{"gene":"KRR1","run_date":"2026-06-10T02:59:49","timeline":{"discoveries":[{"year":2000,"finding":"Krr1p is localized to the nucleolus and is required for 40S ribosomal subunit biogenesis; depletion leads to failure to produce 18S rRNA (but not 25S rRNA), with reduced steady-state 18S rRNA and 20S pre-rRNA levels, establishing its specific role in small subunit pre-rRNA processing.","method":"Nucleolar localization by microscopy; polysome analysis; pulse-chase rRNA labeling; Northern blot in temperature-sensitive krr1 mutants and galactose-shutoff strains","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (pulse-chase, polysome profiling, Northern blot, co-IP) in a single focused study, independently corroborated by a second paper (PMID:11996121)","pmids":["11027267"],"is_preprint":false},{"year":2000,"finding":"Krr1p physically interacts with Kri1p (a novel essential nucleolar protein); co-immunoprecipitation of HA-Krr1p with Myc-Kri1p confirmed the interaction, and a temperature-sensitive krr1 mutant protein was defective in Kri1p binding, functionally linking the interaction to 40S biogenesis.","method":"Co-immunoprecipitation (reciprocal); two-hybrid screen; temperature-sensitive mutant analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP combined with mutant abrogation of interaction, replicated functionally in the same study","pmids":["11027267"],"is_preprint":false},{"year":2000,"finding":"Overexpression of RPS14A (encoding ribosomal protein rpS14p) suppresses the krr1 temperature-sensitive mutant; a C-terminally truncated rpS14p with diminished 18S rRNA binding activity failed to suppress, placing Krr1p genetically upstream of rpS14p-18S rRNA interaction in 40S assembly.","method":"Multicopy suppressor screen; complementation with truncated rpS14 construct","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with functional validation of suppressor specificity, single lab","pmids":["11027267"],"is_preprint":false},{"year":2000,"finding":"The KRR1 gene product (Krr1p) is essential for yeast viability; deletion prevents spore germination and cell division, and Krr1p is expressed in dividing cells but expression ceases in stationary phase; Krr1p is nucleolus-localized.","method":"Gene deletion; nucleolar localization by fractionation/immunofluorescence; growth-phase expression analysis","journal":"Acta biochimica Polonica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization and loss-of-function with defined phenotype, single lab with two reports","pmids":["11996121"],"is_preprint":false},{"year":2004,"finding":"Krr1p is a bona fide component of the small-subunit (SSU) processome, co-immunoprecipitating with Mpp10 (an SSU processome component), the U3 snoRNA, and pre-rRNAs, confirming its membership in this large ribonucleoprotein complex.","method":"Co-immunoprecipitation with SSU processome components (Mpp10, U3 snoRNA, pre-rRNAs)","journal":"Eukaryotic cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple co-IP targets used as criteria, part of a larger characterization study","pmids":["15590835"],"is_preprint":false},{"year":2004,"finding":"Faf1p is a novel nucleolar protein that physically interacts with Krr1p (identified by two-hybrid with Krr1p as bait); depletion of Faf1p impairs 40S ribosomal subunit biogenesis by decreasing 18S rRNA production via inefficient processing at A0, A1, and A2 cleavage sites.","method":"Two-hybrid screen using Krr1p as bait; depletion analysis; Northern blot for rRNA processing","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two-hybrid plus functional depletion analysis with rRNA processing readout, single lab","pmids":["15178413"],"is_preprint":false},{"year":2004,"finding":"Krr1p interacts physically with 13 S. cerevisiae ribosomal proteins as identified by tandem affinity purification (TAP); multicopy suppressors of a cold-sensitive krr1-21 mutant include translation elongation factor EF-1α, a putative ribose methyltransferase, and ribosomal protein genes.","method":"Tandem affinity purification (TAP); multicopy suppressor screen in cold-sensitive krr1-21 mutant","journal":"Acta biochimica Polonica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — TAP-MS for physical interactions combined with genetic suppressor screen, single lab","pmids":["15094838"],"is_preprint":false},{"year":2014,"finding":"Co-crystal