SHR3

UniProt ID: Q02774
Organism: Saccharomyces cerevisiae
Review Status: COMPLETE
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Gene Description

SHR3 encodes an endoplasmic-reticulum membrane packaging chaperone required for folding, quality control, and ER exit of yeast amino acid permeases. Shr3 is a multi-pass ER membrane protein that assists substrate-specific folding of polytopic amino acid transporters, prevents their aggregation and premature ER-associated degradation, and promotes COPII-dependent packaging for trafficking from the ER toward the Golgi and plasma membrane. Shr3 is not itself an amino acid transporter; its core role is client-specific membrane protein chaperoning in the early secretory pathway.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0005789 endoplasmic reticulum membrane
IBA
GO_REF:0000033
ACCEPT
Summary: PANTHER IBA to endoplasmic reticulum membrane is consistent with the specific Shr3 family, UniProt localization, and direct experimental evidence.
Reason: Shr3 is an integral ER membrane protein and functions at the ER membrane during amino acid permease biogenesis.
Supporting Evidence:
file:yeast/SHR3/SHR3-deep-research-falcon.md
Shr3 localizes to the endoplasmic reticulum membrane
GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport
IBA
GO_REF:0000033
ACCEPT
Summary: Family-transfer annotation to ER-to-Golgi vesicle transport is appropriate for Shr3 because it promotes ER exit of amino acid permease cargo.
Reason: Shr3 is required for efficient packaging of permeases into ER-derived COPII vesicles and therefore supports ER-to-Golgi transport of those clients.
Supporting Evidence:
file:yeast/SHR3/SHR3-deep-research-falcon.md
promoting COPII-dependent packaging of amino acid permeases
GO:0051082 unfolded protein binding
IBA
GO_REF:0000033
MODIFY
Summary: Shr3 is a substrate-specific chaperone for polytopic permeases, but "unfolded protein binding" is a vague binding term.
Reason: The evidence supports protein folding chaperone activity for amino acid permease clients rather than a generic unfolded-protein binding annotation.
Proposed replacements: protein folding chaperone
Supporting Evidence:
PMID:15623581
Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER.
GO:0005789 endoplasmic reticulum membrane
IEA
GO_REF:0000044
ACCEPT
Summary: UniProt subcellular-location mapping to ER membrane is consistent with direct Shr3 localization.
Reason: Shr3 is a multi-pass ER membrane protein, and this localization is central to its permease-chaperone function.
GO:0015031 protein transport
IEA
GO_REF:0000043
ACCEPT
Summary: The keyword-derived protein transport annotation is broad but reflects Shr3's role in ER export of amino acid permeases.
Reason: More specific experimental terms capture COPII budding and ER-to-Golgi transport, but the broad transport term remains accurate.
GO:0005515 protein binding
IPI
PMID:10688190
A comprehensive analysis of protein-protein interactions in ...
MARK AS OVER ANNOTATED
Summary: This high-throughput interaction supports physical association with the amino acid permease Gnp1 but the term protein binding is uninformative.
Reason: The curated molecular function should describe Shr3's client-specific chaperone activity rather than retain generic protein binding.
GO:0005515 protein binding
IPI
PMID:16093310
Large-scale identification of yeast integral membrane protei...
MARK AS OVER ANNOTATED
Summary: These interaction data are consistent with Shr3 contacts with membrane cargo or related proteins, but protein binding does not convey the specific function.
Reason: A generic protein-binding annotation should not be treated as a core molecular function when the biological role is permease folding and packaging chaperone activity.
GO:0005515 protein binding
IPI
PMID:18467557
An in vivo map of the yeast protein interactome.
MARK AS OVER ANNOTATED
Summary: Large-scale interaction evidence does not provide a specific molecular function beyond physical association.
Reason: This annotation is too generic for curation; the better-supported role is Shr3 chaperoning and ER export of amino acid permeases.
GO:0005515 protein binding
IPI
PMID:27107014
An inter-species protein-protein interaction network across ...
MARK AS OVER ANNOTATED
Summary: The inter-species interaction screen reports a physical interaction but does not establish a yeast Shr3 molecular activity.
Reason: The xeno interaction is not suitable as a core function annotation and is much less informative than the experimentally supported Shr3 chaperone mechanism.
GO:0005515 protein binding
IPI
PMID:37968396
The social and structural architecture of the yeast protein ...
MARK AS OVER ANNOTATED
Summary: Modern high-throughput interactome data reinforce Shr3 physical associations but still use a generic binding term.
Reason: Protein binding is not an informative endpoint for Shr3; specific client-chaperone and ER-export annotations should carry the curation.
GO:0005789 endoplasmic reticulum membrane
IDA
PMID:1423607
SHR3: a novel component of the secretory pathway specificall...
ACCEPT
Summary: Direct experimental evidence from the original SHR3 study identified Shr3 as an ER integral membrane component.
Reason: This localization is the correct compartment for Shr3's role in amino acid permease processing and ER exit.
Supporting Evidence:
PMID:1423607
SHR3 is a novel integral membrane protein component of the endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
IDA
PMID:15623581
Specialized membrane-localized chaperones prevent aggregatio...
ACCEPT
Summary: Direct experimental evidence supports Shr3 as an integral ER membrane chaperone for amino acid permeases.
Reason: The ER membrane location is required for Shr3 to act on nascent or newly inserted polytopic permease clients.
Supporting Evidence:
PMID:15623581
The integral endoplasmic reticulum (ER) membrane protein Shr3p
GO:0090114 COPII-coated vesicle budding
IGI
PMID:10564255
Shr3p mediates specific COPII coatomer-cargo interactions re...
ACCEPT
Summary: Genetic-interaction evidence supports Shr3 participation in COPII-coated vesicle budding for amino acid permease cargo.
Reason: Shr3 mediates specific COPII coatomer-cargo interactions needed for packaging permeases into ER-derived transport vesicles.
Supporting Evidence:
PMID:10564255
Shr3p mediates specific COPII coatomer-cargo interactions
GO:0005783 endoplasmic reticulum
HDA
PMID:26928762
One library to make them all: streamlining the creation of y...
ACCEPT
Summary: High-throughput SWAp-Tag localization supports ER localization, consistent with direct ER membrane evidence.
Reason: The high-throughput annotation is congruent with multiple direct studies placing Shr3 in the ER membrane.
Supporting Evidence:
PMID:26928762
streamlining the creation of yeast libraries via a SWAp-Tag strategy
GO:0043332 mating projection tip
HDA
PMID:19053807
Systematic definition of protein constituents along the majo...
KEEP AS NON CORE
Summary: High-throughput pheromone-treatment localization suggests a condition- specific signal at the mating projection tip.
Reason: This may reflect condition-specific relocalization of ER/cortical membrane-associated Shr3, but it is not the core compartment for the permease-chaperone mechanism.
GO:0006457 protein folding
IMP
PMID:15623581
Specialized membrane-localized chaperones prevent aggregatio...
ACCEPT
Summary: Mutant phenotype evidence supports Shr3's role in folding of polytopic amino acid permease clients and preventing their aggregation in the ER.
Reason: Protein folding is a core biological process for Shr3 because failure of Shr3 causes permease misfolding/aggregation and ER retention.
Supporting Evidence:
PMID:15623581
prevent aggregation of polytopic proteins in the ER
GO:0051082 unfolded protein binding
IMP
PMID:10564255
Shr3p mediates specific COPII coatomer-cargo interactions re...
MODIFY
Summary: Shr3's activity involves chaperoning amino acid permease cargo, but unfolded protein binding is less precise than a chaperone activity term.
Reason: The evidence supports specific protein folding/packaging chaperone activity in the ER membrane rather than a generic binding term.
Proposed replacements: protein folding chaperone
Supporting Evidence:
PMID:10564255
Shr3p acts as a packaging chaperone
GO:0051082 unfolded protein binding
IMP
PMID:15623581
Specialized membrane-localized chaperones prevent aggregatio...
MODIFY
Summary: The evidence shows Shr3 prevents aggregation of polytopic permeases during folding, which is better represented as protein folding chaperone activity.
Reason: The more informative curation is GO:0044183 protein folding chaperone coupled to ER membrane permease biogenesis.
Proposed replacements: protein folding chaperone
Supporting Evidence:
PMID:15623581
Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER.

