{"gene":"NOB1","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2004,"finding":"The PIN domain of Nob1p is required for D-site cleavage of 20S pre-rRNA to generate mature 18S rRNA. A homology model of the PIN domain revealed structural mimicry of Mg2+-dependent exonucleases, and a point mutation predicted to abolish enzymatic activity abolished 20S pre-rRNA cleavage in vivo.","method":"Homology modeling, site-directed mutagenesis, in vivo pre-rRNA processing assay","journal":"RNA","confidence":"High","confidence_rationale":"Tier 1 / Moderate — active-site mutagenesis with in vivo functional readout, structural model validated by mutagenesis, single lab but multiple orthogonal methods","pmids":["15388878"],"is_preprint":false},{"year":2009,"finding":"Recombinant yeast Nob1 forms a tetramer that binds directly to pre-rRNA analogs containing the D-site cleavage region. RNA truncation and footprinting analyses showed Nob1's binding site centers around the single-stranded 3'-end of 18S rRNA, co-localizing with the proposed active site, positioning Nob1 for cleavage at site D.","method":"Recombinant protein binding assays, RNA truncation series, in vitro and in vivo Nob1-dependent RNA protection assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with recombinant protein, multiple orthogonal RNA binding assays, in vivo footprinting, single lab","pmids":["19706509"],"is_preprint":false},{"year":2009,"finding":"In vivo cleavage of yeast pre-rRNA at site D requires functional interaction between the PIN domain endonuclease Nob1 and the DEAH-box RNA helicase Prp43 and its cofactor Pfa1. Nob1 cleaved a D-site substrate analogue in vitro; mutations in the Nob1 PIN domain or RNA substrate abolished this cleavage. Genetic epistasis showed that increased dosage of wild-type Nob1, but not catalytic-site mutants, suppressed 20S pre-rRNA accumulation caused by ltv1/pfa1 mutations.","method":"In vitro endonuclease assay with PIN domain mutants, genetic epistasis (suppressor dosage analysis), in vivo pre-rRNA processing analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro cleavage assay with mutagenesis corroborated by genetic epistasis, independently consistent with PMID:19706509 and 15388878","pmids":["19801658"],"is_preprint":false},{"year":2011,"finding":"The archaeal (Pyrococcus horikoshii) Nob1 homolog efficiently cleaves RNA substrates containing the D-site of pre-ribosomal RNA in a manganese-dependent manner. NMR structure revealed a PIN domain (required for substrate binding) connected by a flexible linker to a zinc ribbon domain that binds helix 40 of the small subunit rRNA and acts as an anchor on the nascent subunit.","method":"In vitro RNA cleavage assay, NMR structure determination, domain mutagenesis/deletion analysis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structure with functional validation by in vitro cleavage assay and domain-dissection experiments, single lab but multiple orthogonal methods","pmids":["22156373"],"is_preprint":false},{"year":2002,"finding":"Yeast Nob1p forms a complex with the 19S regulatory particle of the 26S proteasome and with nuclear protein Pno1p. Temperature-sensitive nob1 mutants show defects in beta-subunit processing and 20S/26S proteasome assembly. Nob1p acts as a chaperone to join the 20S proteasome with the 19S regulatory particle in the nucleus, facilitate Ump1p degradation, and is then itself internalized and degraded to complete 26S proteasome biogenesis.","method":"Genetic analysis (ts mutants), overexpression rescue, co-fractionation, immunolocalization, proteasome assembly assays","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and cell-biological evidence with multiple readouts (assembly assays, localization, rescue), single lab","pmids":["12502737"],"is_preprint":false},{"year":2000,"finding":"Nob1p interacts with Nin1p/Rpn12 (a 19S regulatory particle subunit) of the yeast 26S proteasome as identified by two-hybrid screening, and co-immunoprecipitates with the ATPase component Rpt1. Nob1p is found exclusively in proteasomal fractions on glycerol gradients, and is degraded by the 26S proteasome during transition to stationary phase.","method":"Two-hybrid screening, glycerol gradient fractionation, co-immunoprecipitation, Western blot","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two-hybrid plus reciprocal co-IP plus fractionation, single lab","pmids":["10675611"],"is_preprint":false},{"year":2005,"finding":"The human NOB1 protein contains a PIN domain and a zinc ribbon domain. When expressed in mammalian culture cells, the NOB1 protein is mainly localized to the nucleus.","method":"Cloning, sequence analysis, Western blot, subcellular localization by imaging of expressed protein","journal":"Molecular biology reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, localization by overexpression without functional consequence reported","pmids":["16172919"],"is_preprint":false},{"year":2011,"finding":"NOB1 is an archaeal/eukaryotic endonuclease with a PIN domain (residues required for substrate binding) and a zinc ribbon domain sufficient to bind helix 40 of the small subunit rRNA; NMR resonance assignments for the archaeal PhNob1 were determined as a structural prerequisite.","method":"NMR resonance assignment (backbone and side chain)","journal":"Biomolecular NMR assignments","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — NMR assignments only (prerequisite study), no functional validation in this paper alone; consistent with PMID:22156373","pmids":["21732055"],"is_preprint":false},{"year":2013,"finding":"miR-326 directly targets the 3'-UTR of human NOB1 mRNA (validated by luciferase reporter assay), reducing NOB1 protein levels. NOB1 silencing in glioma cells (shRNA) causes G1 cell cycle arrest, reduced proliferation, enhanced apoptosis, and decreased colony formation, phenocopying miR-326 overexpression. NOB1 overexpression partially rescues miR-326-mediated growth inhibition. These effects involve the MAPK pathway.","method":"Dual-luciferase reporter assay (3'-UTR targeting), shRNA knockdown, cell cycle analysis, apoptosis assay, colony formation, xenograft model","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase reporter validation plus