structure of the core domain of Krr1 bound to a 19-residue fragment of Faf1 at 2.8 Å resolution reveals that Krr1 consists of two packed KH domains (KH1 and KH2): KH1 is a divergent KH domain lacking the canonical RNA-binding GXXG motif and mediates binding to Kri1, while KH2 contains a canonical RNA-binding surface and associates with an α-helix of Faf1.","method":"X-ray crystallography (co-crystal structure at 2.8 Å); site-directed mutagenesis of Krr1-Faf1 interface; in vivo functional assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with mutagenesis and in vivo functional validation in a single rigorous study","pmids":["24990943"],"is_preprint":false},{"year":2014,"finding":"Specific disruption of the Krr1-Faf1 interaction (by structure-guided mutagenesis) impaired early 18S rRNA processing at sites A0, A1, and A2 and caused cell lethality, but did not prevent incorporation of either protein into pre-ribosomes, indicating the Krr1-Faf1 interaction maintains a critical 90S pre-ribosome conformation for pre-rRNA processing.","method":"Structure-guided mutagenesis of the Krr1-Faf1 interface; Northern blot for rRNA processing; cell viability assay; pre-ribosome incorporation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — mutagenesis guided by crystal structure with multiple functional readouts, rigorous controls","pmids":["24990943"],"is_preprint":false},{"year":2015,"finding":"Krr1 is a component of the small subunit processome (SSUP) in mouse embryonic stem cells (ESCs); RNAi-mediated knockdown of Krr1 impairs 18S rRNA biogenesis, reduces global translational rate, and causes failure to maintain pluripotency factor protein levels (Nanog, Esrrb), establishing a functional link between Krr1-dependent ribosome biogenesis and stem cell pluripotency maintenance.","method":"RNAi screen; knockdown with pluripotency and translation phenotype readouts; 18S rRNA biogenesis assay","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic RNAi screen with defined molecular and cellular phenotypes, single lab","pmids":["26443847"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM analysis of 90S pre-ribosome assembly reveals that the snR30 snoRNP coordinates recruitment of the Krr1-Utp23-Kri1 subcomplex and ribosomal proteins uS11-uS15 to enable isolated platform subdomain assembly; Krr1-dependent release of snR30 culminates in integration of the platform into the 90S pre-ribosome.","method":"Cryo-EM structural analysis of 90S pre-ribosomes; RNA hybridization blocking assays; genetic and biochemical reconstitution","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure combined with biochemical validation, establishing mechanistic sequence of snR30 release and platform integration","pmids":["40399280"],"is_preprint":false}],"current_model":"KRR1 (Krr1p) is a conserved nucleolar protein that forms part of the small subunit (SSU) processome/90S pre-ribosome, where its two KH domains mediate distinct protein interactions: KH1 (lacking the canonical GXXG motif) binds assembly factor Kri1, while KH2 (canonical RNA-binding surface) binds assembly factor Faf1; the Krr1-Faf1 interaction is essential for maintaining the 90S pre-ribosome conformation required for early pre-18S rRNA processing at sites A0, A1, and A2, and Krr1-dependent release of the snR30/U17 snoRNP drives integration of the 40S platform subdomain into the 90S particle, ultimately producing the 18S rRNA and 40S small ribosomal subunit."},"narrative":{"mechanistic_narrative":"KRR1 (Krr1p) is a conserved, essential nucleolar protein that functions in early biogenesis of the small (40S) ribosomal subunit as a component of the small-subunit (SSU) processome/90S pre-ribosome [PMID:11027267, PMID:15590835]. It is specifically required for production of 18S rRNA: its depletion blocks pre-rRNA processing and reduces 18S and 20S pre-rRNA levels without affecting 25S rRNA, placing it genetically upstream of the rpS14-18S rRNA assembly interaction [PMID:11027267]. Krr1 is built from two packed KH domains with divergent roles: KH1, which lacks the canonical RNA-binding GXXG motif, binds the assembly factor Kri1, while the canonical KH2 surface engages an α-helix of the assembly factor Faf1 [PMID:11027267, PMID:15178413, PMID:24990943]. The Krr1-Faf1 interaction does not control incorporation of either protein into pre-ribosomes