YAR1

UniProt ID: P46683
Organism: Saccharomyces cerevisiae
Review Status: COMPLETE
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Gene Description

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. The conserved ankyrin-repeat/PANTHER family context explains domain architecture but does not support transferred MBF/SBF transcription-complex annotations for yeast Yar1.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific
IBA
GO_REF:0000033
REMOVE
Summary: The IBA transcription-activator annotation is not supported for yeast Yar1.
Reason: The direct literature establishes Yar1 as an Rps3-specific ribosomal-protein chaperone, not as a DNA-binding transcription activator; this appears to be an inappropriate family transfer.
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.
GO:0045944 positive regulation of transcription by RNA polymerase II
IBA
GO_REF:0000033
REMOVE
Summary: Positive regulation of RNA polymerase II transcription is not supported as a direct Yar1 function.
Reason: Yar1's experimentally supported role is Rps3 chaperoning and 40S biogenesis; the transcription regulation annotation is inconsistent with the yeast evidence.
GO:0030907 MBF transcription complex
IBA
GO_REF:0000033
REMOVE
Summary: MBF transcription complex membership is not supported for yeast Yar1.
Reason: The PANTHER ankyrin-repeat family is broad and does not justify transferring MBF complex membership to Yar1; yeast evidence supports Rps3 binding instead.
Supporting Evidence:
file:interpro/panther/PTHR24198/PTHR24198-metadata.yaml
PTHR24198 is a broad ankyrin repeat domain-containing protein family rather than a Yar1-specific transcription complex family.
GO:0033309 SBF transcription complex
IBA
GO_REF:0000033
REMOVE
Summary: SBF transcription complex membership is not supported for yeast Yar1.
Reason: The experimentally supported Yar1 function is as a dedicated Rps3 chaperone in ribosome biogenesis, not as an SBF subunit.
GO:0005515 protein binding
IPI
PMID:15611164
Genetic and biochemical interactions among Yar1, Ltv1 and Rp...
MARK AS OVER ANNOTATED
Summary: Generic protein binding is uninformative for Yar1.
Reason: PMID:15611164 supports a specific Yar1-Rps3/Ltv1 ribosome-biogenesis context; the generic protein binding term should not replace the more informative chaperone and ribosome-biogenesis annotations.
GO:0005515 protein binding
IPI
PMID:37968396
The social and structural architecture of the yeast protein ...
MARK AS OVER ANNOTATED
Summary: Interactome-derived protein binding is too generic to retain as core.
Reason: The core molecular role is Rps3-specific chaperoning, not undifferentiated protein binding from a broad interactome.
GO:0051082 unfolded protein binding
IDA
PMID:26112308
Co-translational capturing of nascent ribosomal proteins by ...
MODIFY
Summary: Yar1 acts as a dedicated protein-carrier chaperone for Rps3, so the broader term should be replaced.
Reason: Yar1 protects Rps3 from aggregation and keeps it soluble before pre-ribosome incorporation; GO:0140597 captures this carrier-chaperone role better than generic unfolded-protein binding.
Proposed replacements: protein carrier chaperone
Supporting Evidence:
PMID:22570489
Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo.
file:yeast/YAR1/YAR1-deep-research-falcon.md
Falcon synthesis supports Yar1 as a dedicated Rps3 carrier chaperone rather than a general unfolded-protein binding factor.
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.
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 captures Yar1's direct effect on Rps3 localization before pre-40S assembly.
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.
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.
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: Yar1's substrate binding is a specific carrier-chaperone function for Rps3.
Reason: The replacement term 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.

Core Functions

Yar1 is a dedicated carrier chaperone for Rps3. It binds nascent Rps3, maintains Rps3 solubility, and accompanies Rps3 from cytoplasm to nucleus so it can be incorporated into pre-40S ribosomal particles.

Supporting Evidence:
  • PMID:22570489
    Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo.
  • PMID:26112308
    Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients.
  • file:yeast/YAR1/YAR1-deep-research-falcon.md
    Falcon literature synthesis supports Yar1 as an Rps3-specific ribosomal protein carrier chaperone.

References

Annotation inferences using phylogenetic trees
Global analysis of protein localization in budding yeast.
Genetic and biochemical interactions among Yar1, Ltv1 and Rps3 define novel links between environmental stress and ribosome biogenesis in Saccharomyces cerevisiae.
Yar1 protects the ribosomal protein Rps3 from aggregation.
Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones.
The social and structural architecture of the yeast protein interactome.
file:yeast/YAR1/YAR1-deep-research-falcon.md
Falcon deep research synthesis for YAR1
file:interpro/panther/PTHR24198/PTHR24198-metadata.yaml
PANTHER family PTHR24198 ankyrin repeat metadata

Suggested Questions for Experts

Q: Should yeast Yar1 annotations explicitly distinguish Rps3 carrier-chaperone activity from downstream 40S export phenotypes?

Suggested Experiments

Experiment: Test whether point mutations that disrupt the Yar1-Rps3 interface abolish Rps3 solubility and nuclear delivery without broadly altering stress-response pathways.

📚 Additional Documentation

Deep Research Falcon

(YAR1-deep-research-falcon.md)

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organism: yeast
gene_id: YAR1
gene_symbol: YAR1
uniprot_accession: P46683
protein_description: 'RecName: Full=Ankyrin repeat-containing protein YAR1;'
gene_info: Name=YAR1; OrderedLocusNames=YPL239W;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Not specified in UniProt
protein_domains: Ankyrin_rpt. (IPR002110); Ankyrin_rpt-contain_sf. (IPR036770);
Ank_2 (PF12796)
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P46683
  • Protein Description: RecName: Full=Ankyrin repeat-containing protein YAR1;
  • Gene Information: Name=YAR1; OrderedLocusNames=YPL239W;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Not specified in UniProt
  • Key Domains: Ankyrin_rpt. (IPR002110); Ankyrin_rpt-contain_sf. (IPR036770); Ank_2 (PF12796)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "YAR1" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'YAR1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene YAR1 (gene ID: YAR1, UniProt: P46683) in yeast.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

  • UniProt Accession: P46683
  • Protein Description: RecName: Full=Ankyrin repeat-containing protein YAR1;
  • Gene Information: Name=YAR1; OrderedLocusNames=YPL239W;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Not specified in UniProt
  • Key Domains: Ankyrin_rpt. (IPR002110); Ankyrin_rpt-contain_sf. (IPR036770); Ank_2 (PF12796)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "YAR1" matches the protein description above
  2. Verify the organism is correct: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  3. Check if protein family/domains align with what you find in literature
  4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'YAR1' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene YAR1 (gene ID: YAR1, UniProt: P46683) in yeast.