Core Functions

Shr3 is a substrate-specific ER membrane chaperone for amino acid permeases. It stabilizes polytopic permease clients, prevents aggregation and premature ERAD, and promotes their packaging into COPII-coated ER-derived vesicles.

Supporting Evidence:
  • PMID:15623581
    prevent aggregation of polytopic proteins in the ER
  • PMID:10564255
    Shr3p acts as a packaging chaperone
  • file:yeast/SHR3/SHR3-deep-research-falcon.md
    ER membrane-localized, substrate-specific chaperone

References

Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Shr3p mediates specific COPII coatomer-cargo interactions required for the packaging of amino acid permeases into ER-derived transport vesicles.
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.
SHR3: a novel component of the secretory pathway specifically required for localization of amino acid permeases in yeast.
Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER.
Large-scale identification of yeast integral membrane protein interactions.
An in vivo map of the yeast protein interactome.
Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast.
One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.
An inter-species protein-protein interaction network across vast evolutionary distance.
The social and structural architecture of the yeast protein interactome.
file:yeast/SHR3/SHR3-deep-research-falcon.md
Falcon deep research report for SHR3

Suggested Questions for Experts

Q: For Shr3 and related ER-resident packaging factors, should GO curation distinguish folding chaperone activity from cargo-receptor or COPII-adaptor activity with a more specific child term?

Suggested Experiments

Experiment: Reconstitute Shr3 with defined amino acid permease transmembrane segments and COPII components to separate its folding/stabilization activity from any direct COPII recruitment activity.

Hypothesis: Shr3 first stabilizes early permease transmembrane segments and then promotes COPII packaging indirectly by producing export-competent cargo.

Type: biochemical reconstitution

📚 Additional Documentation

Deep Research Falcon

(SHR3-deep-research-falcon.md)

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organism: yeast
gene_id: SHR3
gene_symbol: SHR3
uniprot_accession: Q02774
protein_description: 'RecName: Full=Secretory component protein SHR3;'
gene_info: Name=SHR3; OrderedLocusNames=YDL212W; ORFNames=D1022;
organism_full: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
protein_family: Not specified in UniProt
protein_domains: Psh3/Shr3. (IPR013248); SHR3_chaperone (PF08229)
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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: Q02774
  • Protein Description: RecName: Full=Secretory component protein SHR3;
  • Gene Information: Name=SHR3; OrderedLocusNames=YDL212W; ORFNames=D1022;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Not specified in UniProt
  • Key Domains: Psh3/Shr3. (IPR013248); SHR3_chaperone (PF08229)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "SHR3" 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 'SHR3' 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 SHR3 (gene ID: SHR3, UniProt: Q02774) 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: Q02774
  • Protein Description: RecName: Full=Secretory component protein SHR3;
  • Gene Information: Name=SHR3; OrderedLocusNames=YDL212W; ORFNames=D1022;
  • Organism (full): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Protein Family: Not specified in UniProt
  • Key Domains: Psh3/Shr3. (IPR013248); SHR3_chaperone (PF08229)

MANDATORY VERIFICATION STEPS:

  1. Check if the gene symbol "SHR3" 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 'SHR3' 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 SHR3 (gene ID: SHR3, UniProt: Q02774) 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.

