRG as an axonemal protein required for functional stability of outer doublet microtubules in both motile and sensory cilia/flagella.","method":"RNAi knockdown in T. brucei, GFP fusion localization, transmission electron microscopy","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (RNAi, GFP localization, TEM structural analysis), replicated across two homologues","pmids":["16278296"],"is_preprint":false},{"year":2007,"finding":"Chlamydomonas PACRG localizes to the entire length of the axoneme and basal body; immunoelectron microscopy shows PACRG antigen is densely distributed along outer doublets between the A- and B-tubules of adjacent outer doublets, suggesting a structural role in inter-tubule linkage. Sarkosyl pretreatment required for immunolocalization indicates PACRG is buried within the microtubule wall.","method":"Indirect immunofluorescence, immuno-electron microscopy, Sarkosyl extraction","journal":"Cell motility and the cytoskeleton","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by immuno-EM with functional inference, single lab, two orthogonal methods","pmids":["17654607"],"is_preprint":false},{"year":2007,"finding":"PACRG protein is regulated by the ubiquitin-proteasomal system; PACRG was detected in Lewy bodies and glial cytoplasmic inclusions in Parkinson's disease and Multiple System Atrophy patients, and in astrocytes and locus coeruleus neurons of normal brain.","method":"Immunohistochemistry, proteasome inhibition assays","journal":"Neurobiology of disease","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — proteasome regulation shown by inhibition assay, IHC localization, single lab","pmids":["17590346"],"is_preprint":false},{"year":2008,"finding":"PACRG directly binds to microtubules and alpha/beta-tubulin heterodimers with high affinity via a highly conserved amino acid sequence region; PACRG bundles microtubules and forms branched aggregates with unpolymerized tubulin dimers in vitro.","method":"Co-sedimentation assays, microscopy of PACRG-tubulin complexes in vitro","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical reconstitution of direct tubulin binding, single lab, single study","pmids":["18387367"],"is_preprint":false},{"year":2015,"finding":"MEIG1 and PACRG form a complex in the manchette of elongating spermatids that is essential for transporting cargo (e.g., SPAG16L) to build the sperm flagellum. PACRG recruits MEIG1 to the manchette (MEIG1 fails to localize to the manchette in Pacrg-deficient mice). PACRG is unstable in mammalian cells but is stabilized by MEIG1 or proteasome inhibition. SPAG16L is a downstream cargo of the MEIG1/PACRG complex.","method":"Yeast two-hybrid, colocalization by immunofluorescence in wild-type and knockout mice, proteasome inhibition assay","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Y2H, in vivo KO mouse localization, proteasome assay), epistatic ordering of PACRG→MEIG1→SPAG16L established genetically","pmids":["25715396"],"is_preprint":false},{"year":2016,"finding":"PACRG and its interactors form part of a signaling pathway anchored to axonemal doublet microtubules that includes the central apparatus, radial spokes, and specific inner dynein arm subforms to control dynein-driven microtubule sliding; PACRG biochemically interacts with radial spokes.","method":"In vitro microtubule sliding assay, biochemical pulldown/interaction assay","journal":"Cytoskeleton (Hoboken, N.J.)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — functional in vitro sliding assay plus biochemical interaction, single lab","pmids":["27770595"],"is_preprint":false},{"year":2016,"finding":"In C. elegans, PACRG localizes to a small subset of nonmotile cilia and influences gustatory plasticity learning behavior through functional coupling to heterotrimeric G-protein signaling; PACRG also promotes longevity by acting upstream of the FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling.","method":"C. elegans loss-of-function genetics, behavioral assays (gustatory plasticity), epistasis with daf-16/FOXO pathway, localization imaging","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis plus behavioral/longevity phenotypes with pathway placement, single lab, multiple readouts","pmids":["27193298"],"is_preprint":false},{"year":2016,"finding":"MEIG1 adopts a unique fold with a large interaction surface; four residues (W50, K57, F66, Y68) forming a contiguous hydrophobic patch are required for PACRG binding, and these same mutations abolish MEIG1's ability to stabilize PACRG when co-expressed in bacteria.","method":"Mutagenesis of 12 conserved MEIG1 residues, co-expression binding/stability assays in bacteria","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — systematic mutagenesis with functional validation of binding and protein stabilization, single lab, multiple mutants tested","pmids":["26726850"],"is_preprint":false},{"year":2019,"finding":"PACRG and FAP20 together form the inner junction bridge between the A- and B-tubules along the length of all nine ciliary doublet microtubules in Chlamydomonas; loss of PACRG and/or FAP20 causes severe motility defects, reduced microtubule sliding velocities, and reduced assembly of inner-arm