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Saccharomyces cerevisiae YAR1 (UniProt P46683; SGD locus YPL239W) — Functional Annotation

0. Target verification (critical disambiguation)

The gene/protein reviewed here is YAR1 / YPL239W from Saccharomyces cerevisiae strain S288c, matching UniProt accession P46683 and the protein name “Ankyrin repeat-containing protein Yar1”. Primary yeast studies explicitly refer to Yar1 as an ankyrin-repeat protein and experimentally connect it to ribosomal protein Rps3 (uS3) as its dedicated chaperone, aligning with the UniProt description and expected ankyrin-repeat domain function (protein–protein interaction) (koch2012yar1protectsthe pages 1-2, koch2012yar1protectsthe pages 1-1, pillet2017holdonto pages 3-4).

1. Key concepts and definitions (current understanding)

1.1 Dedicated ribosomal-protein chaperones

A central concept for YAR1 is the class of “dedicated chaperones”: specialized factors that bind a specific ribosomal protein (r-protein) to prevent its aggregation/misinteraction and to promote proper delivery to the ribosome assembly pathway. Reviews cite Yar1 as a canonical dedicated chaperone for Rps3/uS3, binding the Rps3 N-terminus (aa ~14–29) (pillet2017holdonto pages 3-4).

1.2 What Yar1 is (and is not)

Yar1 is not an enzyme and no catalytic reaction has been assigned in the cited primary literature; rather, it is best understood as an anti-aggregation, escort-type chaperone whose function is implemented by direct binding to its client ribosomal protein Rps3 (koch2012yar1protectsthe pages 1-2, koch2012yar1protectsthe pages 2-3).

2. Molecular function and mechanism

2.1 Primary molecular function: Rps3 anti-aggregation chaperone

Direct Yar1–Rps3 binding is supported by in vivo affinity purification (near-stoichiometric co-purification) and in vitro complex formation (co-expression/co-elution), consistent with a dedicated chaperone–client relationship (koch2012yar1protectsthe pages 2-3, koch2012yar1protectsthe pages 3-4). Yar1 increases Rps3 solubility and prevents Rps3 aggregation in vitro and in vivo, including experiments where Rps3 is largely insoluble unless Yar1 is present/co-expressed (koch2012yar1protectsthe pages 8-9, koch2012yar1protectsthe pages 2-3, koch2012yar1protectsthe pages 7-8). Mechanistically, an “RNA-mimic/shielding” interpretation has been proposed based on charge complementarity: Rps3 is highly basic while Yar1 is acidic, consistent with shielding basic rRNA-binding surfaces from aberrant interactions (koch2012yar1protectsthe pages 8-9).

2.2 Co-translational capture of nascent Rps3

A 2015 Nature Communications study tested the general hypothesis that dedicated r-protein chaperones capture their clients co-translationally. In that work, affinity purification of Yar1 enriched the mRNA encoding its client Rps3, supporting co-translational association of Yar1 with nascent Rps3 (publication date: 2015-06-26; URL: https://doi.org/10.1038/ncomms8494) (pausch2015cotranslationalcapturingof pages 1-2).

2.3 Nuclear import and handoff: coupling chaperoning to karyopherins

A 2016 Scientific Reports paper provides a detailed model for nuclear import of Rps3 together with Yar1. Key points:

  • Rps3 contains an N-terminal monopartite NLS (reported motif 7–10: KKRK) adjacent to the Yar1-binding region (publication date: 2016-11; URL: https://doi.org/10.1038/srep36714) (mitterer2016nuclearimportof pages 1-2, mitterer2016nuclearimportof pages 2-4).
  • The major import route is Kap60/Kap95 (importin α/β), with additional karyopherins contributing redundantly (mitterer2016nuclearimportof pages 1-2, mitterer2016nuclearimportof pages 2-4).
  • Kap60 and Yar1 compete for binding on the Rps3 N-domain in vitro, yet Kap60 is still found in Rps3/Yar1 complexes in vivo; this is explained by the fact that Rps3 is dimeric, allowing Yar1 to occupy one Rps3 N-domain while Kap60 binds the other, coordinating import while maintaining protection (mitterer2016nuclearimportof pages 1-2, mitterer2016nuclearimportof pages 2-4).

The key biochemical evidence for importin competition and the co-import model is shown in figures from this paper (mitterer2016nuclearimportof media 8e76864a, mitterer2016nuclearimportof media 4e812712).

3. Cellular localization

Steady-state localization of Yar1 is predominantly cytoplasmic, with evidence that Yar1 transiently enters the nucleus and is exported via Xpo1/CRM1 (based on nuclear accumulation upon Xpo1 inhibition). Because no Yar1 NLS was identified whereas Rps3’s N-terminus acts as an NLS, Yar1 is inferred to piggyback with Rps3 into the nucleus (koch2012yar1protectsthe pages 4-6, koch2012yar1protectsthe pages 3-4).

4. Biological role and pathways

4.1 Role in 40S small subunit biogenesis

Loss of YAR1 produces clear 40S ribosome biogenesis/maturation phenotypes. Yar1 acts upstream of Rps3 incorporation by ensuring a soluble supply of Rps3 for assembly. Consistent phenotypes reported include:

  • Accumulation of 20S pre-rRNA and defects consistent with impaired cytoplasmic maturation/export of pre-40S particles (koch2012yar1protectsthe pages 4-6, koch2012yar1protectsthe pages 6-7, koch2012yar1protectsthe pages 1-1).
  • Polysome/ribosome profile alterations: reduced 40S peak with excess free 60S and reduced polysomes (koch2012yar1protectsthe pages 6-7, loar2004geneticandbiochemical pages 9-11).