Comprehensive Functional Annotation Report: SHR3 (UniProt: Q02774; ORF YDL212W) in Saccharomyces cerevisiae (S288c)

0) Scope and gene/protein identity verification

All retrieved yeast-focused sources consistently describe Shr3 (Shr3p) as an endoplasmic reticulum (ER) membrane-localized, substrate-specific “packaging chaperone” required for the biogenesis/ER export of amino-acid permeases (AAPs/YATs) and for preventing their aggregation and premature ER-associated degradation (ERAD) (ring2019ssy1functionsat pages 9-9, mochizuki2015retentionofchimeric pages 8-9, dancourt2010proteinsortingreceptors pages 16-17, bianchi2019regulationofamino pages 19-21). No conflicting usage of the symbol SHR3 for a different gene/protein in another organism was encountered within the retrieved corpus (mochizuki2015retentionofchimeric pages 8-9, dancourt2010proteinsortingreceptors pages 16-17, ring2019ssy1functionsat pages 2-3).

Note on domain verification: the retrieved articles did not explicitly name the UniProt/InterPro/Pfam domains (e.g., Psh3/Shr3 domain; PF08229) in the accessible text snippets; thus domain statements are not asserted here beyond the user-provided UniProt context.


1) Key concepts and definitions (current understanding)

1.1. “Packaging chaperone” / membrane-localized chaperone (MLC)

In yeast membrane protein biogenesis, certain cargo classes require substrate-specific ER membrane proteins that act as chaperones and/or packaging factors to enable correct folding and efficient entry into COPII vesicles for ER export. Shr3 is a canonical example of this class, acting on amino-acid transporter clients (dancourt2010proteinsortingreceptors pages 16-17, bianchi2019regulationofamino pages 19-21).

1.2. Client class: yeast amino-acid transporters (YATs/AAPs)

Shr3’s principal clients are yeast amino acid transport (YAT) family permeases. A quantitative framing in the reviewed primary literature is that yeast amino-acid permeases comprise a family of 24 homologous APC transporters, and individual permeases are predicted to have 12 transmembrane domains (TMDs) (mochizuki2015retentionofchimeric pages 1-2). In an authoritative review, Shr3-dependent clients explicitly include Gap1 and other YATs such as Agp1 and Gnp1 (bianchi2019regulationofamino pages 19-21).

1.3. ER quality control and ERAD (ER-associated degradation)

When polytopic membrane proteins fail to fold properly in the ER, they can be removed by ERAD, which includes ubiquitination, extraction from the ER membrane, and proteasomal degradation. In the case of Shr3-dependent permeases, Shr3 is positioned upstream of ERAD by preventing misfolding/aggregation that would otherwise trigger ERAD (mochizuki2015retentionofchimeric pages 1-2, bianchi2019regulationofamino pages 19-21).


2) Molecular function: what SHR3 does (and does not do)

2.1. Primary molecular function (supported)

Shr3 is not a transporter and does not catalyze a chemical reaction. Instead, Shr3 functions as an ER membrane-localized, substrate-specific chaperone/packaging factor required for the functional expression and secretory-pathway export of amino acid permeases (ring2019ssy1functionsat pages 9-9, mochizuki2015retentionofchimeric pages 8-9, bianchi2019regulationofamino pages 19-21).

2.2. Mechanistic model (folding assistance)

A central mechanistic concept supported by both review synthesis and primary data is that Shr3 stabilizes early transmembrane segments of permease clients to prevent nonproductive interactions and aggregation during folding.

  • Quantitative mechanistic detail: Shr3 is described as an ER-resident integral membrane protein with 4 transmembrane segments that “holds the first 5 TMDs” of YAT clients in a stable conformation, allowing the remaining TMDs to fold properly (bianchi2019regulationofamino pages 19-21).
  • Primary mechanistic statement consistent with this model: Shr3 interacts with early TMDs of Gap1 to promote native folding and prevent aggregation (mochizuki2015retentionofchimeric pages 8-9).

2.3. Mechanistic model (ER export/COPII packaging)

Shr3 is also implicated in promoting COPII-dependent packaging of amino acid permeases into ER-derived transport vesicles.

  • A key literature synthesis referenced in primary work: Shr3p mediates specific COPII coatomer–cargo interactions needed for packaging amino acid permeases into ER-derived transport vesicles (mochizuki2015retentionofchimeric pages 9-10).
  • Review-level integration: Shr3 is positioned as a chaperone that stabilizes YATs in the ER and sorts them into vesicles for export (bianchi2019regulationofamino media 260fd4cf, bianchi2019regulationofamino pages 19-21).

3) Subcellular localization: where Shr3 acts

Shr3 localizes to the endoplasmic reticulum membrane, consistent with its role in co-/peri-translational folding and ER export of polytopic permeases (ring2019ssy1functionsat pages 2-3, ring2019ssy1functionsat pages 3-4, bianchi2019regulationofamino pages 19-21).

In cell biology practice, Shr3 has been used as an ER marker: Shr3-GFP highlights ER morphology (perinuclear rim and peripheral ER), supporting ER residency in vivo (ring2019ssy1functionsat pages 3-4).


4) Client proteins and substrate specificity

4.1. Best-supported clients

The most directly supported client is Gap1, the general amino-acid permease, which becomes aggregated/ER-retained in shr3 mutants (mochizuki2015retentionofchimeric pages 1-2, dancourt2010proteinsortingreceptors pages 16-17).

The authoritative review explicitly provides additional YAT examples: Agp1 and Gnp1 (bianchi2019regulationofamino pages 19-21).

4.2. Limits of Shr3’s “rescue” capacity (specificity and folding quality)

Primary evidence indicates that Shr3 is not a universal remedy for all permease folding defects. For example, in an experimental survey of 64 Gap1 mutants, 17 mutants were retained in the ER and SHR3 overexpression did not suppress growth defects associated with these mutants, indicating client mutations can exceed Shr3’s chaperoning capacity and/or reflect distinct folding lesions (mochizuki2015retentionofchimeric pages 8-9).


5) Pathways and biological processes

5.1. Early secretory pathway integration

Shr3 operates at the interface of ER folding quality control and ER export of membrane cargo. It is conceptually distinguished from canonical cycling cargo receptors; rather, Shr3 behaves as a dedicated folding/packaging factor for a client class (dancourt2010proteinsortingreceptors pages 16-17).

