{"gene":"PWP2","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":1996,"finding":"PWP2 is an essential gene in S. cerevisiae encoding an 8-WD-repeat protein; depletion causes defects in bud site selection, cytokinesis, and hydrolysis of the septal junction between mother and daughter cells. Cell fractionation showed HA-Pwp2p localizes to a particulate, high-salt/alkaline-solubilizable complex, suggesting it exists in a proteinaceous complex possibly associated with the cytoskeleton.","method":"Gene disruption, conditional depletion (GAL1-controlled expression), indirect immunofluorescence microscopy, cell fractionation","journal":"Molecular & general genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO/depletion with defined cellular phenotypes and fractionation localization, single lab, multiple orthogonal methods","pmids":["8804409"],"is_preprint":false},{"year":2002,"finding":"Pwp2 (Utp1) is a component of the large 80S U3 snoRNP complex (SSU processome) in S. cerevisiae containing U3 snoRNA and 28 proteins. Depletion of Utp proteins including Pwp2/Utp1 impedes 18S rRNA production, placing them in the active pre-rRNA processing complex.","method":"Biochemical purification of U3 snoRNP, mass spectrometry protein identification, depletion analysis with rRNA northern blotting","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — biochemical purification with MS identification, functional depletion confirmed by multiple labs, foundational SSU processome paper","pmids":["12068309"],"is_preprint":false},{"year":2004,"finding":"Pwp2 is required for formation of the 90S pre-ribosomal particle in yeast. Its depletion blocks pre-rRNA processing at sites A0, A1, and A2, preventing U3 snoRNP from associating with 35S pre-rRNA. In its absence, Imp3 and Imp4 also fail to associate with pre-rRNA. Pwp2 forms a stable sub-complex with Dip2, Utp6, Utp13, Utp18, and Utp21 that can directly interact with the 5' end of 35S pre-rRNA independently of U3 snoRNP.","method":"Conditional depletion, pre-ribosomal particle sedimentation analysis, immunoprecipitation, northern blotting, sucrose gradient sedimentation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (IP, gradient sedimentation, northern blot) in single rigorous study establishing pathway position and complex composition","pmids":["15231838"],"is_preprint":false},{"year":2008,"finding":"Mrd1p functionally interacts with the Pwp2 subcomplex within the assembled 90S preribosomal complex, as shown by partial loss-of-function of Mrd1p-GFP perturbing 90S complex composition and cleavage at A0–A2 sites; Pwp2, Mpp10 and U3 snoRNP subcomplexes are functionally interconnected in the 90S preribosomal complex.","method":"GFP fusion protein incorporation into 90S complex, genetic partial loss-of-function, Miller chromatin spreading electron microscopy, northern blotting","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional interaction defined by partial LOF allele in living cells with rRNA processing readout, single lab","pmids":["18586827"],"is_preprint":false},{"year":2009,"finding":"Rrp36p is a novel component of the 90S preribosome that is recruited downstream of the UTP-A and UTP-B (PWP2) subcomplexes; depletion of UTP-B (PWP2) subcomplex components prevents Rrp36p recruitment and reduces its accumulation, placing PWP2/UTP-B upstream of Rrp36p in 90S preribosome assembly. The human orthologue of Rrp36p similarly functions in early pre-rRNA cleavages in HeLa cells.","method":"Conditional depletion epistasis, sucrose gradient sedimentation, northern blotting, co-immunoprecipitation","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis by sequential depletion with defined molecular readout, single lab, multiple methods","pmids":["20038530"],"is_preprint":false},{"year":2010,"finding":"Human PWP2 co-localizes in the nucleolus with WDR36 (a UTP21 homologue) in human trabecular meshwork cells, as shown by immunocytochemistry co-staining with nucleophosmin.","method":"Immunocytochemistry co-localization in cultured human cells","journal":"Human molecular genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single co-localization observation, no functional follow-up for PWP2 itself","pmids":["21051332"],"is_preprint":false},{"year":2013,"finding":"Loss-of-function mutation in zebrafish pwp2h (titania mutant) causes decreased production of mature 18S rRNA, activation of Tp53, impaired ribosome biogenesis, and arrested growth of endodermal