A 2004 Genetics paper reported that Yar1 physically and genetically interacts with Rps3 and functionally relates to the 40S biogenesis factor Ltv1, with both yar1 and ltv1 mutants showing 40S production defects and stress-sensitive phenotypes (publication date: 2004-12; URL: https://doi.org/10.1534/genetics.104.032656) (loar2004geneticandbiochemical pages 8-9, loar2004geneticandbiochemical pages 9-11). Importantly, RPS3 overexpression suppresses yar1 mutant phenotypes, supporting a model where Yar1’s key role is maintaining Rps3 function/availability (loar2004geneticandbiochemical pages 8-9, loar2004geneticandbiochemical pages 9-11).

5. Phenotypes and quantitative/statistical findings

5.1 Essentiality and growth

YAR1 is non-essential, but yar1Δ cells show slow growth, particularly at lower temperature, and phenotypes similar to compromised Rps3 function; combining yar1Δ with defective rps3 alleles can produce stronger defects including synthetic sickness/lethality (koch2012yar1protectsthe pages 4-6, koch2012yar1protectsthe pages 6-7).

5.2 Quantitative data (selected)

  • In early genetic/biochemical analyses, yar1 and ltv1 mutants exhibited an approximately ~50% reduction in the 40S:60S ratio relative to wild type (loar2004geneticandbiochemical pages 9-11).
  • In vitro anti-aggregation assays for Rps3 used ultracentrifugation (reported 200,000 g) and showed that Yar1 keeps Rps3 in the supernatant (soluble fraction) (koch2012yar1protectsthe pages 2-3, koch2012yar1protectsthe pages 7-8).
  • Dedicated-chaperone biology is motivated by very high ribosome production demand: exponentially growing yeast produce about ~2,000 ribosomes/min and thus must synthesize >160,000 ribosomal proteins/min (publication date: 2015-06-26; URL: https://doi.org/10.1038/ncomms8494) (pausch2015cotranslationalcapturingof pages 1-2).

6. Recent developments (prioritizing 2023–2024)

6.1 Ribosome repair under oxidative stress: Yar1 as a negative control for repair activity

A 2023 Molecular Cell study discovered a chaperone-directed ribosome repair mechanism in yeast for oxidatively damaged ribosomal proteins (notably Tsr2/Rps26). In that context, the authors report that chaperone-dependent release was specific to Tsr2/Rps26, because neither Rps2 nor Rps3 were released by their chaperones (Tsr4 and Yar1, respectively). Additionally, H2O2 exposure increased ribosome association for Tsr2 but not for Yar1, supporting that Yar1 is not acting as the cognate “release/repair” factor for oxidized Rps3 in the tested system (publication date: 2023-05; URL: https://doi.org/10.1016/j.molcel.2023.03.030) (yang2023chaperonedirectedribosomerepair pages 5-7).

6.2 Reviews (2024) integrating Yar1 into ribosome assembly/repair landscape

A 2024 Annual Review of Cell and Developmental Biology review synthesizes progress in ribosome assembly and repair and frames dedicated r-protein chaperones (including the Rps3 system) as part of broader ribosome homeostasis (publication date: 2024-10; URL: https://doi.org/10.1146/annurev-cellbio-111822-113326) (yang2024ribosomeassemblyand pages 8-9). A 2024 Biomolecules review focusing on the 40S “beak” region also discusses Rps3/uS3-centric pathways (including quality control and collision signaling at/near uS3) and notes the role of Yar1 in the assembly context (publication date: 2024-07; URL: https://doi.org/10.3390/biom14070882) (martinvillanueva2024thebeakof pages 10-11).

Overall, the 2023–2024 literature primarily extends context (ribosome repair and quality control; assembly–stress interfaces) rather than redefining Yar1’s core, best-supported role as the dedicated chaperone for Rps3 (yang2024ribosomeassemblyand pages 8-9, yang2023chaperonedirectedribosomerepair pages 5-7).

7. Current applications and real-world implementations

YAR1 is widely used as a model factor to study:

  • Protein quality control of ribosomal proteins (anti-aggregation strategies for basic r-proteins) (koch2012yar1protectsthe pages 1-2, koch2012yar1protectsthe pages 7-8).
  • Co-translational chaperoning (mRNA enrichment and nascent-chain capture paradigms) (pausch2015cotranslationalcapturingof pages 1-2).
  • Coordination between chaperoning and nuclear transport (handoff/competition between dedicated chaperone Yar1 and importin Kap60/Kap95) (mitterer2016nuclearimportof pages 1-2, mitterer2016nuclearimportof pages 2-4).

No Yar1-specific industrial or therapeutic application was identified in the retrieved evidence; its “real-world” impact is primarily as an experimentally tractable paradigm for eukaryotic ribosome biogenesis and proteostasis (pillet2017holdonto pages 3-4, yang2024ribosomeassemblyand pages 8-9).

8. Expert opinion and synthesis (authoritative interpretation)

The most consistent expert-level synthesis across primary and review sources is that Yar1’s primary, evolutionarily motivated job is to shield the aggregation-prone, basic N-terminal region of Rps3/uS3 from nonspecific interactions until it is safely delivered for 40S assembly (koch2012yar1protectsthe pages 1-2, pillet2017holdonto pages 3-4). The 2016 mechanistic import model further suggests that Yar1’s function is integrated into nucleocytoplasmic transport by an elegant “division of labor” on an Rps3 dimer: one N-domain protected by Yar1 while the other is engaged by Kap60 for import, enabling both protection and transport (mitterer2016nuclearimportof pages 2-4, mitterer2016nuclearimportof media 4e812712).

Evidence summary table

The following table consolidates key findings (function, partners, localization, phenotypes, quantitative data, and 2023–2024 context) with publication dates and URLs.