5.2. Interaction with ERAD machinery and proteostasis

When Shr3 is absent, YATs such as Gap1 (and other YAT examples) can form high-molecular-weight aggregates that are removed by ERAD (bianchi2019regulationofamino pages 19-21).

A key mechanistic-statistical summary from an authoritative review lists the ERAD machinery implicated in clearing Shr3-client aggregates: E3 ubiquitin ligases Doa10 and Hrd1, extraction by the Cdc48 ATPase complex, and degradation by the cytoplasmic proteasome (bianchi2019regulationofamino pages 19-21).

5.3. Cellular stress responses linked to misfolded permeases

Retention/aggregation of permease constructs in the ER can induce ER stress responses such as the unfolded protein response (UPR); Shr3’s role in preventing aggregation provides a mechanistic link to avoiding this stress trigger (mochizuki2015retentionofchimeric pages 1-2).


6) Recent developments and latest research (2023–2024 prioritized)

6.1. Availability constraint in this tool run

A 2023 Journal of Cell Biology article directly focused on Shr3 (ER-localized Shr3 as a selective co-translational folding chaperone necessary for amino-acid permease biogenesis; DOI shown in search output) was flagged as unobtainable in this environment and could not be read for direct evidence extraction. Consequently, the most detailed Shr3-specific mechanistic evidence in this report is drawn from accessible primary work (2015) and authoritative reviews (2010–2019) (mochizuki2015retentionofchimeric pages 8-9, dancourt2010proteinsortingreceptors pages 16-17, bianchi2019regulationofamino pages 19-21).

6.2. 2023–2024 contextual advances relevant to Shr3-like systems

While not Shr3 itself, recent work continues to develop the broader concept of substrate-specific ER accessory/chaperone proteins controlling multipass membrane cargo biogenesis:

  • 2023 (MBoC): A detailed analysis of quality control mechanisms for yeast chitin synthase Chs3, emphasizing how interaction with its Shr3-like chaperone Chs7 can mask degrons and tune ERAD engagement, reinforcing the conceptual framework of substrate-specific ER chaperones in proteostasis (paper retrieved but not fully evidence-mined for Shr3; included here as contextual) (dimou2020lifeanddeath pages 1-3).
  • 2024 (Plant Physiology): A mechanistic study of plant AXR4 supports a model where an ER accessory protein physically interacts with a multipass transporter (AUX1/LAX2), reduces aggregation, and supports correct trafficking—an analog of Shr3-like logic across eukaryotes (retrieved but not yeast-specific) (dimou2020lifeanddeath pages 1-3).

7) Current applications and real-world implementations

  1. Membrane protein biogenesis paradigm: Shr3 is widely used as a model for how eukaryotic cells ensure successful folding/export of polytopic transporters and how failure routes into ERAD; this informs experimental design in transporter biology and secretory pathway studies (dancourt2010proteinsortingreceptors pages 16-17, bianchi2019regulationofamino pages 19-21).
  2. Cell biology tool/marker: Shr3-GFP is used experimentally as an ER membrane marker to visualize ER morphology in yeast, consistent with ER localization and stable residency (ring2019ssy1functionsat pages 3-4).
  3. Transporter engineering and trafficking studies (inference from authoritative review): Because YAT function depends on correct ER folding/export, Shr3 is a practical consideration when engineering yeast strains for altered nutrient uptake, or when interpreting transporter localization phenotypes in genetics screens (bianchi2019regulationofamino pages 19-21, mochizuki2015retentionofchimeric pages 1-2).

8) Expert opinions and authoritative synthesis

Annu. Rev. Biochem. (2010) frames Shr3 as an ER chaperone assisting folding of specific membrane cargo (e.g., Gap1), and contrasts Shr3-like factors from cycling sorting receptors, emphasizing the quality-control consequence of Shr3 loss (client aggregation and potential ERAD engagement) (dancourt2010proteinsortingreceptors pages 16-17).

Microbiology and Molecular Biology Reviews (2019) provides a high-level and widely cited synthesis: Shr3 is an ER-resident packaging chaperone, stabilizes early TMDs (first five) of YAT clients, and without Shr3, YATs aggregate and are cleared by ERAD involving Doa10/Hrd1, Cdc48, and the proteasome (bianchi2019regulationofamino pages 19-21).


9) Key statistics and data points (from recent/authoritative sources)

  • Shr3 topology: 4 transmembrane segments (bianchi2019regulationofamino pages 19-21).
  • Client topology: YATs are 12-TMD transporters (bianchi2019regulationofamino pages 19-21, mochizuki2015retentionofchimeric pages 1-2).
  • Folding mechanism: Shr3 stabilizes/holds the first 5 TMDs of YAT clients (bianchi2019regulationofamino pages 19-21, mochizuki2015retentionofchimeric pages 8-9).
  • Client family size (yeast amino-acid permeases): 24 homologous APC transporters (mochizuki2015retentionofchimeric pages 1-2).
  • Mutational dataset (Gap1): 64 mutants tested; 17 ER-retained; SHR3 overexpression did not rescue these (mochizuki2015retentionofchimeric pages 8-9).

10) Evidence-backed schematic support (visual)

The following review figure provides a systems-level depiction of Shr3’s position in YAT biogenesis, ER quality control, ERAD, and onward trafficking.

