{"gene":"UTP6","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2004,"finding":"Utp6 (yeast ortholog) is a component of the 90S pre-ribosome and forms a stable subcomplex with Pwp2, Dip2, Utp13, Utp18, and Utp21 that can directly interact with the 35S pre-rRNA 5' end independently of the U3 snoRNP.","method":"Immunoprecipitation, gradient sedimentation analysis, conditional depletion in yeast","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, gradient sedimentation, and genetic depletion with defined molecular phenotype; multiple orthogonal methods in one study","pmids":["15231838"],"is_preprint":false},{"year":2008,"finding":"The HAT (half-a-tetratricopeptide repeat) domain of Utp6 interacts with a specific peptide ligand in Utp21 with a dissociation constant of ~10 µM, while the N-terminal domain of Utp6 interacts with Utp18; an intact HAT domain is essential for efficient pre-rRNA processing and cell growth.","method":"Yeast two-hybrid interaction mapping, point and deletion mutagenesis, biophysical binding assay (dissociation constant measurement), growth assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro biophysical assay with Kd measurement, mutagenesis, and functional (pre-rRNA processing) validation; multiple orthogonal methods in one rigorous study","pmids":["18725399"],"is_preprint":false},{"year":2009,"finding":"A structural homology model of the Utp6 HAT domain was derived, delineating structure-defining and functionally important residues; random and directed mutagenesis in yeast identified loss-of-function residues that map to a potential functional interaction surface on the HAT domain tertiary structure.","method":"Bioinformatics/homology modeling, random and directed mutagenesis in yeast, functional growth assay","journal":"Protein engineering, design & selection : PEDS","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — homology model (computational) combined with mutagenesis functional validation, single lab","pmids":["19515729"],"is_preprint":false},{"year":2007,"finding":"Human HCA66 (UTP6) directly interacts with the CED4 domain of Apaf-1 and positively regulates Apaf-1-dependent apoptosis; HCA66 expression increases downstream caspase activity following cytochrome c release, and HCA66 depletion reduces caspase-9 recruitment to the apoptosome and impairs caspase-3 activation in a cell-free system.","method":"Co-immunoprecipitation, overexpression/knockdown in cells, cell-free apoptosome assay, caspase activity assay","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct interaction mapping to CED4 domain, functional gain- and loss-of-function, cell-free reconstitution of apoptosome activity; multiple orthogonal methods in one study","pmids":["17380155"],"is_preprint":false},{"year":2009,"finding":"HCA66 (UTP6) localizes to the centrosome from S-phase to mitosis and to the nucleolus throughout interphase; silencing of HCA66 causes failure of centrosome duplication, monopolar spindle formation, loss of gamma-tubulin ring complex proteins (gamma-tubulin, GCP2, GCP3) from centrosomes, and reduced protein levels of all gamma-TuSC components, indicating HCA66 stabilizes the gamma-tubulin small complex.","method":"Mass spectrometry of pericentriolar material, siRNA silencing, immunofluorescence microscopy, immunoblotting","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct localization experiment (mass spec + IF), siRNA loss-of-function with specific molecular phenotype (gamma-TuSC protein levels), multiple orthogonal methods","pmids":["19299467"],"is_preprint":false},{"year":2011,"finding":"Apaf1 interacts with HCA66 (UTP6) and regulates its recruitment to the centrosome; Apaf1-depleted cells show centrosome defects in microtubule nucleation, mitotic spindle formation, cell migration, and mitochondrial network regulation, mediated through loss of HCA66 centrosomal recruitment.","method":"Co-immunoprecipitation, Apaf1 depletion (siRNA/KO), immunofluorescence, centrosome functional assays","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and loss-of-function with centrosome phenotype, single lab, mechanistic link to HCA66 centrosomal recruitment","pmids":["21984814"],"is_preprint":false},{"year":2012,"finding":"Mammalian HCA66 (UTP6) is required for nucleolar steps of 40S ribosomal subunit maturation (pre-rRNA processing); overexpression of a dominant-negative HCA66 that accumulates at centrosomes but is absent from nucleoli disrupts centrosome function but not pre-rRNA processing, indicating HCA66 acts independently in ribosome biogenesis and centriole duplication.","method":"siRNA depletion, dominant-negative overexpression, pre-rRNA processing assays, immunofluorescence localization in HeLa cells","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function and dominant-negative dissection of dual functions