but maintains a critical 90S conformation needed for early cleavage at sites A0, A1, and A2, and its disruption is lethal [PMID:24990943]. Within the assembling particle, the snR30 snoRNP coordinates recruitment of a Krr1-Utp23-Kri1 subcomplex and ribosomal proteins uS11-uS15, and Krr1-dependent release of snR30 drives integration of the platform subdomain into the 90S pre-ribosome [PMID:40399280]. This biogenesis role is conserved in mammals, where Krr1 supports 18S rRNA production, global translation, and maintenance of pluripotency factor levels in mouse embryonic stem cells [PMID:26443847].","teleology":[{"year":2000,"claim":"Established that Krr1p is a nucleolar factor dedicated to small-subunit biogenesis rather than general ribosome production, defining its pathway specificity.","evidence":"Nucleolar localization, polysome analysis, pulse-chase and Northern blot in temperature-sensitive and shutoff yeast strains","pmids":["11027267"],"confidence":"High","gaps":["Did not identify which pre-rRNA cleavage step is directly catalyzed or chaperoned","No structural basis for substrate specificity"]},{"year":2000,"claim":"Identified Kri1p as a direct physical partner and linked the interaction functionally to 40S biogenesis, providing the first protein-interaction anchor for Krr1.","evidence":"Reciprocal co-immunoprecipitation, two-hybrid, and temperature-sensitive mutant defective in Kri1p binding in yeast","pmids":["11027267"],"confidence":"High","gaps":["Interaction surface on Krr1 not mapped at this stage","Order of recruitment relative to other factors unknown"]},{"year":2000,"claim":"Placed Krr1p upstream of the rpS14-18S rRNA interaction in 40S assembly through genetic epistasis.","evidence":"Multicopy suppression of krr1-ts by RPS14A and loss of suppression by an rpS14 truncation with reduced 18S binding","pmids":["11027267"],"confidence":"Medium","gaps":["Genetic suppression does not establish direct physical contact with rpS14","Mechanism by which Krr1 promotes rpS14 loading unresolved"]},{"year":2000,"claim":"Confirmed essentiality and growth-phase-restricted expression, tying Krr1p function to active cell division.","evidence":"Gene deletion, fractionation/immunofluorescence localization, and growth-phase expression analysis in yeast","pmids":["11996121"],"confidence":"Medium","gaps":["Regulation of growth-phase expression not mechanistically defined"]},{"year":2004,"claim":"Defined Krr1p as a bona fide SSU processome subunit, integrating it into a defined large RNP complex.","evidence":"Co-immunoprecipitation with Mpp10, U3 snoRNA, and pre-rRNAs in yeast","pmids":["15590835"],"confidence":"Medium","gaps":["Did not establish direct vs indirect association with U3 snoRNA","Position within the processome architecture unknown"]},{"year":2004,"claim":"Identified Faf1p as a second direct Krr1 partner whose depletion phenocopies Krr1 loss at A0/A1/A2 processing, expanding the interaction network controlling 18S production.","evidence":"Two-hybrid with Krr1p bait plus depletion and Northern blot rRNA-processing analysis in yeast","pmids":["15178413"],"confidence":"Medium","gaps":["Whether Faf1 binding is required for the same step as Kri1 binding unresolved at this stage","No structural detail of the interface"]},{"year":2004,"claim":"Broadened the physical interaction landscape of Krr1 to multiple ribosomal proteins and linked genetic suppressors to translation and rRNA modification factors.","evidence":"Tandem affinity purification and multicopy suppressor screen of the cold-sensitive krr1-21 mutant in yeast","pmids":["15094838"],"confidence":"Medium","gaps":["TAP interactions may reflect complex co-purification rather than direct contacts","Functional relevance of individual suppressors not dissected"]},{"year":2014,"claim":"Resolved the dual-KH architecture of Krr1 and assigned distinct partner-binding roles to KH1 (Kri1) and KH2 (Faf1), explaining how one protein bridges two assembly factors.","evidence":"2.8 Å co-crystal structure of the Krr1 core with a Faf1 fragment, interface mutagenesis, and in vivo assays","pmids":["24990943"],"confidence":"High","gaps":["Structure of the KH1-Kri1 interface not directly solved","RNA-binding role of the canonical KH2 surface not separated from Faf1 binding"]},{"year":2014,"claim":"Showed the Krr1-Faf1 contact maintains a required 90S