Functional aspect Key finding Evidence type Source with year and DOI/URL
Molecular function SHR3 encodes an ER-resident integral membrane chaperone/packaging factor required for functional expression of yeast amino acid permeases rather than an enzyme or transporter itself. (ring2019ssy1functionsat pages 9-9, mochizuki2015retentionofchimeric pages 8-9, bianchi2019regulationofamino pages 19-21) Review + primary; genetic, biochemical, cell biology Bianchi et al., 2019, Microbiol Mol Biol Rev; https://doi.org/10.1128/MMBR.00024-19 ; Ring et al., 2019, Traffic; https://doi.org/10.1111/tra.12681 ; Mochizuki et al., 2015, FEMS Yeast Res; https://doi.org/10.1093/femsyr/fov044
Localization Shr3/Shr3p localizes to the endoplasmic reticulum membrane and has been used experimentally as an ER marker showing perinuclear and cortical ER patterns. (ring2019ssy1functionsat pages 2-3, ring2019ssy1functionsat pages 3-4) Primary; cell biology/imaging Ring et al., 2019, Traffic; https://doi.org/10.1111/tra.12681
Client proteins The best-supported clients are yeast amino acid transporters/permeases, including Gap1 and other YAT/AAP family members such as Agp1 and Gnp1. (mochizuki2015retentionofchimeric pages 8-9, mochizuki2015retentionofchimeric pages 1-2, bianchi2019regulationofamino pages 19-21) Review + primary; genetic, biochemical Mochizuki et al., 2015, FEMS Yeast Res; https://doi.org/10.1093/femsyr/fov044 ; Bianchi et al., 2019, Microbiol Mol Biol Rev; https://doi.org/10.1128/MMBR.00024-19
Mechanism Shr3 stabilizes early transmembrane segments of permeases—reviewed as holding the first 5 TMDs in a folding-competent state—thereby preventing nonproductive TMD interactions, aggregation, and premature ERAD. (mochizuki2015retentionofchimeric pages 8-9, mochizuki2015retentionofchimeric pages 1-2, bianchi2019regulationofamino pages 19-21) Review + primary; biochemical, genetic Bianchi et al., 2019, Microbiol Mol Biol Rev; https://doi.org/10.1128/MMBR.00024-19 ; Mochizuki et al., 2015, FEMS Yeast Res; https://doi.org/10.1093/femsyr/fov044
ER export/COPII packaging Shr3 is required for specific COPII coatomer-cargo interactions that package amino acid permeases into ER-derived transport vesicles for forward trafficking. (ring2019ssy1functionsat pages 9-9, mochizuki2015retentionofchimeric pages 9-10) Review + primary; biochemical trafficking assays Ring et al., 2019, Traffic; https://doi.org/10.1111/tra.12681 ; Mochizuki et al., 2015, FEMS Yeast Res; https://doi.org/10.1093/femsyr/fov044
Pathway / biological process SHR3 functions in transporter biogenesis within the early secretory pathway, linking ER folding quality control to ER exit and subsequent Golgi/plasma-membrane delivery of amino acid transporters. (dancourt2010proteinsortingreceptors pages 16-17, bianchi2019regulationofamino media 260fd4cf, bianchi2019regulationofamino pages 19-21) Review; secretory pathway synthesis Dancourt & Barlowe, 2010, Annu Rev Biochem; https://doi.org/10.1146/annurev-biochem-061608-091319 ; Bianchi et al., 2019, Microbiol Mol Biol Rev; https://doi.org/10.1128/MMBR.00024-19
Quality control In shr3-deficient cells, Gap1 and related permeases accumulate as high-molecular-weight ER aggregates and are cleared by ER-associated degradation involving Doa10/Hrd1, Cdc48, and the proteasome. (mochizuki2015retentionofchimeric pages 1-2, bianchi2019regulationofamino pages 19-21) Review + primary; genetic, proteostasis Mochizuki et al., 2015, FEMS Yeast Res; https://doi.org/10.1093/femsyr/fov044 ; Bianchi et al., 2019, Microbiol Mol Biol Rev; https://doi.org/10.1128/MMBR.00024-19
Phenotypes / assays Loss of SHR3 causes defective cell-surface localization and function of amino acid permeases, while ER-retained misfolded permease constructs can trigger UPR-related stress phenotypes. (ring2019ssy1functionsat pages 9-9, mochizuki2015retentionofchimeric pages 1-2, mochizuki2015retentionofchimeric pages 8-9) Primary + review; mutant phenotype, localization, stress-response assays Ring et al., 2019, Traffic; https://doi.org/10.1111/tra.12681 ; Mochizuki et al., 2015, FEMS Yeast Res; https://doi.org/10.1093/femsyr/fov044
Comparative family context Shr3 is part of a broader class of substrate-specific ER-resident packaging chaperones in yeast, analogous in function to Gsf2, Pho86, and Chs7 for other membrane cargos. (bianchi2019regulationofamino media 260fd4cf, bianchi2019regulationofamino pages 19-21) Review; comparative cell biology Bianchi et al., 2019, Microbiol Mol Biol Rev; https://doi.org/10.1128/MMBR.00024-19
Visual summary evidence A recent authoritative review figure summarizes Shr3 in the ER as stabilizing YATs and sorting them into export vesicles while limiting ERAD, providing a concise systems-level annotation. (bianchi2019regulationofamino media 260fd4cf) Review figure/diagram Bianchi et al., 2019, Microbiol Mol Biol Rev; https://doi.org/10.1128/MMBR.00024-19

Table: This table summarizes the main experimentally supported annotations for yeast SHR3/Q02774, including its ER localization, chaperone role, permease clients, and link to COPII export and ER quality control. It is useful as a concise evidence map anchored to review and primary literature.

(Visual evidence: Figure 7 from Bianchi et al. 2019 explicitly places Shr3 in the ER as stabilizing and sorting YATs while limiting ERAD.) (bianchi2019regulationofamino media 260fd4cf)


References (retrieved in this run; with dates and URLs)