with defined molecular readouts; multiple orthogonal approaches in one study; functionally connects to yeast data","pmids":["22434888"],"is_preprint":false},{"year":2026,"finding":"UTP6 from T. brucei was used as a bait for affinity purification to identify components of early SSU processome intermediates; conserved ribosome biogenesis factors co-purified with tagged UTP6, confirming its role as a component of pre-small-subunit complexes in trypanosomatids.","method":"Affinity purification followed by mass spectrometry (AP-MS) in T. brucei","journal":"Journal of proteome research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single AP-MS experiment in a divergent organism (T. brucei), no functional follow-up on UTP6 itself","pmids":["42150138"],"is_preprint":false}],"current_model":"UTP6/HCA66 is a dual-function protein: in the nucleolus it is an essential component of the UtpB subcomplex of the SSU processome, where its HAT domain mediates a specific peptide interaction with Utp21 (Kd ~10 µM) and its N-terminal domain contacts Utp18, and this intact HAT domain is required for efficient pre-rRNA processing and 40S subunit biogenesis; at the centrosome it localizes from S-phase through mitosis, stabilizes the gamma-tubulin small complex (gamma-tubulin/GCP2/GCP3), and is required for centriole duplication and mitotic spindle assembly, a centrosomal function regulated by direct physical interaction with the CED4 domain of Apaf-1; additionally, HCA66 positively regulates Apaf-1-dependent apoptosis by promoting caspase-9 recruitment to the apoptosome and caspase-3 activation downstream of cytochrome c release."},"narrative":{"mechanistic_narrative":"UTP6 (HCA66) is a dual-function protein that operates both in nucleolar ribosome biogenesis and at the centrosome during the cell cycle [PMID:19299467, PMID:22434888]. In the nucleolus it is a stable component of the 90S pre-ribosome/SSU processome, partitioning into a subcomplex with Pwp2, Dip2, Utp13, Utp18, and Utp21 that engages the 5' end of the pre-rRNA independently of the U3 snoRNP [PMID:15231838]; within this assembly its HAT (half-a-tetratricopeptide repeat) domain binds a specific peptide ligand in Utp21 (Kd ~10 µM) while its N-terminal domain contacts Utp18, and an intact HAT domain is required for efficient pre-rRNA processing and growth [PMID:18725399]. This role is conserved in mammals, where UTP6 is required for nucleolar steps of 40S ribosomal subunit maturation [PMID:22434888]. Independently, HCA66 localizes to the centrosome from S-phase through mitosis, where it stabilizes the gamma-tubulin small complex (gamma-tubulin/GCP2/GCP3) and is required for centrosome duplication and bipolar spindle assembly [PMID:19299467]; a dominant-negative that accumulates at centrosomes but not nucleoli dissociates the ribosomal and centrosomal functions [PMID:22434888]. HCA66 directly binds the CED4 domain of Apaf-1, which controls its recruitment to the centrosome and positively regulates Apaf-1-dependent apoptosis by promoting caspase-9 recruitment to the apoptosome and caspase-3 activation downstream of cytochrome c release [PMID:17380155, PMID:21984814].","teleology":[{"year":2004,"claim":"Established that the Utp6 ortholog is an integral, structured component of the early ribosome assembly machinery rather than a transient factor, by placing it in a defined pre-rRNA-binding subcomplex.","evidence":"Immunoprecipitation, gradient sedimentation, and conditional depletion in yeast","pmids":["15231838"],"confidence":"High","gaps":["Did not resolve which domain of Utp6 mediates subcomplex assembly","No direct demonstration of Utp6's individual contribution to pre-rRNA cleavage"]},{"year":2008,"claim":"Defined the molecular interactions anchoring Utp6 within the subcomplex, showing its HAT domain is a peptide-binding module essential for pre-rRNA processing.","evidence":"Yeast two-hybrid mapping, mutagenesis, biophysical Kd measurement, and growth assays","pmids":["18725399"],"confidence":"High","gaps":["No high-resolution structure of the HAT domain bound to the Utp21 peptide","Functional consequence of the Utp18 contact not separately tested"]},{"year":2009,"claim":"Mapped the functionally critical surface of the HAT domain to interpret loss-of-function residues structurally.","evidence":"Homology modeling combined with random and directed mutagenesis and growth assays in yeast","pmids":["19515729"],"confidence":"Medium","gaps":["Model is computational, not an experimental structure","Functional surface not validated by direct binding measurements"]},{"year":2007,"claim":"Revealed an unexpected role for the human protein in apoptosis through direct binding to the Apaf-1 CED4 domain, linking it to apoptosome function.","evidence":"Co-IP, gain/loss-of-function in cells, and cell-free apoptosome and caspase activity