conformation for early processing rather than controlling factor incorporation, refining the mechanistic role from recruitment to conformational scaffolding.","evidence":"Structure-guided interface mutagenesis with rRNA-processing, viability, and pre-ribosome incorporation readouts in yeast","pmids":["24990943"],"confidence":"High","gaps":["The precise conformational change stabilized is not visualized","How conformation couples to A0/A1/A2 cleavage chemistry is unknown"]},{"year":2015,"claim":"Extended Krr1 function to mammals and connected ribosome biogenesis to pluripotency, demonstrating physiological consequences beyond yeast.","evidence":"RNAi knockdown in mouse ESCs with 18S biogenesis, translation rate, and pluripotency factor readouts","pmids":["26443847"],"confidence":"Medium","gaps":["Direct molecular interactions of mammalian KRR1 not mapped","Whether pluripotency effect is purely translational is not fully resolved"]},{"year":2025,"claim":"Placed Krr1 in a defined assembly sequence in which snR30 coordinates recruitment of a Krr1-Utp23-Kri1 subcomplex and uS11-uS15, with Krr1-dependent snR30 release enabling platform integration into the 90S.","evidence":"Cryo-EM of 90S pre-ribosomes with RNA hybridization blocking and biochemical reconstitution","pmids":["40399280"],"confidence":"High","gaps":["The molecular trigger for Krr1-dependent snR30 release is not defined","Whether Krr1 acts catalytically or sterically in release is unresolved"]},{"year":null,"claim":"How Krr1-stabilized 90S conformation and snR30 release are mechanistically coupled to the chemistry of A0/A1/A2 cleavage remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structure capturing the cleavage-competent state","The catalytic nuclease(s) acted upon by Krr1-dependent conformational changes not connected to Krr1 directly"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,5,7]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[0,3]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,4,10]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,10]}],"complexes":["SSU processome / 90S pre-ribosome","Krr1-Utp23-Kri1 subcomplex"],"partners":["KRI1","FAF1","MPP10","UTP23","RPS14"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q13601","full_name":"KRR1 small subunit processome component homolog","aliases":["HIV-1 Rev-binding protein 2","KRR-R motif-containing protein 1","Rev-interacting protein 1","Rip-1"],"length_aa":381,"mass_kda":43.7,"function":"Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit. During the assembly of the SSU processome in the nucleolus, many ribosome biogenesis factors, an RNA chaperone and ribosomal proteins associate with the nascent pre-rRNA and work in concert to generate RNA folding, modifications, rearrangements and cleavage as well as targeted degradation of pre-ribosomal RNA by the RNA exosome","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q13601/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/KRR1","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":"NPM1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/KRR1","total_profiled":1310},"omim":[{"mim_id":"621355","title":"KRI1 HOMOLOG; KRI1","url":"https://www.omim.org/entry/621355"},{"mim_id":"612817","title":"KRR1 SMALL SUBUNITPROCESSOME COMPONENT HOMOLOG; KRR1","url":"https://www.omim.org/entry/612817"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoli","reliability":"Enhanced"},{"location":"Nucleoli rim","reliability":"Enhanced"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Mitotic chromosome","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/KRR1"},"hgnc":{"alias_symbol":["RIP-1"],"prev_symbol":["HRB2"]},"alphafold":{"accession":"Q13601","domains":[{"cath_id":"3.30.1370.10","chopping":"44-139","consensus_level":"medium","plddt":91.946,"start":44,"end":139},{"cath_id":"3.30.1370.10","chopping":"141-249","consensus_level":"medium","plddt":91.7542,"start":141,"end":249},{"cath_id":"1.20.5","chopping":"278-315","consensus_level":"high","plddt":89.2945,"start":278,"end":315}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13601","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13601-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13601-F1-predicted_aligned_error_v6.png","plddt_mean":81.