knockdown/rescue with multiple phenotypic readouts, single lab","pmids":["23869222"],"is_preprint":false},{"year":2016,"finding":"NOB1 silencing in laryngeal cancer cells inhibits proliferation, induces cell cycle arrest and apoptosis, and inhibits migration and invasion with downregulation of MMP-2 and MMP-9. Mechanistically, NOB1 silencing activates the JNK signaling pathway.","method":"siRNA knockdown, proliferation/apoptosis/migration assays, Western blot (MMP-2/9, JNK pathway)","journal":"Oncology reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single knockdown approach, pathway placement by protein level measurement only","pmids":["27035645"],"is_preprint":false},{"year":2014,"finding":"Downregulation of NOB1 in papillary thyroid carcinoma cells by RNAi significantly activates constitutive phosphorylation of p38 MAPK, which may contribute to inhibition of cancer cell growth and enhances radiosensitivity in vitro and in vivo.","method":"Adenovirus-mediated siRNA, clonogenic survival assay, xenograft model, Western blot (p38 MAPK phosphorylation)","journal":"Oncology reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, pathway placement inferred from phospho-protein levels after knockdown, no direct epistasis","pmids":["25231838"],"is_preprint":false},{"year":2018,"finding":"eEF1A1 positively regulates NOB1 expression (mRNA and protein) in hepatocellular carcinoma cells. Knockdown of eEF1A1 reduces NOB1 expression and decreases HCC cell invasion and migration; eEF1A1 overexpression increases NOB1 expression and promotes invasion/migration. Restoring NOB1 in eEF1A1-knockdown cells rescues invasion/migration, while NOB1 knockdown in eEF1A1-overexpressing cells reverses the enhanced invasion/migration.","method":"siRNA knockdown, overexpression, qRT-PCR, Western blot, Transwell invasion/migration assays, RTCA assay, epistasis by rescue experiment","journal":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — bidirectional epistasis with rescue experiments and multiple orthogonal functional assays, single lab","pmids":["30377124"],"is_preprint":false},{"year":2014,"finding":"NOB1 knockdown in osteosarcoma cells (U2OS) decreases cell migration and increases E-cadherin and β-catenin expression, suggesting NOB1 suppresses these epithelial markers to promote migration.","method":"Lentiviral shRNA knockdown, Transwell migration assay, Western blot (E-cadherin, β-catenin)","journal":"Molecular medicine reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single knockdown method, molecular pathway placement limited to protein level measurement","pmids":["24714960"],"is_preprint":false},{"year":2025,"finding":"TurboID proximity labeling identified 1044 proximal proteins for NOB1 (and 871 for PNO1), with 663 overlapping. NOB1 and PNO1 have different intracellular localizations (immunofluorescence). Co-IP validated interactions of both NOB1 and PNO1 with translation-related proteins EIF4B and EIF4G2. Proximal proteins are predominantly enriched in ribosome assembly, rRNA processing, and translation.","method":"TurboID proximity labeling, mass spectrometry, co-immunoprecipitation, immunofluorescence","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proximity proteomics validated by co-IP for specific interactions, single lab, new interactome data","pmids":["40157618"],"is_preprint":false},{"year":2020,"finding":"NOB1 silencing in colorectal cancer cells increases phosphorylation of JNK, ERK, and p38, suppresses proliferation and colony formation, and promotes apoptosis, placing NOB1 upstream of the JNK signaling pathway in these cells.","method":"siRNA knockdown, MTT assay, colony formation, flow cytometry, Western blot (phospho-JNK, -ERK, -p38)","journal":"Journal of investigative surgery","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, pathway placement by phosphorylation level measurement only, no epistasis experiment","pmids":["31906747"],"is_preprint":false},{"year":2017,"finding":"miR-215 directly targets the 3'-UTR of NOB1 mRNA in epithelial ovarian cancer cells (validated by luciferase reporter assay), suppressing NOB1 expression. NOB1 suppression activates the MAPK signaling pathway. NOB1 overexpression rescues the anti-tumor effects of miR-215.","method":"Dual-luciferase reporter assay, miRNA mimic transfection, Western blot (MAPK), rescue overexpression","journal":"American journal of translational research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, MAPK activation inferred from protein levels without direct epistasis","pmids":["28337275"],"is_preprint":false},{"year":2015,"finding":"NOB1 knockdown in ovarian cancer cells upregulates DR5 expression and activates the MAPK pathway, increasing sensitivity to TRAIL-induced apoptosis, including increased caspase-3, -8, and -9 activity.","method":"Lentiviral shRNA knockdown, TRAIL combination treatment, caspase activity assays, Western blot (DR5, MAPK), xenograft model","journal":"International journal of clinical and experimental pathology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mechanistic pathway placement by protein level measurement, no direct epistasis","pmids":["26617713"],"is_preprint":false}],"current_model":"NOB1 is a conserved PIN-domain endonuclease that cleaves pre-rRNA at site D in a manganese-dependent manner to generate the mature 3'-end of 18S rRNA during cytoplasmic maturation of the pre-40S ribosomal subunit; its PIN domain mediates catalysis and substrate binding to the single-stranded D-site, while its zinc ribbon domain anchors it to helix 40 of the small subunit rRNA, and its activity is facilitated by the RNA helicase Prp43 and cofactor Pfa1. In yeast, NOB1 also associates with the 19S regulatory particle of the 26S proteasome via Nin1p/Rpn12 and acts as a chaperone for proteasome assembly before being degraded. In human cancer cells, NOB1 loss-of-function suppresses proliferation and promotes apoptosis, with evidence linking it to the MAPK and JNK signaling pathways, and its expression is regulated by multiple miRNAs targeting its 3'-UTR and by eEF1A1-dependent transcriptional/translational mechanisms."