Aspect Concise finding Key evidence type Citations with URLs and publication dates
identity/domains Verified target is YAR1 / YPL239W / UniProt P46683 from Saccharomyces cerevisiae S288c; literature consistently describes Yar1 as an ankyrin-repeat-containing protein and a dedicated chaperone for ribosomal protein Rps3/uS3. Reviews note ankyrin-repeat architecture; primary studies identify direct Rps3 binding. (koch2012yar1protectsthe pages 1-1, pillet2017holdonto pages 3-4) biochem, review Koch et al., J Biol Chem (2012-06), https://doi.org/10.1074/jbc.m112.365791; Pillet et al., BioEssays (2017-01), https://doi.org/10.1002/bies.201600153
molecular function Yar1’s primary function is not enzymatic; it acts as a dedicated anti-aggregation chaperone for newly synthesized Rps3, maintaining Rps3 solubility until incorporation into pre-40S particles. Direct binding occurs with free, non-ribosome-bound Rps3. (koch2012yar1protectsthe pages 1-2, koch2012yar1protectsthe pages 1-1, koch2012yar1protectsthe pages 2-3) biochem, genetics Koch et al., J Biol Chem (2012-06), https://doi.org/10.1074/jbc.m112.365791
binding partners Best-supported binding partner is Rps3/uS3; Yar1 binds the N-terminal region of Rps3 (aa 14–29). In vivo complexes can also include Kap60/importin-α and Kap95/importin-β bound to dimeric Rps3/Yar1 assemblies during import. Earlier genetics also linked Yar1 functionally to Ltv1. (pausch2015cotranslationalcapturingof pages 1-2, mitterer2016nuclearimportof pages 1-2, mitterer2016nuclearimportof pages 2-4, loar2004geneticandbiochemical pages 8-9) biochem, cell bio, genetics Pausch et al., Nat Commun (2015-06-26), https://doi.org/10.1038/ncomms8494; Mitterer et al., Sci Rep (2016-11), https://doi.org/10.1038/srep36714; Loar et al., Genetics (2004-12), https://doi.org/10.1534/genetics.104.032656
mechanism Current model: Yar1 captures nascent Rps3 co-translationally, binds its N-domain, and protects the basic rRNA-binding region from aggregation. Rps3 contains an N-terminal monopartite NLS (7-KKRK-10) adjacent to the Yar1-binding site; Kap60/Kap95 mediate major nuclear import. Kap60 and Yar1 compete for the same Rps3 N-domain, but in vivo a ternary Rps3/Rps3/Yar1/Kap60/Kap95 import configuration can form because Rps3 is dimeric. (pausch2015cotranslationalcapturingof pages 1-2, mitterer2016nuclearimportof pages 1-2, mitterer2016nuclearimportof pages 2-4, mitterer2016nuclearimportof pages 4-5) biochem, cell bio, review Pausch et al., Nat Commun (2015-06-26), https://doi.org/10.1038/ncomms8494; Mitterer et al., Sci Rep (2016-11), https://doi.org/10.1038/srep36714
localization Yar1 is predominantly cytoplasmic at steady state but transiently enters the nucleus; nuclear accumulation after Xpo1/CRM1 export inhibition supports a shuttling role. Yar1 likely piggybacks into the nucleus with Rps3 because no Yar1 NLS was identified, whereas Rps3 has a functional NLS. (koch2012yar1protectsthe pages 4-6, koch2012yar1protectsthe pages 3-4, koch2012yar1protectsthe pages 8-9) cell bio, biochem Koch et al., J Biol Chem (2012-06), https://doi.org/10.1074/jbc.m112.365791
phenotypes YAR1 is nonessential, but deletion causes slow growth (especially at low temperature), 40S biogenesis defects, 20S pre-rRNA accumulation, 40S export defects, reduced 40S peak with excess free 60S, and fewer polysomes. RPS3 overexpression suppresses many yar1Δ phenotypes; combining yar1 defects with mutant rps3 alleles enhances phenotypes or causes synthetic lethality. (koch2012yar1protectsthe pages 4-6, koch2012yar1protectsthe pages 6-7, koch2012yar1protectsthe pages 1-1, loar2004geneticandbiochemical pages 9-11) genetics, cell bio Koch et al., J Biol Chem (2012-06), https://doi.org/10.1074/jbc.m112.365791; Loar et al., Genetics (2004-12), https://doi.org/10.1534/genetics.104.032656
quantitative stats Recent and foundational sources provide several useful numbers: yeast makes about ~2,000 ribosomes/min and therefore >160,000 ribosomal proteins/min in rapid growth; Yar1 binds Rps3 region aa 14–29; Rps3 NLS is aa 7–10 (KKRK); in vitro anti-aggregation assays used 20-fold excess Yar1 and 200,000 g centrifugation; yar1/ltv1 mutants show an approximately ~50% decrease in 40S:60S ratio relative to WT in early work. (pausch2015cotranslationalcapturingof pages 1-2, mitterer2016nuclearimportof pages 1-2, koch2012yar1protectsthe pages 2-3, loar2004geneticandbiochemical pages 9-11) biochem, genetics, review Pausch et al., Nat Commun (2015-06-26), https://doi.org/10.1038/ncomms8494; Mitterer et al., Sci Rep (2016-11), https://doi.org/10.1038/srep36714; Loar et al., Genetics (2004-12), https://doi.org/10.1534/genetics.104.032656; Koch et al., J Biol Chem (2012-06), https://doi.org/10.1074/jbc.m112.365791
recent developments 2023-2024 No major 2023–2024 primary study appears to redefine Yar1’s core function beyond Rps3 chaperoning/import. However, newer work places Yar1 in broader ribosome homeostasis context: importins can bind nascent cargo co-translationally in yeast proteostasis networks; 2023 ribosome-repair work found Yar1 does not release Rps3 from oxidized ribosomes, unlike Tsr2-Rps26, arguing Yar1 is not currently supported as a ribosome-repair factor; 2024 reviews continue to cite Yar1 as the canonical Rps3 chaperone in small-subunit assembly. (yang2023chaperonedirectedribosomerepair pages 5-7, yang2024ribosomeassemblyand pages 8-9, martinvillanueva2024thebeakof pages 10-11) primary, review Yang et al., Mol Cell (2023-05), https://doi.org/10.1016/j.molcel.2023.03.030; Yang & Karbstein, Annu Rev Cell Dev Biol (2024-10), https://doi.org/10.1146/annurev-cellbio-111822-113326; Martín-Villanueva et al., Biomolecules (2024-07), https://doi.org/10.3390/biom14070882
applications YAR1 is mainly used as a model dedicated ribosomal-protein chaperone for studying ribosome biogenesis, proteostasis, co-translational chaperoning, and nuclear import coordination. It is also a useful genetic tool to probe 40S assembly and stress-linked ribosome homeostasis, but there are no direct translational/industrial applications specific to YAR1 established in the cited literature. (pillet2017holdonto pages 3-4, yang2024ribosomeassemblyand pages 8-9, martinvillanueva2024thebeakof pages 10-11) review, genetics Pillet et al., BioEssays (2017-01), https://doi.org/10.1002/bies.201600153; Yang & Karbstein, Annu Rev Cell Dev Biol (2024-10), https://doi.org/10.1146/annurev-cellbio-111822-113326; Martín-Villanueva et al., Biomolecules (2024-07), https://doi.org/10.3390/biom14070882

Table: This table summarizes the most relevant evidence for the identity, function, mechanism, localization, phenotypes, and recent literature context of S. cerevisiae YAR1 (P46683/YPL239W). It is designed as a compact, citation-ready reference for the final research report.