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=KRR1","jax_strain_url":"https://www.jax.org/strain/search?query=KRR1"},"sequence":{"accession":"Q13601","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13601.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13601/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13601"}},"corpus_meta":[{"pmid":"26416764","id":"PMC_26416764","title":"Causal 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population.","date":"2024","source":"Journal of family medicine and primary care","url":"https://pubmed.ncbi.nlm.nih.gov/38482315","citation_count":0,"is_preprint":false},{"pmid":"42175431","id":"PMC_42175431","title":"Unveiling the proteomic landscape: Exploring differentially expressed proteins in patients with jaw cysts.","date":"2026","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/42175431","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":18710,"output_tokens":2783,"usd":0.048938,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9993,"output_tokens":3443,"usd":0.06802,"stage2_stop_reason":"end_turn"},"total_usd":0.116958,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"Krr1p is localized to the nucleolus and is required for 40S ribosomal subunit biogenesis; depletion leads to failure to produce 18S rRNA (but not 25S rRNA), with reduced steady-state 18S rRNA and 20S pre-rRNA levels, establishing its specific role in small subunit pre-rRNA processing.\",\n      \"method\": \"Nucleolar localization by microscopy; polysome analysis; pulse-chase rRNA labeling; Northern blot in temperature-sensitive krr1 mutants and galactose-shutoff strains\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (pulse-chase, polysome profiling, Northern blot, co-IP) in a single focused study, independently corroborated by a second paper (PMID:11996121)\",\n      \"pmids\": [\"11027267\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Krr1p physically interacts with Kri1p (a novel essential nucleolar protein); co-immunoprecipitation of HA-Krr1p with Myc-Kri1p confirmed the interaction, and a temperature-sensitive krr1 mutant protein was defective in Kri1p binding, functionally linking the interaction to 40S biogenesis.\",\n      \"method\": \"Co-immunoprecipitation (reciprocal); two-hybrid screen; temperature-sensitive mutant analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP combined with mutant abrogation of interaction, replicated functionally in the same study\",\n      \"pmids\": [\"11027267\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Overexpression of RPS14A (encoding ribosomal protein rpS14p) suppresses the krr1 temperature-sensitive mutant; a C-terminally truncated rpS14p with diminished 18S rRNA binding activity failed to suppress, placing Krr1p genetically upstream of rpS14p-18S rRNA interaction in 40S assembly.\",\n      \"method\": \"Multicopy suppressor screen; complementation with truncated rpS14 construct\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with functional validation of suppressor specificity, single lab\",\n      \"pmids\": [\"11027267\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"The KRR1 gene product (Krr1p) is essential for yeast viability; deletion prevents spore germination and cell division, and Krr1p is expressed in dividing cells but expression ceases in stationary phase; Krr1p is nucleolus-localized.\",\n      \"method\": \"Gene deletion; nucleolar localization by fractionation/immunofluorescence; growth-phase expression analysis\",\n      \"journal\": \"Acta biochimica Polonica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization and loss-of-function with defined phenotype, single lab with two reports\",\n      \"pmids\": [\"11996121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Krr1p is a bona fide component of the small-subunit (SSU) processome, co-immunoprecipitating with Mpp10 (an SSU processome component), the U3 snoRNA, and pre-rRNAs, confirming its membership in this large ribonucleoprotein complex.\",\n      \"method\": \"Co-immunoprecipitation with SSU processome components (Mpp10, U3 snoRNA, pre-rRNAs)\",\n      \"journal\": \"Eukaryotic cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple co-IP targets used as criteria, part of a larger characterization study\",\n      \"pmids\": [\"15590835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Faf1p is a novel nucleolar protein that physically interacts with Krr1p (identified by two-hybrid with Krr1p as bait); depletion of Faf1p impairs 40S ribosomal subunit biogenesis by decreasing 18S rRNA production via inefficient processing at A0, A1, and A2 cleavage sites.