},"narrative":{"mechanistic_narrative":"NOB1 is a conserved PIN-domain endonuclease that executes the final processing step of small ribosomal subunit biogenesis by cleaving pre-rRNA at site D to generate the mature 3'-end of 18S rRNA [PMID:15388878, PMID:22156373]. Its catalytic PIN domain both binds the single-stranded D-site region and mediates manganese-dependent cleavage, with active-site point mutations abolishing 20S pre-rRNA processing in vivo and substrate cleavage in vitro [PMID:15388878, PMID:19801658, PMID:22156373]; recombinant NOB1 binds directly to D-site-containing pre-rRNA analogs, positioning the active site over the cleavage site [PMID:19706509]. A separate zinc ribbon domain, connected to the PIN domain by a flexible linker, anchors NOB1 to helix 40 of the small subunit rRNA on the nascent particle [PMID:22156373, PMID:21732055]. Efficient in vivo D-site cleavage requires functional cooperation with the DEAH-box RNA helicase Prp43 and its cofactor Pfa1 [PMID:19801658], and proximity proteomics confirms NOB1 resides in an environment enriched for ribosome assembly, rRNA processing, and translation factors including EIF4B and EIF4G2 [PMID:40157618]. Independently, in yeast NOB1 associates with the 19S regulatory particle of the 26S proteasome via Nin1p/Rpn12 and the ATPase Rpt1, acting as a chaperone for joining the 20S and 19S particles before being itself degraded [PMID:12502737, PMID:10675611]. In multiple human cancer cell types, NOB1 loss-of-function suppresses proliferation and colony formation and promotes apoptosis, with its mRNA directly targeted by miR-326 and miR-215 and its expression positively regulated by eEF1A1 [PMID:23869222, PMID:30377124, PMID:28337275].","teleology":[{"year":2000,"claim":"Established the first physical context for Nob1p, placing it in the 26S proteasome rather than predicting an RNA-processing role.","evidence":"Two-hybrid screen, reciprocal co-IP, and glycerol gradient fractionation in yeast","pmids":["10675611"],"confidence":"Medium","gaps":["Did not establish a catalytic activity","Did not address rRNA processing","Mechanism of proteasome association unresolved"]},{"year":2002,"claim":"Assigned Nob1p a chaperone role in 26S proteasome assembly, defining a function distinct from any ribosomal activity.","evidence":"ts mutants, overexpression rescue, co-fractionation, immunolocalization, and proteasome assembly assays in yeast","pmids":["12502737"],"confidence":"Medium","gaps":["Relationship between proteasome and rRNA roles not reconciled","Direct enzymatic mechanism not shown","Conservation of proteasome role to humans untested"]},{"year":2004,"claim":"Identified the PIN domain as the catalytic module required for D-site cleavage of pre-rRNA, recasting NOB1 as the 18S rRNA 3'-end maturation endonuclease.","evidence":"Homology modeling plus active-site mutagenesis with in vivo pre-rRNA processing readout in yeast","pmids":["15388878"],"confidence":"High","gaps":["Direct in vitro cleavage not yet demonstrated","Metal dependence inferred from homology only","Substrate-binding determinants undefined"]},{"year":2009,"claim":"Demonstrated direct, sequence-specific binding of NOB1 to the D-site region and reconstituted cleavage in vitro, linking binding geometry to catalysis.","evidence":"Recombinant protein binding, RNA truncation/footprinting, and in vitro endonuclease assays with PIN mutants, plus genetic epistasis with Prp43/Pfa1","pmids":["19706509","19801658"],"confidence":"High","gaps":["Trigger for activation within the pre-40S particle unclear","Precise role of Prp43 helicase activity in cleavage not defined","Tetramer relevance in vivo uncertain"]},{"year":2011,"claim":"Resolved the two-domain architecture, showing the PIN domain handles substrate binding/cleavage and a separate zinc ribbon anchors NOB1 to helix 40, and established manganese dependence.","evidence":"NMR structure, resonance assignments, in vitro cleavage, and domain dissection of the archaeal Pyrococcus horikoshii homolog","pmids":["22156373","21732055"],"confidence":"High","gaps":["Structure of the human enzyme not determined","Conformational activation switch not captured","Interplay of the two domains during catalysis on a real particle unresolved"]},{"year":2018,"claim":"Connected NOB1 to cancer cell phenotypes, showing miRNA control of its 3'-UTR and eEF1A1-dependent regulation modulate proliferation, apoptosis, and invasion.","evidence":"Luciferase 3'-UTR reporters (miR-326, miR-215), knockdown/overexpression with rescue, and migration/invasion assays across glioma, ovarian, and hepatocellular carcinoma cells","pmids":["23869222","28337275","30377124"],"confidence":"Medium","gaps":["Whether phenotypes depend on NOB1 catalytic/ribosomal function untested","Direct effectors downstream of NOB1 not defined","Causal link from rRNA processing defect to apoptosis unestablished"]},{"year":2025,"claim":"Defined the human NOB1 proximity interactome, anchoring it in ribosome assembly, rRNA processing, and translation and validating direct contacts with translation factors.","evidence":"TurboID proximity labeling with mass spectrometry, co-IP validation (EIF4B, EIF4G2), and immunofluorescence comparison with PNO1","pmids":["40157618"],"confidence":"Medium","gaps":["Functional consequence of EIF4B/EIF4G2 contacts unknown","Proximity does not establish stable complex membership","Human D-site cleavage activity not directly assayed here"]},{"year":null,"claim":"How NOB1's catalytic role in 18S rRNA maturation mechanistically connects to its observed proliferation/apoptosis phenotypes and signaling-pathway associations in human cancer cells remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No study links NOB1 endonuclease activity to MAPK/JNK signaling readouts","Pathway placements rest on phospho-protein levels without epistasis","No human structural or reconstituted cleavage data"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,1,2,3]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,2,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,3]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4,6]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[13]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,2,3,13]}],"complexes":["pre-40S ribosomal subunit","26S proteasome (19S regulatory