  1. Bianchi F, van’t Klooster JS, Ruiz SJ, Poolman B. Regulation of Amino Acid Transport in Saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews. 2019-11. https://doi.org/10.1128/mmbr.00024-19 (bianchi2019regulationofamino pages 19-21, bianchi2019regulationofamino media 260fd4cf)
  2. Mochizuki T, Kimata Y, Uemura S, Abe F. Retention of chimeric Tat2-Gap1 permease in the endoplasmic reticulum induces unfolded protein response in Saccharomyces cerevisiae. FEMS Yeast Research. 2015-08. https://doi.org/10.1093/femsyr/fov044 (mochizuki2015retentionofchimeric pages 1-2, mochizuki2015retentionofchimeric pages 8-9)
  3. Dancourt J, Barlowe C. Protein sorting receptors in the early secretory pathway. Annual Review of Biochemistry. 2010-06. https://doi.org/10.1146/annurev-biochem-061608-091319 (dancourt2010proteinsortingreceptors pages 16-17)
  4. Ring A, Martins A, Ljungdahl PO. Ssy1 functions at the plasma membrane as a receptor of extracellular amino acids independent of plasma membrane–endoplasmic reticulum junctions. Traffic. 2019-08. https://doi.org/10.1111/tra.12681 (ring2019ssy1functionsat pages 2-3, ring2019ssy1functionsat pages 3-4)

References

  1. (ring2019ssy1functionsat pages 9-9): Andreas Ring, António Martins, and Per O. Ljungdahl. Ssy1 functions at the plasma membrane as a receptor of extracellular amino acids independent of plasma membrane‐endoplasmic reticulum junctions. Traffic, 20:775-784, Aug 2019. URL: https://doi.org/10.1111/tra.12681, doi:10.1111/tra.12681. This article has 5 citations and is from a peer-reviewed journal.

  2. (mochizuki2015retentionofchimeric pages 8-9): Takahiro Mochizuki, Yukio Kimata, Satoshi Uemura, and Fumiyoshi Abe. Retention of chimeric tat2-gap1 permease in the endoplasmic reticulum induces unfolded protein response in saccharomyces cerevisiae. FEMS yeast research, 15 5:fov044, Aug 2015. URL: https://doi.org/10.1093/femsyr/fov044, doi:10.1093/femsyr/fov044. This article has 1 citations and is from a peer-reviewed journal.

  3. (dancourt2010proteinsortingreceptors pages 16-17): Julia Dancourt and Charles Barlowe. Protein sorting receptors in the early secretory pathway. Annual review of biochemistry, 79:777-802, Jun 2010. URL: https://doi.org/10.1146/annurev-biochem-061608-091319, doi:10.1146/annurev-biochem-061608-091319. This article has 378 citations and is from a domain leading peer-reviewed journal.

  4. (bianchi2019regulationofamino pages 19-21): Frans Bianchi, Joury S. van’t Klooster, Stephanie J. Ruiz, and Bert Poolman. Regulation of amino acid transport in saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews, Nov 2019. URL: https://doi.org/10.1128/mmbr.00024-19, doi:10.1128/mmbr.00024-19. This article has 166 citations and is from a domain leading peer-reviewed journal.

  5. (ring2019ssy1functionsat pages 2-3): Andreas Ring, António Martins, and Per O. Ljungdahl. Ssy1 functions at the plasma membrane as a receptor of extracellular amino acids independent of plasma membrane‐endoplasmic reticulum junctions. Traffic, 20:775-784, Aug 2019. URL: https://doi.org/10.1111/tra.12681, doi:10.1111/tra.12681. This article has 5 citations and is from a peer-reviewed journal.

  6. (mochizuki2015retentionofchimeric pages 1-2): Takahiro Mochizuki, Yukio Kimata, Satoshi Uemura, and Fumiyoshi Abe. Retention of chimeric tat2-gap1 permease in the endoplasmic reticulum induces unfolded protein response in saccharomyces cerevisiae. FEMS yeast research, 15 5:fov044, Aug 2015. URL: https://doi.org/10.1093/femsyr/fov044, doi:10.1093/femsyr/fov044. This article has 1 citations and is from a peer-reviewed journal.

  7. (mochizuki2015retentionofchimeric pages 9-10): Takahiro Mochizuki, Yukio Kimata, Satoshi Uemura, and Fumiyoshi Abe. Retention of chimeric tat2-gap1 permease in the endoplasmic reticulum induces unfolded protein response in saccharomyces cerevisiae. FEMS yeast research, 15 5:fov044, Aug 2015. URL: https://doi.org/10.1093/femsyr/fov044, doi:10.1093/femsyr/fov044. This article has 1 citations and is from a peer-reviewed journal.

  8. (bianchi2019regulationofamino media 260fd4cf): Frans Bianchi, Joury S. van’t Klooster, Stephanie J. Ruiz, and Bert Poolman. Regulation of amino acid transport in saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews, Nov 2019. URL: https://doi.org/10.1128/mmbr.00024-19, doi:10.1128/mmbr.00024-19. This article has 166 citations and is from a domain leading peer-reviewed journal.

  9. (ring2019ssy1functionsat pages 3-4): Andreas Ring, António Martins, and Per O. Ljungdahl. Ssy1 functions at the plasma membrane as a receptor of extracellular amino acids independent of plasma membrane‐endoplasmic reticulum junctions. Traffic, 20:775-784, Aug 2019. URL: https://doi.org/10.1111/tra.12681, doi:10.1111/tra.12681. This article has 5 citations and is from a peer-reviewed journal.

  10. (dimou2020lifeanddeath pages 1-3): Sofia Dimou and George Diallinas. Life and death of fungal transporters under the challenge of polarity. International Journal of Molecular Sciences, 21:5376, Jul 2020. URL: https://doi.org/10.3390/ijms21155376, doi:10.3390/ijms21155376. This article has 21 citations.

