YAR1 encodes an ankyrin repeat protein that functions as a dedicated chaperone for the small ribosomal subunit protein Rps3. Yar1 binds newly synthesized Rps3, prevents Rps3 aggregation, supports its solubility and nuclear delivery, and thereby promotes small ribosomal subunit biogenesis and export.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific | IBA GO_REF:0000033 | REMOVE | Summary: The DNA-binding activator transfer is unlikely for the small Rps3-chaperone architecture. Reason: The target consists of a small ankyrin-repeat protein and lacks the APSES DNA-binding domain of SWI4/MBP1-like DNA-binding activators. Its established client-binding architecture and specific Rps3 chaperoning support rejection of this particular DNA-binding MF. This is a domain-specific judgment, not proof that an ankyrin protein cannot regulate transcription or join a transcription complex. The provider did not reconstruct the PAINT tree, and whole-protein acidity alone is not a DNA-binding exclusion test. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000917496 · PTN000917496 SUPPORTS SOURCE BUT NOT TARGET The source node includes APSES-domain transcription factors such as SWI4/MBP1; YAR1 shares ankyrin repeats but lacks the DNA-binding domain that confers GO:0001228 activity. Supporting Evidence: PMID:22570489 Yar1 directly interacts with the small ribosomal subunit protein Rps3 and accompanies newly synthesized Rps3 from the cytoplasm into the nucleus where Rps3 is assembled into pre-ribosomal subunits. file:yeast/YAR1/YAR1-hypotheses/function-hypothesis-go-0001228/openscientist.md The protein contains only two ankyrin repeats (residues 49–121) and no recognizable DNA-binding domain. |
| GO:0045944 positive regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | REMOVE | Summary: Positive Pol II transcription regulation is over-propagated through a broad ankyrin-repeat PAINT node. Reason: The current PAINT snapshot still places positive regulation of Pol II transcription at PTN000917496, a broad ankyrin-repeat fungal node that also covers genuine Swi4/Mbp1/Swi6-like transcription factors. A focused reassessment found no primary evidence that YAR1 promotes Pol II transcription and no MBF/SBF or IntAct support for contact with Swi4, Swi6, or Mbp1. Instead, the accessible direct literature places Yar1 on newly synthesized Rps3, whose solubility and delivery to pre-40S particles it supports. The broad ankyrin repeat is therefore the wrong basis for propagating a transcription-regulator BP term onto the Rps3 chaperone branch. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000917496 · PTN000917496 SUPPORTS SOURCE BUT NOT TARGET The node is supported for Swi4/Mbp1/Swi6-like fungal transcription regulators but also covers the divergent 200-aa YAR1/Rps3 chaperone branch, so the positive-transcription assertion should not descend to YAR1. Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. file:yeast/YAR1/YAR1-hypotheses/transcriptional-regulation-and-mbf-sbf-membership/openscientist.md There is **no primary experimental evidence** that Yar1 promotes RNA Pol II transcription |
| GO:0030907 MBF transcription complex | IBA GO_REF:0000033 | REMOVE | Summary: MBF membership is over-propagated from an ankyrin-repeat node that includes true MBF/SBF subunits. Reason: PTN000917496 currently carries MBF-complex membership from experimentally grounded fungal transcription factors, but Yar1 has target-specific Rps3 carrier-chaperone evidence and no curated placement in MBF. The focused MBF/SBF reassessment verified that the curated yeast MBF complex contains Mbp1 and Swi6 and not Yar1, and that Yar1 lacks Swi4, Swi6, or Mbp1 among its curated IntAct partners. Shared ankyrin repeats explain why the family groups Yar1 near MBF/SBF factors, but they are generic interaction modules and not evidence that the compact YAR1/Rps3-chaperone branch retained MBF membership. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000917496 · PTN000917496 SUPPORTS SOURCE BUT NOT TARGET The source node legitimately captures fungal MBF/SBF ankyrin-repeat regulators, but MBF membership does not transfer to the Yar1/Rps3 chaperone branch. Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. file:yeast/YAR1/YAR1-hypotheses/transcriptional-regulation-and-mbf-sbf-membership/openscientist.md SBF (CPX-946) = Swi4 + Swi6; MBF (CPX-950) = Mbp1 + Swi6; **Yar1/P46683 absent from both** file:yeast/YAR1/YAR1-hypotheses/transcriptional-regulation-and-mbf-sbf-membership/openscientist.md 15 records; partners = Rps3, Ltv1 + Hsp70/Hsp40 chaperones (Ssa1/2, Ssb1, Sse1, Sis1, Ydj1, Hsp78/26, Erj5, Ess1, Sfm1); **no Swi4/Swi6/Mbp1** |