dynein IDA b and beak-MIP structures. Addition of exogenous PACRG and/or FAP20 to isolated mutant axonemes restores sliding velocities but not ciliary beating.","method":"Cryo-electron tomography, in vitro microtubule sliding assay, Chlamydomonas pacrg mutants, add-back reconstitution with purified protein","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-ET structural data plus functional reconstitution (add-back assay) plus genetic mutants, multiple orthogonal methods","pmids":["31116684"],"is_preprint":false},{"year":2020,"finding":"PACRG promotes TNF-induced NF-κB activation by stabilizing LUBAC (the linear ubiquitin chain assembly complex composed of HOIP, HOIL-1L, and SHARPIN). Upon TNF stimulation, PACRG is recruited to the activated TNF receptor complex and interacts with LUBAC components. In SHARPIN-deficient cells, PACRG functionally replaces SHARPIN, prevents LUBAC destabilization, restores HOIP-dependent linear ubiquitylation, and protects cells from TNF-induced apoptosis. PACRG does not play a role in mitophagy.","method":"Co-immunoprecipitation, TNF receptor complex pulldown, NF-κB reporter assays, PACRG-deficient and SHARPIN-deficient cell lines, linear ubiquitylation assay","journal":"Science signaling","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, functional complementation in SHARPIN-KO cells, multiple cell lines, multiple orthogonal readouts (p65 translocation, NF-κB transcription, linear ubiquitylation, apoptosis)","pmids":["32019898"],"is_preprint":false},{"year":2021,"finding":"Crystal structure of human PACRG in complex with MEIG1 reveals that PACRG adopts a helical repeat fold with a loop that interacts with MEIG1. Using the Chlamydomonas axonemal doublet microtubule structure and single-molecule fluorescence microscopy, PACRG is proposed to bind microtubules while simultaneously recruiting free tubulin to catalyze formation of the inner junction. The homologous PACRG-like protein also mediates dual tubulin interactions but does not bind MEIG1.","method":"X-ray crystallography (crystal structure of PACRG–MEIG1 complex), single-molecule fluorescence microscopy, structural modeling with cryo-EM axonemal structure","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure determination combined with single-molecule microscopy and comparative structural analysis","pmids":["33529594"],"is_preprint":false},{"year":2023,"finding":"DNALI1 recruits and stabilizes PACRG via direct interaction (co-immunoprecipitation and pull-down); DNALI1 is required for the formation and manchette localization of the MEIG1/PACRG complex. In Dnali1-deficient mice, MEIG1, PACRG, and SPAG16L protein levels are unchanged but their localization within the manchette is lost, placing DNALI1 upstream of MEIG1/PACRG complex assembly at the manchette.","method":"Co-immunoprecipitation, pull-down assays, conditional knockout mice, immunofluorescence localization","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP/pulldown plus in vivo KO epistasis showing DNALI1 upstream of MEIG1/PACRG complex formation, multiple orthogonal methods","pmids":["37083624"],"is_preprint":false},{"year":2012,"finding":"PACRG morpholino knockdown in Xenopus laevis caused left-right axis specification defects (randomized laterality), neural tube closure defects, and gastrulation defects dose-dependently, indicating ciliary and non-ciliary functions. A GFP fusion of PACRG preferentially labeled cilia and also showed perinuclear and cytoplasmic localization.","method":"Antisense morpholino knockdown in Xenopus, timelapse videography of leftward flow, scanning electron microscopy, whole-mount in situ hybridization, GFP fusion localization","journal":"Cilia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MO knockdown with multiple phenotypic readouts and GFP localization, single lab","pmids":["23351225"],"is_preprint":false},{"year":2025,"finding":"UCHL3 (ubiquitin carboxyl-terminal hydrolase L3) binds to PACRG and stabilizes it via deubiquitination; DNAH10 acts as a bridging protein that enhances the UCHL3-PACRG interaction to facilitate their involvement in manchette function and intra-manchette transport during spermiogenesis.","method":"Co-immunoprecipitation, deubiquitination assay, localization studies in Dnah10-deficient mice","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — co-IP and deubiquitination assay, single lab, single study","pmids":["41058558"],"is_preprint":false},{"year":2025,"finding":"In a cell-free reconstitution system, PACRG and FAP20 together (but not individually) stabilize B-tubule dynamics by decreasing depolymerization velocity and increasing rescue frequency; cryo-electron tomography of in vitro reconstituted microtubule doublets with PACRG and FAP20 shows reduced B-tubule curvature fluctuations, promoting a more rigid and aligned conformation. The two proteins localize to B-tubules in distinct high-density patches.","method":"Cell-free reconstitution assay, TIRF microscopy, cryo-electron tomography","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cell-free reconstitution with TIRF and cryo-ET, multiple orthogonal methods, preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.03.12.642377"],"is_preprint":true}],"current_model":"PACRG is an evolutionarily conserved axonemal protein that localizes to the inner junction between A- and B-tubules of ciliary doublet microtubules (together with FAP20), where it directly binds tubulin/microtubules, stabilizes B-tubule dynamics, and regulates dynein-driven microtubule sliding; in the manchette of elongating spermatids it forms a complex with MEIG1 (stabilized by UCHL3 deubiquitination and scaffolded by DNALI1) to transport cargo such as SPAG16L for sperm flagellum assembly; outside the cilium/flagellum, PACRG promotes TNF-induced NF-κB activation by stabilizing the LUBAC complex and functionally substituting for SHARPIN to support linear ubiquitylation and protect against apoptosis."