Key primary sources (with publication dates and URLs)

  • Loar et al. 2004-12, Genetics: https://doi.org/10.1534/genetics.104.032656 (loar2004geneticandbiochemical pages 8-9, loar2004geneticandbiochemical pages 9-11)
  • Koch et al. 2012-06, J Biol Chem: https://doi.org/10.1074/jbc.m112.365791 (koch2012yar1protectsthe pages 4-6, koch2012yar1protectsthe pages 2-3)
  • Pausch et al. 2015-06-26, Nat Commun: https://doi.org/10.1038/ncomms8494 (pausch2015cotranslationalcapturingof pages 1-2)
  • Mitterer et al. 2016-11, Sci Rep: https://doi.org/10.1038/srep36714 (mitterer2016nuclearimportof pages 1-2, mitterer2016nuclearimportof media 4e812712)
  • Yang et al. 2023-05, Mol Cell: https://doi.org/10.1016/j.molcel.2023.03.030 (yang2023chaperonedirectedribosomerepair pages 5-7)
  • Yang & Karbstein 2024-10, Annu Rev Cell Dev Biol: https://doi.org/10.1146/annurev-cellbio-111822-113326 (yang2024ribosomeassemblyand pages 8-9)
  • Martín‑Villanueva et al. 2024-07, Biomolecules: https://doi.org/10.3390/biom14070882 (martinvillanueva2024thebeakof pages 10-11)

References

  1. (koch2012yar1protectsthe pages 1-2): Barbara Koch, Valentin Mitterer, Johannes Niederhauser, Tamsyn Stanborough, Guillaume Murat, Gerald Rechberger, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Yar1 protects the ribosomal protein rps3 from aggregation. Journal of Biological Chemistry, 287:21806-21815, Jun 2012. URL: https://doi.org/10.1074/jbc.m112.365791, doi:10.1074/jbc.m112.365791. This article has 78 citations and is from a domain leading peer-reviewed journal.

  2. (koch2012yar1protectsthe pages 1-1): Barbara Koch, Valentin Mitterer, Johannes Niederhauser, Tamsyn Stanborough, Guillaume Murat, Gerald Rechberger, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Yar1 protects the ribosomal protein rps3 from aggregation. Journal of Biological Chemistry, 287:21806-21815, Jun 2012. URL: https://doi.org/10.1074/jbc.m112.365791, doi:10.1074/jbc.m112.365791. This article has 78 citations and is from a domain leading peer-reviewed journal.

  3. (pillet2017holdonto pages 3-4): Benjamin Pillet, Valentin Mitterer, Dieter Kressler, and Brigitte Pertschy. Hold on to your friends: dedicated chaperones of ribosomal proteins. BioEssays, 39:1-12, Jan 2017. URL: https://doi.org/10.1002/bies.201600153, doi:10.1002/bies.201600153. This article has 93 citations and is from a peer-reviewed journal.

  4. (koch2012yar1protectsthe pages 2-3): Barbara Koch, Valentin Mitterer, Johannes Niederhauser, Tamsyn Stanborough, Guillaume Murat, Gerald Rechberger, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Yar1 protects the ribosomal protein rps3 from aggregation. Journal of Biological Chemistry, 287:21806-21815, Jun 2012. URL: https://doi.org/10.1074/jbc.m112.365791, doi:10.1074/jbc.m112.365791. This article has 78 citations and is from a domain leading peer-reviewed journal.

  5. (koch2012yar1protectsthe pages 3-4): Barbara Koch, Valentin Mitterer, Johannes Niederhauser, Tamsyn Stanborough, Guillaume Murat, Gerald Rechberger, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Yar1 protects the ribosomal protein rps3 from aggregation. Journal of Biological Chemistry, 287:21806-21815, Jun 2012. URL: https://doi.org/10.1074/jbc.m112.365791, doi:10.1074/jbc.m112.365791. This article has 78 citations and is from a domain leading peer-reviewed journal.

  6. (koch2012yar1protectsthe pages 8-9): Barbara Koch, Valentin Mitterer, Johannes Niederhauser, Tamsyn Stanborough, Guillaume Murat, Gerald Rechberger, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Yar1 protects the ribosomal protein rps3 from aggregation. Journal of Biological Chemistry, 287:21806-21815, Jun 2012. URL: https://doi.org/10.1074/jbc.m112.365791, doi:10.1074/jbc.m112.365791. This article has 78 citations and is from a domain leading peer-reviewed journal.

  7. (koch2012yar1protectsthe pages 7-8): Barbara Koch, Valentin Mitterer, Johannes Niederhauser, Tamsyn Stanborough, Guillaume Murat, Gerald Rechberger, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Yar1 protects the ribosomal protein rps3 from aggregation. Journal of Biological Chemistry, 287:21806-21815, Jun 2012. URL: https://doi.org/10.1074/jbc.m112.365791, doi:10.1074/jbc.m112.365791. This article has 78 citations and is from a domain leading peer-reviewed journal.

  8. (pausch2015cotranslationalcapturingof pages 1-2): Patrick Pausch, Ujjwala Singh, Yasar Luqman Ahmed, Benjamin Pillet, Guillaume Murat, Florian Altegoer, Gunter Stier, Matthias Thoms, Ed Hurt, Irmgard Sinning, Gert Bange, and Dieter Kressler. Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones. Nature Communications, Jun 2015. URL: https://doi.org/10.1038/ncomms8494, doi:10.1038/ncomms8494. This article has 93 citations and is from a highest quality peer-reviewed journal.