particle)"],"partners":["PRP43","PFA1","PNO1","RPN12","RPT1","EIF4B","EIF4G2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9ULX3","full_name":"RNA-binding protein NOB1","aliases":["Phosphorylation regulatory protein HP-10","Protein ART-4"],"length_aa":412,"mass_kda":46.7,"function":"May play a role in mRNA degradation (Probable). Endonuclease required for processing of 20S pre-rRNA precursor and biogenesis of 40S ribosomal subunits (By similarity)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9ULX3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/NOB1","classification":"Common Essential","n_dependent_lines":1167,"n_total_lines":1208,"dependency_fraction":0.9660596026490066},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"BYSL","stoichiometry":10.0},{"gene":"LTV1","stoichiometry":10.0},{"gene":"TSR1","stoichiometry":10.0},{"gene":"RIOK2","stoichiometry":4.0},{"gene":"RIOK3","stoichiometry":4.0},{"gene":"RPS16","stoichiometry":4.0},{"gene":"CLNS1A","stoichiometry":0.2},{"gene":"DRG1","stoichiometry":0.2},{"gene":"G3BP2","stoichiometry":0.2},{"gene":"METAP2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NOB1","total_profiled":1310},"omim":[{"mim_id":"620074","title":"LTV1 RIBOSOME BIOGENESIS FACTOR; LTV1","url":"https://www.omim.org/entry/620074"},{"mim_id":"619357","title":"ADENYLATE KINASE 6; AK6","url":"https://www.omim.org/entry/619357"},{"mim_id":"618710","title":"PARTNER OF NOB1; PNO1","url":"https://www.omim.org/entry/618710"},{"mim_id":"618308","title":"NOP9 NUCLEOLAR PROTEIN; NOP9","url":"https://www.omim.org/entry/618308"},{"mim_id":"617754","title":"RIO KINASE 2; RIOK2","url":"https://www.omim.org/entry/617754"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Focal adhesion sites","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NOB1"},"hgnc":{"alias_symbol":["NOB1P","ART-4","MST158"],"prev_symbol":["PSMD8BP1"]},"alphafold":{"accession":"Q9ULX3","domains":[{"cath_id":"3.40.50.1010","chopping":"5-109_218-254","consensus_level":"high","plddt":89.6098,"start":5,"end":254},{"cath_id":"-","chopping":"265-358","consensus_level":"medium","plddt":83.9064,"start":265,"end":358}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULX3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULX3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULX3-F1-predicted_aligned_error_v6.png","plddt_mean":72.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NOB1","jax_strain_url":"https://www.jax.org/strain/search?query=NOB1"},"sequence":{"accession":"Q9ULX3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9ULX3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9ULX3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULX3"}},"corpus_meta":[{"pmid":"19801658","id":"PMC_19801658","title":"RNA helicase Prp43 and its co-factor Pfa1 promote 20 to 18 S rRNA processing catalyzed by the endonuclease Nob1.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19801658","citation_count":161,"is_preprint":false},{"pmid":"19706509","id":"PMC_19706509","title":"Nob1 binds the single-stranded cleavage site D at the 3'-end of 18S rRNA with its PIN domain.","date":"2009","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/19706509","citation_count":123,"is_preprint":false},{"pmid":"15388878","id":"PMC_15388878","title":"PIN domain of Nob1p is required for D-site cleavage in 20S pre-rRNA.","date":"2004","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/15388878","citation_count":107,"is_preprint":false},{"pmid":"29115574","id":"PMC_29115574","title":"Long non-coding RNA SNHG1 regulates NOB1 expression by sponging miR-326 and promotes tumorigenesis in osteosarcoma.","date":"2017","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/29115574","citation_count":91,"is_preprint":false},{"pmid":"12502737","id":"PMC_12502737","title":"Nob1p is required for biogenesis of the 26S proteasome and degraded upon its maturation in Saccharomyces cerevisiae.","date":"2002","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/12502737","citation_count":79,"is_preprint":false},{"pmid":"23869222","id":"PMC_23869222","title":"MicroRNA-326 functions as a tumor suppressor in glioma by targeting the Nin one binding protein (NOB1).","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23869222","citation_count":75,"is_preprint":false},{"pmid":"27733214","id":"PMC_27733214","title":"miR-326 Inhibits Gastric Cancer Cell Growth Through Downregulating NOB1.","date":"2016","source":"Oncology 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cisplatin-based chemotherapy in patients with advanced non-small cell lung cancer.","date":"2016","source":"Journal of chemotherapy (Florence, Italy)","url":"https://pubmed.ncbi.nlm.nih.gov/25971309","citation_count":7,"is_preprint":false},{"pmid":"29467874","id":"PMC_29467874","title":"Effects of NOB1 on the pathogenesis of osteosarcoma and its expression on the chemosensitivity to cisplatin.","date":"2018","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/29467874","citation_count":7,"is_preprint":false},{"pmid":"26370469","id":"PMC_26370469","title":"Downregulation of NOB1 inhibits proliferation and promotes apoptosis in human oral squamous cell carcinoma.","date":"2015","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/26370469","citation_count":7,"is_preprint":false},{"pmid":"35294329","id":"PMC_35294329","title":"Overexpression of microRNA-107 suppressed proliferation, migration, invasion, and the PI3K/Akt signaling pathway and induced apoptosis by targeting Nin one binding (NOB1) protein in a hypopharyngeal squamous cell carcinoma cell line (FaDu).","date":"2022","source":"Bioengineered","url":"https://pubmed.ncbi.nlm.nih.gov/35294329","citation_count":7,"is_preprint":false},{"pmid":"26617713","id":"PMC_26617713","title":"Anticancer activity of NOB1-targeted shRNA combination with TRAIL in epithelial ovarian cancer cells.","date":"2015","source":"International journal of clinical and experimental pathology","url":"https://pubmed.ncbi.nlm.nih.gov/26617713","citation_count":7,"is_preprint":false},{"pmid":"10075017","id":"PMC_10075017","title":"Analysis of interleukin (IL)-1 beta and transforming growth factor (TGF)-beta-induced signal transduction pathways in IL-2 and TGF-beta secretion and proliferation in the thymoma cell line