| GO:0005515 protein binding | IPI PMID:15611164 Genetic and biochemical interactions among Yar1, Ltv1 and Rp... | REMOVE | Summary: Generic protein binding is uninformative about the demonstrated molecular role. Reason: The reported interactions are not denied. The chaperone mechanism is captured by the evidence-backed carrier-chaperone replacement; this generic interaction annotation does not independently establish a more specific activity. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: Generic protein binding is uninformative about the demonstrated molecular role. Reason: The reported interactions are not denied. The chaperone mechanism is captured by the evidence-backed carrier-chaperone replacement; this generic interaction annotation does not independently establish a more specific activity. |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Cytoplasmic localization is consistent with Yar1's interaction with newly synthesized Rps3. Reason: Yar1 binds nascent Rps3 in the cytoplasm before accompanying it to the nuclear pre-ribosome assembly site. |
| GO:0000056 ribosomal small subunit export from nucleus | IMP PMID:22570489 Yar1 protects the ribosomal protein Rps3 from aggregation. | KEEP AS NON CORE | Summary: Yar1 supports small-subunit export indirectly through Rps3 maturation and pre-40S biogenesis. Reason: yar1 deletion phenocopies ltv1 deletion with a small-subunit export defect; because Yar1 supplies assembly-competent Rps3 rather than performing nuclear export through the NPC, the BP annotation is retained as a non-core downstream consequence of its chaperone activity. Supporting Evidence: PMID:22570489 A yar1 deletion strain displays a similar phenotype as an rps3 mutant strain, showing an accumulation of 20S pre-rRNA and a 40S export defect. |
| GO:0000056 ribosomal small subunit export from nucleus | IGI PMID:22570489 Yar1 protects the ribosomal protein Rps3 from aggregation. | KEEP AS NON CORE | Summary: Genetic interaction evidence supports a Yar1 contribution to 40S export. Reason: The export phenotype follows from defective Rps3 handling and 40S maturation, so this is valid but downstream of Yar1's chaperone activity; Yar1 supplies an Rps3-containing pre-40S intermediate rather than directly executing the export step. |
| GO:0005634 nucleus | IDA PMID:22570489 Yar1 protects the ribosomal protein Rps3 from aggregation. | ACCEPT | Summary: Yar1 accompanies Rps3 into the nucleus during pre-ribosome assembly. Reason: Direct microscopy/biochemical evidence shows Yar1 travels with newly synthesized Rps3 from cytoplasm into the nucleus. Supporting Evidence: PMID:22570489 Yar1 directly interacts with the small ribosomal subunit protein Rps3 and accompanies newly synthesized Rps3 from the cytoplasm into the nucleus where Rps3 is assembled into pre-ribosomal subunits. |
| GO:0005634 nucleus | IGI PMID:22570489 Yar1 protects the ribosomal protein Rps3 from aggregation. | ACCEPT | Summary: Nuclear localization is consistent with Yar1's Rps3 delivery route. Reason: Yar1 escorts Rps3 to the nuclear pre-ribosome assembly compartment. |
| GO:0006970 response to osmotic stress | IMP PMID:15611164 Genetic and biochemical interactions among Yar1, Ltv1 and Rp... | KEEP AS NON CORE | Summary: Osmotic-stress phenotypes are secondary to Yar1's ribosome-biogenesis role. Reason: PMID:15611164 links yar1 deletion to environmental stress sensitivity, but the mechanistic basis is ribosome biogenesis and Rps3 handling rather than a dedicated stress-response function. |