  9. (mitterer2016nuclearimportof pages 1-2): Valentin Mitterer, Nadine Gantenbein, Ruth Birner-Gruenberger, Guillaume Murat, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Nuclear import of dimerized ribosomal protein rps3 in complex with its chaperone yar1. Scientific Reports, Nov 2016. URL: https://doi.org/10.1038/srep36714, doi:10.1038/srep36714. This article has 38 citations and is from a peer-reviewed journal.

  10. (mitterer2016nuclearimportof pages 2-4): Valentin Mitterer, Nadine Gantenbein, Ruth Birner-Gruenberger, Guillaume Murat, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Nuclear import of dimerized ribosomal protein rps3 in complex with its chaperone yar1. Scientific Reports, Nov 2016. URL: https://doi.org/10.1038/srep36714, doi:10.1038/srep36714. This article has 38 citations and is from a peer-reviewed journal.

  11. (mitterer2016nuclearimportof media 8e76864a): Valentin Mitterer, Nadine Gantenbein, Ruth Birner-Gruenberger, Guillaume Murat, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Nuclear import of dimerized ribosomal protein rps3 in complex with its chaperone yar1. Scientific Reports, Nov 2016. URL: https://doi.org/10.1038/srep36714, doi:10.1038/srep36714. This article has 38 citations and is from a peer-reviewed journal.

  12. (mitterer2016nuclearimportof media 4e812712): Valentin Mitterer, Nadine Gantenbein, Ruth Birner-Gruenberger, Guillaume Murat, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Nuclear import of dimerized ribosomal protein rps3 in complex with its chaperone yar1. Scientific Reports, Nov 2016. URL: https://doi.org/10.1038/srep36714, doi:10.1038/srep36714. This article has 38 citations and is from a peer-reviewed journal.

  13. (koch2012yar1protectsthe pages 4-6): Barbara Koch, Valentin Mitterer, Johannes Niederhauser, Tamsyn Stanborough, Guillaume Murat, Gerald Rechberger, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Yar1 protects the ribosomal protein rps3 from aggregation. Journal of Biological Chemistry, 287:21806-21815, Jun 2012. URL: https://doi.org/10.1074/jbc.m112.365791, doi:10.1074/jbc.m112.365791. This article has 78 citations and is from a domain leading peer-reviewed journal.

  14. (koch2012yar1protectsthe pages 6-7): Barbara Koch, Valentin Mitterer, Johannes Niederhauser, Tamsyn Stanborough, Guillaume Murat, Gerald Rechberger, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Yar1 protects the ribosomal protein rps3 from aggregation. Journal of Biological Chemistry, 287:21806-21815, Jun 2012. URL: https://doi.org/10.1074/jbc.m112.365791, doi:10.1074/jbc.m112.365791. This article has 78 citations and is from a domain leading peer-reviewed journal.

  15. (loar2004geneticandbiochemical pages 9-11): Jesse W Loar, Robert M Seiser, Alexandra E Sundberg, Holly J Sagerson, Nasreen Ilias, Pamela Zobel-Thropp, Elizabeth A Craig, and Deborah E Lycan. Genetic and biochemical interactions among yar1, ltv1 and rps3 define novel links between environmental stress and ribosome biogenesis in saccharomyces cerevisiae. Genetics, 168:1877-1889, Dec 2004. URL: https://doi.org/10.1534/genetics.104.032656, doi:10.1534/genetics.104.032656. This article has 70 citations and is from a domain leading peer-reviewed journal.

  16. (loar2004geneticandbiochemical pages 8-9): Jesse W Loar, Robert M Seiser, Alexandra E Sundberg, Holly J Sagerson, Nasreen Ilias, Pamela Zobel-Thropp, Elizabeth A Craig, and Deborah E Lycan. Genetic and biochemical interactions among yar1, ltv1 and rps3 define novel links between environmental stress and ribosome biogenesis in saccharomyces cerevisiae. Genetics, 168:1877-1889, Dec 2004. URL: https://doi.org/10.1534/genetics.104.032656, doi:10.1534/genetics.104.032656. This article has 70 citations and is from a domain leading peer-reviewed journal.

  17. (yang2023chaperonedirectedribosomerepair pages 5-7): Yoon-Mo Yang, Youngeun Jung, Daniel Abegg, Alexander Adibekian, Kate S. Carroll, and Katrin Karbstein. Chaperone-directed ribosome repair after oxidative damage. Molecular Cell, 83:1527-1537.e5, May 2023. URL: https://doi.org/10.1016/j.molcel.2023.03.030, doi:10.1016/j.molcel.2023.03.030. This article has 70 citations and is from a highest quality peer-reviewed journal.

  18. (yang2024ribosomeassemblyand pages 8-9): Yoon-Mo Yang and Katrin Karbstein. Ribosome assembly and repair. Annual Review of Cell and Developmental Biology, 40:241-264, Oct 2024. URL: https://doi.org/10.1146/annurev-cellbio-111822-113326, doi:10.1146/annurev-cellbio-111822-113326. This article has 18 citations and is from a domain leading peer-reviewed journal.

  19. (martinvillanueva2024thebeakof pages 10-11): Sara Martín-Villanueva, Carla V. Galmozzi, Carmen Ruger-Herreros, Dieter Kressler, and Jesús de la Cruz. The beak of eukaryotic ribosomes: life, work and miracles. Biomolecules, 14:882, Jul 2024. URL: https://doi.org/10.3390/biom14070882, doi:10.3390/biom14070882. This article has 4 citations.

  20. (mitterer2016nuclearimportof pages 4-5): Valentin Mitterer, Nadine Gantenbein, Ruth Birner-Gruenberger, Guillaume Murat, Helmut Bergler, Dieter Kressler, and Brigitte Pertschy. Nuclear import of dimerized ribosomal protein rps3 in complex with its chaperone yar1. Scientific Reports, Nov 2016. URL: https://doi.org/10.1038/srep36714, doi:10.1038/srep36714. This article has 38 citations and is from a peer-reviewed journal.