assays","pmids":["17380155"],"confidence":"High","gaps":["Did not define how HCA66 promotes caspase-9 recruitment mechanistically","Did not connect this role to its nucleolar/ribosomal function"]},{"year":2009,"claim":"Identified a centrosomal function distinct from ribosome biogenesis, showing HCA66 stabilizes the gamma-tubulin small complex required for spindle assembly.","evidence":"Mass spectrometry of pericentriolar material, siRNA silencing, immunofluorescence, and immunoblotting","pmids":["19299467"],"confidence":"High","gaps":["Molecular mechanism by which HCA66 stabilizes gamma-TuSC not defined","Whether centrosomal and nucleolar pools are the same molecules unresolved"]},{"year":2011,"claim":"Connected the Apaf-1 interaction to the centrosomal function, showing Apaf-1 controls HCA66 recruitment to the centrosome.","evidence":"Co-IP, Apaf1 depletion, immunofluorescence, and centrosome functional assays","pmids":["21984814"],"confidence":"Medium","gaps":["Single-lab loss-of-function without reciprocal structural mapping of the recruitment interface","Apoptotic versus centrosomal roles of the Apaf-1 interaction not cleanly separated"]},{"year":2012,"claim":"Demonstrated genetically that the ribosome biogenesis and centriole duplication functions are mechanistically independent, using a localization-restricted dominant negative.","evidence":"siRNA depletion, dominant-negative overexpression, pre-rRNA processing assays, and immunofluorescence in HeLa cells","pmids":["22434888"],"confidence":"High","gaps":["Does not explain how a single protein partitions between two organelles","Regulatory cues controlling pool distribution unknown"]},{"year":2026,"claim":"Extended the conserved SSU processome role to trypanosomatids, confirming UTP6 as a component of early pre-small-subunit complexes across divergent eukaryotes.","evidence":"Affinity purification-mass spectrometry in T. brucei (bait pulldown)","pmids":["42150138"],"confidence":"Low","gaps":["Single AP-MS experiment with no functional follow-up on UTP6 in T. brucei","No confirmation that the trypanosome complex mirrors the yeast/human subcomplex composition"]},{"year":null,"claim":"How a single protein is partitioned and regulated between its nucleolar ribosome-assembly role and its Apaf-1-coupled centrosomal/apoptotic roles remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the human protein in either complex","Signals governing centrosome versus nucleolus localization unknown","Direct mechanistic link between HAT-domain peptide binding and gamma-TuSC stabilization not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,1,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,4]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[4,6]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[4,5]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,6]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[3]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[4]}],"complexes":["SSU processome (UtpB subcomplex)","gamma-tubulin small complex","apoptosome"],"partners":["UTP21","UTP18","PWP2","APAF1","TUBG1","GCP2","GCP3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NYH9","full_name":"U3 small nucleolar RNA-associated protein 6 homolog","aliases":["Hepatocellular carcinoma-associated antigen 66","Multiple hat domains protein"],"length_aa":597,"mass_kda":70.2,"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. Involved in nucleolar processing of pre-18S ribosomal RNA","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q9NYH9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/UTP6","classification":"Common Essential","n_dependent_lines":989,"n_total_lines":1208,"dependency_fraction":0.8187086092715232},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000108651","cell_line_id":"CID001073","localizations":[{"compartment":"nucleolus_gc","grade":3}],"interactors":[],"url":"https://opencell.sf.czbiohub.org/target/CID001073","total_profiled":1310},"omim":[{"mim_id":"620948","title":"UTP6 SMALL SUBUNIT PROCESSOME COMPONENT; UTP6","url":"https://www.omim.org/entry/620948"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoli","reliability":"Enhanced"},{"location":"Mitotic chromosome","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/UTP6"},"hgnc":{"alias_symbol":["HCA66"],"prev_symbol":["C17orf40"]},"alphafold":{"accession":"Q9NYH9","domains":[{"cath_id":"1.20.1440","chopping":"2-104","consensus_level":"medium","plddt":87.1805,"start":2,"end":104},{"cath_id":"1.25.40","chopping":"508-597","consensus_level":"medium","plddt":80.583,"start":508,"end":597}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NYH9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NYH9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NYH9-F1-predicted_aligned_error_v6.png","plddt_mean":82.