EL4.NOB-1.","date":"1999","source":"Scandinavian journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/10075017","citation_count":7,"is_preprint":false},{"pmid":"31906747","id":"PMC_31906747","title":"Silencing NOB1 Can Affect Cell Proliferation and Apoptosis Via the C-Jun N-Terminal Kinase Pathway in Colorectal Cancer.","date":"2020","source":"Journal of investigative surgery : the official journal of the Academy of Surgical Research","url":"https://pubmed.ncbi.nlm.nih.gov/31906747","citation_count":6,"is_preprint":false},{"pmid":"26178254","id":"PMC_26178254","title":"Lentivirus-mediated gene silencing of NOB1 suppresses non-small cell lung cancer cell proliferation.","date":"2015","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/26178254","citation_count":5,"is_preprint":false},{"pmid":"30628685","id":"PMC_30628685","title":"MicroRNA‑744 suppresses cell proliferation and invasion of papillary thyroid cancer by directly targeting NOB1.","date":"2019","source":"Molecular medicine 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agents","url":"https://pubmed.ncbi.nlm.nih.gov/26122232","citation_count":4,"is_preprint":false},{"pmid":"34849026","id":"PMC_34849026","title":"Integrated Analysis of the m6A-Related lncRNA Identified lncRNA ABALON/miR-139-3p/NOB1 Axis Was Involved in the Occurrence of Lung Cancer.","date":"2021","source":"Cancer management and research","url":"https://pubmed.ncbi.nlm.nih.gov/34849026","citation_count":4,"is_preprint":false},{"pmid":"2018210","id":"PMC_2018210","title":"Biological assays for interleukin 1 detection. Comparison of human T lymphocyte, murine thymocyte and NOB-1 assays.","date":"1991","source":"Allergy","url":"https://pubmed.ncbi.nlm.nih.gov/2018210","citation_count":4,"is_preprint":false},{"pmid":"21732055","id":"PMC_21732055","title":"Backbone and side chain NMR resonance assignments for an archaeal homolog of the endonuclease Nob1 involved in ribosome biogenesis.","date":"2011","source":"Biomolecular NMR assignments","url":"https://pubmed.ncbi.nlm.nih.gov/21732055","citation_count":4,"is_preprint":false},{"pmid":"23172535","id":"PMC_23172535","title":"[Effect of lentivirus-mediated NOB1 gene silencing by RNA interference on proliferation and apoptosis of human colon cancer cells].","date":"2012","source":"Zhonghua wei chang wai ke za zhi = Chinese journal of gastrointestinal surgery","url":"https://pubmed.ncbi.nlm.nih.gov/23172535","citation_count":3,"is_preprint":false},{"pmid":"32020218","id":"PMC_32020218","title":"[Retracted] Downregulation of NOB1 suppresses the proliferation and tumor growth of non‑small cell lung cancer in vitro and in vivo.","date":"2020","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/32020218","citation_count":3,"is_preprint":false},{"pmid":"30377124","id":"PMC_30377124","title":"[Eukaryotic translation elongation factor 1A1 positively regulates NOB1 expression to promote invasion and metastasis of hepatocellular carcinoma cells in vitro].","date":"2018","source":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/30377124","citation_count":2,"is_preprint":false},{"pmid":"39143880","id":"PMC_39143880","title":"Ribosome Biogenesis and Cancer: Insights into NOB1 and PNO1 Mechanisms.","date":"2024","source":"Current pharmaceutical design","url":"https://pubmed.ncbi.nlm.nih.gov/39143880","citation_count":1,"is_preprint":false},{"pmid":"35836846","id":"PMC_35836846","title":"miRNA-612 suppresses ovarian cancer cell tumorigenicity by downregulating NOB1.","date":"2022","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/35836846","citation_count":1,"is_preprint":false},{"pmid":"36484386","id":"PMC_36484386","title":"[Corrigendum] Gene silencing of NOB1 by lentivirus suppresses growth and migration of human osteosarcoma cells.","date":"2022","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/36484386","citation_count":1,"is_preprint":false},{"pmid":"27097067","id":"PMC_27097067","title":"Establishment of a Novel Monoclonal Antibody L6 Specific to NOB1.","date":"2016","source":"Monoclonal antibodies in immunodiagnosis and immunotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/27097067","citation_count":1,"is_preprint":false},{"pmid":"35288316","id":"PMC_35288316","title":"Expression and distribution of Nob1 in the developing rat cochleae.","date":"2022","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/35288316","citation_count":0,"is_preprint":false},{"pmid":"40157618","id":"PMC_40157618","title":"The proximity proteome of pre-40S pre-ribosomal particle components PNO1 and NOB1 using turboID proximity labeling technology.","date":"2025","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/40157618","citation_count":0,"is_preprint":false},{"pmid":"37594052","id":"PMC_37594052","title":"[Retracted] MicroRNA‑744 suppresses cell proliferation and invasion of papillary thyroid cancer by directly targeting NOB1.","date":"2023","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/37594052","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":32725,"output_tokens":4197,"usd":0.080565,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12101,"output_tokens":2875,"usd":0.06619,"stage2_stop_reason":"end_turn"},"total_usd":0.146755,"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\": 2004,\n      \"finding\": \"The PIN domain of Nob1p is required for D-site cleavage of 20S pre-rRNA to generate mature 18S rRNA. A homology model of the PIN domain revealed structural mimicry of Mg2+-dependent exonucleases, and a point mutation predicted to abolish enzymatic activity abolished 20S pre-rRNA cleavage in vivo.\",\n      \"method\": \"Homology modeling, site-directed mutagenesis, in vivo pre-rRNA processing assay\",\n      \"journal\": \"RNA\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — active-site mutagenesis with in vivo functional readout, structural model validated by mutagenesis, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"15388878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Recombinant yeast Nob1 forms a tetramer that binds directly to pre-rRNA analogs containing the D-site cleavage region. RNA truncation and footprinting analyses showed Nob1's binding site centers around the single-stranded 3'-end of 18S rRNA, co-localizing with the proposed active site, positioning Nob1 for cleavage at site D.