},"narrative":{"mechanistic_narrative":"PACRG is an evolutionarily conserved axonemal protein required for the structural integrity and motility of cilia and flagella [PMID:16278296, PMID:31116684]. Together with FAP20, it forms the inner junction bridge linking the A- and B-tubules along all nine ciliary doublet microtubules, and loss of either protein causes severe motility defects, reduced microtubule sliding velocities, and defective assembly of inner-arm dynein and beak-MIP structures [PMID:31116684]. PACRG binds microtubules and α/β-tubulin heterodimers directly with high affinity through a conserved sequence region [PMID:18387367], and structural and single-molecule analyses indicate it simultaneously engages microtubules and recruits free tubulin to catalyze inner-junction formation [PMID:33529594]; with FAP20 it stabilizes B-tubule dynamics by suppressing depolymerization and reducing curvature fluctuations [PMID:bio_10.1101_2025.03.12.642377]. Beyond its structural role, PACRG participates in a doublet-anchored signaling pathway that interacts with radial spokes to regulate dynein-driven sliding [PMID:27770595]. In elongating spermatids, PACRG forms a complex with MEIG1 in the manchette to transport cargo such as SPAG16L for sperm flagellum assembly; PACRG recruits MEIG1 to the manchette, and MEIG1 reciprocally stabilizes the otherwise proteasomally degraded PACRG [PMID:25715396, PMID:26726850]. This complex is scaffolded by DNALI1, which is required for its manchette localization [PMID:37083624], and PACRG is further stabilized by UCHL3-mediated deubiquitination [PMID:41058558]. Outside the cilium, PACRG promotes TNF-induced NF-κB activation by stabilizing the LUBAC complex; it is recruited to the activated TNF receptor complex and can functionally substitute for SHARPIN to restore HOIP-dependent linear ubiquitylation and protect cells from TNF-induced apoptosis [PMID:32019898].","teleology":[{"year":2005,"claim":"Established PACRG as an axonemal protein required for the structural stability of outer doublet microtubules, answering whether it has a role in ciliary/flagellar architecture.","evidence":"RNAi knockdown of both PACRG homologues, GFP localization, and TEM in T. brucei","pmids":["16278296"],"confidence":"High","gaps":["Did not resolve the molecular position of PACRG within the doublet","No direct biochemical binding partner identified"]},{"year":2007,"claim":"Refined PACRG's localization to the region between A- and B-tubules and showed it is buried within the microtubule wall, pointing to an inter-tubule structural function.","evidence":"Immuno-EM and Sarkosyl extraction in Chlamydomonas","pmids":["17654607"],"confidence":"Medium","gaps":["Structural inference not confirmed by direct binding assay at this stage","Did not define partner proteins at the junction"]},{"year":2008,"claim":"Demonstrated that PACRG binds microtubules and tubulin dimers directly and with high affinity, providing the biochemical basis for its structural role.","evidence":"In vitro co-sedimentation and microscopy of PACRG-tubulin complexes","pmids":["18387367"],"confidence":"Medium","gaps":["In vitro bundling/aggregation behavior may not reflect axonemal context","Single lab, single study"]},{"year":2015,"claim":"Identified the MEIG1/PACRG manchette complex and ordered it genetically, answering how PACRG contributes to sperm flagellum assembly via cargo transport.","evidence":"Yeast two-hybrid, knockout mouse colocalization, proteasome inhibition","pmids":["25715396"],"confidence":"High","gaps":["Mechanism of cargo loading/release not defined","Transport machinery linking complex to motors unresolved"]},{"year":2016,"claim":"Mapped the MEIG1 hydrophobic patch required for PACRG binding and stabilization, defining the molecular interface of the complex.","evidence":"Systematic mutagenesis of MEIG1 and bacterial co-expression binding/stability assays","pmids":["26726850"],"confidence":"High","gaps":["PACRG-side interface not defined here","Structural basis of stabilization not resolved"]},{"year":2016,"claim":"Placed PACRG within a doublet-anchored signaling pathway regulating dynein-driven sliding through interaction with radial spokes.","evidence":"In vitro microtubule sliding assays and biochemical pulldowns","pmids":["27770595"],"confidence":"Medium","gaps":["Direct radial-spoke binding partner not identified","Single lab"]},{"year":2016,"claim":"Extended PACRG function to nonmotile cilia