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=UTP6","jax_strain_url":"https://www.jax.org/strain/search?query=UTP6"},"sequence":{"accession":"Q9NYH9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NYH9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NYH9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NYH9"}},"corpus_meta":[{"pmid":"11468690","id":"PMC_11468690","title":"Molecular characterization and gene content of breakpoint boundaries in patients with neurofibromatosis type 1 with 17q11.2 microdeletions.","date":"2001","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11468690","citation_count":104,"is_preprint":false},{"pmid":"15231838","id":"PMC_15231838","title":"Functional characterization of Pwp2, a WD family protein essential for the assembly of the 90 S pre-ribosomal particle.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15231838","citation_count":75,"is_preprint":false},{"pmid":"23875536","id":"PMC_23875536","title":"SISH/CISH or qPCR as alternative techniques to FISH for determination of HER2 amplification status on breast tumors core needle biopsies: a multicenter experience based on 840 cases.","date":"2013","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/23875536","citation_count":43,"is_preprint":false},{"pmid":"18725399","id":"PMC_18725399","title":"A direct interaction between the Utp6 half-a-tetratricopeptide repeat domain and a specific peptide in Utp21 is essential for efficient pre-rRNA processing.","date":"2008","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18725399","citation_count":42,"is_preprint":false},{"pmid":"21984814","id":"PMC_21984814","title":"Apaf1 plays a pro-survival role by regulating centrosome morphology and function.","date":"2011","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/21984814","citation_count":42,"is_preprint":false},{"pmid":"12696059","id":"PMC_12696059","title":"Complete physical map and gene content of the human NF1 tumor suppressor region in human and mouse.","date":"2003","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/12696059","citation_count":35,"is_preprint":false},{"pmid":"17380155","id":"PMC_17380155","title":"Positive regulation of apoptosis by HCA66, a new Apaf-1 interacting protein, and its putative role in the physiopathology of NF1 microdeletion syndrome patients.","date":"2007","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/17380155","citation_count":29,"is_preprint":false},{"pmid":"24711647","id":"PMC_24711647","title":"ADAP2 in heart development: a candidate gene for the occurrence of cardiovascular malformations in NF1 microdeletion syndrome.","date":"2014","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24711647","citation_count":26,"is_preprint":false},{"pmid":"19299467","id":"PMC_19299467","title":"Stability of the small gamma-tubulin complex requires HCA66, a protein of the centrosome and the nucleolus.","date":"2009","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/19299467","citation_count":23,"is_preprint":false},{"pmid":"31703719","id":"PMC_31703719","title":"NF1 microdeletion syndrome: case report of two new patients.","date":"2019","source":"Italian journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/31703719","citation_count":23,"is_preprint":false},{"pmid":"31817495","id":"PMC_31817495","title":"Novel and Rare Fusion Transcripts Involving Transcription Factors and Tumor Suppressor Genes in Acute Myeloid Leukemia.","date":"2019","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/31817495","citation_count":21,"is_preprint":false},{"pmid":"23876478","id":"PMC_23876478","title":"Translatome analysis of CHO cells to identify key growth genes.","date":"2013","source":"Journal of biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/23876478","citation_count":20,"is_preprint":false},{"pmid":"16138909","id":"PMC_16138909","title":"Evidence by expression analysis of candidate genes for congenital heart defects in the NF1 microdeletion interval.","date":"2005","source":"Annals of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16138909","citation_count":17,"is_preprint":false},{"pmid":"18850118","id":"PMC_18850118","title":"Expression analysis of genes lying in the NF1 microdeletion interval points to four candidate modifiers for neurofibroma formation.","date":"2008","source":"Neurogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/18850118","citation_count":17,"is_preprint":false},{"pmid":"22434888","id":"PMC_22434888","title":"Mammalian HCA66 protein is required for both ribosome synthesis and centriole duplication.","date":"2012","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/22434888","citation_count":13,"is_preprint":false},{"pmid":"37659689","id":"PMC_37659689","title":"4D-DIA quantitative proteomics revealed the core mechanism of diabetic retinopathy after berberine treatment.","date":"2023","source":"European journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/37659689","citation_count":12,"is_preprint":false},{"pmid":"19515729","id":"PMC_19515729","title":"A structural model for the HAT domain of Utp6 incorporating bioinformatics and genetics.","date":"2009","source":"Protein engineering, design & selection : PEDS","url":"https://pubmed.ncbi.nlm.nih.gov/19515729","citation_count":11,"is_preprint":false},{"pmid":"39095659","id":"PMC_39095659","title":"Differentially localized protein identification for breast cancer based on deep learning in immunohistochemical images.","date":"2024","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/39095659","citation_count":4,"is_preprint":false},{"pmid":"32524281","id":"PMC_32524281","title":"Anti-infective nitazoxanide disrupts transcription of ribosome biogenesis-related genes in yeast.","date":"2020","source":"Genes & 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failure","url":"https://pubmed.ncbi.nlm.nih.gov/42219284","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14138,"output_tokens":2166,"usd":0.037452,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9131,"output_tokens":2910,"usd":0.059202,"stage2_stop_reason":"end_turn"},"total_usd":0.096654,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"Utp6 (yeast ortholog) is a component of the 90S pre-ribosome and forms a stable subcomplex with Pwp2, Dip2, Utp13, Utp18, and Utp21 that can directly interact with the 35S pre-rRNA 5' end independently of the U3 snoRNP.\",\n      \"method\": \"Immunoprecipitation, gradient sedimentation analysis, conditional depletion in yeast\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, gradient sedimentation, and genetic depletion with defined molecular phenotype; multiple orthogonal methods in one study\",\n      \"pmids\": [\"15231838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The HAT (half-a-tetratricopeptide repeat) domain of Utp6 interacts with a specific peptide ligand in Utp21 with a dissociation constant of ~10 µM, while the N-terminal domain of Utp6 interacts with Utp18; an intact HAT domain is essential for efficient pre-rRNA processing and cell growth.\",\n      \"method\": \"Yeast two-hybrid interaction mapping, point and deletion mutagenesis, biophysical binding assay (dissociation constant measurement), growth assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro biophysical assay with Kd measurement, mutagenesis, and functional (pre-rRNA processing) validation; multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"18725399\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"A structural homology model of the Utp6 HAT domain was derived, delineating structure-defining and functionally important residues; random and directed mutagenesis in yeast identified loss-of-function residues that map to a potential functional interaction surface on the HAT domain tertiary structure.\",\n      \"method\": \"Bioinformatics/homology modeling, random and directed mutagenesis in yeast, functional growth assay\",\n      \"journal\": \"Protein engineering, design & selection : PEDS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — homology model (computational) combined with mutagenesis functional validation, single lab\",\n      \"pmids\": [\"19515729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Human HCA66 (UTP6) directly interacts with the CED4 domain of Apaf-1 and positively regulates Apaf-1-dependent apoptosis; HCA66 expression increases downstream caspase activity following cytochrome c release, and HCA66 depletion reduces caspase-9 recruitment to the apoptosome and impairs caspase-3 activation in a cell-free system.\",\n      \"method\": \"Co-immunoprecipitation, overexpression/knockdown in cells, cell-free apoptosome assay, caspase activity assay\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct interaction mapping to CED4 domain, functional gain- and loss-of-function, cell-free reconstitution of apoptosome activity; multiple orthogonal methods in one study\",\n      \"pmids\": [\"17380155\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"HCA66 (UTP6) localizes to the centrosome from S-phase to mitosis and to the nucleolus throughout interphase; silencing of HCA66 causes failure of centrosome duplication, monopolar spindle formation, loss of gamma-tubulin ring complex proteins (gamma-tubulin, GCP2, GCP3) from centrosomes, and reduced protein levels of all gamma-TuSC components, indicating HCA66 stabilizes the gamma-tubulin small complex.