\",\n      \"method\": \"Recombinant protein binding assays, RNA truncation series, in vitro and in vivo Nob1-dependent RNA protection assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with recombinant protein, multiple orthogonal RNA binding assays, in vivo footprinting, single lab\",\n      \"pmids\": [\"19706509\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"In vivo cleavage of yeast pre-rRNA at site D requires functional interaction between the PIN domain endonuclease Nob1 and the DEAH-box RNA helicase Prp43 and its cofactor Pfa1. Nob1 cleaved a D-site substrate analogue in vitro; mutations in the Nob1 PIN domain or RNA substrate abolished this cleavage. Genetic epistasis showed that increased dosage of wild-type Nob1, but not catalytic-site mutants, suppressed 20S pre-rRNA accumulation caused by ltv1/pfa1 mutations.\",\n      \"method\": \"In vitro endonuclease assay with PIN domain mutants, genetic epistasis (suppressor dosage analysis), in vivo pre-rRNA processing analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro cleavage assay with mutagenesis corroborated by genetic epistasis, independently consistent with PMID:19706509 and 15388878\",\n      \"pmids\": [\"19801658\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The archaeal (Pyrococcus horikoshii) Nob1 homolog efficiently cleaves RNA substrates containing the D-site of pre-ribosomal RNA in a manganese-dependent manner. NMR structure revealed a PIN domain (required for substrate binding) connected by a flexible linker to a zinc ribbon domain that binds helix 40 of the small subunit rRNA and acts as an anchor on the nascent subunit.\",\n      \"method\": \"In vitro RNA cleavage assay, NMR structure determination, domain mutagenesis/deletion analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structure with functional validation by in vitro cleavage assay and domain-dissection experiments, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"22156373\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Yeast Nob1p forms a complex with the 19S regulatory particle of the 26S proteasome and with nuclear protein Pno1p. Temperature-sensitive nob1 mutants show defects in beta-subunit processing and 20S/26S proteasome assembly. Nob1p acts as a chaperone to join the 20S proteasome with the 19S regulatory particle in the nucleus, facilitate Ump1p degradation, and is then itself internalized and degraded to complete 26S proteasome biogenesis.\",\n      \"method\": \"Genetic analysis (ts mutants), overexpression rescue, co-fractionation, immunolocalization, proteasome assembly assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and cell-biological evidence with multiple readouts (assembly assays, localization, rescue), single lab\",\n      \"pmids\": [\"12502737\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Nob1p interacts with Nin1p/Rpn12 (a 19S regulatory particle subunit) of the yeast 26S proteasome as identified by two-hybrid screening, and co-immunoprecipitates with the ATPase component Rpt1. Nob1p is found exclusively in proteasomal fractions on glycerol gradients, and is degraded by the 26S proteasome during transition to stationary phase.\",\n      \"method\": \"Two-hybrid screening, glycerol gradient fractionation, co-immunoprecipitation, Western blot\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two-hybrid plus reciprocal co-IP plus fractionation, single lab\",\n      \"pmids\": [\"10675611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"The human NOB1 protein contains a PIN domain and a zinc ribbon domain. When expressed in mammalian culture cells, the NOB1 protein is mainly localized to the nucleus.\",\n      \"method\": \"Cloning, sequence analysis, Western blot, subcellular localization by imaging of expressed protein\",\n      \"journal\": \"Molecular biology reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, localization by overexpression without functional consequence reported\",\n      \"pmids\": [\"16172919\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"NOB1 is an archaeal/eukaryotic endonuclease with a PIN domain (residues required for substrate binding) and a zinc ribbon domain sufficient to bind helix 40 of the small subunit rRNA; NMR resonance assignments for the archaeal PhNob1 were determined as a structural prerequisite.\",\n      \"method\": \"NMR resonance assignment (backbone and side chain)\",\n      \"journal\": \"Biomolecular NMR assignments\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — NMR assignments only (prerequisite study), no functional validation in this paper alone; consistent with PMID:22156373\",\n      \"pmids\": [\"21732055\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"miR-326 directly targets the 3'-UTR of human NOB1 mRNA (validated by luciferase reporter assay), reducing NOB1 protein levels. NOB1 silencing in glioma cells (shRNA) causes G1 cell cycle arrest, reduced proliferation, enhanced apoptosis, and decreased colony formation, phenocopying miR-326 overexpression. NOB1 overexpression partially rescues miR-326-mediated growth inhibition. These effects involve the MAPK pathway.\",\n      \"method\": \"Dual-luciferase reporter assay (3'-UTR targeting), shRNA knockdown, cell cycle analysis, apoptosis assay, colony formation, xenograft model\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase reporter validation plus knockdown/rescue with multiple phenotypic readouts, single lab\",\n      \"pmids\": [\"23869222\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"NOB1 silencing in laryngeal cancer cells inhibits proliferation, induces cell cycle arrest and apoptosis, and inhibits migration and invasion with downregulation of MMP-2 and MMP-9. Mechanistically, NOB1 silencing activates the JNK signaling pathway.\",\n      \"method\": \"siRNA knockdown, proliferation/apoptosis/migration assays, Western blot (MMP-2/9, JNK pathway)\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single knockdown approach, pathway placement by protein level measurement only\",\n      \"pmids\": [\"27035645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Downregulation of NOB1 in papillary thyroid carcinoma cells by RNAi significantly activates constitutive phosphorylation of p38 MAPK, which may contribute to inhibition of cancer cell growth and enhances radiosensitivity in vitro and in vivo.