organs, eyes, brain, and craniofacial structures. Autophagy is upregulated in intestinal epithelial cells as a survival response, independently of the Tor pathway and Tp53.","method":"Forward genetic screen, zebrafish mutant analysis, northern blotting for rRNA intermediates, autophagy assays, genetic epistasis with Tp53 and Tor pathway mutants","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean LOF mutant with defined molecular (18S rRNA) and cellular phenotypes, multiple orthogonal methods, pathway epistasis","pmids":["23408911"],"is_preprint":false},{"year":2014,"finding":"Human PWP2-GFP localizes predominantly to the dense fibrillar component and granular component of nucleoli in living HeLa cells. PWP2-GFP shows very low mobility by FRAP, consistent with tight binding to large protein complexes in the nucleolus; when rRNA transcription is suppressed, PWP2-GFP redistributes to cap and body regions and its mobility increases but remains slow.","method":"Live-cell fluorescence microscopy, FRAP, rRNA transcription inhibition","journal":"Biochemistry and cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct live-cell localization with FRAP quantification and functional perturbation, single lab","pmids":["24754225"],"is_preprint":false},{"year":2017,"finding":"Pwp2p mediates UTP-B subcomplex assembly via two structurally independent domains: the N-terminal tandem WD-repeat (tWD) domain associates with Utp21p, Utp18p, and Utp6p to form a core complex; the C-terminal domains of Pwp2p and Utp21p together mediate assembly of the Utp12p:Utp13p heterodimer, which is required for stable incorporation of UTP-B into the SSU processome. UTP-B also serves as a platform for assembly factors during 20S rRNA precursor maturation.","method":"Structural analysis, domain deletion and mutagenesis, yeast two-hybrid, co-immunoprecipitation, in vivo depletion with rRNA processing assays","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — structural domain dissection combined with mutagenesis, protein interaction assays, and functional rRNA processing readouts in a single study","pmids":["28600509"],"is_preprint":false},{"year":2011,"finding":"Zebrafish Pwp2h protein localizes to the nucleolus during development, as shown by a protein-trap GFP fusion line. Expression is widespread in early embryos but later restricted to highly proliferative regions including the forebrain ventricular zone and endoderm-derived organs.","method":"Protein-trap live fluorescence imaging in zebrafish, subcellular localization","journal":"Developmental dynamics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct live imaging of endogenous tagged protein with subcellular resolution, single lab","pmids":["21954116"],"is_preprint":false}],"current_model":"PWP2 (Utp1) is an essential WD-repeat protein that forms the scaffold of the UTP-B subcomplex within the SSU processome: its N-terminal tandem-WD domain binds Utp21/Utp18/Utp6 to form a core, while its C-terminal domain recruits Utp12:Utp13 to enable stable pre-rRNA association; the assembled UTP-B complex is required for 90S pre-ribosome formation and early endonucleolytic cleavages (A0/A1/A2) that produce the 18S rRNA and 40S ribosomal subunit, with PWP2 localizing to the dense fibrillar and granular components of the nucleolus in human and zebrafish cells."},"narrative":{"mechanistic_narrative":"PWP2 (Utp1) is an essential WD-repeat protein that scaffolds the UTP-B subcomplex of the SSU processome (90S pre-ribosome), the machinery that carries out the earliest steps of small ribosomal subunit biogenesis [PMID:12068309, PMID:15231838]. It assembles UTP-B through two structurally independent regions: its N-terminal tandem WD-repeat domain associates with Utp21, Utp18, and Utp6 to form a core, while the C-terminal domains of PWP2 and Utp21 together recruit the Utp12:Utp13 heterodimer, an interaction required for stable incorporation of UTP-B into the processome [PMID:28600509]. Depletion of PWP2 blocks formation of the 90S particle and abolishes the early endonucleolytic cleavages at sites A0, A1, and A2 that generate 18S rRNA, and prevents U3 snoRNP, Imp3, and Imp4 from associating with the 35S pre-rRNA; the PWP2 subcomplex can directly contact the 5' end of the 35S pre-rRNA independently of U3 snoRNP, placing it early in the assembly hierarchy upstream of factors such as Rrp36 [PMID:15231838, PMID:20038530]. This nucleolar function is conserved: human PWP2 