\",\n      \"method\": \"Mass spectrometry of pericentriolar material, siRNA silencing, immunofluorescence microscopy, immunoblotting\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct localization experiment (mass spec + IF), siRNA loss-of-function with specific molecular phenotype (gamma-TuSC protein levels), multiple orthogonal methods\",\n      \"pmids\": [\"19299467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Apaf1 interacts with HCA66 (UTP6) and regulates its recruitment to the centrosome; Apaf1-depleted cells show centrosome defects in microtubule nucleation, mitotic spindle formation, cell migration, and mitochondrial network regulation, mediated through loss of HCA66 centrosomal recruitment.\",\n      \"method\": \"Co-immunoprecipitation, Apaf1 depletion (siRNA/KO), immunofluorescence, centrosome functional assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and loss-of-function with centrosome phenotype, single lab, mechanistic link to HCA66 centrosomal recruitment\",\n      \"pmids\": [\"21984814\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Mammalian HCA66 (UTP6) is required for nucleolar steps of 40S ribosomal subunit maturation (pre-rRNA processing); overexpression of a dominant-negative HCA66 that accumulates at centrosomes but is absent from nucleoli disrupts centrosome function but not pre-rRNA processing, indicating HCA66 acts independently in ribosome biogenesis and centriole duplication.\",\n      \"method\": \"siRNA depletion, dominant-negative overexpression, pre-rRNA processing assays, immunofluorescence localization in HeLa cells\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function and dominant-negative dissection of dual functions with defined molecular readouts; multiple orthogonal approaches in one study; functionally connects to yeast data\",\n      \"pmids\": [\"22434888\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"UTP6 from T. brucei was used as a bait for affinity purification to identify components of early SSU processome intermediates; conserved ribosome biogenesis factors co-purified with tagged UTP6, confirming its role as a component of pre-small-subunit complexes in trypanosomatids.\",\n      \"method\": \"Affinity purification followed by mass spectrometry (AP-MS) in T. brucei\",\n      \"journal\": \"Journal of proteome research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single AP-MS experiment in a divergent organism (T. brucei), no functional follow-up on UTP6 itself\",\n      \"pmids\": [\"42150138\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"UTP6/HCA66 is a dual-function protein: in the nucleolus it is an essential component of the UtpB subcomplex of the SSU processome, where its HAT domain mediates a specific peptide interaction with Utp21 (Kd ~10 µM) and its N-terminal domain contacts Utp18, and this intact HAT domain is required for efficient pre-rRNA processing and 40S subunit biogenesis; at the centrosome it localizes from S-phase through mitosis, stabilizes the gamma-tubulin small complex (gamma-tubulin/GCP2/GCP3), and is required for centriole duplication and mitotic spindle assembly, a centrosomal function regulated by direct physical interaction with the CED4 domain of Apaf-1; additionally, HCA66 positively regulates Apaf-1-dependent apoptosis by promoting caspase-9 recruitment to the apoptosome and caspase-3 activation downstream of cytochrome c release.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"UTP6 (HCA66) is a dual-function protein that operates both in nucleolar ribosome biogenesis and at the centrosome during the cell cycle [#4, #6]. In the nucleolus it is a stable component of the 90S pre-ribosome/SSU processome, partitioning into a subcomplex with Pwp2, Dip2, Utp13, Utp18, and Utp21 that engages the 5' end of the pre-rRNA independently of the U3 snoRNP [#0]; within this assembly its HAT (half-a-tetratricopeptide repeat) domain binds a specific peptide ligand in Utp21 (Kd ~10 µM) while its N-terminal domain contacts Utp18, and an intact HAT domain is required for efficient pre-rRNA processing and growth [#1]. This role is conserved in mammals, where UTP6 is required for nucleolar steps of 40S ribosomal subunit maturation [#6]. Independently, HCA66 localizes to the centrosome from S-phase through mitosis, where it stabilizes the gamma-tubulin small complex (gamma-tubulin/GCP2/GCP3) and is required for centrosome duplication and bipolar spindle assembly [#4]; a dominant-negative that accumulates at centrosomes but not nucleoli dissociates the ribosomal and centrosomal functions [#6]. HCA66 directly binds the CED4 domain of Apaf-1, which controls its recruitment to the centrosome and positively regulates Apaf-1-dependent apoptosis by promoting caspase-9 recruitment to the apoptosome and caspase-3 activation downstream of cytochrome c release [#3, #5].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established that the Utp6 ortholog is an integral, structured component of the early ribosome assembly machinery rather than a transient factor, by placing it in a defined pre-rRNA-binding subcomplex.