\",\n      \"method\": \"Two-hybrid screen using Krr1p as bait; depletion analysis; Northern blot for rRNA processing\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two-hybrid plus functional depletion analysis with rRNA processing readout, single lab\",\n      \"pmids\": [\"15178413\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Krr1p interacts physically with 13 S. cerevisiae ribosomal proteins as identified by tandem affinity purification (TAP); multicopy suppressors of a cold-sensitive krr1-21 mutant include translation elongation factor EF-1α, a putative ribose methyltransferase, and ribosomal protein genes.\",\n      \"method\": \"Tandem affinity purification (TAP); multicopy suppressor screen in cold-sensitive krr1-21 mutant\",\n      \"journal\": \"Acta biochimica Polonica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — TAP-MS for physical interactions combined with genetic suppressor screen, single lab\",\n      \"pmids\": [\"15094838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Co-crystal structure of the core domain of Krr1 bound to a 19-residue fragment of Faf1 at 2.8 Å resolution reveals that Krr1 consists of two packed KH domains (KH1 and KH2): KH1 is a divergent KH domain lacking the canonical RNA-binding GXXG motif and mediates binding to Kri1, while KH2 contains a canonical RNA-binding surface and associates with an α-helix of Faf1.\",\n      \"method\": \"X-ray crystallography (co-crystal structure at 2.8 Å); site-directed mutagenesis of Krr1-Faf1 interface; in vivo functional assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with mutagenesis and in vivo functional validation in a single rigorous study\",\n      \"pmids\": [\"24990943\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Specific disruption of the Krr1-Faf1 interaction (by structure-guided mutagenesis) impaired early 18S rRNA processing at sites A0, A1, and A2 and caused cell lethality, but did not prevent incorporation of either protein into pre-ribosomes, indicating the Krr1-Faf1 interaction maintains a critical 90S pre-ribosome conformation for pre-rRNA processing.\",\n      \"method\": \"Structure-guided mutagenesis of the Krr1-Faf1 interface; Northern blot for rRNA processing; cell viability assay; pre-ribosome incorporation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — mutagenesis guided by crystal structure with multiple functional readouts, rigorous controls\",\n      \"pmids\": [\"24990943\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Krr1 is a component of the small subunit processome (SSUP) in mouse embryonic stem cells (ESCs); RNAi-mediated knockdown of Krr1 impairs 18S rRNA biogenesis, reduces global translational rate, and causes failure to maintain pluripotency factor protein levels (Nanog, Esrrb), establishing a functional link between Krr1-dependent ribosome biogenesis and stem cell pluripotency maintenance.\",\n      \"method\": \"RNAi screen; knockdown with pluripotency and translation phenotype readouts; 18S rRNA biogenesis assay\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic RNAi screen with defined molecular and cellular phenotypes, single lab\",\n      \"pmids\": [\"26443847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM analysis of 90S pre-ribosome assembly reveals that the snR30 snoRNP coordinates recruitment of the Krr1-Utp23-Kri1 subcomplex and ribosomal proteins uS11-uS15 to enable isolated platform subdomain assembly; Krr1-dependent release of snR30 culminates in integration of the platform into the 90S pre-ribosome.\",\n      \"method\": \"Cryo-EM structural analysis of 90S pre-ribosomes; RNA hybridization blocking assays; genetic and biochemical reconstitution\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure combined with biochemical validation, establishing mechanistic sequence of snR30 release and platform integration\",\n      \"pmids\": [\"40399280\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"KRR1 (Krr1p) is a conserved nucleolar protein that forms part of the small subunit (SSU) processome/90S pre-ribosome, where its two KH domains mediate distinct protein interactions: KH1 (lacking the canonical GXXG motif) binds assembly factor Kri1, while KH2 (canonical RNA-binding surface) binds assembly factor Faf1; the Krr1-Faf1 interaction is essential for maintaining the 90S pre-ribosome conformation required for early pre-18S rRNA processing at sites A0, A1, and A2, and Krr1-dependent release of the snR30/U17 snoRNP drives integration of the 40S platform subdomain into the 90S particle, ultimately producing the 18S rRNA and 40S small ribosomal subunit.