localizes to the dense fibrillar and granular components of nucleoli and binds tightly to large complexes, redistributing upon transcription arrest [PMID:24754225], and zebrafish loss of pwp2h reduces mature 18S rRNA, triggers Tp53 activation and compensatory autophagy, and arrests growth of proliferative tissues [PMID:23408911].","teleology":[{"year":1996,"claim":"Established PWP2 as an essential gene whose product resides in a stable proteinaceous complex, the first clue that it acts as part of a larger assembly rather than alone.","evidence":"Gene disruption, GAL1-conditional depletion, immunofluorescence, and cell fractionation in S. cerevisiae","pmids":["8804409"],"confidence":"Medium","gaps":["Phenotypes (bud-site selection, cytokinesis) were interpreted before its ribosome biogenesis role was known","Complex composition and molecular function not yet defined"]},{"year":2002,"claim":"Placed PWP2/Utp1 within the 80S U3 snoRNP (SSU processome) and showed its depletion impairs 18S rRNA production, defining its true molecular context as pre-rRNA processing.","evidence":"Biochemical purification of U3 snoRNP with MS identification and depletion analysis by rRNA northern blotting","pmids":["12068309"],"confidence":"High","gaps":["Did not resolve which sub-complex PWP2 belongs to within the processome","Direct RNA contacts unknown"]},{"year":2004,"claim":"Defined PWP2's pathway position by showing it is required for 90S particle formation and the A0/A1/A2 cleavages, and that it forms a discrete subcomplex able to contact 35S pre-rRNA independently of U3 snoRNP.","evidence":"Conditional depletion, particle sedimentation, immunoprecipitation, and northern blotting in yeast","pmids":["15231838"],"confidence":"High","gaps":["Architecture of the subcomplex and how PWP2 organizes it not yet resolved","Direct vs indirect RNA binding not distinguished"]},{"year":2008,"claim":"Showed the PWP2 subcomplex is functionally interconnected with Mpp10 and U3 snoRNP subcomplexes inside the assembled 90S particle, framing it as one interdependent module of a coordinated machine.","evidence":"GFP-fusion incorporation, partial loss-of-function allele, Miller spread EM, and northern blotting","pmids":["18586827"],"confidence":"Medium","gaps":["Molecular nature of the inter-subcomplex contacts unresolved","Functional interaction defined genetically, not structurally"]},{"year":2009,"claim":"Ordered the assembly hierarchy by demonstrating that UTP-B (PWP2) acts upstream of Rrp36 recruitment, establishing PWP2 as an early-acting scaffold in 90S maturation with conserved human function.","evidence":"Sequential depletion epistasis, sucrose gradient sedimentation, co-IP, and northern blotting in yeast and HeLa cells","pmids":["20038530"],"confidence":"Medium","gaps":["Mechanism by which UTP-B licenses Rrp36 binding unknown","Human PWP2 not directly tested in this study"]},{"year":2017,"claim":"Resolved how PWP2 builds UTP-B at the domain level, showing the tWD domain nucleates a Utp21/Utp18/Utp6 core while C-terminal domains recruit Utp12:Utp13 for stable processome incorporation.","evidence":"Structural analysis, domain deletion/mutagenesis, yeast two-hybrid, co-IP, and depletion with rRNA processing assays","pmids":["28600509"],"confidence":"High","gaps":["Full atomic structure of PWP2 within the assembled processome not reported here","Dynamics of UTP-B assembly in vivo not captured"]},{"year":2013,"claim":"Demonstrated organismal consequences of PWP2 loss, linking its 18S rRNA function to Tp53 activation, compensatory autophagy, and arrested growth of proliferative tissues.","evidence":"Forward genetic screen, zebrafish pwp2h mutant analysis, rRNA northern blotting, autophagy assays, and Tp53/Tor epistasis","pmids":["23408911"],"confidence":"High","gaps":["Whether autophagy induction is a direct consequence of ribosome biogenesis stress is not mechanistically defined","No human disease linkage established"]},{"year":2014,"claim":"Mapped human PWP2 to the dense fibrillar and granular nucleolar compartments and showed transcription-dependent dynamics, confirming conserved nucleolar engagement in rRNA-processing complexes.","evidence":"Live-cell fluorescence microscopy, FRAP, and rRNA transcription inhibition in HeLa cells","pmids":["24754225"],"confidence":"Medium","gaps":["Identity of the human-specific binding partners not resolved","Functional rRNA processing role in human cells not directly assayed