\",\n      \"evidence\": \"Immunoprecipitation, gradient sedimentation, and conditional depletion in yeast\",\n      \"pmids\": [\"15231838\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which domain of Utp6 mediates subcomplex assembly\", \"No direct demonstration of Utp6's individual contribution to pre-rRNA cleavage\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defined the molecular interactions anchoring Utp6 within the subcomplex, showing its HAT domain is a peptide-binding module essential for pre-rRNA processing.\",\n      \"evidence\": \"Yeast two-hybrid mapping, mutagenesis, biophysical Kd measurement, and growth assays\",\n      \"pmids\": [\"18725399\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of the HAT domain bound to the Utp21 peptide\", \"Functional consequence of the Utp18 contact not separately tested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Mapped the functionally critical surface of the HAT domain to interpret loss-of-function residues structurally.\",\n      \"evidence\": \"Homology modeling combined with random and directed mutagenesis and growth assays in yeast\",\n      \"pmids\": [\"19515729\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Model is computational, not an experimental structure\", \"Functional surface not validated by direct binding measurements\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Revealed an unexpected role for the human protein in apoptosis through direct binding to the Apaf-1 CED4 domain, linking it to apoptosome function.\",\n      \"evidence\": \"Co-IP, gain/loss-of-function in cells, and cell-free apoptosome and caspase activity assays\",\n      \"pmids\": [\"17380155\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define how HCA66 promotes caspase-9 recruitment mechanistically\", \"Did not connect this role to its nucleolar/ribosomal function\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identified a centrosomal function distinct from ribosome biogenesis, showing HCA66 stabilizes the gamma-tubulin small complex required for spindle assembly.\",\n      \"evidence\": \"Mass spectrometry of pericentriolar material, siRNA silencing, immunofluorescence, and immunoblotting\",\n      \"pmids\": [\"19299467\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism by which HCA66 stabilizes gamma-TuSC not defined\", \"Whether centrosomal and nucleolar pools are the same molecules unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Connected the Apaf-1 interaction to the centrosomal function, showing Apaf-1 controls HCA66 recruitment to the centrosome.\",\n      \"evidence\": \"Co-IP, Apaf1 depletion, immunofluorescence, and centrosome functional assays\",\n      \"pmids\": [\"21984814\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab loss-of-function without reciprocal structural mapping of the recruitment interface\", \"Apoptotic versus centrosomal roles of the Apaf-1 interaction not cleanly separated\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated genetically that the ribosome biogenesis and centriole duplication functions are mechanistically independent, using a localization-restricted dominant negative.\",\n      \"evidence\": \"siRNA depletion, dominant-negative overexpression, pre-rRNA processing assays, and immunofluorescence in HeLa cells\",\n      \"pmids\": [\"22434888\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not explain how a single protein partitions between two organelles\", \"Regulatory cues controlling pool distribution unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Extended the conserved SSU processome role to trypanosomatids, confirming UTP6 as a component of early pre-small-subunit complexes across divergent eukaryotes.\",\n      \"evidence\": \"Affinity purification-mass spectrometry in T. brucei (bait pulldown)\",\n      \"pmids\": [\"42150138\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single AP-MS experiment with no functional follow-up on UTP6 in T. brucei\", \"No confirmation that the trypanosome complex mirrors the yeast/human subcomplex composition\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single protein is partitioned and regulated between its nucleolar ribosome-assembly role and its Apaf-1-coupled centrosomal/apoptotic roles remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the human protein in either complex\", \"Signals governing centrosome versus nucleolus localization unknown\", \"Direct mechanistic link between HAT-domain peptide binding and gamma-TuSC stabilization not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [4, 6]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [\"SSU processome (UtpB subcomplex)\", \"gamma-tubulin small complex\", \"apoptosome\"],\n    \"partners\": [\"UTP21\", \"UTP18\", \"PWP2\", \"APAF1\", \"TUBG1\", \"GCP2\", \"GCP3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}