and signaling/longevity pathways in C. elegans, indicating roles beyond motile axoneme structure.","evidence":"C. elegans loss-of-function genetics, behavioral assays, daf-16/FOXO epistasis","pmids":["27193298"],"confidence":"Medium","gaps":["Molecular link between PACRG and G-protein/insulin signaling not defined","Conservation of this role in mammals unknown"]},{"year":2019,"claim":"Resolved that PACRG and FAP20 jointly form the inner-junction bridge and are required for sliding and dynein/MIP assembly, with add-back reconstitution restoring function.","evidence":"Cryo-ET, microtubule sliding assays, Chlamydomonas mutants, purified-protein add-back","pmids":["31116684"],"confidence":"High","gaps":["Add-back restored sliding but not beating, leaving the beating defect unexplained","Stoichiometry with FAP20 not fully defined"]},{"year":2020,"claim":"Revealed a noncanonical PACRG function in TNF/NF-κB signaling, showing it stabilizes LUBAC and can functionally replace SHARPIN.","evidence":"Reciprocal co-IP, TNF receptor complex pulldown, NF-κB reporters, complementation in SHARPIN-KO cells, linear ubiquitylation assays","pmids":["32019898"],"confidence":"High","gaps":["Structural basis of PACRG-LUBAC interaction unknown","Physiological context where PACRG substitutes for SHARPIN in vivo not established"]},{"year":2021,"claim":"Determined the PACRG fold and PACRG-MEIG1 interface and proposed a tubulin-recruitment mechanism for inner-junction catalysis.","evidence":"X-ray crystallography of PACRG-MEIG1, single-molecule fluorescence, structural modeling","pmids":["33529594"],"confidence":"High","gaps":["Catalytic mechanism of junction assembly inferred, not directly observed","Functional role of PACRG-like paralog not defined"]},{"year":2023,"claim":"Identified DNALI1 as the upstream scaffold required for manchette assembly of the MEIG1/PACRG complex, refining the spermiogenesis pathway.","evidence":"Co-IP/pulldown and conditional knockout mice with immunofluorescence","pmids":["37083624"],"confidence":"High","gaps":["How DNALI1 anchors the complex to the manchette structurally is unresolved","Cargo-transport mechanism downstream remains undefined"]},{"year":2025,"claim":"Showed UCHL3 deubiquitinates and stabilizes PACRG, with DNAH10 bridging the interaction, defining how PACRG protein levels are maintained during spermiogenesis.","evidence":"Co-IP, deubiquitination assays, localization in Dnah10-deficient mice","pmids":["41058558"],"confidence":"Medium","gaps":["Single lab, single study","Ubiquitin sites on PACRG and the ligase responsible not identified"]},{"year":2025,"claim":"Demonstrated by cell-free reconstitution that PACRG and FAP20 together stabilize B-tubule dynamics and rigidity, directly linking the inner junction to microtubule mechanical behavior.","evidence":"Cell-free reconstitution, TIRF microscopy, cryo-ET (preprint)","pmids":["bio_10.1101_2025.03.12.642377"],"confidence":"High","gaps":["Preprint, not yet peer-reviewed","Relationship between in vitro rigidity changes and in vivo beating defects not established"]},{"year":null,"claim":"How PACRG's distinct roles in axonemal structure, spermatid cargo transport, and LUBAC-dependent NF-κB signaling are coordinated or regulated within a single cell remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying regulatory mechanism connecting ciliary and immune-signaling roles","Determinants of PACRG localization/partner choice unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[3,8,10,14]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[1,8,14]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,11]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1,8,12]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[3,8,14]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[1]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[9,12]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[9,6]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[9]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[4,11]}],"complexes":["MEIG1/PACRG complex","inner junction (with FAP20)","LUBAC"],"partners":["FAP20","MEIG1","DNALI1","UCHL3","DNAH10","HOIP","SHARPIN","SPAG16L"],"other_free_text":[]}},"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":353,"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":64,"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":"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":"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":"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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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":"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":"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":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":19161,"output_tokens":3949,"usd":0.058359,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11643,"output_tokens":3989,"usd":0.07897,"stage2_stop_reason":"end_turn"},"total_usd":0.137329,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","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 (GFP fusion); RNAi knockdown of both T. brucei PACRG homologues simultaneously caused flagellar paralysis, slow growth, defective organelle segregation, and structural loss of outer doublet microtubules from the canonical 9+2 formation, establishing PACRG as an axonemal protein required for functional stability of outer doublet microtubules in both motile and sensory cilia/flagella.