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 · PANTHER: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 | UNDECIDED | Summary: The transcription-regulatory or complex-membership inference requires a role-specific assessment. Reason: Absence of an APSES DNA-binding domain challenges the DNA-binding activator MF but does not exclude a non-DNA-binding transcriptional subunit or regulator; Swi6/Cdc10-like source roles make that distinction material. Small size, Rps3 chaperoning and lack of a retrieved target promoter assay do not by themselves establish a misplaced PAINT node or loss of complex participation. PTN000917496 is recovered for transcription regulation and MBF membership; the older SBF source row is absent from the current PAINT snapshot, which is a version discrepancy rather than evidence of biological impossibility. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN000917496 · PTN000917496 UNRESOLVED The source includes DNA-binding activators and non-DNA-binding transcription-complex regulators. Domain loss must be evaluated against the specific asserted role; no target complex-membership exclusion experiment or reconstructed loss event was provided. Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. |
| GO:0030907 MBF transcription complex | IBA GO_REF:0000033 | UNDECIDED | Summary: The transcription-regulatory or complex-membership inference requires a role-specific assessment. Reason: Absence of an APSES DNA-binding domain challenges the DNA-binding activator MF but does not exclude a non-DNA-binding transcriptional subunit or regulator; Swi6/Cdc10-like source roles make that distinction material. Small size, Rps3 chaperoning and lack of a retrieved target promoter assay do not by themselves establish a misplaced PAINT node or loss of complex participation. PTN000917496 is recovered for transcription regulation and MBF membership; the older SBF source row is absent from the current PAINT snapshot, which is a version discrepancy rather than evidence of biological impossibility. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN000917496 · PTN000917496 UNRESOLVED The source includes DNA-binding activators and non-DNA-binding transcription-complex regulators. Domain loss must be evaluated against the specific asserted role; no target complex-membership exclusion experiment or reconstructed loss event was provided. Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. |
| GO:0033309 SBF transcription complex | IBA GO_REF:0000033 | UNDECIDED | Summary: The transcription-regulatory or complex-membership inference requires a role-specific assessment. Reason: Absence of an APSES DNA-binding domain challenges the DNA-binding activator MF but does not exclude a non-DNA-binding transcriptional subunit or regulator; Swi6/Cdc10-like source roles make that distinction material. Small size, Rps3 chaperoning and lack of a retrieved target promoter assay do not by themselves establish a misplaced PAINT node or loss of complex participation. PTN000917496 is recovered for transcription regulation and MBF membership; the older SBF source row is absent from the current PAINT snapshot, which is a version discrepancy rather than evidence of biological impossibility. Propagation Review Root cause: UNRESOLVED Sources checked: PANTHER:PTN000917496 · PTN000917496 UNRESOLVED The source includes DNA-binding activators and non-DNA-binding transcription-complex regulators. Domain loss must be evaluated against the specific asserted role; no target complex-membership exclusion experiment or reconstructed loss event was provided. Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. |
| 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:0051082 unfolded protein binding | IDA PMID:26112308 Co-translational capturing of nascent ribosomal proteins by ... | MODIFY | Summary: GO:0051082 is obsolete; Yar1 acts as a dedicated protein-carrier chaperone for Rps3. Reason: Current GO marks GO:0051082 obsolete and recommends replacement by an activity term, with GO:0044183 and GO:0140309 as generic consider targets. Yar1 protects Rps3 from aggregation and keeps it soluble before pre-ribosome incorporation; the more specific GO:0140597 captures this carrier-chaperone role. Proposed replacements: protein carrier chaperone Supporting Evidence: PMID:22570489 Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo. |
| 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. | ACCEPT | 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 acts upstream by stabilizing Rps3, the BP annotation is retained. 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. | ACCEPT | 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. |
| 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:0051082 unfolded protein binding | IMP PMID:22570489 Yar1 protects the ribosomal protein Rps3 from aggregation. | MODIFY | Summary: GO:0051082 is obsolete; Yar1's substrate binding is a specific carrier-chaperone function for Rps3. Reason: Current GO marks GO:0051082 obsolete and recommends replacement by an activity term, with GO:0044183 and GO:0140309 as generic consider targets. The more specific GO:0140597 reflects Yar1's dedicated role in binding and carrying nascent Rps3 to prevent aggregation. Proposed replacements: protein carrier chaperone Supporting Evidence: PMID:26112308 Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients (Rpl3, Rpl5, Rpl10 and Rps3). |
Loading supporting content…
Download this section (compressed HTML)Q: Do endogenous Yar1 interaction or localization data support a secondary role with MBF/SBF or another transcription complex, distinct from its Rps3 chaperoning function?
Experiment: Test whether point mutations that disrupt the Yar1-Rps3 interface abolish Rps3 solubility and nuclear delivery without broadly altering stress-response pathways.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)