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"KRR1 (Krr1p) is a conserved, essential nucleolar protein that functions in early biogenesis of the small (40S) ribosomal subunit as a component of the small-subunit (SSU) processome/90S pre-ribosome [#0, #4]. It is specifically required for production of 18S rRNA: its depletion blocks pre-rRNA processing and reduces 18S and 20S pre-rRNA levels without affecting 25S rRNA, placing it genetically upstream of the rpS14-18S rRNA assembly interaction [#0, #2]. Krr1 is built from two packed KH domains with divergent roles: KH1, which lacks the canonical RNA-binding GXXG motif, binds the assembly factor Kri1, while the canonical KH2 surface engages an \\u03b1-helix of the assembly factor Faf1 [#1, #5, #7]. The Krr1-Faf1 interaction does not control incorporation of either protein into pre-ribosomes but maintains a critical 90S conformation needed for early cleavage at sites A0, A1, and A2, and its disruption is lethal [#8]. Within the assembling particle, the snR30 snoRNP coordinates recruitment of a Krr1-Utp23-Kri1 subcomplex and ribosomal proteins uS11-uS15, and Krr1-dependent release of snR30 drives integration of the platform subdomain into the 90S pre-ribosome [#10]. This biogenesis role is conserved in mammals, where Krr1 supports 18S rRNA production, global translation, and maintenance of pluripotency factor levels in mouse embryonic stem cells [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established that Krr1p is a nucleolar factor dedicated to small-subunit biogenesis rather than general ribosome production, defining its pathway specificity.\",\n      \"evidence\": \"Nucleolar localization, polysome analysis, pulse-chase and Northern blot in temperature-sensitive and shutoff yeast strains\",\n      \"pmids\": [\"11027267\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify which pre-rRNA cleavage step is directly catalyzed or chaperoned\", \"No structural basis for substrate specificity\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Identified Kri1p as a direct physical partner and linked the interaction functionally to 40S biogenesis, providing the first protein-interaction anchor for Krr1.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, two-hybrid, and temperature-sensitive mutant defective in Kri1p binding in yeast\",\n      \"pmids\": [\"11027267\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Interaction surface on Krr1 not mapped at this stage\", \"Order of recruitment relative to other factors unknown\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Placed Krr1p upstream of the rpS14-18S rRNA interaction in 40S assembly through genetic epistasis.\",\n      \"evidence\": \"Multicopy suppression of krr1-ts by RPS14A and loss of suppression by an rpS14 truncation with reduced 18S binding\",\n      \"pmids\": [\"11027267\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Genetic suppression does not establish direct physical contact with rpS14\", \"Mechanism by which Krr1 promotes rpS14 loading unresolved\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Confirmed essentiality and growth-phase-restricted expression, tying Krr1p function to active cell division.\",\n      \"evidence\": \"Gene deletion, fractionation/immunofluorescence localization, and growth-phase expression analysis in yeast\",\n      \"pmids\": [\"11996121\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Regulation of growth-phase expression not mechanistically defined\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Defined Krr1p as a bona fide SSU processome subunit, integrating it into a defined large RNP complex.