Citations

  1. pillet2017holdonto pages 3-4
  2. pausch2015cotranslationalcapturingof pages 1-2
  3. loar2004geneticandbiochemical pages 9-11
  4. yang2023chaperonedirectedribosomerepair pages 5-7
  5. yang2024ribosomeassemblyand pages 8-9
  6. martinvillanueva2024thebeakof pages 10-11
  7. mitterer2016nuclearimportof pages 1-2
  8. mitterer2016nuclearimportof pages 2-4
  9. loar2004geneticandbiochemical pages 8-9
  10. mitterer2016nuclearimportof pages 4-5
  11. https://doi.org/10.1038/ncomms8494
  12. https://doi.org/10.1038/srep36714
  13. https://doi.org/10.1534/genetics.104.032656
  14. https://doi.org/10.1016/j.molcel.2023.03.030
  15. https://doi.org/10.1146/annurev-cellbio-111822-113326
  16. https://doi.org/10.3390/biom14070882
  17. https://doi.org/10.1074/jbc.m112.365791;
  18. https://doi.org/10.1002/bies.201600153
  19. https://doi.org/10.1074/jbc.m112.365791
  20. https://doi.org/10.1038/ncomms8494;
  21. https://doi.org/10.1038/srep36714;
  22. https://doi.org/10.1534/genetics.104.032656;
  23. https://doi.org/10.1016/j.molcel.2023.03.030;
  24. https://doi.org/10.1146/annurev-cellbio-111822-113326;
  25. https://doi.org/10.1002/bies.201600153;
  26. https://doi.org/10.1074/jbc.m112.365791,
  27. https://doi.org/10.1002/bies.201600153,
  28. https://doi.org/10.1038/ncomms8494,
  29. https://doi.org/10.1038/srep36714,
  30. https://doi.org/10.1534/genetics.104.032656,
  31. https://doi.org/10.1016/j.molcel.2023.03.030,
  32. https://doi.org/10.1146/annurev-cellbio-111822-113326,
  33. https://doi.org/10.3390/biom14070882,