Citations

  1. mochizuki2015retentionofchimeric pages 1-2
  2. bianchi2019regulationofamino pages 19-21
  3. mochizuki2015retentionofchimeric pages 8-9
  4. mochizuki2015retentionofchimeric pages 9-10
  5. dancourt2010proteinsortingreceptors pages 16-17
  6. dimou2020lifeanddeath pages 1-3
  7. https://doi.org/10.1128/MMBR.00024-19
  8. https://doi.org/10.1111/tra.12681
  9. https://doi.org/10.1093/femsyr/fov044
  10. https://doi.org/10.1146/annurev-biochem-061608-091319
  11. https://doi.org/10.1128/mmbr.00024-19
  12. https://doi.org/10.1111/tra.12681,
  13. https://doi.org/10.1093/femsyr/fov044,
  14. https://doi.org/10.1146/annurev-biochem-061608-091319,
  15. https://doi.org/10.1128/mmbr.00024-19,
  16. https://doi.org/10.3390/ijms21155376,

📄 View Raw YAML

id: Q02774
gene_symbol: SHR3
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: >-
  SHR3 encodes an endoplasmic-reticulum membrane packaging chaperone required
  for folding, quality control, and ER exit of yeast amino acid permeases. Shr3
  is a multi-pass ER membrane protein that assists substrate-specific folding of
  polytopic amino acid transporters, prevents their aggregation and premature
  ER-associated degradation, and promotes COPII-dependent packaging for
  trafficking from the ER toward the Golgi and plasma membrane. Shr3 is not
  itself an amino acid transporter; its core role is client-specific membrane
  protein chaperoning in the early secretory pathway.
existing_annotations:
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      PANTHER IBA to endoplasmic reticulum membrane is consistent with the
      specific Shr3 family, UniProt localization, and direct experimental
      evidence.
    action: ACCEPT
    reason: >-
      Shr3 is an integral ER membrane protein and functions at the ER membrane
      during amino acid permease biogenesis.
    supported_by:
    - reference_id: file:yeast/SHR3/SHR3-deep-research-falcon.md
      supporting_text: "Shr3 localizes to the endoplasmic reticulum membrane"
- term:
    id: GO:0006888
    label: endoplasmic reticulum to Golgi vesicle-mediated transport
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      Family-transfer annotation to ER-to-Golgi vesicle transport is appropriate
      for Shr3 because it promotes ER exit of amino acid permease cargo.
    action: ACCEPT
    reason: >-
      Shr3 is required for efficient packaging of permeases into ER-derived
      COPII vesicles and therefore supports ER-to-Golgi transport of those
      clients.
    supported_by:
    - reference_id: file:yeast/SHR3/SHR3-deep-research-falcon.md
      supporting_text: "promoting COPII-dependent packaging of amino acid permeases"
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      Shr3 is a substrate-specific chaperone for polytopic permeases, but
      "unfolded protein binding" is a vague binding term.
    action: MODIFY
    reason: >-
      The evidence supports protein folding chaperone activity for amino acid
      permease clients rather than a generic unfolded-protein binding
      annotation.
    proposed_replacement_terms:
    - id: GO:0044183
      label: protein folding chaperone
    supported_by:
    - reference_id: PMID:15623581
      supporting_text: "Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER."
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      UniProt subcellular-location mapping to ER membrane is consistent with
      direct Shr3 localization.
    action: ACCEPT
    reason: >-
      Shr3 is a multi-pass ER membrane protein, and this localization is central
      to its permease-chaperone function.
- term:
    id: GO:0015031
    label: protein transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      The keyword-derived protein transport annotation is broad but reflects
      Shr3's role in ER export of amino acid permeases.
    action: ACCEPT
    reason: >-
      More specific experimental terms capture COPII budding and ER-to-Golgi
      transport, but the broad transport term remains accurate.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10688190
  supporting_entities:
  - UniProtKB:P48813
  review:
    summary: >-
      This high-throughput interaction supports physical association with the
      amino acid permease Gnp1 but the term protein binding is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The curated molecular function should describe Shr3's client-specific
      chaperone activity rather than retain generic protein binding.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16093310
  supporting_entities:
  - UniProtKB:P35206
  - UniProtKB:P38084
  - UniProtKB:P48813
  review:
    summary: >-
      These interaction data are consistent with Shr3 contacts with membrane
      cargo or related proteins, but protein binding does not convey the
      specific function.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      A generic protein-binding annotation should not be treated as a core
      molecular function when the biological role is permease folding and
      packaging chaperone activity.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:18467557
  supporting_entities:
  - UniProtKB:P35206
  - UniProtKB:P38084
  - UniProtKB:P38264
  review:
    summary: >-
      Large-scale interaction evidence does not provide a specific molecular
      function beyond physical association.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This annotation is too generic for curation; the better-supported role is
      Shr3 chaperoning and ER export of amino acid permeases.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27107014
  supporting_entities:
  - UniProtKB:Q96BA8
  review:
    summary: >-
      The inter-species interaction screen reports a physical interaction but
      does not establish a yeast Shr3 molecular activity.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The xeno interaction is not suitable as a core function annotation and is
      much less informative than the experimentally supported Shr3 chaperone
      mechanism.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37968396
  supporting_entities:
  - UniProtKB:P38264
  - UniProtKB:P48813
  review:
    summary: >-
      Modern high-throughput interactome data reinforce Shr3 physical
      associations but still use a generic binding term.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Protein binding is not an informative endpoint for Shr3; specific
      client-chaperone and ER-export annotations should carry the curation.
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IDA
  original_reference_id: PMID:1423607
  review:
    summary: >-
      Direct experimental evidence from the original SHR3 study identified Shr3
      as an ER integral membrane component.
    action: ACCEPT
    reason: >-
      This localization is the correct compartment for Shr3's role in amino acid
      permease processing and ER exit.
    supported_by:
    - reference_id: PMID:1423607
      supporting_text: "SHR3 is a novel integral membrane protein component of the endoplasmic reticulum"
- term:
    id: GO:0005789
    label: endoplasmic reticulum membrane
  evidence_type: IDA
  original_reference_id: PMID:15623581