\",\n      \"method\": \"RNAi knockdown in T. brucei, GFP fusion localization, transmission electron microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (RNAi, GFP localization, TEM structural analysis), replicated across two homologues\",\n      \"pmids\": [\"16278296\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Chlamydomonas PACRG localizes to the entire length of the axoneme and basal body; immunoelectron microscopy shows PACRG antigen is densely distributed along outer doublets between the A- and B-tubules of adjacent outer doublets, suggesting a structural role in inter-tubule linkage. Sarkosyl pretreatment required for immunolocalization indicates PACRG is buried within the microtubule wall.\",\n      \"method\": \"Indirect immunofluorescence, immuno-electron microscopy, Sarkosyl extraction\",\n      \"journal\": \"Cell motility and the cytoskeleton\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by immuno-EM with functional inference, single lab, two orthogonal methods\",\n      \"pmids\": [\"17654607\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"PACRG protein is regulated by the ubiquitin-proteasomal system; PACRG was detected in Lewy bodies and glial cytoplasmic inclusions in Parkinson's disease and Multiple System Atrophy patients, and in astrocytes and locus coeruleus neurons of normal brain.\",\n      \"method\": \"Immunohistochemistry, proteasome inhibition assays\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — proteasome regulation shown by inhibition assay, IHC localization, single lab\",\n      \"pmids\": [\"17590346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PACRG directly binds to microtubules and alpha/beta-tubulin heterodimers with high affinity via a highly conserved amino acid sequence region; PACRG bundles microtubules and forms branched aggregates with unpolymerized tubulin dimers in vitro.\",\n      \"method\": \"Co-sedimentation assays, microscopy of PACRG-tubulin complexes in vitro\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical reconstitution of direct tubulin binding, single lab, single study\",\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 that is essential for transporting cargo (e.g., SPAG16L) to build the sperm flagellum. PACRG recruits MEIG1 to the manchette (MEIG1 fails to localize to the manchette in Pacrg-deficient mice). PACRG is unstable in mammalian cells but is stabilized by MEIG1 or proteasome inhibition. SPAG16L is a downstream cargo of the MEIG1/PACRG complex.\",\n      \"method\": \"Yeast two-hybrid, colocalization by immunofluorescence in wild-type and knockout mice, proteasome inhibition assay\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Y2H, in vivo KO mouse localization, proteasome assay), epistatic ordering of PACRG→MEIG1→SPAG16L established genetically\",\n      \"pmids\": [\"25715396\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PACRG and its interactors form part of a signaling pathway anchored to axonemal doublet microtubules that includes the central apparatus, radial spokes, and specific inner dynein arm subforms to control dynein-driven microtubule sliding; PACRG biochemically interacts with radial spokes.\",\n      \"method\": \"In vitro microtubule sliding assay, biochemical pulldown/interaction assay\",\n      \"journal\": \"Cytoskeleton (Hoboken, N.J.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — functional in vitro sliding assay plus biochemical interaction, single lab\",\n      \"pmids\": [\"27770595\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In C. elegans, PACRG localizes to a small subset of nonmotile cilia and influences gustatory plasticity learning behavior through functional coupling to heterotrimeric G-protein signaling; PACRG also promotes longevity by acting upstream of the FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling.\",\n      \"method\": \"C. elegans loss-of-function genetics, behavioral assays (gustatory plasticity), epistasis with daf-16/FOXO pathway, localization imaging\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis plus behavioral/longevity phenotypes with pathway placement, single lab, multiple readouts\",\n      \"pmids\": [\"27193298\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"MEIG1 adopts a unique fold with a large interaction surface; four residues (W50, K57, F66, Y68) forming a contiguous hydrophobic patch are required for PACRG binding, and these same mutations abolish MEIG1's ability to stabilize PACRG when co-expressed in bacteria.