\",\n      \"evidence\": \"Co-immunoprecipitation with Mpp10, U3 snoRNA, and pre-rRNAs in yeast\",\n      \"pmids\": [\"15590835\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not establish direct vs indirect association with U3 snoRNA\", \"Position within the processome architecture unknown\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Identified Faf1p as a second direct Krr1 partner whose depletion phenocopies Krr1 loss at A0/A1/A2 processing, expanding the interaction network controlling 18S production.\",\n      \"evidence\": \"Two-hybrid with Krr1p bait plus depletion and Northern blot rRNA-processing analysis in yeast\",\n      \"pmids\": [\"15178413\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether Faf1 binding is required for the same step as Kri1 binding unresolved at this stage\", \"No structural detail of the interface\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Broadened the physical interaction landscape of Krr1 to multiple ribosomal proteins and linked genetic suppressors to translation and rRNA modification factors.\",\n      \"evidence\": \"Tandem affinity purification and multicopy suppressor screen of the cold-sensitive krr1-21 mutant in yeast\",\n      \"pmids\": [\"15094838\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"TAP interactions may reflect complex co-purification rather than direct contacts\", \"Functional relevance of individual suppressors not dissected\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved the dual-KH architecture of Krr1 and assigned distinct partner-binding roles to KH1 (Kri1) and KH2 (Faf1), explaining how one protein bridges two assembly factors.\",\n      \"evidence\": \"2.8 \\u00c5 co-crystal structure of the Krr1 core with a Faf1 fragment, interface mutagenesis, and in vivo assays\",\n      \"pmids\": [\"24990943\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of the KH1-Kri1 interface not directly solved\", \"RNA-binding role of the canonical KH2 surface not separated from Faf1 binding\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed the Krr1-Faf1 contact maintains a required 90S conformation for early processing rather than controlling factor incorporation, refining the mechanistic role from recruitment to conformational scaffolding.\",\n      \"evidence\": \"Structure-guided interface mutagenesis with rRNA-processing, viability, and pre-ribosome incorporation readouts in yeast\",\n      \"pmids\": [\"24990943\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The precise conformational change stabilized is not visualized\", \"How conformation couples to A0/A1/A2 cleavage chemistry is unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Extended Krr1 function to mammals and connected ribosome biogenesis to pluripotency, demonstrating physiological consequences beyond yeast.\",\n      \"evidence\": \"RNAi knockdown in mouse ESCs with 18S biogenesis, translation rate, and pluripotency factor readouts\",\n      \"pmids\": [\"26443847\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular interactions of mammalian KRR1 not mapped\", \"Whether pluripotency effect is purely translational is not fully resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed Krr1 in a defined assembly sequence in which snR30 coordinates recruitment of a Krr1-Utp23-Kri1 subcomplex and uS11-uS15, with Krr1-dependent snR30 release enabling platform integration into the 90S.\",\n      \"evidence\": \"Cryo-EM of 90S pre-ribosomes with RNA hybridization blocking and biochemical reconstitution\",\n      \"pmids\": [\"40399280\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The molecular trigger for Krr1-dependent snR30 release is not defined\", \"Whether Krr1 acts catalytically or sterically in release is unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How Krr1-stabilized 90S conformation and snR30 release are mechanistically coupled to the chemistry of A0/A1/A2 cleavage remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure capturing the cleavage-competent state\", \"The catalytic nuclease(s) acted upon by Krr1-dependent conformational changes not connected to Krr1 directly\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 5, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 4, 10]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 10]}\n    ],\n    \"complexes\": [\n      \"SSU processome / 90S pre-ribosome\",\n      \"Krr1-Utp23-Kri1 subcomplex\"\n    ],\n    \"partners\": [\n      \"KRI1\",\n      \"FAF1\",\n      \"MPP10\",\n      \"UTP23\",\n      \"RPS14\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}