here"]},{"year":null,"claim":"How PWP2-dependent ribosome biogenesis stress is transduced into Tp53 activation and autophagy in metazoans, and whether human PWP2 variants cause disease, remain open.","evidence":"No timeline discovery resolves the signaling link or a human Mendelian association","pmids":[],"confidence":"Medium","gaps":["Molecular signal connecting impaired 18S production to Tp53 not identified","No causative human disease mutation reported in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[2]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[2,8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[8]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[5,7,9]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,2,6]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[2,8]}],"complexes":["UTP-B subcomplex","SSU processome (90S pre-ribosome)","U3 snoRNP"],"partners":["UTP21","UTP18","UTP6","UTP12","UTP13","DIP2","WDR36"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q15269","full_name":"Periodic tryptophan protein 2 homolog","aliases":[],"length_aa":919,"mass_kda":102.5,"function":"Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q15269/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PWP2","classification":"Common Essential","n_dependent_lines":1197,"n_total_lines":1208,"dependency_fraction":0.9908940397350994},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PWP2","total_profiled":1310},"omim":[{"mim_id":"601475","title":"PWP2 SMALL SUBUNIT PROCESSOME COMPONENT; PWP2","url":"https://www.omim.org/entry/601475"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoli","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PWP2"},"hgnc":{"alias_symbol":["EHOC-17","UTP1"],"prev_symbol":["PWP2H"]},"alphafold":{"accession":"Q15269","domains":[{"cath_id":"2.110.10.10","chopping":"287-372","consensus_level":"medium","plddt":92.6336,"start":287,"end":372},{"cath_id":"2.130.10.10","chopping":"554-656_701-733","consensus_level":"medium","plddt":91.7818,"start":554,"end":733},{"cath_id":"-","chopping":"735-779","consensus_level":"medium","plddt":92.3633,"start":735,"end":779},{"cath_id":"-","chopping":"783-868","consensus_level":"medium","plddt":90.607,"start":783,"end":868}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15269","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q15269-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q15269-F1-predicted_aligned_error_v6.png","plddt_mean":86.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PWP2","jax_strain_url":"https://www.jax.org/strain/search?query=PWP2"},"sequence":{"accession":"Q15269","fasta_url":"https://rest.uniprot.org/uniprotkb/Q15269.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q15269/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15269"}},"corpus_meta":[{"pmid":"12068309","id":"PMC_12068309","title":"A 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Cell fractionation showed HA-Pwp2p localizes to a particulate, high-salt/alkaline-solubilizable complex, suggesting it exists in a proteinaceous complex possibly associated with the cytoskeleton.\",\n      \"method\": \"Gene disruption, conditional depletion (GAL1-controlled expression), indirect immunofluorescence microscopy, cell fractionation\",\n      \"journal\": \"Molecular & general genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO/depletion with defined cellular phenotypes and fractionation localization, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"8804409\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Pwp2 (Utp1) is a component of the large 80S U3 snoRNP complex (SSU processome) in S. cerevisiae containing U3 snoRNA and 28 proteins. Depletion of Utp proteins including Pwp2/Utp1 impedes 18S rRNA production, placing them in the active pre-rRNA processing complex.\",\n      \"method\": \"Biochemical purification of U3 snoRNP, mass spectrometry protein identification, depletion analysis with rRNA northern blotting\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — biochemical purification with MS identification, functional depletion confirmed by multiple labs, foundational SSU processome paper\",\n      \"pmids\": [\"12068309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Pwp2 is required for formation of the 90S pre-ribosomal particle in yeast. Its depletion blocks pre-rRNA processing at sites A0, A1, and A2, preventing U3 snoRNP from associating with 35S pre-rRNA. In its absence, Imp3 and Imp4 also fail to associate with pre-rRNA. Pwp2 forms a stable sub-complex with Dip2, Utp6, Utp13, Utp18, and Utp21 that can directly interact with the 5' end of 35S pre-rRNA independently of U3 snoRNP.