📄 View Raw YAML

id: P46683
gene_symbol: YAR1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  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. The conserved
  ankyrin-repeat/PANTHER family context explains domain architecture but does
  not support transferred MBF/SBF transcription-complex annotations for yeast
  Yar1.
existing_annotations:
- term:
    id: GO:0001228
    label: DNA-binding transcription activator activity, RNA polymerase II-specific
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: The IBA transcription-activator annotation is not supported for yeast Yar1.
    action: REMOVE
    reason: The direct literature establishes Yar1 as an Rps3-specific ribosomal-protein chaperone, not as a DNA-binding transcription activator; this appears to be an inappropriate family transfer.
    supported_by:
    - reference_id: PMID:22570489
      supporting_text: Yar1 directly interacts with the small ribosomal subunit protein Rps3 and accompanies newly synthesized Rps3 from the cytoplasm into the nucleus.
- term:
    id: GO:0045944
    label: positive regulation of transcription by RNA polymerase II
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Positive regulation of RNA polymerase II transcription is not supported as a direct Yar1 function.
    action: REMOVE
    reason: Yar1's experimentally supported role is Rps3 chaperoning and 40S biogenesis; the transcription regulation annotation is inconsistent with the yeast evidence.
- term:
    id: GO:0030907
    label: MBF transcription complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: MBF transcription complex membership is not supported for yeast Yar1.
    action: REMOVE
    reason: The PANTHER ankyrin-repeat family is broad and does not justify transferring MBF complex membership to Yar1; yeast evidence supports Rps3 binding instead.
    supported_by:
    - reference_id: file:interpro/panther/PTHR24198/PTHR24198-metadata.yaml
      supporting_text: PTHR24198 is a broad ankyrin repeat domain-containing protein family rather than a Yar1-specific transcription complex family.
- term:
    id: GO:0033309
    label: SBF transcription complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: SBF transcription complex membership is not supported for yeast Yar1.
    action: REMOVE
    reason: The experimentally supported Yar1 function is as a dedicated Rps3 chaperone in ribosome biogenesis, not as an SBF subunit.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15611164
  review:
    summary: Generic protein binding is uninformative for Yar1.
    action: MARK_AS_OVER_ANNOTATED
    reason: PMID:15611164 supports a specific Yar1-Rps3/Ltv1 ribosome-biogenesis context; the generic protein binding term should not replace the more informative chaperone and ribosome-biogenesis annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37968396
  review:
    summary: Interactome-derived protein binding is too generic to retain as core.
    action: MARK_AS_OVER_ANNOTATED
    reason: The core molecular role is Rps3-specific chaperoning, not undifferentiated protein binding from a broad interactome.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:26112308
  review:
    summary: Yar1 acts as a dedicated protein-carrier chaperone for Rps3, so the broader term should be replaced.
    action: MODIFY
    reason: Yar1 protects Rps3 from aggregation and keeps it soluble before pre-ribosome incorporation; GO:0140597 captures this carrier-chaperone role better than generic unfolded-protein binding.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
    supported_by:
    - reference_id: PMID:22570489
      supporting_text: Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo.
    - reference_id: file:yeast/YAR1/YAR1-deep-research-falcon.md
      supporting_text: Falcon synthesis supports Yar1 as a dedicated Rps3 carrier chaperone rather than a general unfolded-protein binding factor.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:14562095
  review:
    summary: Cytoplasmic localization is consistent with Yar1's interaction with newly synthesized Rps3.
    action: ACCEPT
    reason: Yar1 binds nascent Rps3 in the cytoplasm before accompanying it to the nuclear pre-ribosome assembly site.
- term:
    id: GO:0000056
    label: ribosomal small subunit export from nucleus
  evidence_type: IMP
  original_reference_id: PMID:22570489
  review:
    summary: Yar1 supports small-subunit export indirectly through Rps3 maturation and pre-40S biogenesis.
    action: ACCEPT
    reason: yar1 deletion phenocopies ltv1 deletion with a small-subunit export defect; because Yar1 acts upstream by stabilizing Rps3, the BP annotation is retained.
    supported_by:
    - reference_id: PMID:22570489
      supporting_text: 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.
- term:
    id: GO:0000056
    label: ribosomal small subunit export from nucleus
  evidence_type: IGI
  original_reference_id: PMID:22570489
  review:
    summary: Genetic interaction evidence supports a Yar1 contribution to 40S export.
    action: ACCEPT
    reason: The export phenotype follows from defective Rps3 handling and 40S maturation, so this is valid but downstream of Yar1's chaperone activity.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IDA
  original_reference_id: PMID:22570489
  review:
    summary: Yar1 accompanies Rps3 into the nucleus during pre-ribosome assembly.
    action: ACCEPT
    reason: Direct microscopy/biochemical evidence shows Yar1 travels with newly synthesized Rps3 from cytoplasm into the nucleus.
    supported_by:
    - reference_id: PMID:22570489
      supporting_text: Yar1 directly interacts with the small ribosomal subunit protein Rps3 and accompanies newly synthesized Rps3 from the cytoplasm into the nucleus.
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IGI
  original_reference_id: PMID:22570489
  review:
    summary: Nuclear localization is consistent with Yar1's Rps3 delivery route.
    action: ACCEPT
    reason: Yar1 escorts Rps3 to the nuclear pre-ribosome assembly compartment.
- term:
    id: GO:0006970
    label: response to osmotic stress
  evidence_type: IMP
  original_reference_id: PMID:15611164
  review:
    summary: Osmotic-stress phenotypes are secondary to Yar1's ribosome-biogenesis role.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0032880
    label: regulation of protein localization
  evidence_type: IMP
  original_reference_id: PMID:22570489
  review:
    summary: Yar1 regulates Rps3 localization by keeping Rps3 soluble and escorting it to the nucleus.
    action: ACCEPT
    reason: The term captures Yar1's direct effect on Rps3 localization before pre-40S assembly.
    supported_by:
    - reference_id: PMID:22570489
      supporting_text: Yar1 directly interacts with the small ribosomal subunit protein Rps3 and accompanies newly synthesized Rps3 from the cytoplasm into the nucleus.
- term:
    id: GO:0032880
    label: regulation of protein localization
  evidence_type: IPI
  original_reference_id: PMID:22570489
  review:
    summary: Protein-localization regulation is supported by Yar1-Rps3 interaction evidence.
    action: ACCEPT
    reason: Yar1 binding promotes productive Rps3 delivery and suppresses defects caused by yar1 deletion.
- term:
    id: GO:0034599
    label: cellular response to oxidative stress
  evidence_type: IMP
  original_reference_id: PMID:15611164
  review:
    summary: Oxidative-stress phenotypes are retained as non-core.
    action: KEEP_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.
- term:
    id: GO:0042274
    label: ribosomal small subunit biogenesis
  evidence_type: IMP
  original_reference_id: PMID:15611164
  review:
    summary: Ribosomal small subunit biogenesis is a core Yar1 biological role.
    action: ACCEPT
    reason: Yar1 acts through Rps3, a 40S subunit protein; yar1 deletion causes ribosome-biogenesis defects that are suppressed by RPS3 overexpression.
    supported_by:
    - reference_id: PMID:15611164
      supporting_text: Overexpression of RPS3 suppresses both the stress sensitivity and the ribosome biogenesis defect of Deltayar1.
- term:
    id: GO:0042274
    label: ribosomal small subunit biogenesis
  evidence_type: IGI
  original_reference_id: PMID:15611164
  review:
    summary: Genetic interaction evidence supports Yar1 function in 40S biogenesis.
    action: ACCEPT
    reason: Yar1, Ltv1, and Rps3 interactions define a pathway connecting Rps3 handling to small ribosomal subunit production.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IMP
  original_reference_id: PMID:22570489
  review:
    summary: Yar1's substrate binding is a specific carrier-chaperone function for Rps3.
    action: MODIFY
    reason: The replacement term GO:0140597 reflects Yar1's dedicated role in binding and carrying nascent Rps3 to prevent aggregation.
    proposed_replacement_terms:
    - id: GO:0140597
      label: protein carrier chaperone
    supported_by:
    - reference_id: PMID:26112308
      supporting_text: Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients.
core_functions:
- molecular_function:
    id: GO:0140597
    label: protein carrier chaperone
  directly_involved_in:
  - id: GO:0042274
    label: ribosomal small subunit biogenesis
  - id: GO:0032880
    label: regulation of protein localization
  locations:
  - id: GO:0005737
    label: cytoplasm
  - id: GO:0005634
    label: nucleus
  description: >-
    Yar1 is a dedicated carrier chaperone for Rps3. It binds nascent Rps3,
    maintains Rps3 solubility, and accompanies Rps3 from cytoplasm to nucleus so
    it can be incorporated into pre-40S ribosomal particles.
  supported_by:
  - reference_id: PMID:22570489
    supporting_text: Yar1 protects Rps3 from aggregation in vitro and increases its solubility in vivo.
  - reference_id: PMID:26112308
    supporting_text: Affinity purification of four chaperones (Rrb1, Syo1, Sqt1 and Yar1) selectively enriched the mRNAs encoding their specific ribosomal protein clients.
  - reference_id: file:yeast/YAR1/YAR1-deep-research-falcon.md
    supporting_text: Falcon literature synthesis supports Yar1 as an Rps3-specific ribosomal protein carrier chaperone.
proposed_new_terms: []
suggested_questions:
- question: >-
    Should yeast Yar1 annotations explicitly distinguish Rps3 carrier-chaperone
    activity from downstream 40S export phenotypes?
suggested_experiments:
- description: >-
    Test whether point mutations that disrupt the Yar1-Rps3 interface abolish
    Rps3 solubility and nuclear delivery without broadly altering stress-response
    pathways.
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: PMID:14562095
  title: Global analysis of protein localization in budding yeast.
  findings: []
- id: PMID:15611164
  title: Genetic and biochemical interactions among Yar1, Ltv1 and Rps3 define novel links between environmental stress and ribosome biogenesis in Saccharomyces cerevisiae.
  findings: []
- id: PMID:22570489
  title: Yar1 protects the ribosomal protein Rps3 from aggregation.
  findings: []
- id: PMID:26112308
  title: Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones.
  findings: []
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome.
  findings: []
- id: file:yeast/YAR1/YAR1-deep-research-falcon.md
  title: Falcon deep research synthesis for YAR1
  findings: []
- id: file:interpro/panther/PTHR24198/PTHR24198-metadata.yaml
  title: PANTHER family PTHR24198 ankyrin repeat metadata
  findings: []