\",\n      \"method\": \"Adenovirus-mediated siRNA, clonogenic survival assay, xenograft model, Western blot (p38 MAPK phosphorylation)\",\n      \"journal\": \"Oncology reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, pathway placement inferred from phospho-protein levels after knockdown, no direct epistasis\",\n      \"pmids\": [\"25231838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"eEF1A1 positively regulates NOB1 expression (mRNA and protein) in hepatocellular carcinoma cells. Knockdown of eEF1A1 reduces NOB1 expression and decreases HCC cell invasion and migration; eEF1A1 overexpression increases NOB1 expression and promotes invasion/migration. Restoring NOB1 in eEF1A1-knockdown cells rescues invasion/migration, while NOB1 knockdown in eEF1A1-overexpressing cells reverses the enhanced invasion/migration.\",\n      \"method\": \"siRNA knockdown, overexpression, qRT-PCR, Western blot, Transwell invasion/migration assays, RTCA assay, epistasis by rescue experiment\",\n      \"journal\": \"Nan fang yi ke da xue xue bao = Journal of Southern Medical University\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — bidirectional epistasis with rescue experiments and multiple orthogonal functional assays, single lab\",\n      \"pmids\": [\"30377124\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NOB1 knockdown in osteosarcoma cells (U2OS) decreases cell migration and increases E-cadherin and β-catenin expression, suggesting NOB1 suppresses these epithelial markers to promote migration.\",\n      \"method\": \"Lentiviral shRNA knockdown, Transwell migration assay, Western blot (E-cadherin, β-catenin)\",\n      \"journal\": \"Molecular medicine reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single knockdown method, molecular pathway placement limited to protein level measurement\",\n      \"pmids\": [\"24714960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TurboID proximity labeling identified 1044 proximal proteins for NOB1 (and 871 for PNO1), with 663 overlapping. NOB1 and PNO1 have different intracellular localizations (immunofluorescence). Co-IP validated interactions of both NOB1 and PNO1 with translation-related proteins EIF4B and EIF4G2. Proximal proteins are predominantly enriched in ribosome assembly, rRNA processing, and translation.\",\n      \"method\": \"TurboID proximity labeling, mass spectrometry, co-immunoprecipitation, immunofluorescence\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proximity proteomics validated by co-IP for specific interactions, single lab, new interactome data\",\n      \"pmids\": [\"40157618\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NOB1 silencing in colorectal cancer cells increases phosphorylation of JNK, ERK, and p38, suppresses proliferation and colony formation, and promotes apoptosis, placing NOB1 upstream of the JNK signaling pathway in these cells.\",\n      \"method\": \"siRNA knockdown, MTT assay, colony formation, flow cytometry, Western blot (phospho-JNK, -ERK, -p38)\",\n      \"journal\": \"Journal of investigative surgery\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, pathway placement by phosphorylation level measurement only, no epistasis experiment\",\n      \"pmids\": [\"31906747\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"miR-215 directly targets the 3'-UTR of NOB1 mRNA in epithelial ovarian cancer cells (validated by luciferase reporter assay), suppressing NOB1 expression. NOB1 suppression activates the MAPK signaling pathway. NOB1 overexpression rescues the anti-tumor effects of miR-215.\",\n      \"method\": \"Dual-luciferase reporter assay, miRNA mimic transfection, Western blot (MAPK), rescue overexpression\",\n      \"journal\": \"American journal of translational research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, MAPK activation inferred from protein levels without direct epistasis\",\n      \"pmids\": [\"28337275\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"NOB1 knockdown in ovarian cancer cells upregulates DR5 expression and activates the MAPK pathway, increasing sensitivity to TRAIL-induced apoptosis, including increased caspase-3, -8, and -9 activity.\",\n      \"method\": \"Lentiviral shRNA knockdown, TRAIL combination treatment, caspase activity assays, Western blot (DR5, MAPK), xenograft model\",\n      \"journal\": \"International journal of clinical and experimental pathology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mechanistic pathway placement by protein level measurement, no direct epistasis\",\n      \"pmids\": [\"26617713\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NOB1 is a conserved PIN-domain endonuclease that cleaves pre-rRNA at site D in a manganese-dependent manner to generate the mature 3'-end of 18S rRNA during cytoplasmic maturation of the pre-40S ribosomal subunit; its PIN domain mediates catalysis and substrate binding to the single-stranded D-site, while its zinc ribbon domain anchors it to helix 40 of the small subunit rRNA, and its activity is facilitated by the RNA helicase Prp43 and cofactor Pfa1. In yeast, NOB1 also associates with the 19S regulatory particle of the 26S proteasome via Nin1p/Rpn12 and acts as a chaperone for proteasome assembly before being degraded. In human cancer cells, NOB1 loss-of-function suppresses proliferation and promotes apoptosis, with evidence linking it to the MAPK and JNK signaling pathways, and its expression is regulated by multiple miRNAs targeting its 3'-UTR and by eEF1A1-dependent transcriptional/translational mechanisms.