\",\n      \"method\": \"Conditional depletion, pre-ribosomal particle sedimentation analysis, immunoprecipitation, northern blotting, sucrose gradient sedimentation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (IP, gradient sedimentation, northern blot) in single rigorous study establishing pathway position and complex composition\",\n      \"pmids\": [\"15231838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Mrd1p functionally interacts with the Pwp2 subcomplex within the assembled 90S preribosomal complex, as shown by partial loss-of-function of Mrd1p-GFP perturbing 90S complex composition and cleavage at A0–A2 sites; Pwp2, Mpp10 and U3 snoRNP subcomplexes are functionally interconnected in the 90S preribosomal complex.\",\n      \"method\": \"GFP fusion protein incorporation into 90S complex, genetic partial loss-of-function, Miller chromatin spreading electron microscopy, northern blotting\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional interaction defined by partial LOF allele in living cells with rRNA processing readout, single lab\",\n      \"pmids\": [\"18586827\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Rrp36p is a novel component of the 90S preribosome that is recruited downstream of the UTP-A and UTP-B (PWP2) subcomplexes; depletion of UTP-B (PWP2) subcomplex components prevents Rrp36p recruitment and reduces its accumulation, placing PWP2/UTP-B upstream of Rrp36p in 90S preribosome assembly. The human orthologue of Rrp36p similarly functions in early pre-rRNA cleavages in HeLa cells.\",\n      \"method\": \"Conditional depletion epistasis, sucrose gradient sedimentation, northern blotting, co-immunoprecipitation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis by sequential depletion with defined molecular readout, single lab, multiple methods\",\n      \"pmids\": [\"20038530\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Human PWP2 co-localizes in the nucleolus with WDR36 (a UTP21 homologue) in human trabecular meshwork cells, as shown by immunocytochemistry co-staining with nucleophosmin.\",\n      \"method\": \"Immunocytochemistry co-localization in cultured human cells\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single co-localization observation, no functional follow-up for PWP2 itself\",\n      \"pmids\": [\"21051332\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Loss-of-function mutation in zebrafish pwp2h (titania mutant) causes decreased production of mature 18S rRNA, activation of Tp53, impaired ribosome biogenesis, and arrested growth of endodermal organs, eyes, brain, and craniofacial structures. Autophagy is upregulated in intestinal epithelial cells as a survival response, independently of the Tor pathway and Tp53.\",\n      \"method\": \"Forward genetic screen, zebrafish mutant analysis, northern blotting for rRNA intermediates, autophagy assays, genetic epistasis with Tp53 and Tor pathway mutants\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean LOF mutant with defined molecular (18S rRNA) and cellular phenotypes, multiple orthogonal methods, pathway epistasis\",\n      \"pmids\": [\"23408911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Human PWP2-GFP localizes predominantly to the dense fibrillar component and granular component of nucleoli in living HeLa cells. PWP2-GFP shows very low mobility by FRAP, consistent with tight binding to large protein complexes in the nucleolus; when rRNA transcription is suppressed, PWP2-GFP redistributes to cap and body regions and its mobility increases but remains slow.\",\n      \"method\": \"Live-cell fluorescence microscopy, FRAP, rRNA transcription inhibition\",\n      \"journal\": \"Biochemistry and cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct live-cell localization with FRAP quantification and functional perturbation, single lab\",\n      \"pmids\": [\"24754225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Pwp2p mediates UTP-B subcomplex assembly via two structurally independent domains: the N-terminal tandem WD-repeat (tWD) domain associates with Utp21p, Utp18p, and Utp6p to form a core complex; the C-terminal domains of Pwp2p and Utp21p together mediate assembly of the Utp12p:Utp13p heterodimer, which is required for stable incorporation of UTP-B into the SSU processome. UTP-B also serves as a platform for assembly factors during 20S rRNA precursor maturation.