  review:
    summary: >-
      Direct experimental evidence supports Shr3 as an integral ER membrane
      chaperone for amino acid permeases.
    action: ACCEPT
    reason: >-
      The ER membrane location is required for Shr3 to act on nascent or newly
      inserted polytopic permease clients.
    supported_by:
    - reference_id: PMID:15623581
      supporting_text: "The integral endoplasmic reticulum (ER) membrane protein Shr3p"
- term:
    id: GO:0090114
    label: COPII-coated vesicle budding
  evidence_type: IGI
  original_reference_id: PMID:10564255
  review:
    summary: >-
      Genetic-interaction evidence supports Shr3 participation in COPII-coated
      vesicle budding for amino acid permease cargo.
    action: ACCEPT
    reason: >-
      Shr3 mediates specific COPII coatomer-cargo interactions needed for
      packaging permeases into ER-derived transport vesicles.
    supported_by:
    - reference_id: PMID:10564255
      supporting_text: "Shr3p mediates specific COPII coatomer-cargo interactions"
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: HDA
  original_reference_id: PMID:26928762
  review:
    summary: >-
      High-throughput SWAp-Tag localization supports ER localization, consistent
      with direct ER membrane evidence.
    action: ACCEPT
    reason: >-
      The high-throughput annotation is congruent with multiple direct studies
      placing Shr3 in the ER membrane.
    supported_by:
    - reference_id: PMID:26928762
      supporting_text: "streamlining the creation of yeast libraries via a SWAp-Tag strategy"
- term:
    id: GO:0043332
    label: mating projection tip
  evidence_type: HDA
  original_reference_id: PMID:19053807
  review:
    summary: >-
      High-throughput pheromone-treatment localization suggests a condition-
      specific signal at the mating projection tip.
    action: KEEP_AS_NON_CORE
    reason: >-
      This may reflect condition-specific relocalization of ER/cortical
      membrane-associated Shr3, but it is not the core compartment for the
      permease-chaperone mechanism.
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IMP
  original_reference_id: PMID:15623581
  review:
    summary: >-
      Mutant phenotype evidence supports Shr3's role in folding of polytopic
      amino acid permease clients and preventing their aggregation in the ER.
    action: ACCEPT
    reason: >-
      Protein folding is a core biological process for Shr3 because failure of
      Shr3 causes permease misfolding/aggregation and ER retention.
    supported_by:
    - reference_id: PMID:15623581
      supporting_text: "prevent aggregation of polytopic proteins in the ER"
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IMP
  original_reference_id: PMID:10564255
  review:
    summary: >-
      Shr3's activity involves chaperoning amino acid permease cargo, but
      unfolded protein binding is less precise than a chaperone activity term.
    action: MODIFY
    reason: >-
      The evidence supports specific protein folding/packaging chaperone
      activity in the ER membrane rather than a generic binding term.
    proposed_replacement_terms:
    - id: GO:0044183
      label: protein folding chaperone
    supported_by:
    - reference_id: PMID:10564255
      supporting_text: "Shr3p acts as a packaging chaperone"
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IMP
  original_reference_id: PMID:15623581
  review:
    summary: >-
      The evidence shows Shr3 prevents aggregation of polytopic permeases during
      folding, which is better represented as protein folding chaperone activity.
    action: MODIFY
    reason: >-
      The more informative curation is GO:0044183 protein folding chaperone
      coupled to ER membrane permease biogenesis.
    proposed_replacement_terms:
    - id: GO:0044183
      label: protein folding chaperone
    supported_by:
    - reference_id: PMID:15623581
      supporting_text: "Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER."
core_functions:
- molecular_function:
    id: GO:0044183
    label: protein folding chaperone
  directly_involved_in:
  - id: GO:0006457
    label: protein folding
  - id: GO:0006888
    label: endoplasmic reticulum to Golgi vesicle-mediated transport
  - id: GO:0090114
    label: COPII-coated vesicle budding
  locations:
  - id: GO:0005789
    label: endoplasmic reticulum membrane
  description: >-
    Shr3 is a substrate-specific ER membrane chaperone for amino acid permeases.
    It stabilizes polytopic permease clients, prevents aggregation and premature
    ERAD, and promotes their packaging into COPII-coated ER-derived vesicles.
  supported_by:
  - reference_id: PMID:15623581
    supporting_text: "prevent aggregation of polytopic proteins in the ER"
  - reference_id: PMID:10564255
    supporting_text: "Shr3p acts as a packaging chaperone"
  - reference_id: file:yeast/SHR3/SHR3-deep-research-falcon.md
    supporting_text: "ER membrane-localized, substrate-specific chaperone"
proposed_new_terms: []
suggested_questions:
- question: >-
    For Shr3 and related ER-resident packaging factors, should GO curation
    distinguish folding chaperone activity from cargo-receptor or COPII-adaptor
    activity with a more specific child term?
suggested_experiments:
- description: >-
    Reconstitute Shr3 with defined amino acid permease transmembrane segments and
    COPII components to separate its folding/stabilization activity from any
    direct COPII recruitment activity.
  experiment_type: biochemical reconstitution
  hypothesis: >-
    Shr3 first stabilizes early permease transmembrane segments and then promotes
    COPII packaging indirectly by producing export-competent cargo.
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
  findings: []
- id: PMID:10564255
  title: Shr3p mediates specific COPII coatomer-cargo interactions required for the packaging of amino acid permeases into ER-derived transport vesicles.
  findings: []
- id: PMID:10688190
  title: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.
  findings: []
- id: PMID:1423607
  title: 'SHR3: a novel component of the secretory pathway specifically required for localization of amino acid permeases in yeast.'
  findings: []
- id: PMID:15623581
  title: Specialized membrane-localized chaperones prevent aggregation of polytopic proteins in the ER.
  findings: []
- id: PMID:16093310
  title: Large-scale identification of yeast integral membrane protein interactions.
  findings: []
- id: PMID:18467557
  title: An in vivo map of the yeast protein interactome.
  findings: []
- id: PMID:19053807
  title: Systematic definition of protein constituents along the major polarization axis reveals an adaptive reuse of the polarization machinery in pheromone-treated budding yeast.
  findings: []
- id: PMID:26928762
  title: 'One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.'
  findings: []
- id: PMID:27107014
  title: An inter-species protein-protein interaction network across vast evolutionary distance.
  findings: []
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome.
  findings: []
- id: file:yeast/SHR3/SHR3-deep-research-falcon.md
  title: Falcon deep research report for SHR3
  findings: []