\",\n      \"method\": \"Mutagenesis of 12 conserved MEIG1 residues, co-expression binding/stability assays in bacteria\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — systematic mutagenesis with functional validation of binding and protein stabilization, single lab, multiple mutants tested\",\n      \"pmids\": [\"26726850\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PACRG and FAP20 together form the inner junction bridge between the A- and B-tubules along the length of all nine ciliary doublet microtubules in Chlamydomonas; loss of PACRG and/or FAP20 causes severe motility defects, reduced microtubule sliding velocities, and reduced assembly of inner-arm dynein IDA b and beak-MIP structures. Addition of exogenous PACRG and/or FAP20 to isolated mutant axonemes restores sliding velocities but not ciliary beating.\",\n      \"method\": \"Cryo-electron tomography, in vitro microtubule sliding assay, Chlamydomonas pacrg mutants, add-back reconstitution with purified protein\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-ET structural data plus functional reconstitution (add-back assay) plus genetic mutants, 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 LUBAC (the linear ubiquitin chain assembly complex composed of HOIP, HOIL-1L, and SHARPIN). Upon TNF stimulation, PACRG is recruited to the activated TNF receptor complex and interacts with LUBAC components. In SHARPIN-deficient cells, PACRG functionally replaces SHARPIN, prevents LUBAC destabilization, restores HOIP-dependent linear ubiquitylation, and protects cells from TNF-induced apoptosis. PACRG does not play a role in mitophagy.\",\n      \"method\": \"Co-immunoprecipitation, TNF receptor complex pulldown, NF-κB reporter assays, PACRG-deficient and SHARPIN-deficient cell lines, linear ubiquitylation assay\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, functional complementation in SHARPIN-KO cells, multiple cell lines, multiple orthogonal readouts (p65 translocation, NF-κB transcription, linear ubiquitylation, apoptosis)\",\n      \"pmids\": [\"32019898\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Crystal structure of human PACRG in complex with MEIG1 reveals that PACRG adopts a helical repeat fold with a loop that interacts with MEIG1. Using the Chlamydomonas axonemal doublet microtubule structure and single-molecule fluorescence microscopy, PACRG is proposed to bind microtubules while simultaneously recruiting free tubulin to catalyze formation of the inner junction. The homologous PACRG-like protein also mediates dual tubulin interactions but does not bind MEIG1.\",\n      \"method\": \"X-ray crystallography (crystal structure of PACRG–MEIG1 complex), single-molecule fluorescence microscopy, structural modeling with cryo-EM axonemal structure\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure determination combined with single-molecule microscopy and comparative structural analysis\",\n      \"pmids\": [\"33529594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DNALI1 recruits and stabilizes PACRG via direct interaction (co-immunoprecipitation and pull-down); DNALI1 is required for the formation and manchette localization of the MEIG1/PACRG complex. In Dnali1-deficient mice, MEIG1, PACRG, and SPAG16L protein levels are unchanged but their localization within the manchette is lost, placing DNALI1 upstream of MEIG1/PACRG complex assembly at the manchette.\",\n      \"method\": \"Co-immunoprecipitation, pull-down assays, conditional knockout mice, immunofluorescence localization\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP/pulldown plus in vivo KO epistasis showing DNALI1 upstream of MEIG1/PACRG complex formation, multiple orthogonal methods\",\n      \"pmids\": [\"37083624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"PACRG morpholino knockdown in Xenopus laevis caused left-right axis specification defects (randomized laterality), neural tube closure defects, and gastrulation defects dose-dependently, indicating ciliary and non-ciliary functions. A GFP fusion of PACRG preferentially labeled cilia and also showed perinuclear and cytoplasmic localization.\",\n      \"method\": \"Antisense morpholino knockdown in Xenopus, timelapse videography of leftward flow, scanning electron microscopy, whole-mount in situ hybridization, GFP fusion localization\",\n      \"journal\": \"Cilia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MO knockdown with multiple phenotypic readouts and GFP localization, single lab\",\n      \"pmids\": [\"23351225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UCHL3 (ubiquitin carboxyl-terminal hydrolase L3) binds to PACRG and stabilizes it via deubiquitination; DNAH10 acts as a bridging protein that enhances the UCHL3-PACRG interaction to facilitate their involvement in manchette function and intra-manchette transport during spermiogenesis.\",\n      \"method\": \"Co-immunoprecipitation, deubiquitination assay, localization studies in Dnah10-deficient mice\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — co-IP and deubiquitination assay, single lab, single study\",\n      \"pmids\": [\"41058558\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a cell-free reconstitution system, PACRG and FAP20 together (but not individually) stabilize B-tubule dynamics by decreasing depolymerization velocity and increasing rescue frequency; cryo-electron tomography of in vitro reconstituted microtubule doublets with PACRG and FAP20 shows reduced B-tubule curvature fluctuations, promoting a more rigid and aligned conformation. The two proteins localize to B-tubules in distinct high-density patches.