\",\n      \"method\": \"Structural analysis, domain deletion and mutagenesis, yeast two-hybrid, co-immunoprecipitation, in vivo depletion with rRNA processing assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — structural domain dissection combined with mutagenesis, protein interaction assays, and functional rRNA processing readouts in a single study\",\n      \"pmids\": [\"28600509\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Zebrafish Pwp2h protein localizes to the nucleolus during development, as shown by a protein-trap GFP fusion line. Expression is widespread in early embryos but later restricted to highly proliferative regions including the forebrain ventricular zone and endoderm-derived organs.\",\n      \"method\": \"Protein-trap live fluorescence imaging in zebrafish, subcellular localization\",\n      \"journal\": \"Developmental dynamics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct live imaging of endogenous tagged protein with subcellular resolution, single lab\",\n      \"pmids\": [\"21954116\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PWP2 (Utp1) is an essential WD-repeat protein that forms the scaffold of the UTP-B subcomplex within the SSU processome: its N-terminal tandem-WD domain binds Utp21/Utp18/Utp6 to form a core, while its C-terminal domain recruits Utp12:Utp13 to enable stable pre-rRNA association; the assembled UTP-B complex is required for 90S pre-ribosome formation and early endonucleolytic cleavages (A0/A1/A2) that produce the 18S rRNA and 40S ribosomal subunit, with PWP2 localizing to the dense fibrillar and granular components of the nucleolus in human and zebrafish cells.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PWP2 (Utp1) is an essential WD-repeat protein that scaffolds the UTP-B subcomplex of the SSU processome (90S pre-ribosome), the machinery that carries out the earliest steps of small ribosomal subunit biogenesis [#1, #2]. It assembles UTP-B through two structurally independent regions: its N-terminal tandem WD-repeat domain associates with Utp21, Utp18, and Utp6 to form a core, while the C-terminal domains of PWP2 and Utp21 together recruit the Utp12:Utp13 heterodimer, an interaction required for stable incorporation of UTP-B into the processome [#8]. Depletion of PWP2 blocks formation of the 90S particle and abolishes the early endonucleolytic cleavages at sites A0, A1, and A2 that generate 18S rRNA, and prevents U3 snoRNP, Imp3, and Imp4 from associating with the 35S pre-rRNA; the PWP2 subcomplex can directly contact the 5' end of the 35S pre-rRNA independently of U3 snoRNP, placing it early in the assembly hierarchy upstream of factors such as Rrp36 [#2, #4]. This nucleolar function is conserved: human PWP2 localizes to the dense fibrillar and granular components of nucleoli and binds tightly to large complexes, redistributing upon transcription arrest [#7], and zebrafish loss of pwp2h reduces mature 18S rRNA, triggers Tp53 activation and compensatory autophagy, and arrests growth of proliferative tissues [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Established PWP2 as an essential gene whose product resides in a stable proteinaceous complex, the first clue that it acts as part of a larger assembly rather than alone.\",\n      \"evidence\": \"Gene disruption, GAL1-conditional depletion, immunofluorescence, and cell fractionation in S. cerevisiae\",\n      \"pmids\": [\"8804409\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phenotypes (bud-site selection, cytokinesis) were interpreted before its ribosome biogenesis role was known\", \"Complex composition and molecular function not yet defined\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Placed PWP2/Utp1 within the 80S U3 snoRNP (SSU processome) and showed its depletion impairs 18S rRNA production, defining its true molecular context as pre-rRNA processing.\",\n      \"evidence\": \"Biochemical purification of U3 snoRNP with MS identification and depletion analysis by rRNA northern blotting\",\n      \"pmids\": [\"12068309\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which sub-complex PWP2 belongs to within the processome\", \"Direct RNA contacts unknown\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Defined PWP2's pathway position by showing it is required for 90S particle formation and the A0/A1/A2 cleavages, and that it forms a discrete subcomplex able to contact 35S pre-rRNA independently of U3 snoRNP.