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NOB1 is a conserved PIN-domain endonuclease that executes the final processing step of small ribosomal subunit biogenesis by cleaving pre-rRNA at site D to generate the mature 3'-end of 18S rRNA [#0, #3]. Its catalytic PIN domain both binds the single-stranded D-site region and mediates manganese-dependent cleavage, with active-site point mutations abolishing 20S pre-rRNA processing in vivo and substrate cleavage in vitro [#0, #2, #3]; recombinant NOB1 binds directly to D-site-containing pre-rRNA analogs, positioning the active site over the cleavage site [#1]. A separate zinc ribbon domain, connected to the PIN domain by a flexible linker, anchors NOB1 to helix 40 of the small subunit rRNA on the nascent particle [#3, #7]. Efficient in vivo D-site cleavage requires functional cooperation with the DEAH-box RNA helicase Prp43 and its cofactor Pfa1 [#2], and proximity proteomics confirms NOB1 resides in an environment enriched for ribosome assembly, rRNA processing, and translation factors including EIF4B and EIF4G2 [#13]. Independently, in yeast NOB1 associates with the 19S regulatory particle of the 26S proteasome via Nin1p/Rpn12 and the ATPase Rpt1, acting as a chaperone for joining the 20S and 19S particles before being itself degraded [#4, #5]. In multiple human cancer cell types, NOB1 loss-of-function suppresses proliferation and colony formation and promotes apoptosis, with its mRNA directly targeted by miR-326 and miR-215 and its expression positively regulated by eEF1A1 [#8, #11, #15].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established the first physical context for Nob1p, placing it in the 26S proteasome rather than predicting an RNA-processing role.\",\n      \"evidence\": \"Two-hybrid screen, reciprocal co-IP, and glycerol gradient fractionation in yeast\",\n      \"pmids\": [\"10675611\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not establish a catalytic activity\", \"Did not address rRNA processing\", \"Mechanism of proteasome association unresolved\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Assigned Nob1p a chaperone role in 26S proteasome assembly, defining a function distinct from any ribosomal activity.\",\n      \"evidence\": \"ts mutants, overexpression rescue, co-fractionation, immunolocalization, and proteasome assembly assays in yeast\",\n      \"pmids\": [\"12502737\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relationship between proteasome and rRNA roles not reconciled\", \"Direct enzymatic mechanism not shown\", \"Conservation of proteasome role to humans untested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Identified the PIN domain as the catalytic module required for D-site cleavage of pre-rRNA, recasting NOB1 as the 18S rRNA 3'-end maturation endonuclease.\",\n      \"evidence\": \"Homology modeling plus active-site mutagenesis with in vivo pre-rRNA processing readout in yeast\",\n      \"pmids\": [\"15388878\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct in vitro cleavage not yet demonstrated\", \"Metal dependence inferred from homology only\", \"Substrate-binding determinants undefined\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrated direct, sequence-specific binding of NOB1 to the D-site region and reconstituted cleavage in vitro, linking binding geometry to catalysis.\",\n      \"evidence\": \"Recombinant protein binding, RNA truncation/footprinting, and in vitro endonuclease assays with PIN mutants, plus genetic epistasis with Prp43/Pfa1\",\n      \"pmids\": [\"19706509\", \"19801658\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Trigger for activation within the pre-40S particle unclear\", \"Precise role of Prp43 helicase activity in cleavage not defined\", \"Tetramer relevance in vivo uncertain\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Resolved the two-domain architecture, showing the PIN domain handles substrate binding/cleavage and a separate zinc ribbon anchors NOB1 to helix 40, and established manganese dependence.\",\n      \"evidence\": \"NMR structure, resonance assignments, in vitro cleavage, and domain dissection of the archaeal Pyrococcus horikoshii homolog\",\n      \"pmids\": [\"22156373\", \"21732055\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of the human enzyme not determined\", \"Conformational activation switch not captured\", \"Interplay of the two domains during catalysis on a real particle unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Connected NOB1 to cancer cell phenotypes, showing miRNA control of its 3'-UTR and eEF1A1-dependent regulation modulate proliferation, apoptosis, and invasion.\",\n      \"evidence\": \"Luciferase 3'-UTR reporters (miR-326, miR-215), knockdown/overexpression with rescue, and migration/invasion assays across glioma, ovarian, and hepatocellular carcinoma cells\",\n      \"pmids\": [\"23869222\", \"28337275\", \"30377124\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether phenotypes depend on NOB1 catalytic/ribosomal function untested\", \"Direct effectors downstream of NOB1 not defined\", \"Causal link from rRNA processing defect to apoptosis unestablished\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the human NOB1 proximity interactome, anchoring it in ribosome assembly, rRNA processing, and translation and validating direct contacts with translation factors.\",\n      \"evidence\": \"TurboID proximity labeling with mass spectrometry, co-IP validation (EIF4B, EIF4G2), and immunofluorescence comparison with PNO1\",\n      \"pmids\": [\"40157618\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of EIF4B/EIF4G2 contacts unknown\", \"Proximity does not establish stable complex membership\", \"Human D-site cleavage activity not directly assayed here\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NOB1's catalytic role in 18S rRNA maturation mechanistically connects to its observed proliferation/apoptosis phenotypes and signaling-pathway associations in human cancer cells remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No study links NOB1 endonuclease activity to MAPK/JNK signaling readouts\", \"Pathway placements rest on phospho-protein levels without epistasis\", \"No human structural or reconstituted cleavage data\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 1, 2, 3]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 2, 3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4, 6]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 2, 3, 13]}\n    ],\n    \"complexes\": [\"pre-40S ribosomal subunit\", \"26S proteasome (19S regulatory particle)\"],\n    \"partners\": [\"PRP43\", \"PFA1\", \"PNO1\", \"RPN12\", \"RPT1\", \"EIF4B\", \"EIF4G2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}