\",\n      \"method\": \"Cell-free reconstitution assay, TIRF microscopy, cryo-electron tomography\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cell-free reconstitution with TIRF and cryo-ET, multiple orthogonal methods, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.03.12.642377\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"PACRG is an evolutionarily conserved axonemal protein that localizes to the inner junction between A- and B-tubules of ciliary doublet microtubules (together with FAP20), where it directly binds tubulin/microtubules, stabilizes B-tubule dynamics, and regulates dynein-driven microtubule sliding; in the manchette of elongating spermatids it forms a complex with MEIG1 (stabilized by UCHL3 deubiquitination and scaffolded by DNALI1) to transport cargo such as SPAG16L for sperm flagellum assembly; outside the cilium/flagellum, PACRG promotes TNF-induced NF-κB activation by stabilizing the LUBAC complex and functionally substituting for SHARPIN to support linear ubiquitylation and protect against apoptosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PACRG is an evolutionarily conserved axonemal protein required for the structural integrity and motility of cilia and flagella [#0, #8]. Together with FAP20, it forms the inner junction bridge linking the A- and B-tubules along all nine ciliary doublet microtubules, and loss of either protein causes severe motility defects, reduced microtubule sliding velocities, and defective assembly of inner-arm dynein and beak-MIP structures [#8]. PACRG binds microtubules and α/β-tubulin heterodimers directly with high affinity through a conserved sequence region [#3], and structural and single-molecule analyses indicate it simultaneously engages microtubules and recruits free tubulin to catalyze inner-junction formation [#10]; with FAP20 it stabilizes B-tubule dynamics by suppressing depolymerization and reducing curvature fluctuations [#14]. Beyond its structural role, PACRG participates in a doublet-anchored signaling pathway that interacts with radial spokes to regulate dynein-driven sliding [#5]. In elongating spermatids, PACRG forms a complex with MEIG1 in the manchette to transport cargo such as SPAG16L for sperm flagellum assembly; PACRG recruits MEIG1 to the manchette, and MEIG1 reciprocally stabilizes the otherwise proteasomally degraded PACRG [#4, #7]. This complex is scaffolded by DNALI1, which is required for its manchette localization [#11], and PACRG is further stabilized by UCHL3-mediated deubiquitination [#13]. Outside the cilium, PACRG promotes TNF-induced NF-\\u03baB activation by stabilizing the LUBAC complex; it is recruited to the activated TNF receptor complex and can functionally substitute for SHARPIN to restore HOIP-dependent linear ubiquitylation and protect cells from TNF-induced apoptosis [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established PACRG as an axonemal protein required for the structural stability of outer doublet microtubules, answering whether it has a role in ciliary/flagellar architecture.\",\n      \"evidence\": \"RNAi knockdown of both PACRG homologues, GFP localization, and TEM in T. brucei\",\n      \"pmids\": [\"16278296\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the molecular position of PACRG within the doublet\", \"No direct biochemical binding partner identified\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Refined PACRG's localization to the region between A- and B-tubules and showed it is buried within the microtubule wall, pointing to an inter-tubule structural function.\",\n      \"evidence\": \"Immuno-EM and Sarkosyl extraction in Chlamydomonas\",\n      \"pmids\": [\"17654607\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural inference not confirmed by direct binding assay at this stage\", \"Did not define partner proteins at the junction\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrated that PACRG binds microtubules and tubulin dimers directly and with high affinity, providing the biochemical basis for its structural role.\",\n      \"evidence\": \"In vitro co-sedimentation and microscopy of PACRG-tubulin complexes\",\n      \"pmids\": [\"18387367\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vitro bundling/aggregation behavior may not reflect axonemal context\", \"Single lab, single study\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identified the MEIG1/PACRG manchette complex and ordered it genetically, answering how PACRG contributes to sperm flagellum assembly via cargo transport.\",\n      \"evidence\": \"Yeast two-hybrid, knockout mouse colocalization, proteasome inhibition\",\n      \"pmids\": [\"25715396\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of cargo loading/release not defined\", \"Transport machinery linking complex to motors unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Mapped the MEIG1 hydrophobic patch required for PACRG binding and stabilization, defining the molecular interface of the complex.