| GO:0032880 regulation of protein localization | IMP PMID:22570489 Yar1 protects the ribosomal protein Rps3 from aggregation. | ACCEPT | Summary: Yar1 regulates Rps3 localization by keeping Rps3 soluble and escorting it to the nucleus. Reason: The term is retained as the curator's experimentally supported framing of Yar1's direct effect on Rps3 localization before pre-40S assembly; it is not being interpreted as a separate indirect signaling role. Supporting Evidence: PMID:22570489 Yar1 directly interacts with the small ribosomal subunit protein Rps3 and accompanies newly synthesized Rps3 from the cytoplasm into the nucleus where Rps3 is assembled into pre-ribosomal subunits. |
| GO:0032880 regulation of protein localization | IPI PMID:22570489 Yar1 protects the ribosomal protein Rps3 from aggregation. | ACCEPT | Summary: Protein-localization regulation is supported by Yar1-Rps3 interaction evidence. Reason: Yar1 binding promotes productive Rps3 delivery and suppresses defects caused by yar1 deletion. |
| GO:0034599 cellular response to oxidative stress | IMP PMID:15611164 Genetic and biochemical interactions among Yar1, Ltv1 and Rp... | KEEP AS NON CORE | Summary: Oxidative-stress phenotypes are retained as non-core. Reason: Stress sensitivity is experimentally observed in yar1 mutants, but available evidence points to ribosome biogenesis defects as the core molecular basis. |
| GO:0042274 ribosomal small subunit biogenesis | IMP PMID:15611164 Genetic and biochemical interactions among Yar1, Ltv1 and Rp... | ACCEPT | Summary: Ribosomal small subunit biogenesis is a core Yar1 biological role. Reason: Yar1 acts through Rps3, a 40S subunit protein; yar1 deletion causes ribosome-biogenesis defects that are suppressed by RPS3 overexpression. Supporting Evidence: PMID:15611164 Overexpression of RPS3 suppresses both the stress sensitivity and the ribosome biogenesis defect of Deltayar1 mutants, but does not suppress either defect in Deltaltv1 mutants. |
| GO:0042274 ribosomal small subunit biogenesis | IGI PMID:15611164 Genetic and biochemical interactions among Yar1, Ltv1 and Rp... | ACCEPT | Summary: Genetic interaction evidence supports Yar1 function in 40S biogenesis. Reason: Yar1, Ltv1, and Rps3 interactions define a pathway connecting Rps3 handling to small ribosomal subunit production. |
| GO:0000082 G1/S transition of mitotic cell cycle | IBA GO_REF:0000033 | REMOVE | Summary: The G1/S transition IBA is over-propagated from fungal MBF/SBF regulators. Reason: The refreshed 2026 GOA now propagates G1/S transition from PTN000917496, the same broad fungal ankyrin-repeat PAINT node that carries MBF/SBF and Pol II transcription terms. The source assertion is supported on Swi4/Mbp1/Swi6-like cell-cycle transcription regulators; Yar1's reported slow-proliferation phenotype is compatible with an indirect ribosome-biogenesis defect, not direct MBF/SBF transcriptional control by this compact Rps3 holdase-carrier chaperone. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000917496 · PTN000917496 SUPPORTS SOURCE BUT NOT TARGET The 2026 G1/S IBD at this node is appropriate for the fungal MBF/SBF regulator branch but should not descend to the Yar1/Rps3 carrier-chaperone branch. Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. |
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | REMOVE | Summary: The cis-regulatory DNA-binding IBA is a bad transfer from APSES-domain transcription factors. Reason: The 2026 GOA refresh newly propagates GO:0000978 from PTN000917496, but RNA polymerase II cis-regulatory region sequence-specific DNA binding requires the APSES DNA-binding domain present in Swi4/Mbp1-like sources and absent from Yar1. Yar1's ankyrin repeats mediate Rps3 binding, and the focused transcription/MBF/SBF reassessment found no primary evidence placing Yar1 on promoter DNA. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN000917496 · PTN000917496 SUPPORTS SOURCE BUT NOT TARGET The sequence-specific DNA-binding IBD reflects APSES-domain fungal transcription factors, not the divergent Yar1/Rps3 chaperone branch. Supporting Evidence: file:yeast/YAR1/YAR1-hypotheses/function-hypothesis-go-0001228/openscientist.md The protein contains only two ankyrin repeats (residues 49–121) and no recognizable DNA-binding domain. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: Cytoplasmic Yar1 is consistent with direct localization and its Rps3 capture step. Reason: Although this IBA descends from the same broad PTN000917496 node as the removed transcriptional assertions, the transferred compartment is a generic cytoplasmic location that agrees with independent SGD HDA evidence and with Yar1's direct capture of newly synthesized Rps3 before nuclear pre-40S assembly. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000917496 · PTN000917496 SUPPORTS TRANSFER Cytoplasmic localization is inherited and agrees with direct target evidence for the Rps3 carrier-chaperone cycle. Supporting Evidence: PMID:22570489 Yar1 directly interacts with the small ribosomal subunit protein Rps3 and accompanies newly synthesized Rps3 from the cytoplasm into the nucleus where Rps3 is assembled into pre-ribosomal subunits. |
| GO:0006457 protein folding | IEA GO_REF:0000108 | REMOVE | Summary: This electronic protein-folding BP follows from an over-broad MF edge. Reason: GO:0006457 entered the refreshed GOA by logical inference from the broad GO:0044183 protein folding chaperone assertion. Yar1's established activity is the more specific holdase-carrier capture and delivery of nascent Rps3 into the ribosome-biogenesis pathway, not a demonstrated role in folding the client protein itself; the existing Rps3 localization and 40S-biogenesis BP rows capture the supported process context. |
| GO:0044183 protein folding chaperone | IDA PMID:22570489 Yar1 protects the ribosomal protein Rps3 from aggregation. | MODIFY | Summary: Yar1 is a specific holdase-carrier rather than a generic protein folding chaperone. Reason: PMID:22570489 establishes Yar1-dependent protection of Rps3 from aggregation and increased Rps3 solubility, but GO:0044183 is broad and its current comment warns not to confuse folding chaperones with holdases that keep an unfolded protein soluble for delivery. GO:0140309 is the more specific term for Yar1's Rps3 holdase-carrier activity. Proposed replacements: unfolded protein holdase activity Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. |
| GO:0140309 unfolded protein holdase activity | IDA PMID:26112308 Co-translational capturing of nascent ribosomal proteins by ... | ACCEPT | Summary: Co-translational Rps3 capture supports Yar1 holdase-carrier activity. Reason: PMID:26112308 directly shows that Yar1 selectively associates with the mRNA encoding its cognate ribosomal-protein client Rps3 and fits the same mechanism established for Yar1/Rps3, binding a nascent aggregation-prone ribosomal protein and keeping that client assembly-competent until delivery to a ribosome-biogenesis acceptor. Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. |
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Download this section (compressed HTML)Q: Could wet-lab co-IP or proximity-labeling assays detect any endogenous Yar1 association with Swi4, Swi6, Mbp1, or another transcription complex that is absent from current Complex Portal and IntAct records?
Q: Should Yar1's direct cytoplasm-to-nucleus escort of Rps3 continue to be represented as regulation of protein localization, or should SGD migrate it to a non-regulatory protein localization term?
Experiment: Test whether point mutations that disrupt the Yar1-Rps3 interface abolish Rps3 solubility and nuclear delivery without broadly altering stress-response pathways.
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Download this section (compressed HTML)Nucleocytoplasmic shuttling assembly chaperone; co-translationally associates with nascent Rps3p in the cytoplasm and delivers it to pre-ribosomal subunits in the nucleus; required for 40S ribosomal subunit nuclear export, biogenesis and adaptation to osmotic and oxidative stress; contains ankyrin-repeats; expression repressed by heat shock
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