\",\n      \"evidence\": \"Conditional depletion, particle sedimentation, immunoprecipitation, and northern blotting in yeast\",\n      \"pmids\": [\"15231838\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Architecture of the subcomplex and how PWP2 organizes it not yet resolved\", \"Direct vs indirect RNA binding not distinguished\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Showed the PWP2 subcomplex is functionally interconnected with Mpp10 and U3 snoRNP subcomplexes inside the assembled 90S particle, framing it as one interdependent module of a coordinated machine.\",\n      \"evidence\": \"GFP-fusion incorporation, partial loss-of-function allele, Miller spread EM, and northern blotting\",\n      \"pmids\": [\"18586827\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular nature of the inter-subcomplex contacts unresolved\", \"Functional interaction defined genetically, not structurally\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Ordered the assembly hierarchy by demonstrating that UTP-B (PWP2) acts upstream of Rrp36 recruitment, establishing PWP2 as an early-acting scaffold in 90S maturation with conserved human function.\",\n      \"evidence\": \"Sequential depletion epistasis, sucrose gradient sedimentation, co-IP, and northern blotting in yeast and HeLa cells\",\n      \"pmids\": [\"20038530\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which UTP-B licenses Rrp36 binding unknown\", \"Human PWP2 not directly tested in this study\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolved how PWP2 builds UTP-B at the domain level, showing the tWD domain nucleates a Utp21/Utp18/Utp6 core while C-terminal domains recruit Utp12:Utp13 for stable processome incorporation.\",\n      \"evidence\": \"Structural analysis, domain deletion/mutagenesis, yeast two-hybrid, co-IP, and depletion with rRNA processing assays\",\n      \"pmids\": [\"28600509\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full atomic structure of PWP2 within the assembled processome not reported here\", \"Dynamics of UTP-B assembly in vivo not captured\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Demonstrated organismal consequences of PWP2 loss, linking its 18S rRNA function to Tp53 activation, compensatory autophagy, and arrested growth of proliferative tissues.\",\n      \"evidence\": \"Forward genetic screen, zebrafish pwp2h mutant analysis, rRNA northern blotting, autophagy assays, and Tp53/Tor epistasis\",\n      \"pmids\": [\"23408911\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether autophagy induction is a direct consequence of ribosome biogenesis stress is not mechanistically defined\", \"No human disease linkage established\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Mapped human PWP2 to the dense fibrillar and granular nucleolar compartments and showed transcription-dependent dynamics, confirming conserved nucleolar engagement in rRNA-processing complexes.\",\n      \"evidence\": \"Live-cell fluorescence microscopy, FRAP, and rRNA transcription inhibition in HeLa cells\",\n      \"pmids\": [\"24754225\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the human-specific binding partners not resolved\", \"Functional rRNA processing role in human cells not directly assayed here\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PWP2-dependent ribosome biogenesis stress is transduced into Tp53 activation and autophagy in metazoans, and whether human PWP2 variants cause disease, remain open.\",\n      \"evidence\": \"No timeline discovery resolves the signaling link or a human Mendelian association\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular signal connecting impaired 18S production to Tp53 not identified\", \"No causative human disease mutation reported in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [2, 8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [5, 7, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 2, 6]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [2, 8]}\n    ],\n    \"complexes\": [\n      \"UTP-B subcomplex\",\n      \"SSU processome (90S pre-ribosome)\",\n      \"U3 snoRNP\"\n    ],\n    \"partners\": [\n      \"UTP21\",\n      \"UTP18\",\n      \"UTP6\",\n      \"UTP12\",\n      \"UTP13\",\n      \"DIP2\",\n      \"WDR36\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}