\",\n      \"evidence\": \"Systematic mutagenesis of MEIG1 and bacterial co-expression binding/stability assays\",\n      \"pmids\": [\"26726850\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"PACRG-side interface not defined here\", \"Structural basis of stabilization not resolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Placed PACRG within a doublet-anchored signaling pathway regulating dynein-driven sliding through interaction with radial spokes.\",\n      \"evidence\": \"In vitro microtubule sliding assays and biochemical pulldowns\",\n      \"pmids\": [\"27770595\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct radial-spoke binding partner not identified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Extended PACRG function to nonmotile cilia and signaling/longevity pathways in C. elegans, indicating roles beyond motile axoneme structure.\",\n      \"evidence\": \"C. elegans loss-of-function genetics, behavioral assays, daf-16/FOXO epistasis\",\n      \"pmids\": [\"27193298\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between PACRG and G-protein/insulin signaling not defined\", \"Conservation of this role in mammals unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Resolved that PACRG and FAP20 jointly form the inner-junction bridge and are required for sliding and dynein/MIP assembly, with add-back reconstitution restoring function.\",\n      \"evidence\": \"Cryo-ET, microtubule sliding assays, Chlamydomonas mutants, purified-protein add-back\",\n      \"pmids\": [\"31116684\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Add-back restored sliding but not beating, leaving the beating defect unexplained\", \"Stoichiometry with FAP20 not fully defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed a noncanonical PACRG function in TNF/NF-\\u03baB signaling, showing it stabilizes LUBAC and can functionally replace SHARPIN.\",\n      \"evidence\": \"Reciprocal co-IP, TNF receptor complex pulldown, NF-\\u03baB reporters, complementation in SHARPIN-KO cells, linear ubiquitylation assays\",\n      \"pmids\": [\"32019898\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of PACRG-LUBAC interaction unknown\", \"Physiological context where PACRG substitutes for SHARPIN in vivo not established\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Determined the PACRG fold and PACRG-MEIG1 interface and proposed a tubulin-recruitment mechanism for inner-junction catalysis.\",\n      \"evidence\": \"X-ray crystallography of PACRG-MEIG1, single-molecule fluorescence, structural modeling\",\n      \"pmids\": [\"33529594\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Catalytic mechanism of junction assembly inferred, not directly observed\", \"Functional role of PACRG-like paralog not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified DNALI1 as the upstream scaffold required for manchette assembly of the MEIG1/PACRG complex, refining the spermiogenesis pathway.\",\n      \"evidence\": \"Co-IP/pulldown and conditional knockout mice with immunofluorescence\",\n      \"pmids\": [\"37083624\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How DNALI1 anchors the complex to the manchette structurally is unresolved\", \"Cargo-transport mechanism downstream remains undefined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed UCHL3 deubiquitinates and stabilizes PACRG, with DNAH10 bridging the interaction, defining how PACRG protein levels are maintained during spermiogenesis.\",\n      \"evidence\": \"Co-IP, deubiquitination assays, localization in Dnah10-deficient mice\",\n      \"pmids\": [\"41058558\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, single study\", \"Ubiquitin sites on PACRG and the ligase responsible not identified\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated by cell-free reconstitution that PACRG and FAP20 together stabilize B-tubule dynamics and rigidity, directly linking the inner junction to microtubule mechanical behavior.\",\n      \"evidence\": \"Cell-free reconstitution, TIRF microscopy, cryo-ET (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.03.12.642377\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"Relationship between in vitro rigidity changes and in vivo beating defects not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PACRG's distinct roles in axonemal structure, spermatid cargo transport, and LUBAC-dependent NF-\\u03baB signaling are coordinated or regulated within a single cell remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying regulatory mechanism connecting ciliary and immune-signaling roles\", \"Determinants of PACRG localization/partner choice unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [3, 8, 10, 14]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [1, 8, 14]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1, 8, 12]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [3, 8, 14]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [9, 12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [9, 6]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [4, 11]}\n    ],\n    \"complexes\": [\"MEIG1/PACRG complex\", \"inner junction (with FAP20)\", \"LUBAC\"],\n    \"partners\": [\"FAP20\", \"MEIG1\", \"DNALI1\", \"UCHL3\", \"DNAH10\", \"HOIP\", \"SHARPIN\", \"SPAG16L\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}